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  • 1995-1999  (5,505)
  • 1985-1989  (3,406)
  • 1970-1974  (926)
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  • Biochemistry and Biotechnology  (8,890)
  • Electron microscopy
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  • 1
    Electronic Resource
    Electronic Resource
    Intimal-type primary sarcoma of the aorta (1999)
    Springer
    Virchows Archiv 435 (1999), S. 62-66 
    Details
    ISSN: 1432-2307
    Keywords: Key words Rhabdomyosarcoma ; Aorta ; Immunohistochemistry ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  We report an intimal sarcoma presenting as an aortic aneurysm. A 68-year-old man suffered from chest pain and speech disturbance. Computed tomography showed a sacciform aneurysm of the aorta, which was resected, revealing a polypoid tumour measuring 1.5×2×2.5 cm projecting into the lumen. This proved to be a poorly differentiated high-grade sarcoma having morphological, immunophenotypic and ultrastructural features consistent with rhabdomyosarcomatous differentiation. Primary sarcomas of the aorta are extremely rare. Many cases have been diagnosed as ”intimal” on the basis of their site of origin, and they are not easy to classify from their histological pattern. Electron microscopy and the use of a more comprehensive panel of immunohistochemical markers should be applied in the histological classification of ”intimal” sarcoma.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004280050396
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  • 2
    Electronic Resource
    Electronic Resource
    Melanin pigmented oncocytic metaplasia of the nasopharynx (1999)
    Springer
    Virchows Archiv 434 (1999), S. 455-457 
    Details
    ISSN: 1432-2307
    Keywords: Key words Melanin ; Oncocytic metaplasia ; Nasopharynx ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  A 64-year-old man presented with a history of discomfort of the throat of a few weeks’ duration. Nasoscopic examination revealed multiple small, brown pigmentations at the left suprapharynx, the base of the left nasal cavity and the pharyngeal openings of the auditory tube on both sides. Microscopically, the lesion showed a glandular pattern of oncocytic epithelium with abundant pigmented granules and melanophages in the surrounding stroma. Immunohistochemically, the dendritic cells in the basal layer were positive for S-100 protein. Electron microscopic study revealed numerous fully melanized melanosomes and hypertrophied mitochondria in the oncocytic cells. Oncocytic cells do not produce melanin for themselves, melanin granules apparently being transferred from the adjacent dendritic cells to the oncocytic cells.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004280050366
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  • 3
    Electronic Resource
    Electronic Resource
    A developmental study using three antibodies (VOBM1, VOBM2, and VOM2): immunocytochemical and electron microscopical analysis of the luminal surface of the rat vomeronasal sensory epithelium (1999)
    Springer
    Anatomy and embryology 199 (1999), S. 215-224 
    Details
    ISSN: 1432-0568
    Keywords: Key words Vomeronasal organ ; Microvilli ; Monoclonal antibody ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  The development of the rat vomeronasal organ was studied morphologically and immunocytochemically, using the monoclonal antibodies (MAbs) VOBM1, VOBM2 and VOM2 that react with the luminal surface of the vomeronasal sensory epithelium. Postnatal day (P) 7, 14, 21, 28, 35 and adult animals were examined. The vomeronasal organ and the blood vessel of the organ markedly increased in size and the vomeronasal glands increased in number between P7 and P14. At P35, the shape of the vomeronasal organ was similar to that of the adult but its size was slightly smaller. Electron microscopy showed that only a few scattered microvilli were present on supporting cells, and receptor cells were immature at P7. At P21, well-branched microvilli of the receptor cells and many microvilli of the supporting cells were observed on the luminal surface of the sensory epithelium. At P35, most apical endings of supporting cells and receptor cells were covered with numerous microvilli. Less developed areas were also present at the luminal surface of the epithelium at P35. At P7, immunoreactivities of the three antibodies were observed as discontinuous thin-layered bands only on the luminal surface of the sensory epithelium and no immunoreactivity was observed in other regions of the vomeronasal organ. Immunoreactivities of the VOBM1, VOBM2 and VOM2 increased with age and were observed as continuous thin-layered bands on the luminal surface of the epithelium by P35. These finding suggest that the development of the vomeronasal organ continues after birth and that the organ may reach maturity just before puberty (P42–49).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004290050222
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  • 4
    Electronic Resource
    Electronic Resource
    A new combined Bodian-Luxol technique for staining unmyelinated axons in semithin, resin-embedded peripheral nerves: a comparison with electron microscopy (1999)
    Springer
    Acta neuropathologica 98 (1999), S. 323-329 
    Details
    ISSN: 1432-0533
    Keywords: Key words Unmyelinated fibers ; Peripheral nerve ; Electron microscopy ; Histochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Quantitation of unmyelinated fibers (UF) in peripheral nerves has classically relied upon ultrastructural morphometry. Because this method is time-consuming, it is not typically performed in routine analysis of nerve biopsies. We applied the Bodian-Luxol technique to detect unmyelinated axons by light microscopy on semithin sections from resin-embedded nerve tissue. Estimates were compared to ultrastructural counts. The staining appeared highly specific for axons. Excellent correlation was found between optic densities and the population of UF larger than 0.5 μm. The smallest profiles detected by light microscopy had a diameter close to 0.6 μm. This new technique is not a substitute for ultrastructural quantitative morphometry of UF, as very small unmyelinated axons, especially regenerating ones, can not be reliably visualized. However, it provides a valuable light microscopic method for evaluating axonal loss among UF.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004010051088
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  • 5
    Electronic Resource
    Electronic Resource
    Breached cerebral glia limitans-basal lamina complex in Fukuyama-type congenital muscular dystrophy (1999)
    Springer
    Acta neuropathologica 98 (1999), S. 330-336 
    Details
    ISSN: 1432-0533
    Keywords: Key words Micropolygyria ; Electron microscopy ; Frontal lobe ; Perivascular space ; Dot-like structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We have reported breaches of glia limitans (GL)-basal lamina (BL) complex with protruding neuroglial tissue in Fukuyama-type congenital muscular dystrophy (FCMD) fetus brain and suggested that some basic deficits in the GL-BL complex may have a pivotal role in formation of micropolygyria in FCMD. We therefore investigated the cerebral GL-BL complex in seven FCMD cases (12–27 years of age), in three cases of Duchenne muscular dystrophy (17–25 years of age) and in two non-neurological controls (28 and 33 years of age). The frontal lobe cortex was examined immunocytochemically using antibodies against collagen type IV and laminin in each case, and ultrastructurally in an adult case of FCMD. In FCMD, the BL of the cortical surface was frequently breached with protruding neural tissue that ultrastructurally showed frequent synapses, neurites that had parallel arranged microtubules, and astrocytic processes. The outermost surface of this tissue was only partly lined by a BL. In the region of the gyral adhesion of micropolygyria, the perivascular space of the apparently entrapped meningeal blood vessels was occupied by neuroglial tissue, which is assumed to have invaded through the occasionally seen breaches of the perivascular GL-BL complex. Electron microscopy of the intruding tissue showed frequent synapses, microtubule-containing neurites and astrocytic processes. No breached GL-BL complex was found in any of the non-FCMD cases. These findings indicate that in FCMD, the cerebral GL-BL complex continues to have a crucial deficit with resulting breaches through which neuroglial tissue protrudes, promoting adhesion of the adjacent cerebral gyri during brain development before and after birth.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004010051089
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  • 6
    Electronic Resource
    Electronic Resource
    Motor neuron disease with predominantly upper extremity involvement: a clinicopathological study (1999)
    Springer
    Acta neuropathologica 98 (1999), S. 645-650 
    Details
    ISSN: 1432-0533
    Keywords: Key words Amyotrophic lateral sclerosis ; Autopsy ; Electron microscopy ; Immunocytochemistry ; Motor ; neuron disease
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We report two autopsy cases of motor neuron disease (MND) patients with an unusual type of muscular atrophy predominantly affecting the shoulder girdle and the upper extremities with proximal dominance. Both patients are considered to be clinically categorized into the El Escorial suspected form of amyotrophic lateral sclerosis (ALS). At autopsy, they showed marked loss of spinal anterior horn cells accompanied by astrogliosis positively immunostained with anti-glial fibrillary acidic protein antibody at the cervical level. At the lumbosacral level, anterior horn neurons were relatively well preserved and Bunina bodies, ubiquitin-positive skein-like inclusions and Lewy body-like inclusions were observed in the remaining neurons. In one patient, brain stem motor neurons (nerves V, VII, XII) and motor cortex, including Betz cells, were also affected and the corticospinal tracts were degenerated at the level of the thoracic and lumbar spinal cord. Pathological findings of this patient are consistent with those of ALS. In the other patient, the motor cortex, brain stem motor nuclei and the corticospinal tracts were well preserved, which is pathologically compatible with progressive spinal muscular atrophy. These patients with such a peculiar pattern of progressive muscular atrophy should be placed in a subgroup of ALS.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004010051131
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  • 7
    Electronic Resource
    Electronic Resource
    Subretinal macrophages in the developing eye of eutherian mammals and marsupials (1999)
    Springer
    Anatomy and embryology 200 (1999), S. 551-558 
    Details
    ISSN: 1432-0568
    Keywords: Key words Retina ; Development ; Retinal pigment epithelium ; Microglia ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  Blood-borne mononuclear cells invade the developing retina via the hyaloid vasculature at the optic nerve head. Following removal of apoptotic cell debris they give rise to the network of resident microglia. The population of cells recently described in the peripheral subretinal space of developing human eyes may represent a further population of macrophages destined to become microglia. The aim of the present study was to confirm the presence of subretinal macrophages in the developing eye in other mammalian species and perform preliminary immunophenotypic analysis in rat tissues. The range of species chosen included eutherian mammals (rat and rabbit) and marsupials (wallaby and opossum). Ocular tissues from a range of developmental stages were studied by scanning electron microscopy and transmission electron microscopy. Distinctive networks of dendriform and pleomorphic macrophages were observed by scanning electron microscopy in the peripheral subretinal space of D2 rabbits, newborn and D2 rats and D75 wallaby. Transmission electron microscopic studies of D2 rabbit, newborn and D2 rat and all ages of North American opossum revealed cells with the ultrastructural features of macrophages in the peripheral subretinal space, cilio-retinal junction and between ciliary epithelial cells. Preliminary immunoperoxidase studies using a panel of anti-leukocyte monoclonal antibodies on frozen sections of rat ocular tissues (newborn, D2 and D4) revealed ED1+ Ox42+ ED2+ but Ox6– cells in the peripheral subretinal space, peripheral retina and ciliary body epithelia. The data confirms that subretinal macrophages are a feature of the developing eye in a broad range of mammalian species and immunophenotypic evidence leads the author to postulate that these cells arise from the ciliary body vasculature and may migrate into peripheral neural retina and mature into resident microglia.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004290050303
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  • 8
    Electronic Resource
    Electronic Resource
    Magnetic properties of human liver and brain ferritin (1999)
    Springer
    European biophysics journal 28 (1999), S. 263-267 
    Details
    ISSN: 1432-1017
    Keywords: Key words Human liver ; Human brain ; Ferritin ; Electron microscopy ; Mössbauer spectroscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Human brain (globus pallidus) and liver tissues were investigated by means of electron microscopy (EM), Mössbauer spectroscopy (MS) and SQUID magnetometry techniques. Based on MS measurements, the iron present was identified to be in the ferritin-like form (61–88%) and in the form of a low-spin iron species (the balance). Its overall concentration was estimated as 1.5(3) mg in the brain and 2.4(5) mg in the liver, per gram of lyophilized tissue. The average core diameter was determined by EM measurements to be equal to 7.5(1.3) nm for the liver and 3.3(5) nm for the brain. Magnetization measurements carried out between 5 and 300 K yielded an estimation of an average blocking temperature, KT BL, as equal to 6.7 K and 8.5 K for the liver and the brain, respectively. From the dependence of KT BL on the external magnetic field it was concluded that the ferritin-like cores in the studied samples can be regarded as non-interacting particles. Finally, the uniaxial magnetic anisotropy constant was determined to be 6×103 J/m3 for the liver and 4×104 J/m3 for the brain.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002490050208
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  • 9
    Electronic Resource
    Electronic Resource
    Infraterminal spreading and extrajunctional expression of nicotinic acetylcholine receptors in denervated rat skeletal muscle (1999)
    Springer
    Experimental brain research 125 (1999), S. 426-434 
    Details
    ISSN: 1432-1106
    Keywords: Key words Acetylcholine receptor ; Nicotinic ; Denervation supersensitivity ; Neuromuscular junction ; α-Bungarotoxin ; Immunocytochemistry ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  Through the use of biotinylated-bungarotoxin and monoclonal antibodies, the nicotinic acetylcholine receptor (nAChR) was localized in the subneural apparatus of mammalian motor end plates of the flexor digitorum brevis muscle of the adult rat at the light and electron microscopic levels. Under normal conditions, nAChR was located in the primary post-synaptic membrane of the neuromuscular junction, and the depths of the junctional folds constituting the secondary post-synaptic membrane did not contain any nAChR. Up to 75 days after repeated transection of the related motor nerve (sciatic), there was no major alteration in the light-microscopic localization of junctional nAChR in the subneural apparatus, except for a moderate shrinkage and increased immunocytochemical reactivity of the subneural apparatus. At the electron microscopic level, however, immunocytochemical reactivity gradually occupied the entire extent of the secondary post-synaptic membrane, including the depths of the junctional folds, which exhibited extensive branching. In non-innervated portions of the muscle fibers, nAChR receptor appeared in a linear localization on the surfaces of denervated muscle fibers. This linear reaction was not continuous with the nAChR reaction of the motor end plates. It is concluded that denervation supersensitivity might not be due to spreading of junctional nAChR from the end-plate area, but rather to expression of nAChR in non-innervated portions of the muscle fiber and to the infraterminal (subsynaptic) spreading of nAChR into the depths of junctional folds.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002210050699
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  • 10
    Electronic Resource
    Electronic Resource
    Recovery of synapses in axotomized adult cat spinal motoneurons after reinnervation into muscle (1999)
    Springer
    Experimental brain research 125 (1999), S. 19-27 
    Details
    ISSN: 1432-1106
    Keywords: Key words Nerve injury ; Nerve repair ; Retrograde reaction ; Regeneration ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  Peripheral axotomy of adult cat spinal motoneurons induces a marked loss of synaptic boutons from the cell bodies and dendritic trees. The aim of the present study was to analyze the recovery of synaptic contacts in axotomized motoneurons following reinnervation into muscle. Adult cat spinal motoneurons were first deprived of their muscular contacts for 12 weeks and, then, allowed to reinnervate their target muscle. Two years later, regenerated motoneurons were labeled with horseradish peroxidase to allow quantitative ultrastructural analyses of the synaptic covering of the cell bodies and dendrites. Presynaptic boutons were classified according to their size and the shape of their synaptic vesicles. Results show that a recovery of synaptic covering occurs in the axotomized neurons after muscle reinnervation, but it affects various bouton types to different degrees. The number of S-type boutons synapsing with the soma was 70% higher after reinnervation than at 12 weeks after axotomy, while the number of F-type boutons had increased by only 13%. Compared with the normal situation, the number of S-type boutons synapsing with the proximal dendrites increased from 82% at 12 weeks after axotomy to 180% in the reinnervated state. In conclusion, in adult cat spinal motoneurons, the reestablishment of muscular contact is followed by a normalization of some of the synaptological changes induced by a prolonged state of axotomy. In certain respects restitution is incomplete, but in others it results in overcompensation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002210050653
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  • 11
    Electronic Resource
    Electronic Resource
    Phase and aggregation behaviour of double-chain cationic surfactants from the class of N-alkyl-N-alkyl′-N, N-dimethylammonium bromide surfactants (1999)
    Springer
    Colloid & polymer science 277 (1999), S. 856-867 
    Details
    ISSN: 1435-1536
    Keywords: Key words Double chain surfactants ; Aggregates ; Phase diagrams ; Lamellar phases ; Electron microscopy ; SANS
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract We present the phase diagrams and the properties of newly synthesised double-chain cationic N-alkyl-N-alkyl′-N,N-dimethylammonium bromide surfactants [C x C y DMABr (x = 12, 14 and 16; y = 10, 11, 12, 14 and 16)]. All the systems studied form liquid-crystalline lamellar phases but with different morphologies: unilamellar vesicles at low surfactant concentrations, multilamellar vesicles and tubular aggregates for surfactant concentrations between 2 and 10 wt% and at even higher concentrations planar bilayers of surfactant molecules in the classical Lα phase. The phase diagrams were determined with macroscopic and microscopic methods (polarisation microscopy, freeze-fracture transmission electron microscopy, scanning electron microscopy and differential interference contrast microscopy). The properties of the surfactant solutions were determined with differential scanning calorimetry measurements for Krafft point determination and small-angle neutron scattering measurements for interlamellar spacing and bilayer thickness. Finally, conductivity and viscosity measurements for phase characterisation were carried out.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003960050462
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  • 12
    Electronic Resource
    Electronic Resource
    Synthesis of colloids and films of Pr, Er and Yb with nonaqueous solvents (1999)
    Springer
    Colloid & polymer science 277 (1999), S. 164-173 
    Details
    ISSN: 1435-1536
    Keywords: Keywords Nanostructures ; Thin films ; Vapor deposition ; Electron microscopy ; Optical properties
