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  • 1985-1989  (5,879)
  • 1970-1974  (1,415)
  • Biochemistry and Biotechnology  (3,598)
  • Engineering General  (2,962)
  • Electron microscopy  (734)
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  • 1
    ISSN: 1432-2307
    Keywords: Clear cell sarcoma ; Melanosomes ; Cytochemistry ; Electron microscopy ; Nude mouse
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary In order to clarify the histogenesis of clear cell sarcoma of tendons and aponeuroses (CCS), two cases of human and one nude mouse-transplanted CCS line were studied using an ultrastructural and enzyme cytochemical approach. Most of the tumour cells obtained from the primary and transplanted CCS demonstrated melanosomes in various stages of development within the cytoplasm, whereas no melanosomes could be identified in the metastatic CCS. However, cholinesterase and tyrosinase activities could be demonstrated not only in the melanotic primary and transplanted CCS but also in the amelanotic metastatic CCS. The results therefore support the hypothesis that CCS is a soft tissue tumour derived from the neural crest.
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  • 2
    ISSN: 1432-2307
    Keywords: Human heart ; Papillary muscle ; Hypertrophy ; Mitochondria ; Specific staining ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Biopsy material of the hypertrophied human papillary muscle has been processed according to various electron microscopical techniques in order to study the mitochondrial ultrastructure and the association between mitochondria and sarcoplasmic reticulum (SR).En bloc staining with a Cu-Pb citrate solution resulted in specifically contrasted mitochondrial and sarcotubular membranes, characterized by numerous, discrete, electron-dense particles. The differences in staining patterns between the perinuclear mitochondria and their subsarcolemmal and interfibrillar counterparts suggest differences in chemical properties and/or metabolic activities. The selectively contrasted mitochondrial particles may represent a conglomorate of extrinisic and intrinisic respiratory enzymes and other membrane-associated proteins, while the majority of the electron-dense particles of the sarcotubular membrane may represent positively stained Ca2+-pumps. Ultrastructural findings in the present study strongly indicate that the slender mitochondrial projections represent an initial stage in a process leading to the formation of large and pleomorphic mitochondria. Intimate contact between adjacent mitochondria as well as between mitochondria and SR are documented. In the contact regions some of the specifically contrasted particles of the adjacent membranes had fused with each other. It is suggested that these particles represent membrane-bound transport proteins providing a system for interorganelle exchanges of metabolites and/or ions.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Virchows Archiv 415 (1989), S. 91-95 
    ISSN: 1432-2307
    Keywords: Carcinosarcoma ; Urinary bladder ; Immunohistochemistry ; Electron microscopy ; Rhabdomyoblast
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary A case of urinary bladder carcinosarcoma (UBCS) is reported with light, immunohistochemical and electron microscopical findings. The tumour consisted of a squamous cell carcinoma, variable spindle cell stromal elements compatible with fibrosarcoma, and rhabdomyoblasts. Intermediate filament co-expression of cytokeratin and vimentin was shown by immunohistochemistry. Electron microscopy (EM) confirmed the nature of the three components, and indicated some similarities between the three cell-types present. Comparisons with the previous UBCS in the literature are made.
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  • 4
    ISSN: 1432-2307
    Keywords: Human acute pancreatitis ; Zymogen granules ; Acinar cells ; Electron microscopy ; Immunocytochemistry ; Morphometry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary In the present study fine structural changes of acinar zymogen granules were investigated in human acute pancreatitis. Pancreatic tissue was obtained at surgery from 6 patients, prepared for ultrastructural analysis, and stained immunocytochemically for trypsinogen. Stereological parameters of zymogen granules were evaluated. The density of the immunocytochemical labelling for trypsinogen was estimated over zymogen granules, the rough endoplasmic reticulum, Golgi apparatus and the acinar lumina. In acute pancreatitis the number of zymogen granules was diminished and their size reduced. The density of the labelling for trypsinogen was unchanged over zymogen granules but showed a significant reduction over the rough endoplasmic reticulum, Golgi apparatus, and the acinar lumina. In general the integrity of zymogen granules was well preserved. Focally degenerative changes of zymogen granules and large autophagosomes were observed. From the immunogold labelling a disturbance of enzyme synthesis and secretion was suggested. Evidence is given that a disruption of the zymogen granule membranes and a fusion with lysosomal bodies might contribute to the pathogenesis of human acute pancreatitis.
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  • 5
    ISSN: 1432-2307
    Keywords: Hyperoxia ; Lung broncho-vascular reaction ; Electron microscopy ; Rat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary In order to clarify the early phenomena involved in the lung reaction to hyperoxia, twenty adult male rats were exposed to 100% oxygen at 1 ATA. Morphological pulmonary lesions were detectable after only 24 h hyperoxia, and included vasoconstriction and perivascular oedema, bronchiolar constriction, and pericyte reaction. The lesions were irregularly scattered within the lung parenchyma and occurred preferentially in areas centred on bronchiolo-vascular stems. Even at the latest stages, pulmonary heterogeneity was obvious, from the coexistence of areas damaged at different times. Neuro-epithelial-bodies were found under the bronchiolar epithelium; the morphological aspect of the neuro-endocrine cells observed was consistent with hyperoxia-induced modulation of their secretory activity. Taken together, our findings show the speed of development of hyperoxia-induced pulmonary changes and raise some pathogenic considerations.
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  • 6
    ISSN: 1432-2307
    Keywords: Thyroid neoplasms ; Electron microscopy ; Immunohistochemistry ; Calcitonin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary An ultrastructural study, both morphological and immunohistochemical, has been carried out on eight thyroglobulin-positive and nine thyroglobulin-negative medullary carcinomas of the thyroid. The morphometric analysis of granule size showed that all tumours contained cells with small granules and cells with medium size granules, whereas eight tumours had additional cells with large granules. The small granules had an electron dense core, while the medium and large sized granules were both pale-cored and dense-cored. The cells with small, medium or large secretory granules were all immunoreactive for calcitonin and CGRP. No ultrastructural differences were observed between thyroglobulin-positive and thyroglobulin-negative cases of medullary carcinoma of the thyroid.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Virchows Archiv 415 (1989), S. 1-6 
    ISSN: 1432-2307
    Keywords: Visceral leishmaniasis ; L. donovani ; Parasitism ; Liver pathology ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Liver parenchymal cell parasitism with the amastigotes form ofL. donovani was detected by electron microscopy in human visceral leishmaniasis. Endocytosis was considered to be the mechanism by which the leishmania entered the cell. Evidence of well preserved parasites within hepatocytes suggest this parasitism as a possible reservoir for recrudescence.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Virchows Archiv 415 (1989), S. 297-300 
    ISSN: 1432-2307
    Keywords: Non-Hodgkin's lymphoma ; Electron microscopy ; Immunohistochemistry ; Intercellular junction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary A rare example of pleomorphic B cell non-Hodgkin's lymphoma is described in which tumour cells possessed simple intercellular junctions.
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  • 9
    ISSN: 1432-2307
    Keywords: Collagen secretion granule ; Myofibroblast ; Spindle cell tumour ; Electron microscopy ; Diagnosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Collagen secretion granules, representing stages in the intracellular packaging, transport and secretion of collagen-fibril precursor, have been studied by transmission electron microscopy in non-neoplastic human myofibroblasts and in neoplastic cells from a preliminary study of tumours exclusively or partly of spindle cell type. Vesicles, newly separated from Golgi saccules and containing finely fibrillar material, were identified as early presecretory granules, the most immature type of granule. Later stages exhibited longitudinally arranged, densely fibrillar bundles. Subsequently, secretory granules developed more homogeneously dense content. Fibril-containing cisternae near the plasma membrane were interpreted as either endocytotic or lysosomal structures, or as participants in the final stages of secretion. The features by which collagen secretion granules can be distinguished from other Golgi products, in particular melanosomes, Weibel-Palade bodies and lysosomes, are pointed out. The significance of these organelles for cell identification and tumour diagnosis is discussed.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-2307
    Keywords: Salivary gland ; Myoepithelioma ; Neoplasm ; Electron microscopy ; Immunohistochemistry ; Cytoplasmic filaments
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The histological and ultrastructural features of five major salivary gland tumours, which have little or no evidence of duct- or gland-type differentiation in routine sections, are described. Four of the cases have the tumour cells organized as narrow, anastomosing cords of cells separated by a myxoid and vascularized stroma; we have designated such lesions as reticular-type myoepitheliomas. The fifth case has a solid growth pattern and is largely composed of hyaline cells, that is, a plasmacytoid myoepithelioma. Ultrastructurally, one reticular myoepithelioma reveals myoepithelial cell differentiation with microfilament aggregates, while the other three examples are composed of modified myoepithelial cells displaying widened intercellular spaces, prominent synthesis of extracellular glycosaminoglycans, distinct basal lamina development, and obvious accumulations of cytoplasmic intermediate filaments. In electron micrographs, the modified myoepithelial cells of the plasmacytoid variant closely resemble the tumour cells in the reticular form. Three cases had expression of both glial fibrillary acid protein (GFAP) and vimentin, but only one of the myoepitheliomas contained muscle-specific actin. At least focally, each of the cases exhibited a considerable spectrum of cytokeratin filaments. Using double-labeled immunofluorescent microscopy of one reticular variant and the plasmacytoid myoepithelioma, there was individual tumour cell co-expression of GFAP and vimentin focally in the plasmacytoid myoepithelioma, but co-expression of cytokeratins 13, 16 and GFAP were not noted in either case. As expected, co-expression of high- and low-molecular weight cytokeratin filaments was wide-spread in both myoepitheliomas. Most described myoepitheliomas have a solid growth pattern and are composed of spindle and plasmacytoid cells, but based on cytological features and growth patterns in this series, it is apparent that polygonalshaped cells with novel architecture can occur in myoepitheliomas. The results also indicate the close relationship between pleomorphic adenoma and such variants of myoepithelioma.
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  • 11
    ISSN: 1432-198X
    Keywords: IgA nephropathy ; Electron microscopy ; Glomerular basement membrane lesions ; Prognosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Seventy-three patients with IgA nephropathy (IgAGN), under the age of 15 years at the time of the discovery of the disease, were investigated with respect to glomerular basement membrane (GBM) lesions. Irregular attenuation or widening of GBM, especially on the epithelial side, was observed in 28 cases (38%). These two changes are referred to aslysis of GBM and were considered to be the primary and specific changes among the GBM lesions in IgAGN. GBM thickening with layering of lamina densa was found in 37 of 73 cases (51%), but this change has been observed in other types of glomerular diseases. GBM lesions similar to those seen in IgAGN were also observed in Henoch-Schönlein purpura nephritis (HSPN) and poststreptococcal acute glomerulonephritis (PSAGN). Lysis of GBM was observed only in IgAGN, HSPN and PSAGN. Subepithelial and intramembranous deposits appeared to have an important role in the development of these GBM lesions. The presence of GBM lesions was correlated with a high incidence of cellular crescents but not with other clinical or light microscopic findings. The presence of these GBM lesions in IgAGN does not have a significant effect on the prognosis, at least in childhood. The affected GBM seemed to recover without leaving any significant residual damage in most cases. In the long-term prognosis of the disease non-immunological factors, such as ageing or hypertension, seem to be important.
    Type of Medium: Electronic Resource
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  • 12
    Electronic Resource
    Electronic Resource
    Springer
    Anatomy and embryology 180 (1989), S. 237-242 
    ISSN: 1432-0568
    Keywords: Perineurium ; Lanthanum ; Diffusion barriers ; In vivo ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary While the perineurium as a diffusion barrier has been extensively investigated by light and electron microscopy, copy, such studies have been largely restricted to the use of protein tracers. In the present study the permeability of the perineurium to a physiologically more relevant ionic tracer has been assessed. In vivo the rat sural or tibial nerve was either microinjected with lanthanum nitrate solution for endoneurial application or bathed in the lanthanum solution for epineurial application. The findings generally demonstrated an effective barrier to the tracer which failed to penetrate the inner layers of the perineurium. Only at the highest lanthanum concentration and longest time intervals employed did trace quantities occasionally penetrate the barrier and then only in the presence of some cytopathological changes to the outermost perineurial cells. The usefulness of the microinjection method was limited by the slight but unavoidable trauma to the perineurium. The findings are related to those of other studies which have used electron dense tracers, also to studies using physiological including electrophysiological techniques and morphological including freeze-fracture methods.
