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  • 2020-2023
  • 1995-1999  (1,492)
  • 1985-1989
  • 1970-1974  (145)
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  • 1
    ISSN: 1432-2307
    Keywords: Key words Apoptosis ; Crescent-shaped spaces ; Ultrastructure ; Nivalenol ; Thymus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  There have been many reports on the formation of apoptotic bodies, but little is known about the cellular pathological processes and the morphological changes involved. We induced apoptotic cell death by administering nivalenol (NIV), a trichothecene mycotoxin produced by Fusarium species, and investigated the ultrastructural process of formation of apoptotic bodies. The thymus was examined by electron microscopy 6, 12, and 18 h after administration. Apoptotic cell death was induced in the thymus of NIV-treated mice. The nuclei became invaginated and pinched off to give fragments, and crescent-shaped spaces (CSS) were found around the nuclear envelopes of these cells at quite an early stage. In some of these spaces, myelin figures were observed. We divided the process of formation into four stages and characterized each of them. These are easily recognized in morphological stages and are also useful for clarifying the apoptotic mechanism.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1432-0533
    Keywords: Key words Brittany Spaniel dog ; Immunocytochemistry ; Purkinje cell ; Spinocerebellar degeneration ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Eight Brittany Spaniel dogs, seven females and one male, between 7 and 14 years old presented with clinical neurological signs of spinocerebellar disease of about 6 months to 4 years duration. Clinically the dogs had a dramatic forward “saluting” movement of the thoracic limbs, hypermetria of the pelvic limbs, cerebellar ataxia and intention tremors. Terminally, dogs crawled in a crouched thoracic posture with neck extension. Lesions were confined to cerebellum, medulla oblongata and spinal cord. The most severe lesion was diffuse Purkinje cell loss with massive neurofilament accumulation in degenerating cells. There was some bilateral neuronal degeneration in the dorsal horns of the spinal cord and in the gracilis and cuneate nuclei. There was bilateral sporadic axonal degeneration in the dorsal columns and lateral and ventromedial areas of the spinal cord. The etiology of this syndrome was not determined.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Acta neuropathologica 95 (1998), S. 367-372 
    ISSN: 1432-0533
    Keywords: Key words Amyotrophic lateral sclerosis ; Heterotopic neuron ; Alpha motor neuron ; Immunocytochemistry ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract This report concerns a comparative immunocytochemical, ultrastructural and morphometric investigation on heterotopic neurons in the white matter of the spinal cords of 19 patients with amyotrophic lateral sclerosis (ALS) and 18 age-matched neurologically normal individuals. The study revealed that the heterotopic neurons were scattered in the white matter, often adjacent to gray matter, that they immunoreacted with the antibody to synaptophysin, and that there were synaptic apparatuses on the surface of their somata and their neuronal processes. Bunina bodies and ubiquitin-positive inclusions such as Lewy body-like inclusions and skein-like inclusions, characteristic of anterior horn neurons of ALS, were present in the cytoplasm of the patients’ heterotopic neurons in the anterior or lateral column of the white matter. These findings suggest that heterotopic neurons in the anterior or lateral column have the characteristics of alpha motor neurons. The average number of heterotopic neurons observed in ALS patients was generally less than in normal subjects. This reduction was correlated with the severity of neuronal loss. The heterotopic neurons in ALS were less susceptible to the degenerative process as compared with spinal cord anterior horn cells. We assume that in this disease the heterotopic neurons may be degenerated and their number diminished after or concomitantly with the depletion of anterior horn neurons.
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  • 4
    ISSN: 1432-0533
    Keywords: Key words Dentatorubral-pallidoluysian atrophy ; Nuclear inclusion ; Ubiquitin ; Immunohistochemistry ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract We examined the brains and spinal cords of seven patients with clinicopathologically and genetically confirmed hereditary dentatorubral-pallidoluysian atrophy (DRPLA) using an antibody against ubiquitin, and found small, round immunoreactive intranuclear inclusions in both neurons and glial cells in various brain regions. Ubiquitinated neuronal intranuclear inclusions (uNIIs) were consistently found in the striatum, the pontine nuclei, the inferior olivary complex, the cerebellar cortex and the dentate nucleus. Ubiquitinated glial intranuclear inclusions (uGIIs) were found less frequently than uNIIs. Most of the inclusion-bearing nuclei were of an astrocytic nature. Immunostaining with an antibody against DRPLA protein revealed similar immunoreactive neuronal and glial intranuclear inclusions, but in much smaller in numbers compared with uNIIs and uGIIs. Electron microscopy showed that such inclusions were composed of granular and filamentous structures. These findings strongly suggest that, in DRPLA, the occurrence of uNIIs and uGIIs is directly related to the causative gene abnormality (an expanded CAG repeat encoding polyglutamine), that neurons are affected much more widely than previously recognized and that glial cells are also involved in the disease process.