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract Colloidal dispersions of Yb, Er and Pr have been prepared by chemical liquid deposition. The metals were cocondensed at 77 K with 2-methoxyethanol and ethanol to produce solvated metal atoms. The particle size of the dispersions was determined by transmission electron microscopy to range from 52 to 1080 Å; the particles had spherical shapes. After solvent evaporation under vacuum, active solids and amorphous powder were deposited over Cu and Al metal. Dispersion stability, particle size, UV/Vis absorption and zeta potential were studied. The solids prepared by solvent evaporation were characterized by Fourier transform infrared (FTIR) spectroscopy and thermogravimetric analysis (TGA). The films prepared on Al were studied by scanning electron microscopy. The most stable colloid was obtained using 2-methoxyethanol: several concentrations were stable for several months and the zeta potential indicated that this colloid stability is mainly due to solvation effects. FTIR spectroscopy of the solids indicated solvent incorporation in the film. This observation was corroborated by thermal analysis. Information on the thermal stability of the films was obtained by TGA. The UV/Vis absorption spectrum was measured at several concentrations under different conditions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s003960050381
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  • 13
    Electronic Resource
    Electronic Resource
    Muscle and skin biopsies are a sensitive diagnostic tool in the diagnosis of CADASIL (1999)
    Springer
    Journal of neurology 246 (1999), S. 526-532 
    Details
    ISSN: 1432-1459
    Keywords: Key words CADASIL ; Cerebrovascular disease ; Skin biopsy ; Muscle biopsy ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a microangiopathic syndrome. Although the defective gene has been identified, genetic analysis may be effort some due to its large size and various mutations. Providing a reliable diagnostic marker would therefore be helpful. Electron microscopy has revealed characteristic electron-dense granular deposits in the basal lamina of vessels of patients with CADASIL. We investigated the sensitivity of skin and muscle biopsies for diagnosing CADASIL. We examined 30 family members of three unrelated German families affected by CADASIL. In 14 of the 21 affected individuals we performed skin and muscle biopsies; two patients were clinically asymptomatic. Under electron microscopy all muscle and skin biopsy specimens showed patches of granular and electron-dense material in the basal layer of both arterioles and capillaries. These findings confirm that general microangiopathy is a typical feature of this syndrome and is present in the early phase of the disease with or without clinical manifestation. Thus, as electron microscopy of skin biopsy specimens can establish the diagnosis of CADASIL with high certainty, it may be considered the method of first choice.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004150050398
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  • 14
    Electronic Resource
    Electronic Resource
    A comprehensive analysis of selected diagnostic methods with respect to their usefulness in evaluating the biology of neoplastic cells in patients with laryngeal cancer (1999)
    Springer
    European archives of oto-rhino-laryngology and head & neck 256 (1999), S. 306-311 
    Details
    ISSN: 1434-4726
    Keywords: Key words Laryngeal cancer ; p53 ; Oncoprotein ; Ki67 ; Proliferating cell nuclear antigen (PCNA) ; DNA ploidy ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The difficult and complicated mechanism of cancer development with little knowledge about the biology of existing cancers can lead to a permanent search for new examination techniques to improve the precision of life expectancy in patients and the selection of the most efficient methods of treatment. The aim of this study was to analyze certain prognostic factors, i.e., p53, Ki67, proliferating cell nuclear antigen (PCNA), DNA ploidy and cell proliferating activity, as well as the degree of morphological differentiation and cell maturity evaluated on an ultrastructural level in patients with laryngeal cancers in connection with data obtained from follow-up examinations and the clinical course of the disease. Neoplastic tissue was taken from 120 patients with laryngeal cancers. All underwent surgical treatment, radiotherapy and combined treatment in the Department of Otolaryngology, Karol Marcinkowski University School of Medical Sciences, Poznań, Poland, and the Department of Otolaryngology – Head and Neck Surgery, Haukeland University, Bergen, Norway. Before beginning treatment all patients underwent histological verification of their neoplastic tissues. Histopathological examination proved that the majority of cases (95%) had a squamous cell carcinoma. The occurrence of changes within the lymph nodes of the neck (N) was significantly correlated with T, S, Ki67, metastases to lymph nodes, DNA ploidy, site and surgery performed. The degree of clinical progression (S) was intercorrelated with T, N, p53, Ki67, PCNA, DNA ploidy, site and laryngectomy. The occurrence of oncoprotein p53 in neoplastic cells was measured by the staining degree of their nuclei and was correlated with T, S, DNA ploidy, metastases to lymph nodes, PCNA and site. The degree of staining of neoplastic cells for the nuclear antigen Ki67 was correlated to T, N, G, S, DNA ploidy, metastases to lymph nodes and surgical treatment. The proliferative antigen PCNA in the examined population of patients was intercorrelated with T, p53, Ki67, metastases to lymph nodes and surgical treatment. The results obtained from DNA flow cytometry could be associated with N, G, p53, Ki67 and metastases to lymph nodes. On the basis of the results obtained, the techniques suggested for the morphological and biological evaluation of neoplastic cells in cancer of the larynx should include TNM classification + G + DNA + p53 + Ki67.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004050050252
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  • 15
    Electronic Resource
    Electronic Resource
    The cytoskeleton of the myenteric neurons during murine embryonic life (1999)
    Springer
    Anatomy and embryology 199 (1999), S. 459-469 
    Details
    ISSN: 1432-0568
    Keywords: Key words Differentiation ; Electron microscopy ; Histochemistry ; Microtubules ; Neurofilaments
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  The organization of the cytoskeleton has been studied during mouse differentiation in cells of the myenteric neuronal lineage. The entire gut was examined starting from day 12.5 of embryonic life (E12.5) until birth (P0). Immunocytochemistry was performed to evaluate the expression of five of the most represented neurofilaments proteins (the low, NF-L, medium, NF-M, and heavy, NF-H, molecular weight subunits, α-internexin and peripherin) and of two of the microtubule-associated proteins (MAP1 and MAP2a+2b). In parallel, the appearance in the differentiating myenteric neurons of filamentous and microtubular structures and their intracytoplasmatic distribution were observed under the electron microscope. A differential immunohistochemical expression of the structural proteins was found. Immature cells expressed α-internexin, peripherin, NF-M and MAP1 by day E12.5; α-internexin expression was strong in these cells, but gradually decreased with age and was practically absent in adulthood. Conversely, the expression of the other three proteins increased with cell differentiation and was still present in adulthood. NF-L and NF-H expression appeared later, by day E16.5, and was weak for the entire pre- and postnatal life. MAP2a+2b was never expressed. Under the electron microscope, at day E12.5 the cytoskeleton was already organized in filamentous and microtubular structures. At this age neurofilaments were few and mainly located in the cell processes, and microtubules were numerous and mainly assembled in the neuritic growth cones, together with synaptic vesicles. With ageing, neurofilaments and microtubules were ubiquitous in the neuron. Data obtained demonstrate that cytoskeletal proteins gradually accumulate in the cells of the neuronal lineage in parallel with the organization of the cytoskeletal structures, which in turn mediate important neural events by the earliest stages of murine embryonic life, including growth of nerve processes and initiation of axonal transport.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004290050244
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  • 16
    Electronic Resource
    Electronic Resource
    Outbreaks of gastroenteritis caused by SRSVs from 1987 to 1992 in Kyushu, Japan: Four outbreaks associated with oyster consumption (1999)
    Springer
    European journal of epidemiology 15 (1999), S. 175-180 
    Details
    ISSN: 1573-7284
    Keywords: Electron microscopy ; Epidemiology ; Non-bacterial Gastroenteritis ; Oyster ; Small round structured viruses (SRSVs)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract From 1987 to 1992, 18 outbreaks of acute non-bacterial gastroenteritis occurred in Kyushu district. The most common symptoms were diarrhea, vomiting, nausea and abdominal cramp. Small round structured viruses (SRSVs) were detected in 52 (44.8%) of 116 stool samples from 17 outbreaks by the electron microscopy (EM) method, and a significant increase in the antibody level was noted in 42 (80.7%) of 52 paired serum samples from 12 outbreaks by the immune electron microscopy (IEM) method and in 18 (51.4%) of 35 samples from 8 outbreaks by the western blot (WB) method. However, according to the WB method, antigen-antibody reaction was not observed to reference antigen strips (SRSV-9/Tokyo 86-510, 63kDa) in three of the 8 outbreaks. The detected virus was regarded as an etiologic agent for these outbreaks. In four of 5 outbreaks which appeared associated with eating raw oysters, there was a close relation between SRSV infection and consumption of raw oysters.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1007543924543
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  • 17
    Electronic Resource
    Electronic Resource
    Metaphase-specific cell death in meiotic spermatocytes in mice (1999)
    Springer
    Cell & tissue research 296 (1999), S. 359-369 
    Details
    ISSN: 1432-0878
    Keywords: Key words Apoptosis ; Electron microscopy ; Meiosis ; Spermatocytes ; Spermatogenesis ; Testis ; TUNEL ; Mouse (10 strains)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Apoptosis of male germ cells is a widespread but little-understood phenomenon in many animal species. The elucidation of its mechanisms could be useful in the understanding of male infertility. We have examined the distribution of dying cells with the terminal transferase-mediated nick-end labeling (TUNEL) method and by an electron-microscopic procedure in the testes of 10 mouse strains, viz., C57BL/10 (B10), SL/NiA (SL), C57BL/6 (B6), C3H/He (C3H), BALB/c (BALB), DBA2 (DBA), CBA/J (CBA), MRL/MpJ-+/+ (M+), MRL/MpJ-lpr/lpr (lpr), and wild-type NJL mice (Mus musculus musculus). In the testes of the B10, NJL, SL, B6, C3H, BALB, DBA, and CBA mice, very few TUNEL-positive cells are distributed in the seminiferous tubules, whereas in the testes of the M+ and lpr mice, many TUNEL-positive cells, which are restricted to stage XII seminiferous tubules, have been identified. The most important finding is that many metaphases of meiotic spermatocytes show a marked TUNEL-positive reaction. Some metaphases show apoptotic morphology electron-microscopically. These results suggest that the testes of MRL strains will provide a useful model for the study of the mechanism of metaphase-specific apoptosis in meiotic spermatocytes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004410051296
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  • 18
    Electronic Resource
    Electronic Resource
    Effect of high-level oxygen exposure on the peroxidase activity and the neuromelanin-like pigment content of the nerve net in the earthworm, Lumbricus terrestris (1999)
    Springer
    Cell & tissue research 295 (1999), S. 349-354 
    Details
    ISSN: 1432-0878
    Keywords: Key words Neuromelanin ; Neuron ; Peroxidase ; Oxygen metabolism ; High-definition light microscopy ; Electron microscopy ; Ultrastructure ; Cytochemistry ; Substantia nigra ; Lumbricusterrestris (Annelida)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Histochemical examination of 1-μm tissue sections from the dorsal nerve plexus of the earthworm, Lumbricus terrestris, reveals multiple brown intraneuronal granules. These granules contain material morphologically and histochemically consistent with neuromelanin. When viewed with transmission electron microscopy, these were seen as single membrane-enclosed biphasic granules with diameters of 370–730 nm. Exposure of L. terrestris to high-level environmental oxygen resulted in an increase in the number of neuromelanin-like pigment granules within the neurons of the circular muscle layer. As measured by ortho-phenylenediamine hydrochloride, the endogenous peroxidase activity of extracts from worms incubated in high-level environmental oxygen was 51% more than controls. The endogenous peroxidase activity was localized in situ with 3,3-diaminobenzidine (DAB) and was found to increase in and around the neuromelanin-like pigment-containing neurons within the circular muscle layer. These studies suggest that the nerve net of L. terrestris may serve as a model to study the role of neuromelanin production in oxidative stress and its relationship to endogenous peroxidases.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004410051241
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  • 19
    Electronic Resource
    Electronic Resource
    Op/op mice defective in production of functional colony-stimulating factor-1 lack macrophages in muscularis externa of the small intestine (1999)
    Springer
    Cell & tissue research 295 (1999), S. 485-493 
    Details
    ISSN: 1432-0878
    Keywords: Key words Immunohistochemistry ; Electron microscopy ; Interstitial cells of Cajal ; F4/80 ; CSF-1 ; Kit-receptor ; Mouse (op/op)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The osteopetrotic (op/op) mutant mouse possesses an inactivating mutation in the colony-stimulating factor-1 (CSF-1) gene, which results in the absence of certain macrophages and in osteopetrosis, following a lack of osteoclasts. Studies of the op/op mouse indicate that CSF-1-dependent tissue macrophages may belong to a trophic and/or scavenger subpopulation, which through their effect on other cell types can significantly affect tissue functions, and that cells which are CSF-1 independent have antigen presentation and immunological functions.We have previously identified a cell system of regularly distributed macrophages in the muscularis externa of the small intestine and wanted to extend these studies to the op/op mouse.The present investigations with light- and electron-microscopic methods using fluorescent dextran, methylene blue and immunohistochemistry (F4/80, anti-kit receptor, anti-CD3, anti-CD45R/B220) show that macrophages are absent from the muscle layers, with only an occasional macrophage present in the subserosa. In the lamina propria and submucosa, macrophage numbers are reduced. In all other respects the muscularis externa appears normal, including normal organization and number of interstitial cells of Cajal. Control and op/op mice both lack cells expressing CD3 (T lymphocytes), CD45R/B220 (B lymphocytes) and mast cells in the muscularis externa. This leaves the muscularis externa macrophages as the most likely source of local cytokine production under such conditions as postoperative ileus and intussusception in infants, where the muscularis externa appears to be one target of cytokines. We conclude that the lack of macrophages, combined with the preservation of otherwise normal structure, will make the op/op mouse a valuable model by which to assess the functions and relative importance of the muscularis externa macrophages in relation to intestinal motility under normal and pathological conditions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004410051254
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  • 20
    Electronic Resource
    Electronic Resource
    Caveolin and its cellular and subcellular immunolocalisation in lung alveolar epithelium: implications for alveolar epithelial type I cell function (1999)
    Springer
    Cell & tissue research 295 (1999), S. 111-120 
    Details
    ISSN: 1432-0878
    Keywords: Key words Caveolin ; Caveolae ; Lung ; Alveolar epithelial type I cell ; Immunocytochemistry ; Electron microscopy ; Confocal laser scanning microscopy ; Rat (CD)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Caveolae are flask-shaped invaginations of the plasmalemma which pinch off to form discrete vesicles within the cell cytoplasm. Biochemically, caveolae may be distinguished by the presence of a protein, caveolin, that is the principal component of filaments constituting their striated cytoplasmic coat. Squamous alveolar epithelial type I (ATI) cells, comprising approximately 95% of the surface area of lung alveolar epithelium, possess numerous plasmalemmal invaginations and cytoplasmic vesicles ultrastructurally indicative of caveolae. However, an ultrastructural appearance does not universally imply the biochemical presence of caveolin. This immunocytochemical study has utilised a novel application of confocal laser scanning and electron microscopy unequivocally to localise caveolin-1 to ATI cells. Further, cytoplasmic vesicles and flask-shaped membrane invaginations in the ATI cell were morphologically identified whose membranes were decorated with anti-caveolin-1 immunogold label. Coexistent with this, however, in both ATI and capillary endothelial cells could be seen membrane invaginations morphologically characteristic of caveolae, but which lacked associated caveolin immunogold label. This could reflect a true biochemical heterogeneity in populations of morphologically similar plasmalemmal invaginations or an antigen threshold requirement for labelling. The cuboidal alveolar epithelial type II cell (ATII) also displayed specific label for caveolin-1 but with no ultrastructural evidence for the formation of caveolae. The biochemical association of caveolin with ATI cell vesicles has broad implications for the assignment and further study of ATI cell function.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004410051217
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  • 21
    Electronic Resource
    Electronic Resource
    Types, numbers and distribution of synapses on the dendritic tree of an identified visual interneuron in the brain of the locust (1999)
    Springer
    Cell & tissue research 296 (1999), S. 645-665 
    Details
    ISSN: 1432-0878
    Keywords: Key words Descending contralateral movement detector (DCMD) ; Identified neuron ; Vesicles ; Electron microscopy ; 3-D reconstruction ; Locust ; Schistocercagregaria (Insecta)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The descending contralateral movement detector (DCMD), an identified descending interneuron in the brain of the locust Schistocerca gregaria has been investigated by using light and electron microscopy. We describe the fine structure, distribution and numbers of synapes that it receives from another identified brain neuron, the lobular giant movement detector (LGMD), and from unidentified neurons. The DCMD dendrites emerging from the integrative segment vary in form and number between individuals and sexes but always form a flattened dendritic domain. The arborizations and the integrative segment appear to be exclusively postsynaptic. Two types of synaptic contacts (Type 1 and 2) onto the DCMD can be discerned as having either round (Type 1) or pleiomorphic synaptic vesicles (Type 2) and by large (Type 1) or small (Type 2) subsynaptic appositions. Contact zones of Type 1 synapses are smaller than those of Type 2. LGMD-synapses are of Type 1 and occur intermingled with presynaptic sites of unidentified units. Some branches of the DCMD receiving input from unidentified units are devoid of contacting LGMD processes. Synapses of both types are randomly distributed over the DCMD integrative segment and at fibres with similar sizes.Type 1 synapses are much more frequent than Type 2 synapses and their number is negatively correlated with fibre diameter. For a whole DCMD dendritic arborization, a total of 8500 active zones of chemical synapses has been calculated, including a mininum of 2250 LGMD-synapses and about 1000 Type 2 synapses. The DCMD may thus receive a considerable amount of input from as yet unidentified neurons.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004410051325
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  • 22
    Electronic Resource
    Electronic Resource
    Docetaxel-induced apoptosis in the mitotic phase: electron microscopic and cytochemical studies of human leukemia cells (1999)
    Springer
    Medical electron microscopy 32 (1999), S. 167-174 
    Details
    ISSN: 1437-773X