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  • 13
    Electronic Resource
    Electronic Resource
    Springer
    Archives of dermatological research 281 (1989), S. 165-172 
    ISSN: 1432-069X
    Keywords: Netherton's syndrome ; Retinoid therapy ; Etretin ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary A young female patient, expressing the symptom triad of Netherton's syndrome, i.e., ichthyosis linearis circumflexa Comèl, trichorrhexis invaginata and other hair shaft defects, and atopic diathesis, has been treated successfully with the new retinoid preparation Etretin. Our electron microscopical study especially focused on the ultrastructural effect on the characteristic, active part of the skin lesions, which is only found within a narrow borderline just preceding the lesion's margin. In untreated skin, this part is characterized by dermal inflammation, immigrating inflammatory cells, and specific keratinization disturbances: synthesis of keratinization proteins is suppressed, serum exudates invade the epidermis, either filling the intercellular spaces of the upper spinous and the granular layer as finely granular, amorphous material, or they are partly phagocytosed and lie within intracellular, round-oval inclusions. The portions of the lesions lying towards the center are unspecific and represent recovery stages, ultrastructurally resembling stages of normal wound repair. Oral therapy with Etretin did not heal the basic defect, but drastically reduced exoserosis and the deposition of intra- and extracellular material. Keratinization seemed to normalize. The condition of the hair was also improved.
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  • 14
    ISSN: 1432-0533
    Keywords: Senile plaque-like structure ; Periodicacid methenamine silver (PAM) method ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Numerous diffuse senile plaque-like structures (SPLSs) were found in the cerebral cortex from cases with dementia of the Alzheimer type by means of the methenamine-Bodian method. SPLSs varied in shape and size. They were never recognized in the original Bodian, PAS and Congo red preparations, but were positive with anti-β-protein immunostaining and periodic-acid methenamine silver (PAM) methods, which are thought to specifically stain amyloid substance. With PAM electron microscopy, we found sparse aggregations of amorphous, often ramified, structures with fine granular silver deposits in SPLS. Routine electron microscopic examination on the same portion where SPLS were confirmed by PAM electron microscopy revealed amorphous, partially fibrous structures. These structures might be amyloid or amyloid-precursor substance. In SPLSs only a few degenerated neurites and astrocytic processes with glycogen granules were seen. We consider SPLSs to be a kind of senile plaque.
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  • 15
    ISSN: 1432-0533
    Keywords: Schwann cell ; Oligodendrocyte ; Electron microscopy ; Myelin ; Optic nerve
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Neonatal rats were exposed to Tellurium (Te), via the mother's milk, from the day of birth until sacrifice at 7, 14, 21, and 28 days of age. Light and electron microscopy revealed Schwann cell and myelin degeneration in the sciatic nerves at each age studied. These changes were similar to those described in weanling rats as a result of Te intoxication. In the CNS, hypomyelination of the optic nerves was convincingly demonstrated at 14, 21, and 28 days of age, accompanied by some evidence of myelin degeneration. These changes were also seen in the ventral columns of the cervical spinal cords, although less markedly, and were confirmed by quantitative methods. There was little evidence of oligodendrocyte pathology in the CNS, and it appears that degeneration of these cells is not the primary cause of the CNS hypomyelination, in contrast to the PNS where Schwann cell degeneration has been shown to precede the myelin pathology.
    Type of Medium: Electronic Resource
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  • 16
    Electronic Resource
    Electronic Resource
    Springer
    Acta neuropathologica 78 (1989), S. 472-483 
    ISSN: 1432-0533
    Keywords: Astroblastoma ; Electron microscopy ; Immunohistochemistry ; Organ culture ; Tanycytes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Two examples of cerebral astroblastoma have been studied by electron microscopy and immunohistochemistry, one of them having been maintained in vitro in an organ-culture matrix system for 8 months and the explants studied by light and electron microscopy at different time intervals. The fine structural characteristics were those of a glial cell type with features intermediary between those of astrocytes and ependymocytes. They recapitulated the structure of the tanycyte, a glial precursor cell which is normally found scattered along the ependymal lining of the embryonal and neonatal mammalian brain, but is distinct from epithelial ependymocytes. The possible origin of some astroblastomas from such a cell would account for a number of characteristics in this enigmatic type of glioma.
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  • 17
    Electronic Resource
    Electronic Resource
    Springer
    Anatomy and embryology 180 (1989), S. 273-280 
    ISSN: 1432-0568
    Keywords: Wallerian degeneration ; Myelin breakdown ; Light microscopy ; Electron microscopy ; Marchi staining
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Morphological aspects of myelin breakdown in the posterior funiculus during Wallerian degeneration were studied in kittens subjected to lumbosacral dorsal rhizotomies 6–8 days after birth. The first sign of myelin breakdown was characterized by swollen or shrunken nerve fibers. Shortly thereafter there was an increased occurrence of collapsed myelin sheaths and later of rounded myelin bodies. Myelin was clearly seen in microglial cells. Correlative observations on Marchi-stained material indicated the simultaneous and frequent appearance of Marchi-positive bodies (MPB:s) and myelin bodies. Due to the rapidity of the degeneration process in the kitten, the increase in the occurrence of Marchi-positive granules (MPG:s) seemed to start concomitantly with increased occurrence of MPB:s. However, the frequent occurrence of MPG:s outlasted that for MPB:s. The findings indicate that the MPB:s may be the counterpart to myelin bodies and the MPG:s to lipid droplets. Microglial cells may be responsible for the primary uptake of degenerating myelin and the subsequent transformation of myelin bodies to lipid droplets. The much faster breakdown of myelin and elimination of lipid material in the degenerating posteror funiculus of the kitten, as compared to the adult, seemed to be due not only to the lower myelin content in the kitten, but also to a higher density of microglia and a greater efficiency in the myelin breakdown process in the degenerating posterior funiculus of the kitten.
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  • 18
    Electronic Resource
    Electronic Resource
    Springer
    Acta neuropathologica 79 (1989), S. 10-17 
    ISSN: 1432-0533
    Keywords: Locus ceruleus ; Pick bodies ; Lewy bodies ; Immunocytochemistry ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary In classical Pick's disease with typical Pick bodies, inclusions resembling those present in the cerebral cortex are frequently found in the locus ceruleus. In three such cases Pick bodies were studied by light and electron microscopy and compared with Lewy bodies, inclusions more commonly found in this location. In contrast to the situation in the cerebral cortex, nerve cells with multiple Pick bodies were often found in the locus ceruleus, but in other respects definite light and electron microscopic differences between Pick bodies and Lewy bodies were present. Pick bodies were slightly basophilic and never had a central core or a peripheral halo. They were intensely argyrophilic. Differences in immunocytochemical reactions were especially marked with antibodies to tau and to paired helical filaments. Pick bodies displayed an intense reaction with these two antibodies, contrasting with that of Lewy bodies, which either lacked reactivity or reacted in a peripheral band. By electron microscopy the Pick bodies were composed of random filaments with smooth contour, whereas typical Lewy bodies had fuzzy deposits on filaments that radiated from a central core. Pick bodies in the locus ceruleus therefore maintained their immunocytochemical and electron microscopic characteristics and did not take on the character of Lewy bodies. Such differences point to a different pathogenesis and perhaps etiology of these two types of inclusions and attest to the marked difference clinically and pathologically between Pick's and Parkinson's diseases.
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  • 19
    Electronic Resource
    Electronic Resource
    Springer
    Acta neuropathologica 77 (1989), S. 664-666 
    ISSN: 1432-0533
    Keywords: Hemimegalencephaly ; Golgi study ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Pathological findings in a case of hemimegalencephaly are presented. Hemispherectomy, performed because of intractable seizures, allowed an electron microscopic and Golgi study. Glial abnormalities consisted of hyperplasia of glia cells with giant astrocytes often containing several nuclei and proliferation of numerous Rosenthal fibers. Golgi stain showed many giant neurons with a perikaryon covered by perisomatic processes, and a complex dendritic tree. Glial abnormalities could be correlated with the firmness of the hemisphere and intense hypersignal on magnetic resonance imaging. Giant neurons were associated with an increase in size of the perikaryon and dendritic tree; this pattern suggests a polyploidy.
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  • 20
    ISSN: 1432-0533
    Keywords: Cerebral ischemia ; Ischemic neuronal injury ; Long-term recovery ; Mongolian gerbil ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Unilateral transient cerebral ischemia was produced in Mongolian gerbils by clipping the left common carotid artery for 1h. About 60% of the gerbils with neurological symptoms had post-ischemic seizures. The majority of those that had seizures died within a few days, and sections of their cerebral cortices contained many dark and shrunken neurons. However, the gerbils that did not have seizures survived without any severe complications. In the cerebral cortex of the latter, the neurons with diffuse or peripheral pallor of the perikarya were seen along with a small number of dark and shrunken neurons. Diffuse pallor occurred within a few hours following ischemia in layers III, V and VI, and disappeared 1 or 2 days after recirculation. Electron microscopically, these neurons showed dispersion of ribosomes, simple and elongated profiles of rough endoplasmic reticulum (r-ER), clustered vacuoles, and mild to moderate mitochondrial swelling. Occasional net-like tubulomembranous structures, probably derived from r-ER, were observed. On the other hand, peripheral pallor became apparent after 5 days following ischemia, usually involving layer II first and gradually extending to the deeper layers. Concomitantly, the amount of neuropil decreased and the dendrites exhibited tortuosity and irregularity in layer II. Electron microscopically, these neurons showed marked swelling of peripheral perikarya and polyribosomes and organelles were located peripherally to the nuclei. In addition, numerous degenerated axon terminals and distended dendrites were observed around the neurons. These observations indicate that diffuse pallor represents damage directly induced by ischemia and subsequent recirculation, while peripheral pallor is the delayed and remote effect of ischemia, probably due to degeneration of neuronal processes.
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  • 21
    Electronic Resource
    Electronic Resource
    Springer
    Acta neuropathologica 78 (1989), S. 555-560 
    ISSN: 1432-0533
    Keywords: Sporadic motor neuron disease ; Lewy body-like hyaline inclusions ; Immunocytochemistry ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Lewy body-like hyaline inclusions were immunocytochemically and electron microscopically investigated in a patient with sporadic motor neuron disease. The hyaline inclusions were chiefly observed within the perikarya of both normal-looking and chromatolytic anterior horn cells in the lumbar spinal cord, but some were detected in the axons and dendrites. Usually, a single inclusion was found in the perikaryon, but in rare cases two or more were observed. Immunocytochemically, these inclusions were intensely immunostained with anti-ubiquitin anti-body. Ultrastructurally, the hyaline inclusions were chiefly composed of randomly arranged linear structures associated with ribosome-like granules, varying from compactly arranged linear densities to more loosely packed ones. They contained scattered vesicles of various sizes and occasionally a focal accumulation of randomly arranged 10-nm neurofilaments or 13–25-nm filamentous structures.
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  • 22
    Electronic Resource
    Electronic Resource
    Springer
    Acta neuropathologica 78 (1989), S. 594-604 
    ISSN: 1432-0533
    Keywords: Neurocysticercosis ; Pathogenesis ; Histochemistry ; Immunohistochemistry ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary This study was based on two cases of disseminated human neurocysticercosis from India. The material availabel was examined grossly, and by light microscopy, histochemistry, immunomorphology and electron microscopy. The results showed that the parasites commonly embolized to the anatomically discernable gray-white matter junction of the brain and were located in cavities, the walls of which were dilated vascular channels. The parasite-nutrition process was through endocytosis and microtrichal activity. To camouflage themselves from the host-defense mechanisms, the parasites apparently covered themselves with host-tissue-like material. Host reactivity to the parasite was heralded morphologically by the physical anchoring of the parasite by activated endothelial cells, loss of the host-tissue-like cover and an acute polymorphonuclear leucocytic response.
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  • 23
    Electronic Resource
    Electronic Resource
    Springer
    Acta neuropathologica 79 (1989), S. 340-346 
    ISSN: 1432-0533
    Keywords: Paraganglioma ; Melanin ; Orbit ; Immunocytochemistry ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary A paraganglioma of the orbit in a 21-year-old woman is presented, containing oculo-cutaneous melanin in many tumor cells, occasionally adjacent to neurosecretory granules, and in macrophages. This tumor expands the list of neuroectodermal tumors with potential melaninization.
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  • 24
    Electronic Resource
    Electronic Resource
    Springer
    Anatomy and embryology 180 (1989), S. 243-257 
    ISSN: 1432-0568
    Keywords: Dorsal lateral geniculate nucleus ; Synapse formation ; Synaptic glomerulus ; Rat ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Synapse formation and maturation were examined in the rat dorsal lateral geniculate nucleus (dLGN) from birth to adulthood. Examination of animals, whose ages were closely spaced in time, showed that the maturation of the synaptic organization of the nucleus takes place chiefly during the first 3 weeks of postnatal life. This period of maturation may be divided into 3 broad stages. During the first stage, which spans the first 4 days of life, there are only a few immature synapses scattered throughout the nucleus; occasionally aggregates of 3 or 4 synapses are encountered. Dendrodendritic synapses first appear at the end of this stage. The second stage, which lasts from the end of the first stage through day 8, is characterized by intensive synaptogenesis as well as extensive growth and degeneration. For the first time, large boutons resembling retinal terminals form multiple synaptic contacts with dendrites and dendritic protrusions; these synaptic arrangements are partially covered by glial processes. A feature characteristic of the developing dLGN during the first 2 postnatal weeks, and particularly during the second stage, is the presence of membrane specializations that resemble vacant postsynaptic densities. These specializations, which may be unapposed or opposite another neuronal process, decrease in frequency as the number of synapses increases. It is not known whether these densities are converted to synapses or whether they result from loss of presynaptic elements. The third stage in the process of synaptogenesis, which spans a period between days 10 and 20, is characterized by myelination and by the diminution of growth cones, degenerating profiles and vacant postsynaptic densities. There is also a very significant increase in the number and maturation of synapses including synaptic glomeruli. However, it is not until the end of this stage that synapses appear qualitatively indistinguishable from synaptic arrangements identified in adult animals.
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  • 25
    Electronic Resource
    Electronic Resource
    Springer
    Archives of dermatological research 281 (1989), S. 254-259 
    ISSN: 1432-069X
    Keywords: Innermost cell layer ; Tonofilaments ; Huxley's cells ; Henle's cells ; Anagen hair follicles ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary To elucidate the biologic roles and further cytologic characteristics of the innermost cell (IMC) layer of the outer root sheath (ORS), human anagen hair follicles were ultrastructurally examined. In the lower follicle, the transeversely running tonofilaments in the inner side of the cytoplasm of the IMCs showed a massive accumulation, facing the keratinized part of a Huxley's cell protruding through a Henle's pore. In a rare instance, a spindle-shaped cell was seen between the IMC layer and the keratinized Henle's layer. At the lower isthmus portion, some of the IMCs containing a large number of tonofilaments showed a partial degeneration of the inner side of the cytoplasm. More distally, intercellular spaces between the keratinized IMCs and keratinized Henle's cells were partly dilated and contained amorphous substances. It is suggested that the IMCs in the lower follicle may play a role to support and cover the inner hair structures, tightly as hoops of a barrel. In the isthmus portion, the IMCs may loosely support and guide the keratinized Henle's cells undergoing degeneration.
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  • 26
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    Experimental brain research 75 (1989), S. 563-568 
    ISSN: 1432-1106
    Keywords: Retina ; Diencephalon ; Co-culture ; Synapses ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Explants of chick embryo diencephalon co-cultured with explants of retina display areas of complex neuropil containing large retinal-like endings which establish synaptic contact with conventional and presynaptic dendrites. Transection of fibre bundles linking retinal to diencephalic explants results in the degeneration of endings of this type, suggesting that axons of extrinsic (retinal) origin innervate the diencephalic explants in an in-vivo-like manner.
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  • 27
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    Experimental brain research 78 (1989), S. 425-434 
    ISSN: 1432-1106
    Keywords: Avian forebrain ; Synapses ; Stereology ; Disector ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The lobus parolfactorius (LPO) of the chick has been shown to undergo an increase in the mean synaptic numerical density (Nv syn) in response to one-trial passive avoidance learning (Stewart et al. 1987). The present study was undertaken in order to describe the pattern of normal development of synapses in the LPO, to further investigate the significance of this plastic response. The LPO's from each hemisphere of pre-hatch (16 days), and post-hatch (1 day, 9 day and 22 day old) chicks were processed for electron microscopy. Synapses were classified into asymmetric spine, asymmetric shaft, symmetric spine, and symmetric shaft synapses, on the basis of the density of the post-synaptic thickening and the nature of the post-synaptic target. A 3-dimensional stereological probe was used (the ‘disector’) to calculate Nv syp, and mean projected height (H syp) of the post-synaptic density (PSD). Mean values for each age and hemisphere were compared with a 2-way analysis of variance test using paired samples. A six-fold increase in Nv syp was seen between 16 days in ovo, and 9 days post-hatch. There was a hemispheric asymmetry at 9 days post-hatch, with the left hemisphere LPO containing 1.6 times as many synapses per μm-3. There was a subsequent period of reduction in synaptic density in the left hemisphere LPO between 9 and 22 days post-hatch. The Nv of all classes of synapse increased with age, but the proportions of the symmetrical synapses with respect to the total number of synapses, decreased with age. This decrease was of a similar magnitude for each hemisphere. A hemispheric difference was seen in post-hatch asymmetric synapses, with a greater proportion of asymmetric spine synapses in the left hemisphere. The magnitude of the hemispheric asymmetry was constant throughout the 3 week period of post-hatch development, but was not present in pre-hatch chicks. The PSD increased in length in each hemisphere by approximately 40% between post-hatch day 1 and post-hatch day 9. These data show that the LPO contains a synaptic population which undergoes substantial modification during the first week post-hatch. An asymmetry exists at post-hatch day 9 which is not present at the earlier ages investigated, nor indeed after 22 days post-hatch. This may have significance with regard to studies of passive avoidance learning in the one-day old chick, where an increase in both the size and number of synapses in the LPO has been demonstrated (Stewart et al. 1987). It is possible that ‘training’, in this situation, may simply enhance the timing of synaptic events that result as a consequence of normal development.
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  • 28
    ISSN: 1432-1106
    Keywords: Nerve growth factor ; C6 glioma cells ; Chromaffin cells histofluorescence ; Electron microscopy ; Immunocytochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary In order to maintain a chronic supply of growth factor for medulla cells in vitro, chromaffin cells from rat, African green monkeys and man were co-cultured with C6 glioma cells, which secrete growth factors that sustain sympathetic neurons in vitro. The response of chromaffin cells to coculture was compared to treatment of medullary cells with nerve growth factor (NGF) alone. Dispersed chromaffin cell preparations were obtained by a trypsin-collagenase procedure, and subjected to differential plating on collagen-coated surfaces. With both human and monkey tissue, non-chromaffin cells did attach to the culture plates and an enriched chromaffin cell population could be replated. Rat adrenal medulla cells survived very poorly in vitro and were not enriched in this procedure. Cultured human and monkey chromaffin cells survived as epithelial cells (50%) and showed neuritic outgrowth on 55 to 66% of the cells after eight days when treated with nerve growth factor (NGF). These cells showed strong catecholamine histofluorescence, tyrosine hydroxylase (TH) and dopamine beta hydroxylase (DBH) immunoreactivity. In contrast, only ten percent of adult rat chromaffin cells survived in culture, although NGF treatment rescued an additional 20% of the cells and induced neuritic outgrowth after one week in vitro. C6 glioma cells were treated with mitomycin C bromodeoxyuridine to inhibit mitosis and were plated with the various medulla cells in a one to one ratio. Both human and monkey chromaffin cells expressed extensive and enhanced neuritic arborization within eight days of co-culture, (64–82% respectively) and exhibited intimate contact with the glioma cells as seen at the ultrastructural level. Importantly, survival of adult rat adrenal medulla cells was enhanced to 50% or more with 40% of the cells extending neurites when co-cultured with glioma cells for seven days. Chromaffin cells from all three species reacted for TH, DBH and PNMT in co-culture and were histofluorescent. The majority of these cells were also immunoreactive for serotonin and enkephalin, while only 37% of chromaffin cells indicated the presence of NPY. These data indicate that adrenal medulla can be maintained in vitro as the neuronal phenotype when co-cultured with growth factor producing cells and that this strategy may be useful for in vivo transplantation studies.
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  • 29
    ISSN: 1432-072X
    Keywords: Aggregation substance ; Enterococcus faecalis ; Electron microscopy ; Field emission scanning electron microscopy ; Immunogold labelling technique ; Sex pheromone system
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The distribution of sex pheromone induced aggregation substance was studied on the cell surface of various Enterococcus faecalis strains. In the accompanying paper we have shown that the aggregation substance appears as a layer of hairlike structures. Using direct and indirect immunogold technique, transmission electron microscopy and high resolution scanning electron microscopy we investigated the appearance and distribution of the aggregation substance. The “hairs” increase in number with increasing exposure to sex pheromones (maximum density: 1300/μm2). We show that these structures are unequally distributed over the cell surface, even if the cells were induced by sex pheromones for a long period of time. Statistical analysis of the unequal distribution indicates that aggregation substance is incorporated into pre-existing “old” cell-walls and that this incorporation shows a saturation ca. 40 min after addition of sex pheromones.
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  • 30
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    Archives of gynecology and obstetrics 246 (1989), S. 169-179 
    ISSN: 1432-0711
    Keywords: Human fetal endometrium ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Human fetal endometrium was examined by light and electron microscopy. Our study shows the following new morphological aspects: (1) Glands are already present. (2) Endometrium undergoes a maturation process during gestation and at late gestational age resembles late proliferative endometrium. (3) The nuclear bodies are present in cell nuclei throughout gestation. (4) Nucleolar channel systems (NCS) sometimes appear at a late gestational age. (5) Cells with the same morphology as that of endocrine cells are found in the basal layers of endometrium at a late gestational age. The significance of these morphological aspects is discussed.
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  • 31
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    Rheumatology international 9 (1989), S. 49-51 
    ISSN: 1437-160X
    Keywords: Synovium ; Monoclonal antibodies ; Immunohistochemistry ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The cells making up the lining of the synovium have long been known as type A and B synoviocytes, with an intermediate form sometimes also described. Accumulating evidence shows that the type A cells are macrophages and the type B cells are fibroblasts. Recently, a definite orientation of these cells within the synovial lining has been observed. The number of synovial lining cells increases in joint disease, and this now seems more likely to be due to cellular recruitment rather than local proliferation.
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  • 32
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    Journal of neurology 236 (1989), S. 361-363 
    ISSN: 1432-1459
    Keywords: Mitochondrial encephalomyopathy ; MELAS ; Mitochondrial inclusion ; Pilovacuolar inclusion ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The case of a 33-year-old man with clinical features of mitochondrial encephalomyopathy is presented. He suffered from recurrent cerebral infarctions, cerebellar ataxia, deafness, retinopathy, weakness, and cardiac and renal disorders. Biochemical and light microscope investigations of skeletal muscle did not show any mitochondrial abnormality. Electron microscopy revealed the presence of a hitherto unreported peculiar “pilovacuolar” inclusion in numerous mitochondria, composed of an electron dense pile or rod within a vacuole, while globular or crystalline inclusions were absent.
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  • 33
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    European archives of oto-rhino-laryngology and head & neck 246 (1989), S. 428-432 
    ISSN: 1434-4726
    Keywords: Otitis media with effusion ; Mucociliary system ; Eustachian tube ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary We have examined the function and fine structure of the mucociliary system of the eustachian tube in an experimental study of otitis media with effusion induced by X-ray irradiation. Functional examination demonstrated that the ciliary activity was diminished in such a condition, while morphological observations showed pathological findings including compound cilia, vacuolation of ciliated cells and expansion of intercellular space. These findings show that irradiation-induced otitis media with effusion results in impairment of the mucociliary system. As evidenced by these studies, the mucociliary system in the eustachian tube has an important role in the clearance of fluid produced in the tympanic cavity as well as affording improvement in this disease.
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  • 34
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 125-131 
    ISSN: 0887-3585
    Keywords: protein conformation ; dynamics ; Monte Carlo simulation ; conformational energy ; minimization ; plastic deformation ; conformational heterogeneity ; hierarchy in dynamics ; trypsin inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Differences in atom packing are studied in the minimum energy conformations derived from the record of the Monte Carlo simulation of conformational fluctuation in the native state of a globular protein, bovine pancreatic trypsin inhibitor. It is found that local deformations observed among the minima which are found in the previous paper are accompanied by rearrangement of atom packing. Spatial locations of the local deformations in the three-dimensional folded structure are also studied. It is foundthat the local deformations are distributed in space in several clusters inthe folded structure. The size and location of the clusters characterize the respective fluctuations of the first and the second levels observed in the simulation. In the fluctuations of the first level local deformations, each of which usually involves a few side chains and one main chain local segment, are thermally exited independently of each other near thesurface of the molecule. The observed fluctuation of the second level involves a cooperative deformation involving many side chains and local main chain segments all in one cluster, which goes though the core of the molecule. The collective local deformations observed both in the first and second levels are plastic in the sense that they are accompanied with rearrangement of atom packing.
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  • 35
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 139-148 
    ISSN: 0887-3585
    Keywords: protein architecture ; packing ; evolutionary relationships ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: α/β barrel structures very similar to that first observed in triose phosphate isomerase are now known to occur in 14 enzymes. To understand the origin of this fold, we analyzed in three of these proteins the geometry of the eight-stranded β-sheets and the packing of the residues at the center of the barrel. The Packingin thisregion is seen in its simplest form in glycolate oxidase. It consists of 12 residues arranged in three layers. Each layer contains four side chains. The packing of RubisCO and TIM can be understood in terms of distortions of this simple pattern, caused by residues with small side chains at someof the positions inside the barrel. Two classes of packing are found. In one class, to which RubisCO and TIM belong, the central layer is formed by a residue from the first, third, fifth, and seventh strands; the upper and lower layers are formed by residues fromthe second, fourth, sixth, and eighth strands. In the second class, to which GAO belongs, this is reversed: it is side chains from the even-numbered strands that form the central layer, and side chains from the oddnumbered strands that form the outer layers. Our results suggest that not all proteins with this fold are related by evolution, but that they represent a common favorable solution to the structural problems involved in the creation of a closed β barrel.