    Keywords: Key words Apoptosis ; Docetaxel ; Human leukemia cell ; DNA fragmentation ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We induced apoptosis in cells of the human leukemia cell line HL-60 using an antitumor agent, docetaxel (Taxotere), and investigated apoptosis in various aspects using in situ end-labeling (ISEL) of DNA, DNA fragmentation assay, flow cytometry, and electron microscopy. Because it inhibits depolymerization of tubulin, docetaxel is thought to arrest the cell cycle at the mitotic stage and to exert an antitumor effect. In this study, accumulation of docetaxel-treated cells at the G2/M phase was detected using flow cytometry. On ISEL of DNA, DNA fragmentation was observed at the mitotic stage. On electron microscopy, the nuclei of apoptotic cells lost their nuclear membranes, as do cells at mitosis, demonstrating that the cells were arrested mainly at the M phase in the cell cycle.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007950050024
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  • 23
    Electronic Resource
    Electronic Resource
    Electron microscopic and immunohistochemical studies of gastrointestinal stromal tumors (1999)
    Springer
    Medical electron microscopy 32 (1999), S. 213-220 
    Details
    ISSN: 1437-773X
    Keywords: Key words Gastrointestinal stromal tumor ; Gastrointestinal autonomic nerve tumor ; Electron microscopy ; Immunohistochemistry ; Gastrointestinal tract
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Sixteen gastrointestinal stromal tumors (GISTs) were studied by immunohistochemical analysis and an ultrastructural procedure. The tumor locations were as follows: esophagus (2), stomach (7), small intestine (3), and large intestine (4). Four of the lesions were classified as malignant, 2 as borderline, and 10 as benign. On the basis of the immunohistochemical analysis, the tumors were classified as follows: 1 as myogenic type, 2 as Schwann cell type, 8 as Cajal cell type (including 2 gastrointestinal autonomic nerve tumors, GANTs), and 5 as mixed-cell type. In each subtype the phenotype was compared to the ultrastructural findings. Myogenic and Schwann cell type revealed ultrastructurally smooth muscle differentiation and schwannian tumor. All 8 tumors of the Cajal cell type revealed interdigitating cytoplasmic processes with occasional clusters of filopodia. Two tumors were subdivided as GANT. Five tumors of mixed-cell type were composed of a mixture of cells with variable myogenic features or variable neural differentiation. We confirmed in this study that immunohistochemical analysis reflected electron microscopic findings.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007950050005
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  • 24
    Electronic Resource
    Electronic Resource
    Ultrastructural and immunohistochemical study of small cell neuroendocrine carcinoma of the parotid gland (1999)
    Springer
    Medical electron microscopy 32 (1999), S. 122-126 
    Details
    ISSN: 1437-773X
    Keywords: Key words Small cell neuroendocrine carcinoma ; Parotid gland ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract A case of small cell neuroendocrine carcinoma of the parotid gland is presented with immunohistochemical and electron microscopic studies. Small cell neuroendocrine carcinoma is extremely rare and is often difficult to distinguish from malignant lymphoma, adenoid cystic carcinoma, and undifferentiated carcinoma. Under light microscopy, the tumor cells consisted of solid sheets and nests of small tumor cells. Immunohistochemically, they were positive for KL-1 and EMA, and focally positive for NSE and synaptophysin. Observation using an electron microscope showed membrane-bound neuroendocrine granules in some tumor cells. Histological evaluation indicated that the present case was small cell carcinoma of the parotid gland, showing a neuroendocrine variety.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007950050018
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  • 25
    Electronic Resource
    Electronic Resource
    Reduction of cytochemical ecto-ATPase activities in keratin 8-deficient FVB/N mouse livers (1999)
    Springer
    Medical electron microscopy 32 (1999), S. 209-212 
    Details
    ISSN: 1437-773X
    Keywords: Key words Keratin ; Bile canaliculi ; Ecto-ATPase ; Transgenic mice ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Keratin 8 (K8) and keratin 18 are the intermediate filament proteins that are expressed in hepatocytes. A K8-deficient FVB/N mouse is a unique animal model for assessing the contribution of keratin intermediate filaments (IFs) to the structural and functional integrity of hepatocytes. Hepatocytes from homozygous (−/−) K8-deficient mice manifest a reduced bile acid secretion and an increased fragility to mechanical stress and hepatotoxic drugs. Hepatocytes from heterozygous (+/−) mice are more susceptible to drug-induced injury. Immunofluorescent microscopy revealed that hepatocytes from (+/−) mice maintained K8 IFs and F-actin that are similar to those in wild-type (+/+) mouse hepatocytes. In (−/−) mouse hepatocytes, K8 protein was negative and F-actin presented a coarse and irregular pattern. Ecto-ATPase, detected by enzyme histochemistry and observed by electron microscopy, was reduced in the bile canaliculi of both (+/−) and (−/−) mouse livers, in comparison with that of (+/+) mouse livers. These results reveal for the first time different microscopical findings regarding the livers of these three genotypes. They also suggest that the reduction of ecto-ATPase plays a role in the increased fragility of (+/−) and (−/−) mouse livers.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s007950050004
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  • 26
    Electronic Resource
    Electronic Resource
    Extranodal follicular dendritic cell tumour of the nasopharynx (1998)
    Springer
    Virchows Archiv 432 (1998), S. 293-298 
    Details
    ISSN: 1432-2307
    Keywords: Key words Follicular dendritic cell tumour ; Nasopharynx ; Immunohistochemistry ; Electron microscopy ; PCR
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  We report the first case of an extranodal follicular dendritic cell (FDC) tumour localized in the nasopharynx of a 44-year-old male patient. The tumour cells were characterized immunohistochemically by strong expression of CD21, HLA-DR and vimentin and focal expression of CD68 and cytokeratin. Electron microscopic examination revealed desmosomal cell junctions between adjacent cell processes. Molecular genetic analysis using polymerase chain reaction (PCR) showed germline configuration of immunoglobulin and T-cell receptor genes. Epstein-Barr virus (EBV) genomes were detectable by PCR. After complete surgical tumour removal and radiotherapy the patient is disease-free 20 months after the initial diagnosis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004280050168
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  • 27
    Electronic Resource
    Electronic Resource
    Cutaneous nerves in atopic dermatitis (1998)
    Springer
    Virchows Archiv 432 (1998), S. 363-370 
    Details
    ISSN: 1432-2307
    Keywords: Key words Atopic dermatitis ; Pruritus ; Cutaneous nerve ; Immunohistochemistry ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  Although pruritus is the cardinal symptom of atopic dermatitis, its mechanism is not well understood. Free nerve endings in the skin are involved in pruritus as itching receptors. We studied the cutaneous nerve fibres in lichenified lesions of 16 patients with adult atopic dermatitis. On immunohistochemistry, fibres immunoreactive for neurofilament, neuron-specific enolase, and protein gene product 9.5 were observed in the papillary dermis and dermoepidermal junctions as well as in the epidermis. In these areas, no fibres stained positively for substance P, neuropeptide Y, vasoactive intestinal peptide, beta endorphin, somatostatin or serotonin. On electron microscopy, the ultrastructure of subepidermal and intraepidermal free nerve endings appeared to be essentially normal. However, the distribution density of the cutaneous nerve fibres was much higher than in normal controls, and the diameter of these fibres was much larger, because of the large number of axons in each nerve fibre. Degranulation of mast cells was not seen. These findings suggest that pruritus in lichenified atopic skin is probably not caused by damage to the cutaneous free nerve endings. In such lesions, the number of the cutaneous free nerve endings is greatly increased, but they may have a normal function.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004280050179
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  • 28
    Electronic Resource
    Electronic Resource
    Cell surface and nuclear changes during TNF-α-induced apoptosis in WEHI 164 murine fibrosarcoma cells (1998)
    Springer
    Virchows Archiv 433 (1998), S. 75-83 
    Details
    ISSN: 1432-2307
    Keywords: Key words Apoptosis ; Cell surface ; Cell nucleus ; Blebs ; TNF-α ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  Tumour necrosis factor (TNF)-α-induced apoptosis is associated with several nuclear and cell surface alterations, in particular with the condensation of chromatin and the fragmentation of the cell nucleus, formation of blebs on the cell surface and breakdown of the plasma membrane. However, there is little information about the relationship between the cell surface alterations and the nuclear changes during apoptosis. To study this, cultured WEHI cells were exposed to TNF-α over different time periods. The cytological changes were studied using a correlative approach, which allowed observation of the same cell consecutively under light, scanning and transmission electron microscopy. The earliest sign of cell alteration was a reduction of the number of microvilli after 15 min of TNF-α exposure. This reaction was reversible (reappearance of microvilli) and took place during the first hour, in which neither nuclear alterations nor plasma membrane breakdown were observed. The changes in the nucleus began with condensation of chromatin after approximately 1 h of TNF-α-exposure. After 4–5 h the microvilli disappeared again, particularly in areas where the formation of blebs (blebbing) was observed. Strikingly, cell surface alterations (bleb formation) were detected only in those cells that presented with condensed chromatin, and not in cells with a normal chromatin pattern, proving at least a close correlation between nuclear and cell surface changes during the process of apoptosis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004280050219
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  • 29
    Electronic Resource
    Electronic Resource
    In vivo diagnosis of Kufs’ disease by extracerebral biopsies (1998)
    Springer
    Acta neuropathologica 96 (1998), S. 102-108 
    Details
    ISSN: 1432-0533
    Keywords: Key words Adult ceroid lipofuscinosis ; Kufs’ disease ; Electron microscopy ; Extracerebral biopsies
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract In almost all of the earlier reported cases of Kufs’ disease, the adult form of ceroid lipofuscinosis, the diagnosis was ascertained by cerebral tissue examination, while peripheral biopsy examination revealed an apparent poor diffusion of specific lipofuscinic deposits, the finger print profiles (FPs). We report the ultrastructural data from skin, muscle and rectal biopsy specimens from two siblings, both still living, who present clinical features of Kufs’ disease. We observed the presence of FPs in locations that differ from the previous classic reports. Our results emphasize the value of extracerebral biopsies for the diagnosis of Kufs’ disease in vivo, and suggest some physiopathological assumptions based on vascular wall involvement.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004010050866
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  • 30
    Electronic Resource
    Electronic Resource
    Hypoglycaemic neuropathy in BB/Wor rats treated with insulin implants: electron microscopic observations (1998)
    Springer
    Acta neuropathologica 96 (1998), S. 151-156 
    Details
    ISSN: 1432-0533
    Keywords: Key words Neuropathy ; Hypoglycemia ; Insulin ; implant ; Rat ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Insulin-dependent diabetes mellitus is a chronic metabolic disease that causes long-term secondary complications such as neuropathy. The occurrence of diabetic neuropathy has generally been thought of as being associated with hyperglycaemia. However, in a previous light microscopic examination of plantar nerves in diabetic BB/Wor rats treated with insulin implants we found that eu-/hyperglycaemic rats present a normal picture, whereas eu-/hypoglycaemic rats show severe changes. The aim of the present work is to supplement our previous light microscopic report with electron microsocpic data from the lateral plantar nerve of normal, eu-/hyperglycaemic and eu-/hypoglycaemic BB/Wor rats. Under the electron microscope lateral plantar nerves collected from eu-/hyperglycaemic rats presented a qualitatively normal picture. In addition, the fibre numbers and the size distribution of the myelinated fibres were normal. In contrast, specimens from eu-/hypoglycaemic BB/Wor rats showed severe qualitative changes, interpreted as signs of axonal de- and regeneration. The total number of axons was somewhat subnormal and the sizes of the myelinated fibres were strongly shifted towards smaller diameters. These data confirm our previous light microscopic observations. We conclude that eu-/hypoglycaemic BB/Wor rats treated with insulin implants, but not similarly treated eu-/hyperglycaemic animals, develop a neuropathy in their plantar nerves.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004010050875
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  • 31
    Electronic Resource
    Electronic Resource
    The innervation of the synovium of the knee joint in the guinea pig: an immunohistochemical and ultrastructural study (1998)
    Springer
    Anatomy and embryology 197 (1998), S. 293-303 
    Details
    ISSN: 1432-0568
    Keywords: Key words Sensory neurons ; Autonomic neurons ; Neuropeptides ; Immunohistochemistry ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  The innervation of the knee joint synovial membrane of the guinea pig, i.e., the synoviocyte layer, the subjacent connective tissue and the connective tissue region beneath, was analyzed with immunohistofluorescence and electron microscopy. A screening of the innervation with antibodies against the general axon marker – protein gene product (PGP) 9,5 – revealed the presence of nerve fibers distributed in various regions of the knee joint synovial membrane. Confirmating previous studies, some of these nerve fibers stained with antibodies to tyrosine hydroxylase (TH), neuropeptide Y (NPY), substance P (SP), calcitonin gene-related peptide (CGRP), and vasoactive intestinal polypeptide (VIP). In addition, dynorphin (DYN)-containing fibers were detected, which have not been reported previously in normal joints. In general, the immunoreactive fibers were observed close to the synoviocytes and at blood vessels. Fibers with colocalization of NPY- and TH-like immunoreactivities (LIs), as well as of DYN- and TH-LIs were demonstrated. In the electron microscope, bundles of unmyelinated fibers as well as single fibers were found in the connective tissue region below the synoviocytes. Varicose parts of the nerve fibers contained mainly small, clear vesicles. Small and large dense-cored vesicles were also seen, but less frequently. Denser portions of the plasma membranes of some axons were observed in these regions, facing the extracellular space. Myelinated fibers were also observed in some nerve bundles. These findings emphasize the complex innervation of the synovial membrane, with nerve fibers containing a host of neuroactive substances. Altogether, these fibers are probably involved in many functions such as vasoregulation and control of synovial secretion in addition to being a source of mediators in joint inflammation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004290050139
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  • 32
    Electronic Resource
    Electronic Resource
    Intravenous injection of guanylin induces mucus secretion from goblet cells in rat duodenal crypts (1998)
    Springer
    Anatomy and embryology 197 (1998), S. 359-367 
    Details
    ISSN: 1432-0568
    Keywords: Key words Guanylin ; Mucus secretion ; Goblet cells ; Small intestine ; Edema ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  Guanylin, structurally related to the heat-stable enterotoxin of E. coli, is a 15-amino-acid peptide isolated from rat small intestine. We investigated the morphological effects of an intravenous injection of rat and human guanylin upon the rat intestine. Various doses of rat guanylin were injected intravenously in anesthetized rats. After 5, 10 and 30 min, rats were killed by intracardiac perfusion with aldehyde fixative, and specimens of the intestine were then prepared for light and electron microscopy. Intravenously injected rat guanylin rapidly induced mucus secretion from crypt goblet cells in the duodenum. About half of the crypt goblet cells secreted mucous granules by compound exocytosis within 5 min. The villus goblet cells, in contrast, were not sensitive to guanylin. Goblet cells in the jejunum were less responsive than those in the duodenum. This secretory response was rare in the ileum and colon. Human guanylin produced similar results. The mucus secretion induced by guanylin was inhibited by a prior-injection of atropine, but not hexamethonium. Moreover, guanylin induced intense edema in the mucosa and submucosa of the small intestine 5 min after the injection, which disappeared after 30 min. A prior-injection of atropine did not block the appearance of edema. In conclusion, the intravenous injection of guanylin induces two phenomena related to water movement: (1) compound exocytosis of mucous granules from crypt goblet cells in the rat duodenum and jejunum; (2) perineural, inter-epithelial and intra-epithelial edema in the rat small intestine.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004290050146
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  • 33
    Electronic Resource
    Electronic Resource
    Histopathological and ultrastructural features of feline hereditary cerebellar cortical atrophy: a novel animal model of human spinocerebellar degeneration (1998)
    Springer
    Acta neuropathologica 96 (1998), S. 379-387 
    Details
    ISSN: 1432-0533
    Keywords: Key words Cat ; Spinocerebellar degeneration ; Purkinje cell ; Distal dendrite ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Human spinocerebellar degeneration is one of the intractable diseases. We studied the detailed neuropathology of cats with hereditary cerebellar degeneration obtained from the experimental breeding. The findings included almost total loss of Purkinje cells with an increase in Bergmann’s glia in the cerebellar hemisphere, preservation of some Purkinje cells in the vermis and moderate neuronal depletion of the olive nucleus. Cerebellar and pontine nuclei were normal. The cerebrum and spinal cord as well as the peripheral nervous system appeared normal. Electron microscopic examination revealed swelling of the distal dendrites of Purkinje cells in the less-affected nodule of the vermis, and clusters of presynaptic boutons without any synaptic contact in the severely affected folia where Purkinje cell bodies and dendrites disappeared. Prolonged existence of presynapses in the molecular and Purkinje cell layers was confirmed by positive immunoreactivity to anti-synaptophysin. Quantitative analysis using electron microscopy demonstrated an apparent increase in the density and mean size of presynapses in the molecular layer of the severely affected folia. These findings indicate that degeneration of Purkinje cells started at the most distal part of the dendrite in this animal model of cerebellar degeneration, and that presynapses, axon terminals of the granular cells and basket cells can exist for a long time even after complete degeneration of the Purkinje cells. Further investigation of this novel animal model may promote a better understanding of pathogenesis of human hereditary cerebellar degeneration.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004010050908
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  • 34
    Electronic Resource
    Electronic Resource
    Changes in synaptology of adult cat spinal α-motoneurons after axotomy (1998)
    Springer
    Experimental brain research 118 (1998), S. 1-13 
    Details
    ISSN: 1432-1106