    Additional Material: 8 Ill.
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  • 36
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 170-182 
    ISSN: 0887-3585
    Keywords: modeling ; flavodoxin ; structure prediction ; side chains ; database ; structure analysis ; protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The tertiary structure of flavodoxin has been model build from only the X-ray crystallographic α-carbon coordinates. Main-Chain atoms were generated from a dictionary of backbone structures. Side-chain conformations were initially set according to observed statistical distributions, clashes were resolved with reference to other knowledge-based parameters, and finally, energy minimization was applied. The RMSD of the model was 1.7 Å across all atoms to the native structure. Regular secondary structural elements were modeledmore accurately than other regions. About 40%of the ξ1 torsional angles were modeled correctly. Packing of side chains in the core was energetically stable but diverged significantly from the native structure in some regions.The modeling of protein structures is increasing in popularity but relatively few checks have been applied to determine the accuracy of the approach. In this work a variety of parameters have been examined. It was found that close contact, and hydrogen-bonding patterns could identifypoorly packed residues. These tests, however, did not indicate which residues had a conformation different from the native structure or how to move such residues to bring them into agreement. To assist in the modeling of interacting side chains a database of known interactions has been prepared.
    Additional Material: 8 Ill.
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  • 37
    ISSN: 0887-3585
    Keywords: yeast hexokinase II ; dimerization ; in vivo functions ; glucose repression ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The function of the N-terminal amino acids of Saccharomyces cerevisiae hexokinase II was studied in vivo using strains producing a form of hexokinase II lacking its first 15 amino acids (short form).This short form of hexokinase II was produced from a fusion between the promoter region of the PGK1 gene and the HXK2 coding sequence except the first 15 codons. As expected, the in vitro analysis of the short from protein by gel filtration chromatography indicates that the short protein does not form dimers under conditions where the wild-type protein dimerizes. Kinetic studies show that the enzymatic activities are very similarto wild-type behavior. The physiological experiments performed on the strains containing the fusion allele demonstrate that the short form ofthe enzyme is similar to the wild-type both in terms of phosphorylation of hexoses and glucose repression. We conclude that the N-terminalamino acids of hexokinase II are not required in vivo either for phosporylation of hexoses or for glucose repression.
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  • 38
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 289-312 
    ISSN: 0887-3585
    Keywords: aconitase ; iron-sulfur enzyme ; crystal structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of the 80,000 Da Fe—S enzyme aconitase has been solved and refined at 2.1 Å resolution. The protein contains four domains; the first three from the N-terminus are closely associated around the [3Fe-4S] cluster with all three cysteine ligands to the cluster being provided by the third domain. Associationof the larger C-terminal domain with the first three domains createsan extensive cleft leading to the Fe—S cluster. Residues from all four domains contribute to the active site region, which is defined by the Fe—S cluster and a bound SO42-ion. This region of the structure contains 4 Arg, 3 His, 3 Ser, 2 Asp, 1 Glu, 3 Asn, and 1 Gln residues, as well asseveral bound water molecules. Three of these side chains reside on a threeturn 310 helix in the first domain. The SO42-ion is bound 9.3 Å from the center of the [3Fe-4S] cluster by the side chains of 2 Arg and 1 Gln rsidues. Each of 3 His side chains in the putative active site is paired with Asp or Glu side chains.
    Additional Material: 13 Ill.
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  • 39
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 271-280 
    ISSN: 0887-3585
    Keywords: antifluorescyl monoclonal antibody ; high-affinity binding site ; effects of MPD on hapten binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of a fluorescein-Fab (4-4-20) complex was determined at 2.7 Å resolution by molecularreplacement methods. The starting model was the refined 2.7 Å structure of unliganded Fab from an autoantibody (BV04-01) with specificity for single-stranded DNA. In the 4-4-20 complex fluorescein fits tightly into a relatively deep slot formed by a network of tryptophan and tyrosine side chains. The planar xanthonyl ring of the hapten is accommodated at the bottom of the slot while the phenylcarboxyl group interfaces with solvent. Tyrosine 37 (light chain) and tryptophan 33 (heavy chain) flank the xanthonyl group and tryptophan 101 (light chain) provides the floor of the combining site. Tyrosine 103 (heavy chain) is situated near the phenyl ring of the hapten and tyrosine 102 (heavy chain) forms part of the boundary of the slot. Histidine 31 and arginine 39 of the light chain are located in positions adjacent to the two enolic groups at opposite ends of the xanthonyl ring, and thus account for neutralization of one of two negative charges in the haptenic dianion. Formation of an enol-arginine ion pair in a region of low dielectric constant may account for an incremental increase in affinity of 2-3 orders of magnitude in the 4-4-20 molecules relative to other members of an idiotypic family of monoclonalantifluorescyl antibodies. The phenyl carboxyl group of fluorescein appearsto be hydrogen bonded to the phenolic hydroxyl group of tyrosine 37 of the light chain. A molecule of 2-methyl-2,4-pentanediol (MPD), trapped in the interface of the variable domainsjust below the fluorescein binding site, may be partly responsible for the decrease in affinity for the hapten in MPD.
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  • 40
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 355-373 
    ISSN: 0887-3585
    Keywords: protein ; structure ; prediction ; primary ; secondary ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new approach is introduced for analyzing and ultimately predicting protein structures, defined at the level of Cα coordinates. We analyze hexamers (oligopeptides of six amino acid residues) and show that their structure tends to concentrate in specific clusters rather than vary continuously. Thus, we can use a limited set ofstandard structural building blocks taken from these clusters as representatives of the repertoire of observed hexamers. We demonstrate that protein structures can be approximated by concatenating such building blocks. We have identified about 100 building blocks by applying clustering algorithms, and have shown that they can “replace” about 76% ofall hexamers in well-refined known proteins with an error of less than 1 Å, and can be joined together to cover 99% of the residues. After replacing each hexamer by a standard building block with similar conformation, we can approximately reconstruct the actual structure by smoothly joining the overlapping building blocks into a full protein. The reconstructed structures show, in most cases, high resemblance to the original structure, although using a limited number of building blocks and local criteria of concatenating them is not likely to produce a very precise global match. Since these building blocks reflect, in many cases, some sequence dependency, it may be possible to use the results of this study as a basis for a protein structure prediction procedure.
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  • 41
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 20-31 
    ISSN: 0887-3585
    Keywords: ribonuclease ; active site ; conformational change ; protein-nucleic ; acid interactions ; fluorescence depolarization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations were performed on free RNase T1 and the 2′GMP-RNase T1 complex in vacuum and with water in the active site along with crystallographically identified waters, allowing analysis of both active site and overall structural and dynamics changes due to the presence of 2′GMP. Difference in the active site include a closing in the presence of 2′GMP, which is accompanied by a decrease in mobility of active site residues. The functional relevance of the active site fluctuations is discussed. 2′GMP alters the motion of Tyr-45, suggesting a role for that residue in providing a hydrophobic environment for the protein-nucleic acid interactions responsible for the specificity of RNase T1. The presence of 2′GMP causes a structural change of the C-terminus of the α-helix, indicating the transmission of structural changes from the active site through the protein matrix. Overall fluctuations of both the free and 2′GMP enzyme forms are in good agreement with X-ray temperature factors. The motion of Trp-59 is influenced by 2′GMP, indicating difference in enzyme dynamics away from the active site, with the calculated changes following those previously seen in time-resolved fluorescence experiments.
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  • 42
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 324-337 
    ISSN: 0887-3585
    Keywords: aspartyl protease ; HIV/AIDS ; yeast expression ; polyprotein processing ; α-factor ; secretion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The protease of the human immunodeficiency virus type I (HIV1) was expressed both intracellularly and extracellularly in Saccharomyces cerevisiae. Intracellular expression of the protease was achieved by fusing a 179 amino acid precursor form of the protease to human superoxide dismutase (hSOD). Self-processing of the viral enzyme from the hybrid precursor was demonstrated to ocur within the yeast host. Secretion of the protease was achieved by fusing the leader sequence of yeast α-factor to the precursor form of the protrease or to the 99 amino acid mature form of the protease. Authentic and active forms of the retroviral enzyme were detected in yeast supernatants of cells expressing the precursor or the mature form of the protease. A D25E active site variant of the retroviral enzyme exhibited diminished autocatalytic activity when expressed intracellularly or secreted from yeast. The wild-type protease was active in an in vitro assay on the natural substrate, myristylated gag precursor, Pr53gag. Correct processing of Pr53gag at the Tyr 138-Pro 139 junction was confirmed by amino terminal sequence analysis of the resulting capsid protein (CA, p24). The secreted protease was purified to homogeneity from yeast media using preparative isoelectric focusing and reverse-phase HPLC. Amino terminal sequence analysis showed a sequence beginning at amino acid 1 of the mature enzyme (Pro) and another sequence beginning at amino acid 6 (Trp). This shorter sequence may represent a natural autolytic product of the proteaseaspartyl protease.
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  • 43
    ISSN: 0887-3585
    Keywords: protein tertiary structure ; incorrect and correct folding ; molecular surfaces ; solvation free energy ; solution and crystal structure ; disulfide connectivity determination ; squash inhibitor family ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Refinement of distance geometry (DG) structures of EETI-II (Heitz et al.:Biochemistry 28:2392-2398, 1989), a member of the squash family trypsin inhibitor, have been carried out by restrained molecular dynamics (RMD) in water. The resulting models show better side chain apolar/polar surface ratio and estimated solvation free energy than structures refined “in cacuo.” The consistent lower values of residual NMR constraint violations, apolar/polar surface ration and solvation free energy of one of these refined structures allowed prediction of the 3D folding and disulfide connectivity of EETI-II. Except for the few first residues for which no NMR constraints were available, this computer model fully agree with X-ray structures of CMTI-I (Boe et al.: FEBS Lett. 242:285-292, 1989) and EETI-II complexed with trypsin that appeared after the RMD simulation was completed. Restrained molecular dynamics n water is thus proved to highly valuable for refinement of DG structures Also, the successful use of apolar/polar surface ratio and solvation free energy reinforce the analysis of Novotny et al. (Proteins 4: 19-30, 1988) and shows that these criteria are useful indicators of correct versus misfolded models.
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  • 44
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    Proteins: Structure, Function, and Genetics 5 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 45
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 155-167 
    ISSN: 0887-3585
    Keywords: protein structure comparison ; dihedral angles ; protein conformation ; hemoglobin structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An efficient algorithm was characterized that determines the similarity in main chain conformation between short protein substructures. The algorithm computes Δt, the root mean square difference in φ and ψ torsion angles over a small number of amino acids (typically 3-5). Using this algorithm, large number of protein substrates comparisons were feasible. The parameter Δt was sensitive to variations in local protein conformation, and it correlates with Δr, the root mean square deviation in atomic coordinates. Values for Δt were obtained that define similarity thresholds, which determine whether two substructure are considered structurally similar. To set a lower bound on the similarity threshold, we estimated the component of Δt due to measurement noise fromcomparisons of independently refined coordinates of the same protein. A sample distribution of Δt from nonhomologous protein comparisons identified an upper bound on the similarity threshold, one that refrains from incorporating large numbers of nonmatching comparisons large numbers of nonmatching comparisons. Unlike methods based on Cα atoms alone, Δt was sensitive to rotations in the peptide plane, shown to occur in several proteins. Comparisons of homologus proteins by Δt showed that the active site torsion angles are highly conserved. The Δt method was applied to the α-chain of human hemoglobin, where it readily demonstrated the local differences in the structures of different ligation states.
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  • 46
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 193-209 
    ISSN: 0887-3585
    Keywords: protein folding ; simulated annealing ; empirical potentials ; Monte Carlo dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The current work describes a simplified representation of protein structure with uses in the simulation of protein folding. The model assumes that a protein can be represented by a freely rotating rigid chain with a single atom approximately the effect of each side chains. Potentials describing the attraction or repulsion between different types of amino acids are determined directly from the distribution of amino acids in the database of known protein structures. The optimization technique of simulated annealinghas been used to dynamically sample the conformations available to this sample model, allowing the protein to evolve from an extended, random coil into a compact globular structure. Many characteristics expected of true proteins, such as the sequence-dependent formation of secondary structure, the partitioning of hydrophobic residues, and specific disulfide, suggestion the model may accurately simulate the folding process.
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  • 47
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 249-258 
    ISSN: 0887-3585
    Keywords: DNA binding domain ; etheno-M13 DNA ; single-stranded DNA affinity chromatography ; proteolytic fragments ; truncated topoisomerase ; protein-DNA interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Limited digestion of E. coli DNA topoisomerase I with trypsin or papain generated a DNA-binding domain of MW 14,000 corresponding to the carboxyl terminal of the enzyme. This fragment binds to single-stranded DNA agarose as tightly as the intact enzyme. It required around 400 mM NaCl for elution. A truncated topoisomerase that lacks this C-terminal domain was purified. It was eluted from the single-stranded DNA agarose column at around 150 mM NaCl. Although the truncated enzyme could relax negatively supercoiled DNA as efficiently as the intact enzyme at low ionic strength, its processivity was more sensitive to increasing salt concentration. Measurement of binding to fluorescent etheno-M13 DNA also demonstrated that the presence of the C-terminal domain confers higher affinity to DNA for the enzyme.
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  • 48
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 275-283 
    ISSN: 0887-3585
    Keywords: mutagenesis ; structure-function relationships ; enzymatic catalysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Site saturation mutagenesis has been carried out at Ala-237 in RTEM-1 β-lactamase to assess the role of this site in modulating differences in specificity of β-lactamases for penams vs. cephams as substrates. (An Ala-237 Thr mutation had previously been shown to increase activity on cephems by about 30-80%.1,2) Screening of all 19 possibles mutants on penams and cephems revealed the even more active Ala-237 Asn mutant. Detailed kinnetic analysis showns that this mutant has about four times the activity toward cephalothin and cephalosporin C as the wild-type enzyme. Both mutations reduce the activity toward penams to about 10% that of RETM-1 β-lactamase and lower by about 5°C the tempreature at which the enzyme denatures. Functional properties of the other mutants have also been surveyed. The most intresting aspect of these results is that two quite disparate amino acids, theronine and asparagine, when intorduced for Ala-237, cause such similar changes in enzyme specificity while more similar residues do not alter the catalytic properties of the enzyme to such a significant degree.
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  • 49
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 338-340 
    ISSN: 0887-3585
    Keywords: cytochrome c ; axial ligand ; semisynthesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Semisynthesis has been employed to replace the axial methionine in horse heart cytochrome c with histidine. The reduction potential of the His-80 protein (cyt c-His-80) is 41 mV vs NHE (0.1 M phosphate; pH 7.0; 25°C). The absorption spectra of oxidized and reduced cyt c-His-80 are very similar to those of the native protein in the porphyrin region, but the 695 nm band is absent in the oxidized His-80 protein.
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  • 50
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    Proteins: Structure, Function, and Genetics 6 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 51
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 372-381 
    ISSN: 0887-3585
    Keywords: cytochromec ; Saccharomyces cerevisiae ; protein secondary structures ; protein design ; protein engineering ; protein folding ; protein evolution ; modular exchange ; loop swap ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ω(Omega)-loops are protein secondary structural elements having small distance between segment termini. It should be possible to delete or replace certain of these Ω-loops without greatly distorting the overall structure of the remaining portion of the molecule. Functional requirements of regions of iso-1-cytochrome c from the yeast Saccharomyces cerevisiae were in investigated by determining the biosynthesis and activity in vivo of mutant forms in which four different Ω-loops were individually deleted, or in which one Ω-loop was replaced with five different segments. Deletion encompassing amino acid positions 27-33 and79-83 either prevented synthesis of the holoprotein, or produced highly labile iso-1-cytochromes c, whereas deletions encompassing position 42-45 and 48-55 allowed partial synthesis and activity. These two latter regions, therefore, are not absolutely required for any biosynthetic process such as heme attachment, mitochondrial import, or for enzymatic interactions. All replacements in Loop A (residue position 24-33) with the same size (10 amino acid residues), longer (13 and 15 amino acid residues), or shorter segments (6 amino acid residues), resulted in strains having at least partial levels of iso-1-cytochrome c; however, the relative activities ranged from zero to almost the normal level. Thus, Loop A does not appear to be essential for such biosynthetic steps as heme attachment and mitochondrial import. In contrast, the full range of relative activities suggest that this region interacts with physiological partners to carry out efficient electron transport.
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  • 52
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 418-423 
    ISSN: 0887-3585
    Keywords: accessible area ; power law fit ; bootstrap analyses ; fractal structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The coefficients in a power low fit of accessible area versus molecular weight for high-reslution monomeric protein structures are assessed with respect to statistical accuracy using bootstrap analyses, and with respect to physical significance using model systems and the concept of roughness or fractal structure of the protein surface.
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  • 53
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 38-46 
    ISSN: 0887-3585
    Keywords: reconstitution ; membrane protein folding/unfolding ; pH effects ; differential scanning calorimetry ; circular dichroism ; electron microscopy ; HPLC ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Thermal unfolding experiments on bacteriorhodopsin in mixed Phospholipid/detergent micelles were performed. Bacteriorhodopsin was extracted from the purple membrane in a denatured state and then renatured in the micellar system. The purpose of this study was to compare the changes, if any, in the structure and stability of a membrane protein that has folded in a nonnative environment with results obtained on the native system, i.e., the purple membrane. The purple membrane crystalline lattice is an added factor that may influence the structural stability of bacteriorhodopsin. Micelles containing bacteriorhodopsin are uniformly sized disks 105 ± 13 Å in diameter (by electron microscopy) and have an estimated molecular mass of 210 kDa (by gel filtration HPLC). The near-UV CD spectra (which is indicative of tertiary structure) for micellar bacteriorhodopsin and the purple membrane are very similar. In the visible CD region of retinal absorption, the double band seen in the spectrum of the purple membrane is replaced with a broad positive band for micellar bacteriorhodopsin, indicating that in micelles, bacteriorhodopsin is monomeric. The plot of denaturational temperature vs. pH for micellar bacteriorhodopsin is displaced downward on the temperature axis, illustrating the lower thermal stability of micellar bacteriorhodopsin when compared to the purple membrane at the same pH. Even though micellar bacteriorhodopsin is less stable, similar changes in response to pH and temperature are seen in the visible absorption spectra of micellar bacteriorhodopsin and the purple membrane. This demonstrates that changes in the protonation state or temperature have a similar affect on the local environment of the chromophore and the protein conformation. We conclude that the tertiary structure of the bacteriorhodopsin monomer is essentially the same in micelles and the purple membrane. On the other hand, in the synthetic mixed micelle system, the packing between the nonnative amphiphiles and bacteriorhodopsin is probably not optimal, protein-protein interactions have been lost, and thehelical packing may be looser because the crystalline lattice is absent. Itis likely that a combination of these effects leads to the decreased stability of micellar bacteriorhodopsin.
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  • 54
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 22-37 
    ISSN: 0887-3585
    Keywords: sequence homology ; tertiary structure prediction ; molecular dynamics ; energy minimization ; hydrophobic interactions ; aromatic ring-ring interactions ; salt bridges ; calcium binding ; thermoactinomyces vulgaris ; extracellular protease ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Subtilisin family of proteases has four members of known sequence and structure: subtilisin Carlsberg, Subtilisin novo, proteinase K, and thermitase. Using thermitase as a test case, we ask two questions. How good are methods for model building a three-dimensional structure of a protein based on sequence homology to a known structure? And what are the molecular causes of thermostability? First, we compare predicted models of thermitase, refined by energy minimization and varied by molecular dynamics, with the preliminary crystal structure. The predictions work best in the conserve structural core and less well in seven loop regions involving insertions and deletions relative to Subtilisin. Here, variation of loop regions by molecular dynamics simulation in vacuo followed by energy minimization does not improve the prediction since we find no correlation between in vacuo energy and correctness of structure when comparing local energy minima. Second, in order to identify the molecular case of thermostability we confront hypotheses erived by calculation of the details of interatomic interactions with inactivation experiments. As a result, we can exclude salt bridges and hydrophobic interactions as main cause of thermostability. Based on a combination of theoretical and experimental evidence, the unusually tight binding of calcium by thermitase emerges as the most likely single influence responsible for its increased thermostability.
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  • 55
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 166-169 
    ISSN: 0887-3585
    Keywords: α-crystallin ; enthalpy ; entropy of solution ; light scattering ; second virial coefficient ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Light scattering studies were performed on bovine α-crystallin measuring the scattering intensities as a function of scattering angle, concentration, and temperature. The data yielded the molecular weight, radius of gyration, and second virial coefficient of α-crystallin at different temperatures. The second virial coefficient increased with increasing temperature. Both the enthalpy and entropy of solution of α-crystallin are positive. The Flory thetatemperature was found to be 271 K.
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  • 56
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 202-210 
    ISSN: 0887-3585
    Keywords: enhanced stability ; λCro ; genetic suppression ; intracellular proteolysis ; antibody screen ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A mutant Cro protein, which bears the Ile-30→ Leu substitution, is thermally unstable and degraded more rapidly than wildtype Cro in vivo. Using an antibody screen, we have isolated five different second site suppressor substitutions that reduce the proteolytic hypersensitivity of this mutant Cro protein. Two of the suppressor substitutions increase the thermal stability of Cro by 12°C to 14°C. These amino acid substitutions affect residues 16 and 26, which are substitutions affect residues 16 and 26, which are substantially exposed to solvent in the crystal structure of wild-type Cro.
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  • 57
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 211-217 
    ISSN: 0887-3585
    Keywords: tyrosin ; mutant protein ; amino acid substitution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: CD spectra in the aromatic region of a series of the mutant α-subunits of tryptophan synthase from Escherichia coli, substituted at position 49 buried in the interior of the molecule, were measured at pH 7.0 and 25°C. The measurements were taken to gain information on conformational change produced by single amino acid substitutions. The CD spectra of the mutant proteins, substituted by Tyr or Trp residue in place of Glu residue at position 49, showed more intense positive bands due to one additional Tyr or Trp residue at position 49. The CD spectra of other mutant proteins also differed from that of the wild-type protein, despite the fact that the substituted residues at position 49 were not aromatic. Using the spectrum of the wild-type protein (Glu49) as a standard, the spectra of the other mutants were classified into three major groups. For 10 mutant proteins substituted by Ile, Ala, Leu, Met, Val, Cys, Pro, Ser, His, or Gly, their CD values of bands (due to Tyr residues) decreased in comparison with those of thewild-type protein. The mutant protein substituted by Phe also belonged to this group. These substituted amino acid residues are more hydrophobic than the original residue, Glu. In the second group, three mutant proteins were substituted by Lys, Gln, or Asn, and the CD values of tyrosyl bands increased compared to those of the wild-type proteins. These residues are polar. In the third group, the CDvalues of tyrosyl bands of two mutant proteins substituted by Asp or Thr were similar to those of the wild-type protein, except for oneband at 276.5 nm. these results suggested that the changes in the CD spectra for the mutant proteins were affected by the hydrophobicity of the residuesat position 49.
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  • 58
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    Proteins: Structure, Function, and Genetics 5 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 59
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 266-270 
    ISSN: 0887-3585
    Keywords: crystallization ; purification ; crystals ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Single crystals of T7 RNA polymerase have been grown to a maximum size of 1.8 × 0.3 × 0.3 mm. The crystals are composed of fully intact T7 RNA polymerase which in enzymatically active upon dissolution. These crystals belong to the monoclinic space group P21 and have unit cell parameters a =114.5 Å, b=139.6 Å, c=125.7 Å, β=98.1° Self-rotation function studies indicate that there are three molecules per asymmetricunit. The crystals diffract to at least 3.0 Å resolution. These are the first crystals of a DNA-dependent RNA polymerase suitable for high-resolution X-ray structure determination.
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  • 60
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 233-247 
    ISSN: 0887-3585
    Keywords: protein folding ; crystallographic data base ; structural analysis ; computer program system ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: PKB is a computer program system that combines a data base of three-dimensional protein structures with a series of algorithms for pattern recognition, data analysis, and graphics. By typing relatively simple commands the user may search the data base for instances of a structural motif and analyze in detail the set of individual structures that are found. The application of PKB to the study of protein folding is illustrated in three examples. The first analysis compares the conformations observed for a short sequential motif, sequences similar to the cell-attachment signal Arg-Gly-Asp. The second compares sequences observed for a conformational motif, a 16-residue βαβ unit. The third analysis considers a population of substructures containing ion-pair interaction, examining the relationship offrequency of occurrence to calculated electrostatic energy.
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  • 61
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    Proteins: Structure, Function, and Genetics 6 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 62
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 46-60 
    ISSN: 0887-3585
    Keywords: macromolecular conformation ; protein folding ; helical axis ; secondary structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present a general and mathematically rigorous algorithm which allows the helicoidal structure of a protein to be calculated starting from the atomic coordinated of its peptide backbone. This algorithm yields a unique curved axis which quantifies the folding of the backbone and a full set of helicoidal parameters describing the location of each peptide unit. The parameters obtained form a complete and independent set and can therefore be used for analyzing, comparing, or reconstructing protein backbone geometry. This algorithm has been implemented in a computer program named P-Curve. Several examples of its possible applications are discussed.