    Keywords: Key words Nerve injury ; Retrograde reaction ; Spinal cord ; Electron microscopy ; Cat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The aim of this electron-microscopic study was to analyze the distribution of synaptic contacts on the cell bodies and dendrites of permanently axotomized adult cat spinal α-motoneurons. Following transection and ligation of the medial gastrocnemius nerve, the synaptic covering of the cell bodies and three different dendritic compartments of homonymous α-motoneurons was analyzed quantitatively at 3, 6, and 12 weeks postoperatively. The synaptic boutons were classified according to their size and the shape of their synaptic vesicles. On the soma, a transient increase in the number of boutons was noted at 3 weeks and 6 weeks postoperatively, while after 12 weeks the bouton number had decreased to half of its normal value. The transient increase was mainly due to an increase in the number of F-type boutons. At 12 weeks postoperatively, the synaptic covering was reduced by 83% on the soma and by 57% on the proximal dendrites. In the distal dendritic regions, the values for synaptic covering remained largely unchanged. In summary, axotomized motoneurons exhibit a reduction in synaptic covering which is maximal on the cell body and becomes less pronounced centrifugally along the dendrites. However, if also taking into account the loss of distal dendritic branches that occurs in axotomized motoneurons, the total loss of boutons is several times larger in the dendrites than on the soma.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002210050249
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    Electronic Resource
    Electronic Resource
    Differential localisation of the metabotropic glutamate receptor mGluR1a and the ionotropic glutamate receptor GluR2/3 in neurons of the human cerebral cortex (1998)
    Springer
    Experimental brain research 119 (1998), S. 367-374 
    Details
    ISSN: 1432-1106
    Keywords: Key words Glutamate receptors ; Immunocytochemistry ; Electron microscopy ; Human cortex
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  Specimens of human cerebral cortex were obtained during neurosurgical operations and studied by immunocytochemistry and electron microscopy, using antibodies to the metabotropic glutamate receptor subunit mGluR1a and the ionotropic glutamate receptor GluR2/3. A small number of non-pyramidal neuronal cell bodies were labelled for mGluR1a. Double immunolabelling with mGluR1a and GluR2/3 showed that most pyramidal cell bodies were labelled for GluR2/3 but not for mGluR1a. Despite the non-colocalisation of these two receptor subtypes in cell bodies, however, many dendrites and dendritic spines were double-labelled for mGluR1a and GluR2/3 at electron microscopy. As there is evidence that most neurons positive for GluR2/3 are pyramidal cells, this suggests that mGluR1a is present in dendrites of pyramidal neurons, despite absent or low levels of immunoreactivity in their cell bodies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002210050352
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    Electronic Resource
    Electronic Resource
    Morphological and physical characterization of the capsular layer of Vibrio cholerae O139 (1998)
    Springer
    Archives of microbiology 170 (1998), S. 339-344 
    Details
    ISSN: 1432-072X
    Keywords: Key wordsV. cholerae O139 ; Lipopolysaccharide ; Electron microscopy ; Freeze-substitution technique ; Capsule
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The morphological and physical characteristics of the capsule of Vibrio cholerae O139 were examined. An electron microscopic study using the freeze-substitution technique showed that all of the V. cholerae strains of the O139 serogroup examined have a very thin fibrous layer on the outside of the outer membrane. In contrast, the mutants of strain O139, strain MO10T4 (which lacks capsule synthesis), and strain Bengal-2R1 (which fails to synthesize both the capsule and the O-antigen of lipopolysaccharide) were all found to have lost the surface layer. In addition, the capsule layer could also not be observed on the surface of V. cholerae strain O1. To determine the biological characteristics of the capsule of strains of the O139 serogroup, we investigated the serum killing activity and bacterial phagocytosis by polymorphonuclear leukocytes. The O139 strains were more resistant to the serum killing activity than were the V. cholerae O1 strain and the O139 mutant strains, thus suggesting that the existence of the capsule gave a serum-resistant character to the O139 strains. The surface character of the O139 strains had the same hydrophobic character as did that of the O139 mutant strains and the O1 strain. In addition, all the V. cholerae O1 and O139 strains examined, including the mutant strains, were effectively ingested by the human polymorphonuclear leukocytes. The number of ingested bacteria was not significantly different among the strains, and the ingestion of the acapsular O139 mutants thus showed that the capsule does not play an antiphagocytic role. These data suggest that the capsule of V. cholerae O139 has a physiological function different from that of the ordinal hydrophilic capsule that is found in invasive bacteria such as Klebsiella pneumoniae.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002030050651
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    Electronic Resource
    Electronic Resource
    Phylogenetic affiliation and ultrastructure of uncultured magnetic bacteria with unusually large magnetosomes (1998)
    Springer
    Archives of microbiology 169 (1998), S. 136-147 
    Details
    ISSN: 1432-072X
    Keywords: Key words Magnetic bacteria ; Biomineralization ; Magnetite ; 16S rRNA ; In situ hybridization ; Ultrastructure ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Natural enrichments of magnetic bacteria from the Itaipu lagoon near Rio de Janeiro were dominated by coccoid-to-ovoid morphotypes that produced unusually large magnetosomes. To determine the phylogenetic position of these unusual microorganisms, 16S rRNA genes were retrieved from bacteria magnetically separated from sediment of the Itaipu lagoon by in vitro amplification and cloning of PCR products into a plasmid vector. Partial sequencing of the obtained clones revealed two clusters of closely related sequences affiliated to a distinct lineage consisting exclusively of magnetic bacteria within the α-subclass of Proteobacteria. For a detailed phylogenetic analysis, several almost complete sequences of the 16S rRNA genes were determined. One representative clone of each cluster provided a PCR template for the in vitro transcription of group-specific polynucleotide probes complementary to a variable region of the 16S rRNA molecule. At least three different morphotypes of magnetic bacteria were reliably identified by post-embedding hybridization of ultra-thin sections. Electron microscopic analyses of hybridized cells enabled for the first time a detailed description of the morphological variety and ultrastructure of phylogenetically identified, uncultured magnetic bacteria. Two distinct coccoid bacteria were identified by the transcript probe complementary to the 16S rRNA sequence mabrj12, whereas the probe complementary to the sequence mabrj58 allowed the identification of an ovoid morphotype that displayed magnetosomes with the largest volumes observed to date.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002030050553
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    Electronic Resource
    Cell biology, clinicopathological profile, and classification of gastro-enteropancreatic endocrine tumors (1998)
    Springer
    Journal of molecular medicine 76 (1998), S. 413-420 
    Details
    ISSN: 1432-1440
    Keywords: Key words Endocrine tumors ; Histochemistry ; Electron microscopy ; Pathology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  Recent developments in the field of endocrine cell biology and pathology at both morphological and molecular levels are briefly outlined and discussed as a basis for endocrine tumor characterization. The main tools available for identifying the endocrine nature of the tumors, their pathogenetic interpretation, and experimental reproduction with special emphasis on tumor antecedents are reported. Based on this, classifications of endocrine tumors of the pancreas and gastrointestinal tract are developed, covering most clinical (hyperfunctional syndromes included), pathological, and biological patterns, with special emphasis on tumor prognosis.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001090050233
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    Electronic Resource
    Electronic Resource
    Interaction of the Escherichia coli DnaA protein with bacteriophage k DNA (1998)
    Springer
    Molecular genetics and genomics 259 (1998), S. 679-688 
    Details
    ISSN: 1617-4623
    Keywords: Key words Bacteriophage λ ; DnaA-DNA interactions ; Electron microscopy ; DNA-protein complexes ; Escherichia coli
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Interaction of the Escherichia coli DnaA (replication initiator) protein with restriction fragments of phage λ DNA demonstrated differential binding of DnaA along the whole λ DNA. Interaction of DnaA with the λ replication region (from the promoter p R to the origin of replication, oriλ) demonstrated a strong binding of DnaA to the region around the p o promoter where synthesis of a short antisense oop RNA is initiated. The four sequences protected by DnaA (two 9mers and two 5mers) are not related even to a relaxed DnaA box. The pattern of protection of these four sequences and the location of three DNase I hypersensitive sites in the λ DNA r strand, together with results of mobility shift assays and electron microscopy studies, may indicate an interaction involving DnaA monomers bound to different DNA positions on one side of the helix and the formation of higher-order nucleoprotein structures. Therefore, it is tempting to suggest that DnaA, in addition to its activity in regulation of replication and transcription, could be considered as a factor which structures certain chromosomal regions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004380050863
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  • 40
    Electronic Resource
    Electronic Resource
    Virus assembly inHincksia hincksiae (Ectocarpales, Phaeophyceae) An electron and fluorescence microscopic study (1998)
    Springer
    Protoplasma 203 (1998), S. 153-167 
    Details
    ISSN: 1615-6102
    Keywords: Algae ; Virus assembly ; DAPI staining ; Electron microscopy ; Hincksia hincksiae ; Immunofluorescence ; Marine double-stranded DNA virus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The filamentous brown algaHincksia hincksiae can be infected by a large icosahedral double-stranded DNA virus (HincV-1). The virus shows extended latency and is replicated only in cells homologous to sporangia. Virus formation was studied by transmission electron microscopy, DAPI staining, and β-tubulin immunofluorescence. Inhibition of cytokineses results in multinucleate cells, which are the first indication of virus replication in productive cells; the microtubular cytoskeleton does not seem to be affected by the virus. Replication of viral DNA begins in the nuclei, which increase in size and eventually disintegrate. Virus assembly takes place in a mixed nucleo-/cytoplasm. Capsids bud from cisternae, which are interpreted as modified endoplasmic reticulum aggregated to virus assembly centres. The internal membranous component of the virus is thus derived from the endoplasmic reticulum. The particles are empty (electron translucent) when assembled, and the nucleoprotein core seems to be packaged subsequently through an opening in the capsid. A number of fine structural features not previously reported from brown algae and related to virus formation are described. Our results on Hincksia hincksiae virus are compared with observations made on various other icosahedral DNA viruses infecting eukaryotic algae and animals.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01279472
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    Electronic Resource
    Electron and X-ray microscopic analyses of reaggregated materials obtained after fractionation of dissolved sporopollenin (1998)
    Springer
    Protoplasma 204 (1998), S. 13-21 
    Details
    ISSN: 1615-6102
    Keywords: Sporopollenin ; Solubilisation ; 2-Aminoethanol ; Reaggregation ; Electron microscopy ; X-ray microscopy ; Thypha angustifolia L
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Exines fromTypha angustifolia L. pollen were dissolved in hot 2-aminoethanol. The solubilisate was successively fractionated and reaggregated via a dialysis cascade with dialysis tubings of different exclusion volumina. Four fractions of reaggregated material with different molecular mass were obtained. Fraction 1 with a molecular mass above 25,000 Da, fraction 2 with a molecular mass between 10,000–25,000 Da, fraction 3 with a molecular mass between 5,000–10,000 Da, and fraction 4 of a molecular mass lower than 5,000 Da. The fractions were comparatively analysed by scanning and transmission electron microscopy and X-ray microscopy. The material of the fractions with a molecular mass above 10,000 Da exhibit high congruence to the initial material. Analysis of the reaggregated material with the lowest molecular mass revealed special distinct substructures which in form and size showed high similarities to substructures of exines described in literature. In detail, spherical substructures consisting of an electron-dense core surrounded by an electron-transparent corona and in addition elongated substructures with a distinctive surface sculpture were detected.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01282289
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    Electronic Resource
    Callose deposition and breakdown, followed by phytomelan synthesis in the seed coat ofGasteria verrucosa (Mill.) H. Duval (1998)
    Springer
    Protoplasma 201 (1998), S. 221-230 
    Details
    ISSN: 1615-6102
    Keywords: Callose ; Electron microscopy ; Gasteria verrucosa ; Phenolics ; Phytomelan ; Seed coat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In the seed coat ofGasteria verrucosa the deposition of phytomelan takes place during seed development in three stages. Phytomelan is a black cell wall material which is chemically very inert. First the radial walls and part of the transverse cell wall of the outer epidermis of the outer integument become thickened by exocytosis of dictyosome vesicles. Callose is deposited at the tangential plasma membrane against those walls. After the callose deposition about two thirds of the original cell volume is filled with callose. During the second stage the callose is broken down, probably into glucose monomers or small polymers. At the same time cellulose is deposited at the outer tangential plasma membrane, forming a wall between the dissolving callose and the plasma membrane. In the third phase small granules appear in the solution of dissolved callose. which grow out and finally fuse to form a block of phytomelan, consisting of spherical 15-nm units. Remarkable is the function of the callose: it determines the size of the phytomelan block, and it probably functions as carbohydrate source for the phytomelan synthesis and/or for the cellulose inner layer. In this study transmission electron microscopy and cryo scanning electron microscopy are used to study the three developmental stages of the formation of the phytomelan layer.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01287418
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    Characterization of receptors with a new negative image: Use in molecular docking and lead optimization (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 321-336 
    Details
    ISSN: 0887-3585
    Keywords: surface characterization ; DOCK ; structure-based molecular design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The characterization of receptor binding sites is an important aspect of molecular docking, molecular recognition, and the structure-based design process. This characterization can take several forms: the receptor surface itself can be delineated or described, the space adjacent to the surface can be chemically mapped, or a negative image of the protein binding region can be generated. In this report, we describe a new method of constructing a negative image through generation of a set of spheres. These spheres lie along the receptor surface, and their centers represent possible ligand atom positions. By the method in which they are constructed, these spheres carry a limited amount of energetic and chemical information in addition to their primary geometric information. We test the accuracy of the image by comparing sphere positions to the positions of bound ligand atoms and propose a figure of merit for such tests. Then, we use the spheres to orient ligands in enzyme active sites and show how they can be used to generate low scoring configurations more efficiently than other approaches that search orientation space. In addition, two novel applications of these spheres are described: they are used to help identify structural differences among families of enzymes and to suggest points for ligand modification in analog design. Proteins 30:321-336, 1998. © 1998 Wiley-Liss, Inc.
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    Electronic Resource
    Nitric oxide myoglobin: Crystal structure and analysis of ligand geometry (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 352-356 
    Details
    ISSN: 0887-3585
    Keywords: myoglobin ; nitric oxide ; ligand binding ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of the ferrous nitric oxide form of native sperm whale myoglobin has been determined by X-ray crystallography to 1.7 Å resolution. The nitric oxide ligand is bent with respect to the heme plane: the Fe-N-O angle is 112°. This angle is smaller than those observed in model compounds and in lupin leghemoglobin. The exact angle appears to be influenced by the strength of the proximal bond and hydrogen bonding interactions between the distal histidine and the bound ligand. Specifically, the Nε atom of histidine64 is located 2.8 Å away from the nitrogen atom of the bound ligand, implying electrostatic stabilization of the FeNO complex. This interpretation is supported by mutagenesis studies. When histidine64 is replaced with apolar amino acids, the rate of nitric oxide dissociation from myoglobin increases tenfold. Proteins 30:352-356, 1998. © 1998 Wiley-Liss, Inc.
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  • 45
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    Electronic Resource
    A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 372-380 
    Details
    ISSN: 0887-3585
    Keywords: protein modeling ; crystal structure ; conformation change ; prediction ; mechanism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The occurrence of large domain motions associated with the mechanism of action of many proteins is well established. We present a general method of predicting domain closure applicable to proteins containing domains separated by an apparent hinge. The method attempts to allow for natural directional bias within the closing protein by repeatedly applying a weak pulling force over a short distance between pairs of atoms chosen at random in the two domains in question. Appropriate parameters governing the pulling function were determined empirically. The method was applied to the bi-lobal protein PGK and a closed-form activated ternary complex generated for Bacillus stearothermophilus PGK. This model was compared with the recently determined crystal structure of closed-form Trypanosoma brucei PGK. The model predicts the correct hinge regions, although the magnitude of movement at one hinge point was overestimated, and provides a reasonable representation of the closed-form ternary complex. Proteins 30:372-380, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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  • 46
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    Electronic Resource
    Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 388-400 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; free energy perturbation ; thermodynamics integration ; spherical solvent boundary potential ; cell multipole method ; Nosé-Hoover equation ; component analysis ; chymotrypsin inhibitor 2 ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We developed a software package for improved free energy calculation, in which spherical solvent boundary potential, cell multipole method, and Nosé-Hoover equation are employed. The performance of the developed software package is demonstrated in the case of valine to alanine mutation of the 57th residue in chymotrypsin inhibitor 2. By using this package, we obtained results quantitatively comparable to experimental results. By the free energy component analysis, it is shown that leucine 51, arginine 65, arginine 67, and phenylalanine 69 residues contribute significantly to the total free energy shift, ΔΔG. Among them, contribution from the hydrophilic arginine 67 residue, which is in close contact with the mutation site, is the largest. Structure around the mutation site is largely changed by the mutation. The structure change is caused mainly by two effects, hydrophobic interaction and short-range interaction along the sequence. Effects of Nosé-Hoover algorithm and Kirkwood reaction field are also discussed. Proteins 30:388-400, 1998. © 1998 Wiley-Liss, Inc.
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    Electronic Resource
    Proteolysis as a probe of thermal unfolding of cytochrome C (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 435-441 
    Details
    ISSN: 0887-3585
    Keywords: cytochrome c ; thermal unfolding ; proteolysis ; proteinase K ; thermolysin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recent hydrogen exchange experiments on native cytochrome c implicate a sequential unfolding pathway in contrast to a simple two-state process. We have studied the heat-induced unfolding of this protein by using spectroscopic measurements to detect changes in conformation and proteolytic enzyme digestion to identify regions of the protein that are labile. Several spectroscopic profiles were monitored: CD at 222 nm, a measurement of secondary structure change in the protein, the absorbance at 280 nm, involving the local environment of Trp 59, and absorbance at 420 nm, the Soret band of the heme. The apparent Tm values for these probes differ, consistent with an unfolding pathway containing intermediates. The limited digestion by proteinase K is consistent with population of an intermediate state in unfolding. We find a single strong region of cleavage at low temperature with retention of structure in each fragment. Proteins 30:435-441, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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    Crystallographic and spectroscopic characterization of a molecular hinge: Conformational changes in bothropstoxin I, a dimeric Lys49-phospholipase A2 homologue (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 442-454 
    Details
    ISSN: 0887-3585
    Keywords: venom toxin ; protein-membrane interaction ; X-ray diffraction ; spectroscopy ; quaternary structural change ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Bothropstoxin I (BthTX-I) from the venom of Bothrops jararacussuis a myotoxic phospholipase A2 (PLA2) homologue which, although catalytically inactive due to an Asp49→Lys substitution, disrupts the integrity of lipid membranes by a Ca2+-independent mechanism. The crystal structures of two dimeric forms of BthTX-I which diffract X-rays to resolutions of 3.1 and 2.1 Å have been determined. The monomers in both structures are related by an almost perfect twofold axis of rotation and the dimer interfaces are defined by contacts between the N-terminal α-helical regions and the tips of the β-wings of partner monomers. Significant differences in the relative orientation of the monomers in the two crystal forms results in “open” and “closed” dimer conformations. Spectroscopic investigations of BthTX-I in solution have correlated these conformational differences with changes in the intrinsic fluorescence emission of the single tryptophan residues located at the dimer interface. The possible relevance of this structural transition in the Ca2+-independent membrane damaging activity is discussed. Proteins 30:442-454, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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  • 49
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    Electronic Resource
    Structure-based design of model proteins (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 10-20 
    Details
    ISSN: 0887-3585
    Keywords: protein design ; lattice model ; protein stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A structure-based, sequence-design procedure is proposed in which one considers a set of decoy structures that compete significantly with the target structure in being low energy conformations. The decoy structures are chosen to have strong overlaps in contacts with the putative native state. The procedure allows the design of sequences with large and small stability gaps in a random-bond heteropolymer model in both two and three dimensions by an appropriate assignment of the contact energies to both the native and nonnative contacts. The design procedure is also successfully applied to the two-dimensional HP model. Proteins 31:10-20, 1998. © 1998 Wiley-Liss, Inc.
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  • 50
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    Electronic Resource
    Modelling repressor proteins docking to DNA (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 535-549 
    Details
    ISSN: 0887-3585
    Keywords: docking ; protein-DNA ; prediction ; structure ; base recognition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The docking of repressor proteins to DNA starting from the unbound protein and model-built DNA coordinates is modeled computationally. The approach was evaluated on eight repressor/DNA complexes that employed different modes for protein/ DNA recognition. The global search is based on a protein-protein docking algorithm that evaluates shape and electrostatic complementarity, which was modified to consider the importance of electrostatic features in DNA-protein recognition. Complexes were then ranked by an empirical score for the observed amino acid /nucleotide pairings (i.e., protein-DNA pair potentials) derived from a database of 20 protein/DNA complexes. A good prediction had at least 65% of the correct contacts modeled. This approach was able to identify a good solution at rank four or better for three out of the eight complexes. Predicted complexes were filtered by a distance constraint based on experimental data defining the DNA footprint. This improved coverage to four out of eight complexes having a good model at rank four or better. The additional use of amino acid mutagenesis and phylogenetic data defining residues on the repressor resulted in between 2 and 27 models that would have to be examined to find a good solution for seven of the eight test systems. This study shows that starting with unbound coordinates one can predict three-dimensional models for protein/DNA complexes that do not involve gross conformational changes on association. Proteins 33:535-549, 1998. © 1998 Wiley-Liss, Inc.
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    Influence of protein structure databases on the predictive power of statistical pair potentials (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 139-149 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; statistical potentials ; protein structure database ; assessing protein models ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A long standing goal in protein structure studies is the development of reliable energy functions that can be used both to verify protein models derived from experimental constraints as well as for theoretical protein folding and inverse folding computer experiments. In that respect, knowledge-based statistical pair potentials have attracted considerable interests recently mainly because they include the essential features of protein structures as well as solvent effects at a low computing cost. However, the basis on which statistical potentials are derived have been questioned. In this paper, we investigate statistical pair potentials derived from protein three-dimensional structures, addressing in particular questions related to the form of these potentials, as well as to the content of the database from which they are derived. We have shown that statistical pair potentials depend on the size of the proteins included in the database, and that this dependence can be reduced by considering only pairs of residue close in space (i.e., with a cutoff of 8 Å). We have shown also that statistical potentials carry a memory of the quality of the database in terms of the amount and diversity of secondary structure it contains. We find, for example, that potentials derived from a database containing α-proteins will only perform best on α-proteins in fold recognition computer experiments. We believe that this is an overall weakness of these potentials, which must be kept in mind when constructing a database. Proteins 31:139-149, 1998. © 1998 Wiley-Liss, Inc.
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    Crystal structure of the disulfide-stabilized Fv fragment of anticancer antibody B1: Conformational influence of an engineered disulfide bond (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 128-138 
    Details
    ISSN: 0887-3585
    Keywords: antibody ; antitumor ; single chain Fv ; variable domains ; X-ray crystallography ; protein structure ; protein stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A recombinant Fv construct of the B1 monoclonal antibody that recognizes the LewisY-related carbohydrate epitope on human carcinoma cells has been prepared. The Fv is composed of the polypeptide chains of the VH and VL domains expressed independently and isolated as inclusion bodies. The Fv is prepared by combining and refolding equimolar amounts of guanidine chloride solubilized inclusion bodies. The Fv is stabilized by an engineered interchain disulfide bridge between residues VL100 and VH44. This construct has a similar binding affinity as that of the single-chain construct (Benhar and Pastan, Clin. Cancer Res. 1:1023-1029, 1995). The B1 disulfide-stabilized Fv (B1dsFv) crystallizes in space group P6122 with the unit cell parameters a = b = 80.1 Å, and c = 138.1 Å. The crystal structure of the B1dsFv has been determined at 2.1-Å resolution using the molecular replacement technique. The final structure has a crystallographic R-value of 0.187 with a root mean square deviation in bond distance of 0.014 Å and in bond angle of 2.74°. Comparisons of the B1dsFv structure with known structures of Fv regions of other immunoglobulin fragments shows closely related secondary and tertiary structures. The antigen combining site of B1dsFv is a deep depression 10-Å wide and 17-Å long with the walls of the depression composed of residues, many of which are tyrosines, from complementarity determining regions L1, L3, H1, H2, and H3. Model building studies indicate that the LewisY tetrasaccharide, Fuc-Gal-Nag-Fuc, can be accommodated in the antigen combining site in a manner consistent with the epitope predicted in earlier biochemical studies (Pastan, Lovelace, Gallo, Rutherford, Magnani, and Willingham, Cancer Res. 51:3781-3787, 1991). Thus, the engineered disulfide bridge appears to cause little, if any, distortion in the Fv structure, making it an effective substitute for the B1 Fab. Proteins 31:128-138, 1998. Published 1998 Wiley-Liss, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
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    Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 150-159 
    Details
    ISSN: 0887-3585
    Keywords: photosynthetic reaction center ; bacteriorhodopsin ; cytochrome C oxidase ; zipper ; packing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Membrane-embedded protein domains frequently exist as α-helical bundles, as exemplified by photosynthetic reaction centers, bacteriorhodopsin, and cytochrome C oxidase. The sidechain packing between their transmembrane helices was investigated by a nearest-neighbor analysis which identified sets of interfacial residues for each analyzed helix-helix interface. For the left-handed helix-helix pairs, the interfacial residues almost exclusively occupy positions a, d, e, or g within a heptad motif (abcdefg) which is repeated two to three times for each interacting helical surface. The connectivity between the interfacial residues of adjacent helices conforms to the knobs-into-holes type of sidechain packing known from soluble coiled coils. These results demonstrate on a quantitative basis that the geometry of sidechain packing is similar for left-handed helix-helix pairs embedded in membranes and coiled coils of soluble proteins. The transmembrane helix-helix interfaces studied are somewhat less compact and regular as compared to soluble coiled coils and tolerate all hydrophobic amino acid types to similar degrees. The results are discussed with respect to previous experimental findings which demonstrate that specific interactions between transmembrane helices are important for membrane protein folding and/or oligomerization. Proteins 31:150-159, 1998. © 1998 Wiley-Liss, Inc.
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    Protein folding in the landscape perspective: Chevron plots and non-arrhenius kinetics (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 2-33 
    Details
    ISSN: 0887-3585
    Keywords: chevron plot ; energy landscape ; folding funnel ; kinetic trap ; lattice models ; non-Arrhenius behavior ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We use two simple models and the energy landscape perspective to study protein folding kinetics. A major challenge has been to use the landscape perspective to interpret experimental data, which requires ensemble averaging over the microscopic trajectories usually observed in such models. Here, because of the simplicity of the model, this can be achieved. The kinetics of protein folding falls into two classes: multiple-exponential and two-state (single-exponential) kinetics. Experiments show that two-state relaxation times have “chevron plot” dependences on denaturant and non-Arrhenius dependences on temperature. We find that HP and HP+ models can account for these behaviors. The HP model often gives bumpy landscapes with many kinetic traps and multiple-exponental behavior, whereas the HP+ model gives more smooth funnels and two-state behavior. Multiple-exponential kinetics often involves fast collapse into kinetic traps and slower barrier climbing out of the traps. Two-state kinetics often involves entropic barriers where conformational searching limits the folding speed. Transition states and activation barriers need not define a single conformation; they can involve a broad ensemble of the conformations searched on the way to the native state. We find that unfolding is not always a direct reversal of the folding process. Proteins 30:2-33, 1998. © 1998 Wiley-Liss, Inc.
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    Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 49-60 
    Details
    ISSN: 0887-3585
    Keywords: kohonen network ; mitochondrial processing peptidase (MPP) ; mitochondrial intermediate peptidase (MIP) ; neural network ; protein import ; sequence motif ; mitochondrial targeting ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cleavage sites in nuclear-encoded mitochondrial protein targeting peptides (mTPs) from mammals, yeast, and plants have been analysed for characteristic physicochemical features using statistical methods, perceptrons, multilayer neural networks, and self-organizing feature maps. Three different sequence motifs were found, revealing loosely defined arginine motifs with Arg in positions -10, -3, and -2. A self-organizing feature map was able to cluster these three types of endopeptidase target sites but did not identify any species-specific characteristics in mTPs. Neural networks were used to define local sequence features around precursor cleavage sites. Proteins 30:49-60, 1998. © 1998 Wiley-Liss, Inc.
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    Don Caspar, TMV, and protein-protein interactions (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 109-112 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    A hybrid sequence approach to the paracelsus challenge (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 136-143 
    Details
    ISSN: 0887-3585
    Keywords: protein design ; protein structure ; circular dichroism ; trifluoroethanol ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Inspired by the Paracelsus Challenge of Rose and Creamer (Proteins 19:1-3, 1994), we have designed a protein sequence that is 50% identical to an all-helical protein but is intended to fold into a largely β-sheet structure. Rather than attempt a de novo design, our strategy was to construct a hybrid sequence based on a helical “parent” protein (434 Cro) and a “target” protein with the desired fold (the B1 domain of protein G). The hybrid sequence (Crotein-G) is 50% identical to 434 Cro but is also 62% identical to the B1 domain of protein G. We also created a variant of Crotein-G (ZCrotein-G) that contains a potential His3Cys1 zinc binding site. At low protein concentrations and in the presence of 20% 2,2,2-trifluoroethanol (TFE) (v/v), the circular dichroism spectra of the designed proteins are distinct from that of 434 Cro and similar to that of the B1 domain of protein G. However, the proteins fail to denature in a cooperative manner. Furthermore, aggregation occurs at moderate protein concentrations or in the absence of TFE. Addition of zinc to ZCrotein-G does not promote structure formation. In summary, 434 Cro has been altered to something that may resemble the B1 domain of protein G, but the protein does not adopt a native structure. Proteins 30:136-143, 1998. © 1998 Wiley-Liss, Inc.
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    Monte Carlo simulation of denaturation of adsorbed proteins (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 168-176 
    Details
    ISSN: 0887-3585
    Keywords: denaturation kinetics ; irreversible conformational changes ; metastable states ; folding temperature ; lattice model ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Denaturation of model proteinlike molecules at the liquid-solid interface is simulated over a wide temperature range by employing the lattice Monte Carlo technique. Initially, the molecule containing 27 monomers of two types (A and B) is assumed to be adsorbed in the native folded state (a 3 × 3 × 3 cube) so that one of its sides is in contact with the surface. The details of the denaturation kinetics are found to be slightly dependent on the choice of the side, but the main qualitative conclusions hold for all the sides. In particular, the kinetics obey approximately the conventional first-order law at T 〉 Tc (Tc is the collapse temperature for solution). With decreasing temperature, below Tc but above Tf (Tf is the folding temperature for solution), deviations appear from the first-order kinetics. For the most interesting temperatures, that is, below Tf, the denaturation kinetics are shown to be qualitatively different from the conventional ones. In particular, the denaturation process occurs via several intermediate steps due to trapping in metastable states. Mathematically, this means that (i) the transition to the denatured state of a given molecule is nonexponential, and (ii) the denaturation process cannot be described by a single rate constant kr. One should rather introduce a distribution of values of this rate constant (different values of kr correspond to the transitions to the altered state via different metastable states). Proteins 30:168-176, 1998. © 1998 Wiley-Liss, Inc.
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    Monte Carlo simulation of the kinetics of protein adsorption (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 177-182 
    Details
    ISSN: 0887-3585
    Keywords: adsorption ; irreversible conformational changes ; denaturation rate constant ; kinetic control ; diffusion control ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Adsorption of proteins occurs via diffusion toward the interface, actual adsorption, and subsequent irreversible conformational changes resulting in denaturation of the native protein structure. The conventional kinetic models describing these steps are based on the assumption that the denaturation transitions obey the first-order law with a single value of the denaturation rate constant kr. Meanwhile, recent Monte Carlo simulations indicate that, in general, the denaturation process cannot be described by a single rate constant kr. One should rather introduce a distribution of this rate constant (physically, different values of kr correspond to the transitions to the altered state via different metastable states). We have calculated the kinetics of irreversible adsorption of proteins with and without distribution of the denaturation rate constant kr in the limits when protein diffusion in the solution is, respectively, rapid or slow. In both cases, the adsorption kinetics with distribution of kr are found to be close to those with a single-valued rate constant kr provided that the average value of kr in the former case is equal to kr for the latter case. This conclusion holds even for wide distributions of kr. The consequences of this finding for the fitting of global experimental kinetics on the basis of phenomenological equations are briefly discussed. Proteins 30:177-182, 1998. © 1998 Wiley-Liss, Inc.
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    Structural diversity of sequentially identical subsequences of proteins: Identical octapeptides can have different conformations (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 228-231 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; local vs. non-local interactions ; secondary structure prediction ; fragment matching algorithms ; PDB ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: One of the most important questions in the protein folding problem is whether secondary structures are formed entirely by local interactions. One way to answer this question is to compare identical subsequences of proteins to see if they have identical structures. Such an exercise would also reveal a lower limit on the number of amino acids needed to form unique secondary structures. In this context, we have searched the April 1996 release of the Protein Data Bank for sequentially identical subsequences of proteins and compared their structures. We find that identical octamers can have different conformations. In addition, there are several examples of identical heptamers with different conformations, and the number of identical hexamers with different conformations has increased since the previous PDB releases. These observations imply that secondary structure can be formed entirely by non-local interactions and that an identical match of up to eight amino acids may not imply structural similarity. In addition to the larger context of the protein folding problem, these observations have implications for protein structure prediction methods. Proteins 30:228-231, 1998. © 1998 Wiley-Liss, Inc.