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  • 63
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 61-69 
    ISSN: 0887-3585
    Keywords: peptides ; hormones ; amphipathic helix ; hydrophobic moment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Eisenberg's helical hydrophobic moment (〈μH〉) algorithm was applied to the analysis of the primary structure of amphipathic α-helical peptide hormones and an optimal method for identifying other peptides of this class determined. We quantitate and compare known amphipathic helical peptide hormones with a second group of peptides with proven nonamphipathic properties and determine the best method of distinguishing between them. The respective means of the maximum 11 residue 〈μH〉 for the amphipathic helical and control peptides were 0.46 (±/-0.07) and 0.33 (0.07) (P+0.004). To better reflect the amphipathic potential of the entire peptide, the percent of 11 residue segments in each peptide above a particular 〈μH〉 was plotted vs 〈μH〉. The resulting curves are referred to as HM-C. The mean HM-C (of the two groups) was highly significantly different such that the HM-C method was superior to others in its ability to distinguish amphipathic from nonamphipathic peptides. Several potential new members of this structural class were identified using this approach. Molecular modeling of a portion of one of these, prolactin inhibitory factor, reveals a strongly amphipathic α helix at residues 4-21. This computer-based method may enable rapid identification of peptide of the amphipathic α-helix class.
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  • 64
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 128-138 
    ISSN: 0887-3585
    Keywords: DNA repair ; ultravioletlight ; pyrimidine dimers ; glycosylase ; apurinic/apyrimidinic endonuclease ; DNA repair enzymology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Previous structure/function analyses of the DNA repairenzyme, T4 endonuclease V, have suggested that the extreme carboxyl portion of the enzyme is associated with pyrimidine dimer-specific binding (Recinos and Lloyd, and Stump and Lloyd, Biochemistry 27:1832-1838 and 1839-1843, 1988, respectively). Within the final 11 amino acids there are 5 aromatic, 2 basic, and no acidic residues and it has been proposed that these residues stack with and electrostatically interact with the kinked DNA at the site of a pyrimidine dimer. The role of the tyrosine residue at position 129 has beeninvestigated by oligonucleotide site-directed mutagenesis in which the codon for Tyr-129 has been altered to reflect conservative changesof Trp and Phe and more dramatic changes of Ser- a stop, codon, deletion of the codon or introduction of a frameshift. Both changesto the aromatic amino acids resulted in proteins which accumulated will in E. coli and not only significantly enhanced the UV survival of repair, deficient cells but also complemented a defective denV gene within UV-irradiated T4 phage. Partially purified preparations of the Tyr-129 → Trp and Tyr-129 → Phe mutants were assayed for their ability to processively incise UV-irradiated plasmid DNA (a nicking reaction carried out at low 25 mM salt concentrations). The mutant enzymes Tyr-129 → Phe and Tyr-129 → Trp displayed a 1000% and 500% enhanced specific nicking activity, respectively. These reactions were also shown to be completely processive. Assays performed at higher (100 mM) salt concentrations reduced the specific activities of the mutant enzymes approximately to that of wild type for the Tyr-129 → Phe mutant and to 20% that of wild type for the Tyr1-29 → Trp mutant.
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  • 65
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 168-192 
    ISSN: 0887-3585
    Keywords: salt bridge ; ab initio ; calcium ; magnesium ; carboxylate ; phosphate ; ammonium ; guanidinium ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Equilibrium geometries and binding energies of model “salt” or “ion” bridge systems have been computed by ab initio quantum chemistry techniques (GAUSSIAN82) and by empirical techniques (AMBER2.0). Formate and dimethyl phosphate served as anions in the model compounds while interacting with several organic cations, including methyl ammonium, methyl guanidinium, and divalent metal ion (either Mg2+ or Ca2+) without and with an additional chloride; and a divalent metal ion (either Mg2+ or Ca2+), chloride, and four water molecules of hydration about the metal ion. The majority of the quantum chemical computations were performed using a split-valence basis set. For the model compounds studied we find that the ab initio geometries are in remarkably goodagreement with the molecular mechanics geometries.Several Calculations werealso performed using diffuse fractions. The formate anion binds these modelcations more strongly than does dimethyl phosphate, while the organiccation methyl ammonium binds model anions more strongly than does methyl guanidinium. Finally, in model compounds including organic anions, Mg2+ or Ca2+ and four molecules of water, and a chloride anion, we find that the equilibrium structure of the magnesium complex involves a solvent separated ion pair (the magnesium ion is six coordinate), whereas the calcium ion complex remains seven coordinate. Molecular mechanics overestimates binding energies, but the estimates may be close enough to actual binding energies togive useful insight into the details energies to give useful insight into the details of salt bridges in biological systems.
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  • 66
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 306-315 
    ISSN: 0887-3585
    Keywords: oncogene ; GTP-binding protein ; cancer ; S. cerevisiae adenylyl cyclase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Biologically active forms of Ras complexed to GTP can bind to the GTP ase-activating protein (GAP), which has been implicated as a possible target of Ras in mammalian cells. In order to study the structural features of Ras required for this interaction, we have evaluated a series of mutant ras proteins for the ability to bind GAP and a series of Ras peptides for the ability to interfere with this interaction. Point mutations in the putative effector region of Ras (residues 32-40) that inhibit biological activity also impair Ras binding to GAP. An apparent exception is the Thr to Ser substitution at residue 35; [Ser-35]Ras binds to GAP as effectively as wild-type Ras even though this mutant is biologically weak in both mammalian and S. cerevisiae cells. In vitro, [Ser-35]Ras can also efficiently stimulate the S. cerevisiae target of Ras adenylyl cyclase, indicating that other factors may influence Ras/protein interactions in vivo. Peptides having Ras residues 17-44 and 17-32 competed with the binding of RAS to E. coli-expressed GAP with IC50 values of 2.4 and 0.9 μM, respectively, whereas Ras peptide 17-26 was without effect up to 400 μM. A related peptide from the yeast GTP-binding protein YPT1 analogous to Ras peptide 17-32 competed with an IC50 value of 19 μM even though the YPT1 protein itself is unable to bind to GAP. These results suggest that determinants within Ras peptide 17-32 may be important for Ras binding to GAP.
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  • 67
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 357-371 
    ISSN: 0887-3585
    Keywords: sea anemone toxin ; NMR ; distance geometry ; restrained energy minimization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: With the aid of 1H nuclear magnetic resonance (NMR) spectroscopy, the three-dimensional structure in aqueous solution was determined for ATX Ia, which is a 46 residue polypeptide neurotoxin of the sea anemone Anemonia sulcata. The input for the structure calculations consisted of 263 distance constraints from nuclear Overhauser effects (NOE) and 76 vicinal coupling constants. For the structure calculation several new or ammended programs were used in a revised strategy consisting of five successive computational steps. First, the program HABAS was used for a complete search of all backbone and χ1 conformations that are compatible with the intraresidual and sequential NMR constraints. Second, using the program DISMAN, we extended this approach to pentapeptides by extensive sapling of al conformations that are consistent with the local and medium-range NMR constraints. Both steps resulted in the definition of additional dihedral angle constraints and in stereospecific assignments for a number of β-methylene groups. In the next two steps DISMAN was used to obtain a group of eight conformers that contain no significant residual violations of the NMR constraints or van der Waals contacts. Finally, these structures were subjected to restrained energy refinement with a modified version of the molecular mechanics module of AMBER, which in addition to the energy force field includes potentials for the NOCE distance constraints and the dihedral angle constraints. The average of the pairwise minimal RMS distances between the resulting refined conformers calculated for the well defined molecular core, which contains the backbone atoms of 35 residues and 20 interior side chains, is 1.5 ± 0.3 Å. This core is formed by a four-stranded β-sheet connected by two well-defined loops, and there is an additional flexible loop consisting of the eleven residues 8-18. The core of the protein is stabilized by three disulfide bridges, which are surrounded by hydrophobic residues and shielded on one side by hydrophilic residues.
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 424-430 
    ISSN: 0887-3585
    Keywords: ultracentrifugation ; calcium-binding proteins ; fluorescence resonance energy transfer ; pH effect ; hydrophobic interactions ; troponin C dimer ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have investigated pH-dependent changes of the properties of troponin C from rabbit skeletal muscle. At pH 7.5 this protein is a monomer and at pH 5.2 it is a dimer. In contrast, bovine cardiac troponin C remains essentially monomeric at pH 5.2. Bovine brain calmodulin is not a dimer, but significantly aggregated at the same acidic pH. The dimerization of skeletal troponin C was demonstrated by low-speed (16,000 rpm) sedimentation equilibrium measurements carried out at 20°C and by polyacrylamide gel electrophoresis under nondenaturing conditions. Dimer formation was significantly inhibited in the ultracentrifuge at rotor speeds of 30,000 and 40,000 rpm at 20°C, and was completely prevented at a rotor speed of 40,000 rpm and 4°C. This temperature and pressure dependence of dimerization strongly suggests that hydrophobic bonding is a major factor in promoting skeletal troponin C association at pH 5.2. The intramolecular distance between Met-25 and Cys-98 of rabbit skeletal troponin C deduced from fluorescence resonance energy transfer measurements increased by a factor of two upon lowering the pH from 7.5 to 5.2, indicating a pH-dependent transition in which the protein changed from a relatively compact conformation to an elongated conformation. The protein-induced increase in the energy transfer distance is related to the acid-induced dimerization of the protein. The extended conformation observed at pH 5.2 is compatible with the dumbbell-shaped structure of skeletal troponin C crystals obtained from turkey at pH 5.0 [Herzberg, O., James, M. N. G. Nature (London) 313:653-659, 1985] and chicken at pH 5.1 (Sundaralingam, M., Bergstrome, R., Strasburg, G., Rao, S. T., Roychowdhury, P., Greaser, M., Wang, B. C. Science 227:945-948, 1985). However, the conformation in neural solution deviates form that predicted by crystallography. Intermolecular interactions leading to dimer formation likely play an important role in promoting the extended conformation that exists at acidic pH.
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  • 69
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 8-12 
    ISSN: 0887-3585
    Keywords: ribonuclease A ; protein deamidation ; protein conformation ; disulfide bonds ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The effect of the folded conformation of a protein on the rate of deamidation of a specific asparaginyl residue has been determine. Native and unfolded ribonuclease A (RNase A) could be compared under identical conditions, because stable unfolded protein was generated by breaking irreversibly the protein disulfide bonds.Deamidation of the labile Asn-67 residue of RNase A was followedelectrophoretically and chromatographically. At 80°C, similar rates of deamidation were observed for the disulfidebonded form, which is thermally unfolded, and the reduced form. At 37°C and pH 8, however, the rate of deamidation of native RNase A was negligible, and was more than 30-fold slower than that of reduced, unfolded RNase A. This demonstrates that the Asn-67 residue is located in a local conformation in the native protein that greatly inhibits deamidation. This conformation is the β-turn of residues 66-68.
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  • 70
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 1-7 
    ISSN: 0887-3585
    Keywords: helix stabilization ; helix dipole ; charged group ; pH titration ; electrostatic interaction ; hydrogen bonding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Interactions between the α-helix peptide dipoles and charged groups close to the ends of the helix were found to be an important determinant of α-helix stability in a previous study.1 The charge on the N-terminal residue of the C-peptide from ribonuclease A was varied chiefly by changing the α-NH2 blocking group, and the correlation of helix stability with N-terminal charge was demonstrated. An alternative explanation for some of those results is that the succinyl and acetyl blocking groups stabilize the helix by hydrogen bonding to an unsatisfied main-chain NH group. The helix dipole model is tested here with peptides that contain either a free α-NH3+ α-COO- groups, and no other charged groups that would titrate with similar pKa's. This model predicts that α-NH3α-COO- groups are helix-destabilizingand that the destabilizing interactions are electrostatic in origin. The hydrogen bonding model predicts that α-NH3 and α-COO- groups are not themselves helix-destabilizing, but that an acetyl or amide blocking group at the N- or C- terminus, respectively, stabilizes the helix by hydrogen bonding to an unsatisfied main-chain NH or CO group.The results are as follows: (1) Removal of the charge from α-NH3 and α-COO- groups by pH titration stabilizes an α-helix. (2) The increase in helix stability on pH titration of these groups is close to the increase produced by adding an acetyl or amide blocking group. (3) The helix-stabilizing effect of removing the charge from α-NH3 and α-COO- groups by pH titration is screened by increasing the NaCl concentration, and therefore the effect is electrostatic in origin. (4) Replacing the C-terminal amide blocking group with a methylester blocking group, which cannot donate a hydrogen bond, causes little change in helix stability.
    Additional Material: 6 Ill.