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    Structural modeling of the complex between an acetylcholine receptor-mimicking antibody and its snake toxin antigen (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 249-263 
    Details
    ISSN: 0887-3585
    Keywords: antibody-antigen complex ; snake toxin ; protein docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The antibody Mα2-3 neutralizes the functional, acetylcholine receptor binding activity of its antigen, neurotoxin α, and exhibits several other properties in common with the receptor itself. We present here the results of calculations examining the three-dimensional structure of the toxin α:Mα2-3 complex. The antigen structure, determined by nuclear magnetic resonance spectroscopy,1 was docked to models of the variable fragment of the antibody combining site2 by using a method based on surface complementarity and maximization of buried surface area3,4 while taking into account the possibility of conformational change on complexation. Extensive experimental information on the location of the functional epitope was incorporated into the analysis and used to screen candidate geometries of the complex resulting from the modeling. Eight plausible structures that are in accord with the experimental data were derived. Common structural features of the models are discussed, and residues of the antibody-combining site that are expected to play important roles in complexation are identified. In particular, three epitope residues that, according to mutagenesis experiments, make particularly strong contributions to the binding, interact excentrically and do not make contact with the central loops of the combining site, L3 and H3. Proteins 30:249-263, 1998. © 1998 Wiley-Liss, Inc.
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    Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 287-294 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; side chain contact prediction ; lattice protein models ; CREB-binding protein ; KIX domain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using a recently developed protein folding algorithm, a prediction of the tertiary structure of the KIX domain of the CREB binding protein is described. The method incorporates predicted secondary and tertiary restraints derived from multiple sequence alignments in a reduced protein model whose conformational space is explored by Monte Carlo dynamics. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that was modified for the presence of predicted U-turns, i.e., regions where the chain reverses global direction. Tertiary restraints are obtained via a two-step process: First, seed side-chain contacts are identified from a correlated mutation analysis, and then, a threading-based algorithm expands the number of these seed contacts. Blind predictions indicate that the KIX domain is a putative three-helix bundle, although the chirality of the bundle could not be uniquely determined. The expected root-mean-square deviation for the correct chirality of the KIX domain is between 5.0 and 6.2 Å. This is to be compared with the estimate of 12.9 Å that would be expected by a random prediction, using the model of F. Cohen and M. Sternberg (J. Mol. Biol. 138:321-333, 1980). Proteins 30:287-294, 1998. © 1998 Wiley-Liss, Inc.
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    Mass spectrometric identification and microcharacterization of proteins from electrophoretic gels: Strategies and applications (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 74-89 
    Details
    ISSN: 0887-3585
    Keywords: mass spectrometry ; matrix-assisted laser desorption/ionization ; electrospray ; database searching ; gel electrophoresis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The entire genomic DNA sequences of a number of prokaryotic and eukaryotic species are now available and many more, including the human genome, will be completed in the near future. The state-of-life of a cell at any given time, however, is defined by its protein composition, i.e., its proteome. Gel electrophoresis, mass spectrometry, and bioinformatics will be important tools for protein and proteome analysis in the post-genome era. Protein identification from electrophoretic gels by mass spectrometric peptide mapping or peptide sequencing combined with sequence database searching is established and has been applied to numerous biological systems. We describe current strategies and selected applications in molecular and cell biology. The next challenges are detailed structure/function analyses, which include studying the molecular composition of multiprotein complexes and characterization of secondary modifications of proteins. The advantages and limitations of a number of mass spectrometry-based strategies designed for microcharacterization of low amounts of protein from electrophoretic gels are discussed and illustrated by examples. Proteins Suppl. 2:74-89, 1998. © 1998 Wiley-Liss, Inc.
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    A fusion protein between serum amyloid A and staphylococcal nuclease - synthesis, purification, and structural studies (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 381-387 
    Details
    ISSN: 0887-3585
    Keywords: serum amyloid A ; fluorescence ; circular dichroism ; acute phase ; denaturation ; nuclease ; amyloidosis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We developed a recombinant DNA system to overexpress a fusion protein between the small, minimally soluble acute phase serum protein, serum amyloid A (SAA), and the bacterial enzyme staphylococcal nuclease (SN). This fusion protein is very soluble and is immunoreactive to polyclonal anti-SAA antibodies. Tryptophan fluorescence shows smooth denaturation curves for the fusion protein in guanidinium HCl or potassium thiocyanate. Fluorescence also indicates that only a single tryptophan residue (of the four present) is accessible to iodide quenching and, presumably, is exposed on the surface of the fusion protein. Circular dichroism (CD) shows a significant signal indicating α-helix, which can be attributed to the SAA portion of the molecule; these are the first CD spectral data available for SAA. pH titration shows persistence of helix domains for the fusion protein at pH 3.0, in contrast to the denaturation of SN under the same conditions. (The entire fusion protein shows a random coil pattern below pH 3.0.) By exploiting the structural and solubility properties of SN, this fusion protein has provided the first structural data about SAA - the precursor of the amyloid deposits in secondary amyloidosis. This fusion protein should be useful for further physical and physiologic studies of SAA. Proteins 30:381-387, 1998. © 1998 Wiley-Liss, Inc.
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    The PDP: Past, present, and future (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 1-1 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    Direct observation of an altered quaternary-structure transition in a mutant aspartate transcarbamoylase (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 383-390 
    Details
    ISSN: 0887-3585
    Keywords: time-resolved small-angle X-ray scattering ; allosterism ; domain closure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Time-resolved small-angle X-ray scattering (TR-SAXS) was used to monitor the structural changes that occur upon the binding of the natural substrates to a mutant version of the allosteric enzyme aspartate transcarbamoylase from Escherichia coli, in which the creation of a critical link stabilizing the R state of the enzyme is hindered. Previously, SAXS experiments at equilibrium showed that the structures of the unligated mutant enzyme and the mutant enzyme saturated with a bisubstrate analog are indistinguishable from the T and R state structures, respectively, of the wild-type enzyme (Tauc et al., Protein Sci. 3:1998-2004, 1994). However, as opposed to the wild-type enzyme, the combination of one substrate, carbamoyl phosphate, and succinate, an analog of aspartate, did not convert the mutant enzyme into the R state. By using TR-SAXS we have been able to study the transient steady-state during catalysis using the natural substrates rather than the nonreactive substrate analogs. The steady-state in the presence of saturating amount of substrates is a mixture of 60% T and 40% R structures, which is further converted entirely to R in the additional presence of ATP. These results provide a structural explanation for the reduced cooperativity observed with the mutant enzyme as well as for the stimulation by ATP at saturating concentrations of substrates. They also illustrate the crucial role played by domain motions and quaternary-structure changes for both the homotropic and heterotropic aspects of allostery. Proteins 31:383-390, 1998. © 1998 Wiley-Liss, Inc.
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    Structural investigation of C4b-binding protein by molecular modeling: Localization of putative binding sites (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 391-405 
    Details
    ISSN: 0887-3585
    Keywords: complement control protein ; protein modeling ; blood coagulation ; C4b-binding protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: C4b-binding protein (C4BP) contributes to the regulation of the classical pathway of the complement system and plays an important role in blood coagulation. The main human C4BP isoform is composed of one β-chain and seven α-chains essentially built from three and eight complement control protein (CCP) modules, respectively, followed by a nonrepeat carboxy-terminal region involved in polymerization of the chains. C4BP is known to interact with heparin, C4b, complement factor I, serum amyloid P component, streptococcal Arp and Sir proteins, and factor VIII/VIIIa via its α-chains and with protein S through its β-chain. The principal aim of the present study was to localize regions of C4BP involved in the interaction with C4b, Arp, and heparin. For this purpose, a computer model of the 8 CCP modules of C4BP α-chain was constructed, taking into account data from previous electron microscopy (EM) studies. This structure was investigated in the context of known and/or new experimental data. Analysis of the α-chain model, together with monoclonal antibody studies and heparin binding experiments, suggests that a patch of positively charged residues, at the interface between the first and second CCP modules, plays an important role in the interaction between C4BP and C4b/Arp/Sir/heparin. Putative binding sites, secondary-structure prediction for the central core, and an overall reevaluation of the size of the C4BP molecule are also presented. An understanding of these intermolecular interactions should contribute to the rational design of potential therapeutic agents aiming at interfering specifically some of these protein-protein interactions. Proteins 31:391-405, 1998. © 1998 Wiley-Liss, Inc.
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    Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 406-416 
    Details
    ISSN: 0887-3585
    Keywords: electrostatics ; Brownian dynamics ; triose phosphate isomerase ; diffusion-control ; similarity index ; rate enhancement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Triose phosphate isomerase (TIM) is a diffusion-controlled enzyme whose rate is limited by the diffusional encounter of the negatively charged substrate glyceraldehyde 3-phosphate (GAP) with the homodimeric enzyme's active sites. Translational and orientational steering of GAP toward the active sites by the electrostatic field of chicken muscle TIM has been observed in previous Brownian dynamics (BD) simulations. Here we report simulations of the association of GAP with TIMs from four species with net charges at pH 7 varying from -12e to +12e. Computed second-order rate constants are in good agreement with experimental data. The BD simulations and computation of average Boltzmann factors of substrate-protein interaction energies show that the protein electrostatic potential enhances the rates for all the enzymes. There is much less variation in the computed rates than might be expected on the basis of the net charges. Comparison of the electrostatic potentials by means of similarity indices shows that this is due to conservation of the local electrostatic potentials around the active sites which are the primary determinants of electrostatic steering of the substrate. Proteins 31:406-416, 1998. © 1998 Wiley-Liss, Inc.
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    Functional conformational changes of endo-1,4-xylanase II from Trichoderma reesei: A molecular dynamics study (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 434-444 
    Details
    ISSN: 0887-3585
    Keywords: hinge ; structural change ; xylose ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recent crystallographic studies have revealed a range of structural changes in the three-dimensional structure of endo-1,4-xylanase (XYNII) from Trichoderma reesei. The observed conformational changes can be described as snapshots of an open-close movement of the active site of XYNII. These structures were further analyzed in this study. In addition, a total of four 1 ns molecular dynamics (MD) simulations were performed representing different states of the enzyme. A comparison of the global and local changes found in the X-ray structures and the MD runs suggested that the simulations reproduced a similar kind of active site opening and closing as predicted by the crystal structures. The open-close movement was characterized by the use of distance difference matrixes and the Hingefind program (Wriggers and Schulten, Proteins 29:1-14, 1997) to be a ‘hinge-bending’ motion involving two large rigidly-moving regions and an extended hinge. This conformational feature is probably inherent to this molecular architecture and probably plays a role in the function of XYNII. Proteins 31:434-444, 1998. © 1998 Wiley-Liss, Inc.
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    Interaction of human SRY protein with DNA: A molecular dynamics study (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 417-433 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; sex-determining region Y (SRY) protein ; high mobility group (HMG) box ; DNA-binding proteins ; DNA bending ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations have been conducted to study the interaction of human sex-determining region Y (hSRY) protein with DNA. For this purpose, simulations of the hSRY high mobility group (HMG) domain (hSRY-HMG) with and without its DNA target site, a DNA octamer, and the DNA octamer alone have been carried out, employing the NMR solution structure of hSRY-HMG-DNA complex as a starting model. Analyses of the simulation results demonstrated that the interaction between hSRY and DNA was hydrophobic, just a few hydrogen bonds and only one water molecule as hydrogen-bonding bridge were observed at the protein-DNA interface. These two hydrophobic cores in the hSRY-HMG domain were the physical basis of hSRY-HMG-DNA specific interaction. They not only maintained the stability of the complex, but also primarily caused the DNA deformation. The salt bridges formed between the positive-charged residues of hSRY and phosphate groups of DNA made the phosphate electroneutral, which was advantageous for the deformation of DNA and the formation of a stable complex. We predicted the structure of hSRY-HMG domain in the free state and found that both hSRY and DNA changed their conformations to achieve greater complementarity of geometries and properties during the binding process; that is, the protein increased the angle between its long and short arms to accommodate the DNA, and the DNA became bent severely to adapt to the protein, although the conformational change of DNA was more severe than that of the hSRY-HMG domain. The sequence specificity and the role of residue Met9 are also discussed. Proteins 31:417-433, 1998. © 1998 Wiley-Liss, Inc.
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    Density functional studies on herpes simplex virus type 1 thymidine kinase-substrate interactions: The role of Tyr-172 and Met-128 in thymine fixation (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 453-459 
    Details
    ISSN: 0887-3585
    Keywords: quantum mechanical calculations ; substrate-enzyme interactions ; mutants ; functional role of amino acids ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The enzyme herpes simplex virus type 1 thymidine kinase (HSV1 TK) salvages thymidine into the DNA metabolism of the virus. In the active site, the thymine ring of the nucleoside binds in a pocket, formed by two residues, Tyr-172 and Met-128, in a sandwich-type orientation. To investigate the nature of the thymine-enzyme pocket interactions, we have carried out density functional theory calculations with gradient-corrected exchange-correlation functionals of models of the thymine-HSV1 TK adduct. Our calculations indicate that the role of Met-128 in the substrate fixation is purely steric and hydrophobic, while the substrate-Tyr-172 interaction is essentially electrostatic in nature. These findings are completely consistent with the available catalytic properties of mutants on the 128 position. Proteins 31:453-459, 1998. © 1998 Wiley-Liss, Inc.
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    Electrostatics, allostery, and activity of the yeast chorismate mutase (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 445-452 
    Details
    ISSN: 0887-3585
    Keywords: chorismate mutase ; activity ; allosteric ; electrostatics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The predicted active site of chorismate mutase of baker's yeast Saccharomyces cerevisiae has been studied by continuum electrostatics, molecular surface/volume calculations, and molecular modeling. Our study shows that despite being subject to an allosteric transition, the enzyme's active-site pocket neither decreased in volume nor deformed significantly in shape between the active R state and the inactive T state. We find that the polar atmosphere in the pocket is responsible for the enzyme's affinity. A single amino acid, Glu23, can adequately account for the atmospheric variation. This residue swings into the active-site pocket from the R state to the T state. In the R state, Glu23 on helix H2 doubly pairs with Arg204 and Lys208 of H11, which is packed against H2. In the T state, a slide occurs between H11 and H2 such that Glu23 can no longer interact with Lys208 and competes with Asp24 for interacting with Arg204. Consequently, Glu23 is found in the T state to couple with Arg157, an active-site residue critical to substrate binding. The tandem sliding of H11 in both monomers profoundly changes the interactions in the dimer interface. The loop between H11 and H12 demonstrates the largest conformational change. Hence, we establish a connection between the allosteric transition and the activity of the enzyme. The conformational change in the transition is suggested to propagate into the active-site pocket via a series of polar interactions that result in polarity reversal in the active-site pocket, which regulates the enzyme's activity. Proteins 31:445-452, 1998. © 1998 Wiley-Liss, Inc.
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    Evidence of new cadmium binding sites in recombinant horse L-chain ferritin by anomalous Fourier difference map calculation (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 477-485 
    Details
    ISSN: 0887-3585
    Keywords: X-ray structure ; L-chain apoferritin ; metal binding sites ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We refined the structure of the tetragonal form of recombinant horse L-chain apoferritin to 2.0 Å and we compared it with that of the cubic form previously refined to the same resolution. The major differences between the two structures concern the cadmium ions bound to the residues E130 at the threefold axes of the molecule. Taking advantage of the significant anomalous signal (f′′ = 3.6 e-) of cadmium at 1.375 Å, the wavelength used here, we performed anomalous Fourier difference maps with the refined model phases. These maps reveal the positions of anomalous scatterers at different locations in the structure. Among these, some are found near residues that were known previously to bind metal ions, C48, E57, C126, D127, E130, and H132. But new cadmium binding sites are evidenced near residues E53, E56, E57, E60, and H114, which were suggested to be involved in the iron loading process. The quality of the anomalous Fourier difference map increases significantly with noncrystallographic symmetry map averaging. Such maps reveal density peaks that fit the positions of Met and Cys sulfur atoms, which are weak anomalous scatterers (f′′ = 0.44 e-). Proteins 31:477-485, 1998. © 1998 Wiley-Liss, Inc.
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    The biology workbench - A seamless database and analysis environment for the biologist (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 1-2 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    Calculation of HyHel10-lysozyme binding free energy changes: Effect of ten point mutations (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 39-48 
    Details
    ISSN: 0887-3585
    Keywords: antibody ; antigen ; electrostatics ; binding ; finite difference ; Poisson-Boltzmann ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The change in free energy of binding of hen egg white lysozyme (HEL) to the antibody HyHel-10 arising from ten point mutations in HEL (D101K, D101G, K96M, K97D, K97G, K97G, R21E, R21K, W62Y, and W63Y) was calculated using a combination of the finite difference Poisson-Boltzmann method for the electrostatic contribution, a solvent accessible surface area term for the non-polar contribution, and rotamer counting for the sidechain entropy contribution. Comparison of experimental and calculated results indicate that because of pKa shifts in some of the mutated residues, primarily those involving Aspartate or Glutamate, proton uptake or release occurs in binding. When this effect was incorporated into the binding free energy calculations, the agreement with experiment improved significantly, and resulted in a mean error of about 1.9 kcal/mole. Thus these calculations predict that there should be a significant pH dependence to the change in binding caused by these mutations. The other major contributions to binding energy changes comes from solvation and charge charge interactions, which tend to oppose each other. Smaller contributions come from nonpolar interactions and sidechain entropy changes. The structures of the HyHel-10-HEL complexes with mutant HEL were obtained by modeling, and the effect of the modeled structure on the calculations was also examined. “Knowledge based” modeling and automatic generation of models using molecular mechanics produced comparable results. Proteins 33:39-48, 1998. © 1998 Wiley-Liss, Inc.
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    Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase KAtomic coordinates have been deposited with the Protein Data Bank, Brookhaven National Laboratory. (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 30-38 
    Details
    ISSN: 0887-3585
    Keywords: lactoferrin ; proteinase K ; complex, hydrolysis ; structure ; inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Lactoferrin is an iron binding glycoprotein with a molecular weight of 80 kDa. The molecule is divided into two lobes representing the N-terminal and C-terminal halves of the polypeptide chain, each containing an iron binding site. The serine proteinases such as trypsin, chymotrypsin, and pepsin hydrolyze lactoferrin into two unequal halves while proteinase K divides this protein into two equal halves. In the first step of hydrolysis by proteinase K, the C- and N-lobes, each having a molecular weight of approximately 40 kDa, are generated. In the next step, the lobes are further hydrolyzed into small molecular weight peptides. The proteinase K isolated from the hydrolyzed product does not show enzymatic activity suggesting that the enzyme is inhibited. Furthermore, the hydrolysis experiments on N-lobe and C-lobe showed that the inhibitory fragment came from the C-lobe. The purified lactoferrin fragment was found to be a decapeptide with an amino acid sequence of H2N-Val-Ala-Gln-Gly-Ala-Ala-Gly-Leu-Ala-COOH. The complex formed between proteinase K and lactoferrin fragment was crystallized by microdialysis. The crystals belonged to the monoclinic space group P21with cell dimensions a = 44.4 Å, b = 38.6 Å, c = 79.2 Å, β = 105.8o and Z = 2. The crystal structure has been determined at 2.4 Å resolution. It has been refined to an R factor of 0.163 for 9044 reflections. The Lf-fragment forms several intermolecular interactions with proteinase K. The Ser-224 Oγ and His-57 Nε2 move away to a distance of 3.68 Å in the complex. In the crystal structure, Gln-3I (I indicates inhibitor i.e., lactoferrin fragment) is involved in a direct intermolecular interaction with a symmetry related proteinase K molecule through a strong hydrogen bond with Asp-254. The mode of intermolecular interactions in the complex conformational features of the enzyme and placement of the fragment with respect to the enzyme resemble with the molecular complex of proteinase K with its natural inhibitor PKI3 from wheat. Proteins 33:30-38, 1998. © 1998 Wiley-Liss, Inc.
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    Dictionary of recurrent domains in protein structures (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 88-96 
    Details
    ISSN: 0887-3585
    Keywords: fold classification ; substructures ; Dali ; protein families ; structural similarity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The rapid growth in the number of experimentally determined three-dimensional protein structures has sharpened the need for comprehensive and up-to-date surveys of known structures. Classic work on protein structure classification has made it clear that a structural survey is best carried out at the level of domains, i.e., substructures that recur in evolution as functional units in different protein contexts. We present a method for automated domain identification from protein structure atomic coordinates based on quantitative measures of compactness and, as the new element, recurrence. Compactness criteria are used to recursively divide a protein into a series of successively smaller and smaller substructures. Recurrence criteria are used to select an optimal size level of these substructures, so that many of the chosen substructures are common to different proteins at a high level of statistical significance. The joint application of these criteria automatically yields consistent domain definitions between remote homologs, a result difficult to achieve using compactness criteria alone. The method is applied to a representative set of 1,137 sequence-unique protein families covering 6,500 known structures. Clustering of the resulting set of domains (substructures) yields 594 distinct fold classes (types of substructures). The Dali Domain Dictionary (http://www.embl-ebi.ac.uk/dali) not only provides a global structural classification, but also a comprehensive description of families of protein sequences grouped around representative proteins of known structure. The classification will be continuously updated and can serve as a basis for improving our understanding of protein evolution and function and for evolving optimal strategies to complete the map of all natural protein structures. Proteins 33:88-96, 1998. © 1998 Wiley-Liss, Inc.
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    Crystal structures of HLA-A*0201 complexed with antigenic peptides with either the amino- or carboxyl-terminal group substituted by a methyl group (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 97-106 
    Details
    ISSN: 0887-3585
    Keywords: antigenic peptides ; class I MHC molecules ; HLA-A2 complexes ; hydrogen bonds ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structures of class I major histocompatibility complex (MHC) molecules complexed with antigenic peptides revealed a network of hydrogen bonds between the charged amino- and carboxyl-termini of the peptides and conserved MHC residues at both ends of the peptide binding site. These interactions were shown to contribute substantially to the stability of class I MHC/peptide complexes by thermal denaturation studies using synthetic peptides in which either the amino- or carboxyl-terminal group is substituted by a methyl group. Here we report crystal structures of HLA-A*0201 complexed with these terminally modified synthetic peptides showing that they adopt the same bound conformation as antigenic peptides. A number of variations in peptide conformation were observed for the terminally modified peptides, including in one case, a large conformational difference in four central peptide residues that is apparently caused by the lattice contact. This is reminiscent of the way binding a T-cell receptor changed the conformation of central residues of an MHC-bound peptide. The structures determined identify which conserved hydrogen bonds are eliminated in terminally substituted peptides and suggest an increased energetic importance of the interactions at the peptide termini for MHC-peptide stability. Proteins 33:97-106, 1998. © 1998 Wiley-Liss, Inc.
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    AmbiPack: A systematic algorithm for packing of macromolecular structures with ambiguous distance constraints (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 26-42 
    Details
    ISSN: 0887-3585
    Keywords: intermolecular restraints ; solid-state NMR ; symmetric multimer ; branch and bound ; amyloid ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The determination of structures of multimers presents interesting new challenges. The structure(s) of the individual monomers must be found and the transformations to produce the packing interfaces must be described. A substantial difficulty results from ambiguities in assigning intermolecular distance measurements (from nuclear magnetic resonance, for example) to particular intermolecular interfaces in the structure. Here we present a rapid and efficient method to solve the packing and the assignment problems simultaneously given rigid monomer structures and (potentially ambiguous) intermolecular distance measurements. A promising application of this algorithm is to couple it with a monomer searching protocol such that each monomer structure consistent with intramolecular constraints can be subsequently input to the current algorithm to check whether it is consistent with (potentially ambiguous) intermolecular constraints. The algorithm AmbiPack uses a hierarchical division of the search space and the branch-and-bound algorithm to eliminate infeasible regions of the space. Local search methods are then focused on the remaining space. The algorithm generally runs faster as more constraints are included because more regions of the search space can be eliminated. This is not the case for other methods, for which additional constraints increase the complexity of the search space. The algorithm presented is guaranteed to find all solutions to a predetermined resolution. This resolution can be chosen arbitrarily to produce outputs at various level of detail. Illustrative applications are presented for the P22 tailspike protein (a trimer) and portions of β-amyloid (an ordered aggregate). Proteins 32:26-42, 1998. © 1998 Wiley-Liss, Inc.
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    Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 204-217 
    Details
    ISSN: 0887-3585
    Keywords: rotamer libraries ; energy minimization ; self consistent mean-field theory ; torsion space ; modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The ab initio folding problem can be divided into two sequential tasks of approximately equal computational complexity: the generation of native-like backbone folds and the positioning of side chains upon these backbones. The prediction of side-chain conformation in this context is challenging, because at best only the near-native global fold of the protein is known. To test the effect of displacements in the protein backbones on side-chain prediction for folds generated ab initio, sets of near-native backbones (≤ 4 Å Cα RMS error) for four small proteins were generated by two methods. The steric environment surrounding each residue was probed by placing the side chains in the native conformation on each of these decoys, followed by torsion-space optimization to remove steric clashes on a rigid backbone. We observe that on average 40% of the χ1 angles were displaced by 40° or more, effectively setting the limits in accuracy for side-chain modeling under these conditions. Three different algorithms were subsequently used for prediction of side-chain conformation. The average prediction accuracy for the three methods was remarkably similar: 49% to 51% of the χ1 angles were predicted correctly overall (33% to 36% of the χ1+2 angles). Interestingly, when the inter-side-chain interactions were disregarded, the mean accuracy increased. A consensus approach is described, in which side-chain conformations are defined based on the most frequently predicted χ angles for a given method upon each set of near-native backbones. We find that consensus modeling, which de facto includes backbone flexibility, improves side-chain prediction: χ1 accuracy improved to 51-54% (36-42% of χ1+2). Implications of a consensus method for ab initio protein structure prediction are discussed. Proteins 33:204-217, 1998. © 1998 Wiley-Liss, Inc.
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    Molecular dynamics simulations of human carbonic anhydrase II: Insight into experimental results and the role of solvation (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 119-134 
    Details
    ISSN: 0887-3585
    Keywords: molecular modeling ; proton transfer ; enzyme catalysis ; mutations ; molecular mechanics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this paper, the carbonic anhydrase II (CA II) enzyme active site is modeled using ab initio calculations and molecular dynamics simulations to examine a number of important issues for the enzyme function. It is found that the Zn2+ ion is dominantly tetrahedrally coordinated, which agrees with X-ray crystallographic studies. However, a transient five-fold coordination with an extra water molecule is also found. Studies of His64 conformations upon a change in the protonation states of the Zn-bound water and the His64 residue also confirm the results of an X-ray study which suggest that the His64 conformation is quite flexible. However, the degree of water solvation is found to affect this behavior. Water bridge formation between the Zn-bound water and the His64 residue was found to involve a free energy barrier of 2-3 kcal/mol and an average lifetime of several picoseconds, which supports the concept of a proton transfer mechanism through such a bridge. Mutations of various residues around the active site provide further insight into the corresponding experimental results and, in fact, suggest an important role for the solvent water molecules in the CA II catalytic mechanism. Proteins 33:119-134, 1998. © 1998 Wiley-Liss, Inc.
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    Sequence and structure conservation in a protein core (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 358-366 
    Details
    ISSN: 0887-3585
    Keywords: homologous proteins ; superfamilies ; sequence conservation ; protein structure ; protein evolution ; sequence-structure relationships ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In order to study structural aspects of sequence conservation in families of homologous proteins, we have analyzed structurally aligned sequences of 585 proteins grouped into 128 homologous families. The conservation of a residue in a family is defined as the average residue similarity in a given position of aligned sequences. The residue similarities were expressed in the form of log-odd substitution tables that take into account the environments of amino acids in three-dimensional structures. The protein core is defined as those residues that have less then 7% solvent accessibility. The density of a protein core is described in terms of atom packing, which is investigated as a criterion for residue substitution and conservation. Although there is no significant correlation between sequence conservation and average atom packing around nonpolar residues such as leucine, valine and isoleucine, a significant correlation is observed for polar residues in the protein core. This may be explained by the hydrogen bonds in which polar residues are involved; the better their protection from water access the more stable should be the structure in that position. Proteins 33:358-366, 1998. © 1998 Wiley-Liss, Inc.
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    Extraction of geometrically similar substructures: Least-squares and Chebyshev fitting and the difference distance matrix (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 320-328 
    Details
    ISSN: 0887-3585
    Keywords: structural similarity ; optimal superposition ; common substructure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In analysis, comparison and classification of conformations of proteins, a common computational task involves extractions of similar substructures. Structural comparisons are usually based on either of two measures of similarity: the root-mean-square (r.m.s.) deviation upon optimal superposition, or the maximal element of the difference distance matrix. The analysis presented here clarifies the relationships between different measures of structural similarity, and can provide a basis for developing algorithms and software to extract all maximal common well-fitting substructures from proteins.Given atomic coordinates of two proteins, many methods have been described for extracting some substantial (if not provably maximal) common substructure with low r.m.s. deviation. This is a relatively easy task compared with the problem addressed here, i.e., that of finding all common substructures with r.m.s. deviation less than a prespecified threshold. The combinatorial problems associated with similar subset extraction are more tractable if expressed in terms of the maximal element of the difference distance matrix than in terms of the r.m.s. deviation. However, it has been difficult to correlate these alternative measures of structural similarity. The purpose of this article is to make this connection.We first introduce a third measure of structural similarity: the maximum distance between corresponding pairs of points after superposition to minimize this value. This corresponds to fitting in the Chebyshev norm. Properties of Chebyshev superposition are derived.We describe relationships between the r.m.s. and minimax (Chebyshev) deviations upon optimal superposition, and between the Chebyshev deviation and the maximal element of the difference distance matrix. Combining these produces a relationship between the r.m.s. deviation upon optimal superposition and the maximal element of the difference distance matrix. Based on these results, we can apply algorithms and software for finding subsets of the difference distance matrix for which all elements are less than a specified bound, either to select only subsets for which the r.m.s.deviation is less than or equal to a specified threshold, or to select subsets that include all subsets for which the r.m.s. deviation is less than or equal to a threshold. Proteins 33:320-328, 1998. © 1998 Wiley-Liss, Inc.
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    Flexible docking using tabu search and an empirical estimate of binding affinity (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 367-382 
    Details
    ISSN: 0887-3585
    Keywords: ligand-protein docking ; molecular recognition ; tabu search ; empirical scoring function ; binding affinity prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: This article describes the implementation of a new docking approach. The method uses a Tabu search methodology to dock flexibly ligand molecules into rigid receptor structures. It uses an empirical objective function with a small number of physically based terms derived from fitting experimental binding affinities for crystallographic complexes. This means that docking energies produced by the searching algorithm provide direct estimates of the binding affinities of the ligands. The method has been tested on 50 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. All water molecules are removed from the structures and ligand molecules are minimized in vacuo before docking. The lowest energy geometry produced by the docking protocol is within 1.5 Å root-mean square of the experimental binding mode for 86% of the complexes. The lowest energies produced by the docking are in fair agreement with the known free energies of binding for the ligands. Proteins 33:367-382, 1998. © 1998 Wiley-Liss, Inc.
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    Folding-unfolding energy change of a simple sphere model protein and an energy landscape of the folding process (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 408-416 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; potential energy curve ; two state model ; semi-empirical calculation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have calculated the free energy of a spherical model of a protein or part of a protein generated in the way of protein folding. Two spherical models are examined; one is a homogeneous model consisting of only one residue type - hydrophobic. The other is a heterogeneous model consisting of two residue types - strong hydrophobic and weak hydrophobic. Both models show a folding transition state, and the latter model reproduces the trend of the experimental folded-unfolded energy change. The heterogeneous model suggests that in the folding process of a protein of more than 70 residues, a specific region of the protein folds first to form a stable region, then the other residues follow the folding process. The energy landscape of folding of a small protein is approximately a funnel model, whereas a flatter energy landscape is suggested for larger proteins of more than 55-70 residues. Proteins 33:408-416, 1998. © 1998 Wiley-Liss, Inc.
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    Structural model for family 32 of glycosyl-hydrolase enzymes (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 383-395 
    Details
    ISSN: 0887-3585
    Keywords: glycosidases ; protein structure prediction ; correlated mutations ; sequence space ; phylogenic relationships ; threading ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A structural model is presented for family 32 of the glycosyl-hydrolase enzymes based on the beta-propeller fold. The model is derived from the common prediction of two different threading methods, TOPITS and THREADER. In addition, we used a correlated mutation analysis and prediction of active-site residues to corroborate the proposed model. Physical techniques (circular dichroism and differential scanning calorimetry) confirmed two aspects of the prediction, the proposed all-beta fold and the multi-domain structure. The most reliable three-dimensional model was obtained using the structure of neuraminidase (1nscA) as template. The analysis of the position of the active site residues in this model is compatible with the catalytic mechanism proposed by Reddy and Maley (J. Biol. Chem. 271:13953-13958, 1996), which includes three conserved residues, Asp, Glu, and Cys. Based on this analysis, we propose the participation of one more conserved residue (Asp 162) in the catalytic mechanism. The model will facilitate further studies of the physical and biochemical characteristics of family 32 of the glycosyl-hydrolases. Proteins 33:383-395, 1998. © 1998 Wiley-Liss, Inc.