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  • 71
    ISSN: 0887-3585
    Keywords: template-assembled synthetic protein (TASP) ; 4-helix bundle ; β-barrel structure ; protein de novo design ; peptide synthesis ; peptide conformation ; orthogonal protection ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The construction of a template-assembled synthetic protein (TASP) designed to contain both a 4-helix bundle and a β-barrel as two folding “domains” is described. For the de novo design of proteins, amphiphilic helices (α) and β-sheets (β) are covalently attached to a template peptide (T) carrying functional side chains suitably oriented to promote intarmolecular folding of the secondary structure blocks into a characteristic packing arrangement, i.e., T8-(4α)(4β). The design of this new macromolecule was assisted by computer modeling, which suggested a low-energy conformation with tight hydrophobic packing of the secondary structure subunits. Solid-phase synthesis of the “two-domain” TASP molecule was achieved using orthogonal protection techniques. The solution properties as well as circular dichroism (CD) and infrared spectroscopy (IR) data under various experimental conditions are consistent with the folded conformation suggested by modeling.
    Additional Material: 6 Ill.
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  • 72
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 313-321 
    ISSN: 0887-3585
    Keywords: protein ; electron transfer ; molecular dynamic simulations ; dielectric ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Electrostatic calculations have been carried out on a number of structural conformers of tuna cytochrome c Conformers were generated using molecular dynamics simulations with a range of solvent simulating, macroscopic dielectric formalisms, and one solvent model that explicitly included solvent water molecules. Structures generated using the lowest dielectric models were relatively tight, with-side chains collapsed on the surface, while those from the higher dielectric modelshad more internal and external fluidity, with surface side chains exploring a fuller range of conformational space. The average structure generated with the explicitly solvated model corresponded most closely with the crystal structure. Individual pK values, overall titration curves, and electrostatic potential surfaces were calculated for average structures and along each simulation. Differences between structural conformers within each simulation give rise to substantial changes in calculated local electrostatic interactions, resulting in pK value fluctuations for individual sites in the protein that very by 0.3-2.0 pK units from the calculated time average. These variations are due to the thermal side chain reorientations that produce fluctuations in charge site separations. Properties like overall titration curves and pH dependent stability are not as sensitive to side chain fluctuations within a simulation, but there are substantial effects between simulation due to markeddifferences in average side chain behavior. These findings underscore the importance of proper dielectric formalism in molecular dynamics simulations when used to generate alternate solution structures from a crystal structure, and suggest that conformers significantly removed from the averagestructure have altered electrostatic properties that may prove important inepisodic protein properties such as catalysis.
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  • 73
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 78-92 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 1 Ill.
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  • 74
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 97-103 
    ISSN: 0887-3585
    Keywords: protein conformation ; dynamics ; Monte Carlo simulation ; conformational energy ; minimization ; spin glass ; conformational substates ; conformational heterogeneity ; hierarchy in dynamics ; trypsin inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A computer experiment of protein dynamics is carried out, which consists of two steps: (1) A Monte Carlo simulation of thermal fluctuations in the native state of a globular protein, bovinepancreatic trypsin inhibitor; and (2) a simulation of the quick freezingof fluctuating conformations into energy minima by minimization of the energy of a number of conformations sampled in the Monte Carlo simulations sampled in the Monte Carlo simulation. From the analysis of results of the computer experiment is obtained the following picture of protein dynamics:multiple energy minima exist in the native state, and they are distributedin clusters in the conformational space. The dynamics has a hierarchical structure which has at least two levels. In the first level, dynamics is restricted within one of the clusters of minima. In the second, transitions occur among the clusters. Local parts of a protein molecule, side chains and local main chain segments, can take multiple locally stable conformations in the native state. Many minima result from combinations of these multiple local conformations. The hierarchical structure in the dynamics comes from interactions among the local parts. Protein moleculeshave two types of flexibility, each associated with elastic and plastic deformations, respectively.
    Additional Material: 3 Ill.
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  • 75
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 149-155 
    ISSN: 0887-3585
    Keywords: solution scattering ; low-angle scattering ; spherical averaging ; spherical harmonics ; spherical Fourier transform ; bound water ; solvent structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: If one expands the structure factor equation in spherical coordinates, rotational averaging of the molecular Fourier transform, which leads directly to the solution scattering profile, is greatly simplified. It becomes a projection in the polar and azimuthal angular variables. The profile is given by The index j runs over all atoms; r, θ, φ are atomic coordinates and ε and N are constants; the Ym,n are complex spherical harmonics, and Jn are spherical Bessel functions; R = 2 sin θ/λ. The effects of solvent have been modeled by subtracting from each protein atom a properly weighted water. Hydrogens have been included by using scattering curves fj derived from the spherical averaging ofprotein atoms with their attached hydrogens. This approach may also be satisfactory for neutron scattering. Published scattering profiles2 for lysozyme and BPTI have been accurately matched in less than one-tenth the time required by other methods. Separate, adjustable temperature factors for the protein, solvent waters, and bound watersare used, and appear to be needed. In the case of BPTI, as suggested by NMR observations, the observed diffraction pattern was much better accounted for by including only 4 tightly bound waters rather than the roughly 60 seen by crystallography.
    Additional Material: 5 Ill.
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  • 76
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 156-165 
    ISSN: 0887-3585
    Keywords: retrovirus integrase ; circular dichroism ; homologous proteins ; secondary structural predictions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The retrovirus integrase (IN) protein is essentialfor integration of viral DNA into host DNA. The secondary structure of thepurified IN protein from avian myeloblastosis virus was investigated by bothcircular dichroism (CD) spectroscopy and five empirical prediction methods. The secondary structures determined from the resolving of CD spectra through a least-squares curve fitting procedure were compared with those predicted from four statistical methods, e.g., the Chou-Fasman, arnier-Osguthorpe-Robson, Nishikawa-Ooi, and a JOINT scheme which combined all three of these methods, plus a pure a priori one, the Ptitsyn-Finkelstein method. Among all of the methods used, the Nishikawa-Ooiprediction gave the closest match in the composition of secondary structureto the CD result, although the other methods each correctly predictedoneor more secondary structural group. Most of the α-helix and β-sheet states predicted by the Ptitsyn-Finkelstein methodwere in accord with the Nishikawa-Ooi method. Secondary structural predictions by the Nishikawa-Ooi method were extended further toinclude IN proteins from four phylogenetic distinct retroviruses. The structuralrelationships between the four most conserved amino acid blocks of these IN proteins were compared using sequence homology and secondary structure predictions.
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  • 77
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 183-201 
    ISSN: 0887-3585
    Keywords: crystallographic refinement ; restrained least-squares refinement ; Konnert-Hendrickson refinement ; phosphodiesterase ; protein structure ; enzyme mechanism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of a complex of staphylococcal nuclease with Ca2+ and deoxythymidine 3′,5′-biophosphate (pdTp) has been refined by stereochemically restrained leastsquares minimization to a crystallographic R value of 0.161 at Å resolution. The estimated root-mean-square (rms) error in the coordinates in 0.16 Å. The final model comprises 1082 protein atoms, onecalcium ion, the pdTp molecule, and 82 protein atoms, onecalcium ion, the pdTp molecule, and 82 solvent water molecules;it displays an rms deviation from ideality of 0.017 Å for bond distances and 1.8° for bond angles.The mean distance between corresponding α carbons in the refined and unrefined structures is 0.6 Å we observe small but significant differences between the refined and unrefined models in the turn between residues 27 and 30, the loop between residues 44 and 50, the first helix, and the extended strand between residues 112 and 117 which forms part of the active site binding pocket.The details of the calcium liganding and solvent structure in the activesite are clearly shown in the final electron density map. The structure ofthe catalytic site is consistent with mechanism that has been proposed for this enzyme. However, we note that two lysines from a symmetry-related molecule in the crystal lattice may play an important role in determining the geometry of inhibitor binding, and that only one of the two required calcium ions is observed in the crystal structure; thus, caution is advised in extrapolating from the structure of the complex of enzyme and inhibitor to that enzyme and substrate.
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  • 78
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    Proteins: Structure, Function, and Genetics 5 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 79
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 224-232 
    ISSN: 0887-3585
    Keywords: effective pore's radius ; α-ketoglutarate dehydrogenase complex ; branched chain α-keto acid dehydrogenase complex ; electron microscopy ; multienzyme complex ; two-dimensional ; electrophoresis ; multienzyme complex ; aggregation of Pyruvate dehydrogenase complex ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In the studies of the size and structure of multienzyme complexes, a procedure complementary to electron microscopy for determining the molecular dimensions of hydrated multisubunit complexes is needed. For some applications this procedure must be capable of detecting aggregation of complexes and must be applicable to impure preparations. In the present study, a procedure of two-dimensional agarose gel electrophoresis (2d-AGE) (Serwer, P. et al. Anal. Biochem. 152: 339-345, 1986) was modified and employed to provide accurate sizemeasurements of several classical multienzyme complexes. To improve band clarity and to achieve required gel pore sizes, a hydroxyethylated agarose was used. The effective pore's radius (PE) as a function of gel concentration was determined for this agarose inthe range of PE value needed for multienzyme complexes (effective radius, R = 10-30 nm). Appropriate conditions wereestablished to measure R value ± 1% of the pyruvate (PDC), α-ketoglutarate (α-KGDC), and the branched chain α-keto acid (BCDC) dehydrogenase multienzyme complexes; the accuracy of R was limited by the accuracy of the determinations of the R value for the sizestandards. The PDC from bovine heart was found to have an R = 22.4 ± 0.2 nm following cross-linking with glutaraldehyde that was necessary for stabilization of the complex. Dimers and trimers of PDC, present in the preparations used, were separated from monomeric PDCduring 2d-AGE. All R values for the enzyme complexes studied were agreement with, though more accurate than, R valuesobtained by use of electron microscopy. In contrast to this statement, the internal dihydrolipoyl transacetylase core of PDC (E2) had an R of 18.8 ± 0.2 nm using 2d-AGE, but 10.5 nm by electron microscopy. This observation confirms the proposal that the core of the PDC has externally projecting fibrous domains invisibleto electron microscopy.
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  • 80
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 259-265 
    ISSN: 0887-3585
    Keywords: cDNA expression ; deletion mutagenesis ; zymogen activation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cultured mouse myeloma cells were transfected with expression vectors encoding the aspartyl proteinase, human renin. The full construct, encoding the renin precursor prorenin, allows transfected cellsto secrete the enzymically inactive pro-protein. Activity is detectable only following trypsin treatment which mimics the physiological activation step. Accordingly, it appears that myeloma cells do not contain detectable levels of an appropriate activating proteinase. However, when these cells are transfected with a construct from which the pro-peptide coding sequence has been deleted, they secrete an apparently fully active enzyme which is indistinguishable from mature renin. We conclude that expression of the pro-peptide is not necessary to allow correct folding of the molecule and its passage through the secretory pathway.
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  • 81
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 281-288 
    ISSN: 0887-3585
    Keywords: Hu protein ; integration host factor ; transcription factor 1 ; DNA bending protein ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The prokaryotic protein HU, integration host factor (IHF) from Escherichia coli and transcription factor 1 (TF1) from bacteriophage SPO1 are closely related molecules. Biochemical results suggest that the role of these proteins is to bind and bend DNA. From the high-resolution structure of HU, we propose a model for thisinteraction with DNA. Crucial amino acid differences between the proteins can be rationalized in terms of their different specific functions.
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  • 82
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    Proteins: Structure, Function, and Genetics 5 (1989), S. 322-336 
    ISSN: 0887-3585
    Keywords: sequence conservation ; exon ; gene duplication ; protein folding ; structure-function ; X-ray structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Detailed analysis of the CuZn superoxide dismutase (SOD) structure provides new results concerning the significance and molecular basis for sequence conservation, intron-exon boundary locations, gene duplication, and Greek key β-barrel evolution. Using 15 aligned sequences, including a new mouse sequence, specific roles have been assigned to all 23 invariant residues and additional residues exhibiting functional equivalence. Sequence invariance is dominated by 15 residues that form the active site stereochemistry, supporting a primary biological function of uperoxide dismutation. The β-strands have no sequence insertions and deletions, whereas insertions occur within the loops connecting the β-strands and at both termini. Thus, the β-barrel with only four invariant residues is apparently over determined, but dependent on multiple cooperative side chain interactions. The regions encoded by exon I, a proposed nucleation site for protein folding, and exon III, the Zn loop involved in stability and catalysis, are the major structural subdomains not included in the internal twofold axis of symmetry passing near the catalytic Cu ion. This provides strong confirmatory evidence for gene evolution by duplication and fusion followed by the addition of these two exons. The proposed evolutionary pathway explains the structural versatility ofthe Greek key β-barrel through functional specialization and subdomain insertions in new loop connections, and provides a rationale for the size of the present day enzyme.
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  • 83
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 1-19 
    ISSN: 0887-3585
    Keywords: virus crystallography ; molecular dynamics ; hydrophobic pockets ; antiviral agents ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: X-Ray diffraction data have been obtained for nine related antiviral agents (“WIN compounds”) while bound to human rhinovirus 14 (HRV14).These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (∼60percnt;) occupancies of these compounds in the crystal, (2) the large (up to 7.9 Å) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps.The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the β-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the β-barrel.
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  • 84
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    Proteins: Structure, Function, and Genetics 6 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 85
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 104-127 
    ISSN: 0887-3585
    Keywords: lac repressor; lac operator ; lac headpiece-operator complex ; protein-DNA specificity ; molecular dynamics ; computer simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The results of a 125 psec molecular dynamics simulation of a lac headpiece-operator complex in aqueous solution are reported. The complexsatisfies essentially all experimental distance information derived from two-dimensional nuclear magnetic resonance (2-D-NMR) studies. The interaction between lac repressor headpiece and its operator based on many direct- and water-mediated hydrogenbonds and nonpolar contacts which allow the formation of a tight complex. Nostable hydrogen bonds between side chains and bases and found, while specific contacts occur between both nonpolar groups and, to a lesserextent, through water-mediated hydrogen bonds. The simulated complex structure in water is intrinsically stable without application of nuclear Overhauser effect (NOE) distance restraints, while being compatible with most of the available biochemical, genetic, andchemically induced dynamic nuclear polarization (CIDNP) data.
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  • 86
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    Proteins: Structure, Function, and Genetics 6 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 87
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 217-221 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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  • 88
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 240-248 
    ISSN: 0887-3585
    Keywords: substrate-assisted catalysis ; serine protease ; fusion proteins ; site-directed mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A combination of protein engineering and substrate optimization was used to create variants of the serine protease, subtilisin BPN′, which efficiently and specifically cleave a designed target sequence in a fusion protein. The broad substrate specificity of wildtype subtilisin BPN′ is greatly restricted by substitution of the catalytic histidine 64 with alanine (H64A) so that certain histidine-containing substrates are preferentially hydrolysed (Carter, P., Wells, J. A. Science 237:394-399, 1987). The catalytic efficiency, (kcat/Km), of this H64A variant was increased almost 20-fold by judicious choice of substrate and by installing three additional mutations which increase the activity of wild-type subtilisin. The most favorable substrate sequence identified was introduced as a linker in a fusion protein between a synthetic IgG binding domain of Staphylococcus aureus protein A and Escherichia coli alkaline phosphatase. The fusion protein (affinity purified on an IgG column) was cleaved by the prototype H64A enzyme and its improved variant, efficiently and exclusively at the target site, to liberate an alkaline phosphatase product of the expected size and N-terminal sequence. Several features of H64A variants of subtilisin make them attractive for site-specific proteolysis of fusion proteins: they have exquisite substrate specificity on the N-terminal side of the cleavage site and yet are broadly specific on the C-terminal side; they can be produced in large quantities and remain highly active even in the presence of detergents, reductants (modest concentrations), protease inhibitors, at high temperatures, or when specifically immobilized on a solid support.
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  • 89
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 284-293 
    ISSN: 0887-3585
    Keywords: calmodulin ; peptides ; fluorescence spectroscopy ; photoaffinity labeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Calmodulin is known to bind target enzymes and basic, amphiphilic peptides in a Ca2+-dependent manner. Recently, we introduced a photoaffinity label, p-benzoylphenylalanine (Bpa), into the sequence of a model, α-helical, calmodulin-binding peptide. When the Bpa residue was introduced at the third position of the peptide, Met-144 on the C-terminal domain of calmodulin was labeled, whereas when the photolabel was placed at the thirteenth position, Met-71 on the N-terminal do main was labeled. Assuming that both peptides bind in similar orientations, these results are not consistent with the crystal structure of calmodulin, in which the domains are held at a significant distance from one another by a long α-helical segment. To test the assumption that both peptides bind in similar orientations, we have synthesized a calmodulin-binding peptide with the photolabel in both the third and the thirteenth positions. Upon photolysis, this peptide forms a cross-link between Met-71 and Met 124 on the N- and C-terminal domains, respectively. Furthermore, a peptide with a Bpa in the thirteenth position and a Trp residue in the third position was also synthsized. After photocross-linking the Bpa redidue of this peptide to Met-71 of calmodulin, it could be shown that the fluorescence properties of the Trp residue were consistent with its side chain being buried in a hydrophobic pocket on the C-terminal domain of calmodulin. These data indicate that, when complexed with basic, amphiphi peptides, calmodulin can adopt a conformation in which its two domains are significantly closer than in the crystal sturcture of the uncommplexed protein.
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  • 90
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 231-239 
    ISSN: 0887-3585
    Keywords: phosphotyrosine linkage ; protein-DNA transesterification ; enzyme mechanism ; DNA-protein covalent complex ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Tyrosine 319 of E. coli topoisomerase I is shown to be the activesite tyrosine that becomes covalently attached to a DNA 5′ phosphoryl group during the transient breakage of a DNA internucleotide bond by the enzyme. The tyrosine was mapped by trapping the covalent complex between the DNA and DNA topoisomerase I, digesting the complex exhaustively with trypsin, and sequencing the DNA-linked tryptic peptide. Site-directed mutagenesis converting Tyr-319 to a serine or phenylalanine completely inactivates the enzyme. The structure of the enzyme andits catalysis of DNA strand breakage, passage, and rejoining are discussed in terms of the available information.
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  • 91
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    Proteins: Structure, Function, and Genetics 6 (1989), S. 259-266 
    ISSN: 0887-3585
    Keywords: protein folding ; folding intermediate ; hydrophobic effect ; tryptophan fluorescence ; site-directed mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The rapid kinetic phase that leads from unfolded species to transient folding intermediates in dihydrofolate reductase from Escherichia coli was examined by site-directed mutagenesis and by physicochemical means. The absence of this fluorescence-detected phase in the refolding of the Trp-74Phe mutant protein strongly implies that this early phase in refolding can be assigned to just one of the five Trp residues in the protein, Trp-74. In addition, water-soluble fluorescence quenching agents, iodide and cesium, have a much less significant effect on this early step in refolding than on the slower phases that lead to native and nativelike conformers. These and other data imply that an important early event in the folding of dihydrofolate reductase is the formation of a hydrophobic cluster which protects Trp-74 fromsolvent.
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  • 92
    ISSN: 0887-3585
    Keywords: α-helix ; EPR ; trypsinolysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Colicin E1 is an E. coli plasmid-lencoded water-soluble protein that spontaneously inserts into lipid membranes to form a voltage-gated ion channel. We have employed a novel approach is which site-directed mutagenesis is used to provide highly specific attachment points for nitroxide spin labels. A series of colicin mutants, differing only by the position of a single cysteine residue, were prepared and selectively labeled at that cysteine. A hydrophilic sequence (398-406) within the C-terminal domain of the water-soluble form of the protein was investigated and exhibited an electron paramagnetic resonancc (EPR) spectral periodicity strongly suggesting an amphiphilic α-helix. After removal of the N—terminus of the protein with trypsin, the spectra for this sequence indicate increased label mobility and a more flexible structure.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 93
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 382-394 
    ISSN: 0887-3585
    Keywords: immunoglobulins ; hydrogen bonding ; hairpin loops ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Loops are integral components of protein structures, providing links between elements of secondary structure, and in many cases contributing to catalytic and binding sites.The conformations of short loops are now understood to depend primarily on their amino acid sequences. In contrast, the structural determinants of longer loops involve hydrogen-bonding and packing interactions within the loop and with other parts of the protein. By searching solved protein structures for regions similar in main chain conformation to the antigen-binding loops in immunoglobulins, we identified medium-sized loops of similar structure in unrelated proteins, and compared the determinants of their conformations.For loops that form compact substructures the major determinant of the conformation is the formation of hydrogen bonds to inward-pointing main chain atoms. For oops that have more extended conformations, the major determinant of their structure is the packing of a particular residue or residues against the rest of the protein.The following picture emerges: Medium-sized lops of similar conformation are stabilized by similar interaction. The groups that interact with the loop have very similar spatial dispositions with respect to the loop. However, the residues that provide these interactions may arise from dissimilar parts of the protein: The conformation of the loop requires certain interactions that the protein may provide in a variety of ways.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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  • 94
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 341-356 
    ISSN: 0887-3585
    Keywords: neuraminidase (sialidase) of influenza virus ; structure ; enzyme active site ; escape mutants ; structure of epitopes ; structures of neuraminidase ; Fab complexes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: It is the enzyme neuraminidase, projecting form the surface of influenza virus particles, which allows the virus to leave infected cells and spread in the body. Antibodies which inhibit the enzyme limit the infection, but antigenic variation of the neuraminidase renders it ineffective in a vaccine. This article describes the crystal structure of influenza virus neuraminidase, information about the active site which may lead to development of specific and effective inhibitors of the enzyme, and the structure of epitopes (antigenic determinants) on the neuraminidase. The 3-dimensional structure of the epitopes was obtained by X-ray diffraction methods using crystals of neuraminidase complexed with monoclonal antibody Fab fragments. Escape mutants, selected by growing virus in the presence of monoclonal antibodies to the neuraminidase, possess single amino acid sequence changes. The crystal structure of two mutants showed that the change in structure was restricted to that particular sidechain, but the change in the epitope was sufficient to abolish antibody binding even though it is known in one case that 21 other amino acids on the neuraminidase are in contact with the antibody.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
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  • 95
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 395-404 
    ISSN: 0887-3585
    Keywords: folding pathway ; tryptophan synthase ; acid denaturation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The β2 subunit of Escherichia coli tryptophan synthase can be either unfolded in 6 M guanidine, or extensively denatured at acidic pH. These two denatured form of β2 have different circular dichroism spectra and thus correspond to distinct physical states. Here we compare the folding pathways of these two different denatured forms of β chains. We describe the kinetics of regain of a variety of physical, functional, ad immunochemical signals characteristic of six successive steps previously identified on the folding pathway of guanidine unfolded β2. It is shown that whereas identical molecular events over with the same kinetics, the two folding pathways are different, and involve different structural intermediates.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 96
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 47-65 
    ISSN: 0887-3585
    Keywords: crystal growth ; helical conformation ; repetitive octapeptide ; icelike molecular surface ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The active conformation of an icenucleation protein, whose major portion consists of a long polypeptide segment of nearly repetitive octapeptides, is predicted by the analyses of conformational energy and the mechanism of crystal growth. The protein ideally has an exact octapeptide repetition and is assumed to have a helical conformation. The present study searched for low-energy helical conformations and each of the obtained low-energy conformations examined as to whether it has a surface structure that can promote crystal formation. Two conformations obtained were good candidates for an ice nucleus. Both were found to have on their surfaces an arrangement of hydrogen-bonding sites, which fits well with those of hydrogen bonds in hexagonal ice crystal. Further, one of the two conformations had a hexagonal conformational symmetry consistent with the hexagonal ice crystal structure. The other conformation had apentagonal conformational symmetry that could enable the growth of an ice crystal-dendritic polycrystalline snow crystal-which grows on metastable cubic ice.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 97
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 66-77 
    ISSN: 0887-3585
    Keywords: subunit interactions ; allosteric regulation ; solvent accessibility ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Although ionizable groups are known to play important roles in the assembly, catalytic, and regulatory mechanisms of Escherichia coli aspartate transcarbamylase, these groups have not been characterized in detail. We report the application of static accessibility modified Tanford-Kirkwood theory to model electrostatic effects associated with the assembly of pair of chains, subunits, and the holoenzyme. All of the interchain interfaces except R1-R6 are stabilized by electrostatic interactions by -2 to -4 kcal-m-1 at pH 8. The pH dependence of the electrostatic component of the free energy of stabilization of intrasubunit contacts (C1-C2 and R1-R6) is qualitatively different from that of intersubunit contacts (C1-C4, C1-R1, and C1-R4). This difference may allow the transmission of information across subunit interfaces to be selectively regulated. Groups whose calculated pK or charge changes as a result of protein-protein interactions have been identified and the results correlated with available information about their function. Both the 240s loop of the c chain and the region near the Zn(II) ion of the r chain contain clusters of ionizable groups whose calculated pK values change by relatively large amounts upon assembly. These pK changes in turn extend to regions of the protein remote from the interface. The possibility that networks of ionizable groups are involved in transmitting information between binding sites is suggested.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 98
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 99
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. 93-95 
    ISSN: 0887-3585
    Keywords: folding intermediate ; molten globule state ; protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Previous results from equilibrium and kinetic studies of the folding of bovine growth hormone (bGH) have demonstrated that bGH does not follow a simple two-step folding mechanism. These results are summarized and interpreted according to the “molten globule” model. The molten globule state of bGH is characterized as a folding intermediate which largely a-helical, retains a compact hydrodynamic radius, has packing of the aromatic side chains that is similar to the unfolded state, and possesses a solvent-exposed hydrophobic surface along helix 106127 that readily leads association.
    Additional Material: 1 Ill.
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  • 100
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 5 (1989), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
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