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    Molecular dynamics simulations of epidermal growth factor and transforming growth factor-α structures in water (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 396-407 
    Details
    ISSN: 0887-3585
    Keywords: AMBER ; epidermal growth factor ; transforming growth factor-alpha ; conformation ; receptor binding ; domain movement ; weakly polar interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: AMBER v. 4.1 force field in 1.5 ns NPT molecular dynamics simulations of murine epidermal growth factor (mEGF), human epidermal growth factor (hEGF), and human transforming growth factor-α (hTGF-α) structures with explicit TIP3P solvation were used to investigate differences in backbone stability, changes in secondary structure, interdomain flexibility, and weakly polar interactions. Backbone root mean square deviations of sections of each peptide show that the most stable regions in mEGF and hEGF are the A-, B-, and C-loops, whereas the most stable regions in hTGF-α are the A- and B-loops. The secondary structure in the B-loops of mEGF and hEGF differ significantly from the nuclear magnetic resonance (NMR) structures of mEGF and hEGF. The position and type of turns in the B-loop of mEGF and hEGF increase the interstrand distance of the antiparallel β-sheets thereby disrupting their structure. The interdomain flexibility of simulated hTGF-α structure is greater than in either mEGF or hEGF. The φ, ψ dihedrals of hTGF-α occupy two distinct populations of phase space corresponding to either a C7eq or an α-helical conformation. This change in dihedral angle is stabilized by Phe15 with Arg42 and Phe17 with Arg42 N-π weakly polar interactions that are present only in hTGF-α but not in mEGF or hEGF. Proteins 33:396-407, 1998. © 1998 Wiley-Liss, Inc.
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    Analysis of domain motions by approximate normal mode calculations (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 417-429 
    Details
    ISSN: 0887-3585
    Keywords: protein energy surface ; crambin ; lysozyme ; ATCase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The identification of dynamical domains in proteins and the description of the low-frequency domain motions are one of the important applications of numerical simulation techniques. The application of these techniques to large proteins requires a substantial computational effort and therefore cannot be performed routinely, if at all. This article shows how physically motivated approximations permit the calculation of low-frequency normal modes in a few minutes on standard desktop computers. The technique is based on the observation that the low-frequency modes, which describe domain motions, are independent of force field details and can be obtained with simplified mechanical models. These models also provide a useful measure for rigidity in proteins, allowing the identification of quasi-rigid domains. The methods are validated by application to three well-studied proteins, crambin, lysozyme, and ATCase. In addition to being useful techniques for studying domain motions, the success of the approximations provides new insight into the relevance of normal mode calculations and the nature of the potential energy surface of proteins. Proteins 33:417-429, 1998. © 1998 Wiley-Liss, Inc.
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  • 89
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    Helix-helix packing angle preferences for finite helix axes (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 457-459 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recently, James Bowie addressed the question of how to normalize correctly the distribution of observed helix-helix packing angles in proteins (Bowie, Nature Struct. Biol. 4:915-917, 1997). A hitherto unrealized yet significant bias toward crossed packing angles was revealed. However, the derived random reference distribution of packing angles requires that helices have to be assumed as infinite in length. Here, we complement Bowie's analysis by consideration of the more realistic case where helices are of finite length. As a result, the statistical bias toward near perpendicular packings appears to be even stronger. Proteins 33:457-459, 1998. © 1998 Wiley-Liss, Inc.
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  • 90
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    A homology model for the human theta-class glutathione transferase T1-1 (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 444-454 
    Details
    ISSN: 0887-3585
    Keywords: hGSTT1-1 ; homology modeling ; menaphthyl sulfate ; dichloromethane ; dehalogenase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A manual threading approach is used to model the human glutathione transferase T1-1 based on the coordinates of the related Theta class enzyme T2-2. The low level of sequence identity (about 20%), found in the C-terminal extension in conjunction with a relative deletion of about five residues makes this a challenging modeling problem. The C-terminal extension contributes to the active site of the molecule and is thus of particular interest for understanding the molecular mechanism of the enzyme. Manual docking of known substrates and non-substrates has implicated potential candidates for the T1-1 catalytic residues involved in the dehalogenation and epoxide-ring opening activities. These include the conserved Theta class residues Arg 107, Trp 115, and the conserved GSTT1 subclass residue His 176. Also, the residue at position 234 is implicated in the modulation of T1-1 activity with different substrates between species. Proteins 33:444-454, 1998. © 1998 Wiley-Liss, Inc.
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  • 91
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    Intersubunit hydrogen bond acts as a global molecular switch in Escherichia coli aspartate transcarbamoylase (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 430-443 
    Details
    ISSN: 0887-3585
    Keywords: pyrimidine biosynthesis ; protein crystallography ; allostery ; long-range interactions ; site-directed mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Tyr 165 in the catalytic subunit of Escherichia coli aspartate transcarbamoylase (ATCase, EC 2.1.3.2) forms an intersubunit hydrogen bond in the T state with Glu 239 in the 240s loop of a second catalytic subunit, which is broken in the T to R transition. Substitution of Tyr 165 by Phe lowers substrate affinity by approximately an order of magnitude and alters the pH profile for enzyme function. We have determined the crystal structure of Y165F at 2.4 Å resolution by molecular replacement, using a wild-type T state structure as the probe, and refined it to an R value of 25.2%. The Y165F mutation induces a global conformational change that is in the opposite direction to the T to R transition and therefore results in an extreme T state. The two catalytic trimers move closer by ∼0.14 Å and rotate by ∼0.2°, in the opposite direction to the T→R rotation; the two domains of each catalytic chain rotate by ∼2.1°, also in the opposite direction to the T→R transition; and the 240s loop adopts a new conformation. Residues 229 to 236 shift by ∼2.4 Å so that the active site is more open. Residues 237 to 244 rotate by ∼24.1°, altering interactions within the 240s loop and at the C1-C4 and C1-R4 interfaces. Arg 167, a key residue in domain closure and interactions with L-Asp, swings out from the active site to interact with Tyr 197. This crystal structure is consistent with the functional properties of Y165F, expands our knowledge of the conformational repertoire of ATCase, and indicates that the canonical T state does not represent an extreme. Proteins 33:430-443, 1998. © 1998 Wiley-Liss, Inc.
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  • 92
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    A hierarchical method for generating low-energy conformers of a protein-ligand complex (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 475-495 
    Details
    ISSN: 0887-3585
    Keywords: docking ; landscape ; dynamics ; dielectric ; affinity ; binding ; methotrexate ; thermolysin ; dihydrofolate reductase ; HIV protease ; generalized Born ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A novel dynamical protocol for finding the low-energy conformations of a protein-ligand complex is described. The energy functions examined consist of an empirical force field with four different dielectric screening models; the generalized Born/surface area model also is examined. Application of the method to three complexes of known crystal structure provides insights into the energy functions used for selecting low-energy docked conformations and into the structure of the binding-energy surface. Evidence is presented that the local energy minima of a ligand in a binding site are arranged in a hierarchical fashion. This observation motivates the construction of a hierarchical docking algorithm that substantially enriches the population of ligand conformations close to the crystal conformation. The algorithm is also adapted to permit docking into a flexible binding site and preliminary tests of this method are presented. Proteins 33:475-495, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 24 Ill.
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  • 93
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    Energy landscape of a native protein: Jumping-among-minima model (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 496-517 
    Details
    ISSN: 0887-3585
    Keywords: energy landscape ; hierarchical conformational substates ; molecular dynamics ; normal mode analysis ; principal component analysis ; jumping-among-minima model ; human lysozyme ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have investigated energy landscape of human lysozyme in its native state by using principal component analysis and a model, jumping-among-minima (JAM) model. These analyses are applied to 1 nsec molecular dynamics trajectory of the protein in water. An assumption embodied in the JAM model allows us to divide protein motions into intra-substate and inter-substate motions. By examining intra-substate motions, it is shown that energy surfaces of individual conformational substates are nearly harmonic and mutually similar. As a result of principal component analysis and JAM model analysis, protein motions are shown to consist of three types of collective modes, multiply hierarchical modes, singly hierarchical modes, and harmonic modes. Multiply hierarchical modes, the number of which accounts only for 0.5% of all modes, dominate contributions to total mean-square atomic fluctuation. Inter-substate motions are observed only in a small-dimensional subspace spanned by the axes of multiplyhierarchical and singly hierarchical modes. Inter-substate motions have two notable time components: faster component seen within 200 psec and slower component. The former involves transitions among the conformational substates of the low-level hierarchy, whereas the latter involves transitions of the higher level substates observed along the first four multiply hierarchical modes. We also discuss dependence of the subspace, which contains conformational substates, on time duration of simulation. Proteins 33:496-517, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 13 Ill.
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  • 94
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    Patterns of protein-fold usage in eight microbial genomes: A comprehensive structural census (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 518-534 
    Details
    ISSN: 0887-3585
    Keywords: structure databank ; superfold ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Eight microbial genomes are compared in terms of protein structure. Specifically, yeast, H. influenzae, M. genitalium, M. jannaschii, Synechocystis, M. pneumoniae, H. pylori, and E. coli are compared in terms of patterns of fold usage - whether a given fold occurs in a particular organism. Of the ∼340 soluble protein folds currently in the structure databank (PDB), 240 occur in at least one of the eight genomes, and 30 are shared amongst all eight. The shared folds are depleted in all-helical structure and enriched in mixed helix-sheet structure compared to the folds in the PDB. The top-10 most common of the shared 30 are enriched in superfolds, uniting many non-homologous sequence families, and are especially similar in overall architecture - eight having helices packed onto a central sheet. They are also very different from the common folds in the PBD, highlighting databank biases. Folds can be ranked in terms of expression as well as genome duplication. In yeast the top-10 most highly expressed folds are considerably different from the most highly duplicated folds. A tree can be constructed grouping genomes in terms of their shared folds. This has a remarkably similar topology to more conventional classifications, based on very different measures of relatedness. Finally, folds of membrane proteins can be analyzed through transmembrane-helix (TM) prediction. All the genomes appear to have similar usage patterns for these folds, with the occurrence of a particular fold falling off rapidly with increasing numbers of TM-elements, according to a “Zipf-like” law. This implies there are no marked preferences for proteins with particular numbers of TM-helices (e.g. 7-TM) in microbial genomes. Further information pertinent to this analysis is available at http://bioinfo.mbb.yale.edu/genome. Proteins 33:518-534, 1998. © 1998 Wiley-Liss, Inc.
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  • 95
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    The slow step of folding of Staphylococcus aureus PC1 β-lactamase involves the collapse of a surface loop rate limited by the Trans to Cis isomerization of a non-proline peptide bond (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 550-557 
    Details
    ISSN: 0887-3585
    Keywords: mutagenesis ; c.d. spectroscopy ; unfolding ; Ω-loop ; molten-globule ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We wished to test the hypothesis that the non proline cis to trans isomerization of the peptide bond at position 167 in the S. aureus β-lactamase PC1 exerts a significant controlling effect on the folding pathway of this enzyme. The previous data presented in support of this hypothesis could not rule out the effect of factors unrelated to non-proline cis/trans isomerization. We have used the plasmid pET9d to direct soluble overproduction of the S. aureus β-lactamase PC1 and a site-directed mutant (Ile 167 to Pro) in Escherichia coli. Following purification the proteins were subjected to a comparative analysis of the kinetics of unfolding and refolding using the techniques of near- and far-UV circular dichroism spectroscopy and fluorescence spectroscopy in conjunction with “double-jump” experiments. Results show that the fully-unfolded I167P mutant enzyme retains 20% of molecules in a fast-refolding form and that slower-refolding molecules fold faster than the recombinant wild-type enzyme. The final stage of folding involves folding of the Ω-loop into a conformation essential for enzymatic activity. In support of the original hypothesis, the folding of this Ω-loop is rate limited by the isomerization of the Glu 166-Ile 167 peptide bond. Proteins 33:550-557, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
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  • 96
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    Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 116-127 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; X-ray crystallography ; essential dynamics ; lysozyme ; hinge bending ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A comparison of a series of extended molecular dynamics (MD) simulations of bacteriophage T4 lysozyme in solvent with X-ray data is presented. Essential dynamics analyses were used to derive collective fluctuations from both the simulated trajectories and a distribution of crystallographic conformations. In both cases the main collective fluctuations describe domain motions. The protein consists of an N- and C-terminal domain connected by a long helix. The analysis of the distribution of crystallographic conformations reveals that the N-terminal helix rotates together with either of these two domains. The main domain fluctuation describes a closure mode of the two domains in which the N-terminal helix rotates concertedly with the C-terminal domain, while the domain fluctuation with second largest amplitude corresponds to a twisting mode of the two domains, with the N-terminal helix rotating concertedly with the N-terminal domain. For the closure mode, the difference in hinge-bending angle between the most open and most closed X-ray structure along this mode is 49 degrees. In the MD simulation that shows the largest fluctuation along this mode, a rotation of 45 degrees was observed. Although the twisting mode has much less freedom than the closure mode in the distribution of crystallographic conformations, experimental results suggest that it might be functionally important. Interestingly, the twisting mode is sampled more extensively in all MD simulations than it is in the distribution of X-ray conformations. Proteins 31:116-127, 1998. © 1998 Wiley-Liss, Inc.
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  • 97
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    Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing potential sequence alignments (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 558-566 
    Details
    ISSN: 0887-3585
    Keywords: Drosophila melanogaster couch potato protein ; Werner's syndrome ; restrained molecular dynamics ; simulated annealing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have recently described an automated approach for homology modeling using restrained molecular dynamics and simulated annealing procedures (Li et al, Protein Sci., 6:956-970,1997). We have employed this approach for constructing a homology model of the putative RNA-binding domain of the human RNA-binding protein with multiple splice sites (RBP-MS). The regions of RBP-MS which are homologous to the template protein snRNP U1A were constrained by “homology distance constraints,” while the conformation of the non-homologous regions were defined only by a potential energy function. A full energy function without explicit solvent was employed to ensure that the calculated structures have good conformational energies and are physically reasonable. The effects of misalignment of the unknown and the template sequences were also explored in order to determine the feasibility of this homology modeling method for distinguishing possible sequence alignments based on considerations of the resulting conformational energies of modeled structures. Differences in the alignments of the unknown and the template sequences result in significant differences in the conformational energies of the calculated homology models. These results suggest that conformational energies and residual constraint violations in these homology-constrained simulated annealing calculations can be used as criteria to distinguish between correct and incorrect sequence alignments and chain folds. Proteins 33:558-566, 1998. © 1998 Wiley-Liss, Inc.
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  • 98
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    Structural basis of increased resistance to thermal denaturation induced by single amino acid substitution in the sequence of β-glucosidase A from Bacillus polymyxa (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 567-576 
    Details
    ISSN: 0887-3585
    Keywords: bacterial cellobiase ; mutated β-glucosidase ; family 1 ; thermoresistance ; X-ray structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The increasing development of the biotechnology industry demands the design of enzymes suitable to be used in conditions that often require broad resistance against adverse conditions. β-glucosidase A from Bacillus polymyxa is an interesting model for studies of protein engineering. This is a well-characterized enzyme, belonging to glycosyl hydrolase family 1. Its natural substrate is cellobiose, but is also active against various artificial substrates. In its native state has an octameric structure. Its subunit conserves the general (α/β)8 barrel topology of its family, with the active site being in a cavity defined along the axis of the barrel. Using random-mutagenesis, we have identified several mutations enhancing its stability and it was found that one them, the E96K substitution, involved structural changes. The crystal structure of this mutant has been determined by X-ray diffraction and compared with the native structure. The only difference founded between both structures is a new ion pair linking Lys96 introduced at the N-terminus of helix α2, to Asp28, located in one of the loops surrounding the active-site cavity. The new ion pair binds two segments of the chain that are distant in sequence and, therefore, this favorable interaction must exert a determinant influence in stabilizing the tertiary structure. Furthermore, analysis of the crystallographic isotropic temperature factors reveals that, as a direct consequence of the introduced ion pair, an unexpected decreased mobility of secondary structure units of the barrel which are proximal to the site of mutation is observed. However, this effect is observed only in the surrounding of one of the partners forming the salt bridge and not around the other. These results show that far-reaching effects can be achieved by a single amino acid replacement within the protein structure. Consequently, the identification and combination of a few single substitutions affecting stability may be sufficient to obtain a highly resistant enzyme, suitable to be used under extreme conditions. Proteins 33:567-576, 1998. © 1998 Wiley-Liss, Inc.
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  • 99
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    Mass spectrometry (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 1-2 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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  • 100
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    Kinetics and interaction studies between cytochrome c3 and Fe-only hydrogenase from Desulfovibrio vulgaris hildenborough (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 590-600 
    Details
    ISSN: 0887-3585
    Keywords: [Fe] hydrogenase ; protein-protein interaction ; BIAcore analysis ; crystallization ; cooperativity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hydrogenases from Desulfovibrio are found to catalyze hydrogen uptake with low potential multiheme cytochromes, such as cytochrome c3, acting as acceptors. The production of Fe-only hydrogenase from Desulfovibrio vulgaris Hildenborough was improved with respect to the growth phase and media to determine the best large-scale bacteria growth conditions. The interaction and electron transfer from Fe-only hydrogenase to multiheme cytochrome has been studied in detail by both BIAcore and steady-state measurements. The electron transfer between [Fe] hydrogenase and cytochrome c3 appears to be a cooperative phenomenon (h = 1.37). This behavior could be related to the conductivity properties of multihemic cytochromes. An apparent dissociation constant was determined (2 × 10-7 M). The importance of the cooperativity for contrasting models proposed to describe the functional role of the hydrogenase/cytochrome c3 complex is discussed. Presently, the only determined structure is from [NiFe] hydrogenase and there are no obvious similarities between [NiFe] and [Fe] hydrogenase. Furthermore, no crystallographic data are available concerning [Fe] hydrogenase. The first results on crystallization and X-ray crystallography are reported. Proteins 33:590-600, 1998. © 1998 Wiley-Liss, Inc.
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