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  • 5
    ISSN: 1432-0533
    Keywords: Key words Congenital myopathy ; Muscle fibers ; Ultrastructure ; Myofibrillar disarray
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract A 44-year-old man presenting with dyspnoic attacks was found to be affected with congenital myopathy, rigid spine, restrictive respiratory insufficiency and cardiomyopathy. Muscle biopsy showed type 1 fiber predominance (65.7%) and hypotrophy, and characteristic changes in 43.9% of the type 1 fibers, consisting in alternating pale and dark staining on alkaline ATPase reacted sections in a mosaic pattern. Ultrastructural examination demonstrated bands of myofibrils at right angles or skew to the remaining myofibrils transversing the fibers. Myofibrillar disarray was always associated with loss of the Z-discs and actin filaments, and often with aggregation of mitochondria. The muscle biopsy findings in this patient suggest a new entity of congenital myopathy with clinical features of rigid spine, cardiomyopathy and restrictive respiratory insufficiency, characterized by peculiar abnormalities of ATPase staining in a mosaic pattern and, ultrastructurally, by zones of disorientation of the sarcomeres.
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  • 6
    ISSN: 1432-0568
    Keywords: Key words Adult-type Leydig cells ; Endothelium ; 3β-HSD ; Ultrastructure ; Differentiation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  In the biosynthesis of steroid hormones 3β-hydroxysteroid dehydrogenase (3β-HSD) is a key enzyme. The present report describes the subcellular localization of the enzyme in the fetal-type Leydig cells, the fibroblast-like precursors of adult-type Leydig cells and in endothelial cells of interstitial capillaries. Histochemical methods for light microscopy and ultracytochemical methods for electron microscopy were used on rat testes of postnatal day 15. 3β-HSD reactivity was located at subcellular levels by means of the ferricyanide method. A specific, distinct localization of reaction product in the form of copper ferrocyanide precipitates was observed on the membranes of the smooth endoplasmic reticulum not only in the fetal-type Leydig cells and the fibroblast-like precursors of adult-type Leydig cells, but also focally in the endothelial cells of interstitial blood capillaries. Topographically, the 3β-HSD-positive precursors were most often found in the outer layer of the boundary tissue and surrounding interstitial blood vessels. The capillaries with 3β-HSD-positive endothelial cells were usually located in the vicinity of 3β-HSD-positive Leydig cells. For the first time, 3β-HSD has been located at the subcellular level in precursors of adult-type Leydig cells and focally in capillary endothelial cells associated with them. Due to the close association between 3β-HSD-positive vascular endothelial cells and Leydig cells a paracrine relationship between the two cell types may be involved in the acute regulation of steroidogenesis by blood-borne luteinizing hormone.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1432-0533
    Keywords: Key words Anorexia nervosa ; Myopathy ; Muscle biopsy ; Ultrastructure ; Protein-energy malnutrition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Protein-energy malnutrition in anorexia nervosa is an under-recognised cause of muscle dysfunction. To characterise the skeletal myopathy that occurs in patients with severe anorexia nervosa, muscle function and structure were comprehensively examined in eight young adult female patients with severe (40%) self-induced weight loss. All of the patients showed impaired muscle function on strength and exercise measurement. The maximum voluntary contraction force for the patient group was significantly less than predicted values. Electromyography revealed myopathy in five of the patients, four of whom also had electro-physiological evidence of neuropathy. However, muscle biopsy specimens consistently showed myopathic changes with severe type 2 fibre atrophy but with no evidence of neuropathic changes. Ultrastructurally, there was separation and segmental loss of myofibrils and most biopsy samples contained abundant glycogen granules; we have previously reported that one of the most consistent biochemical abnormalities in these patients is impaired ischaemic lactate responses to forearm exercise. The result of severe protein-energy malnutrition on the musculo-skeletal system is a metabolic myopathy. Although the patients admitted to a variety of abnormal dieting behaviours, such as over-exercising and self-induced vomiting, no association was found between any of these and quantitative histological changes in the muscle biopsy samples. It is recommended that myopathy in anorexia nervosa be treated by instituting an appropriate refeeding programme.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Anatomy and embryology 197 (1998), S. 135-141 
    ISSN: 1432-0568
    Keywords: Key words Interstitial cells of Cajal ; Ultrastructure ; Gap junction ; Intestine ; Motility
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract  Interstitial cells forming many large gap junctions in the region of the deep muscular plexus of the rat small intestine were studied by electron microscopy and by three-dimensional cell models reconstructed from serial ultrathin sections. Two different profiles of cells were observed. Cells of the first profile are characterized by an elongated cell shape and by less electron-dense cytoplasm, containing many mitochondria, well-developed Golgi apparatus and free ribosomes. They mainly connect with smooth muscle cells of the main circular layer. In a three-dimensional cell model, the total area of the gap junctions occupies 1.3% of the cell surface. Cells of the second profile are characterized by the frequent occurrence of slender cytoplasmic processes, higher electron-dense cytoplasm, containing mitochondria, Golgie apparatus and well-developed rough endoplasmic reticulum, and numerous caveolae on the cell membrane. In this cell model, gap junctions occupy 0.8% of the cell surface. The ratio of gap junctions with the same profile of cells to the total gap junction area is 37.7%, which is more than three times greater than the 9.9% in cells of the first profile. These cells were closely associated with nerve terminals. It is likely that these cells with different profiles constitute subtypes with each other and cooperate for regulation of intestinal motility via the transmission of nerve signals.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1432-0533
    Keywords: Key words Congenital myopathy ; morphometry ; Ultrastructure ; Fetal myogenesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Centronuclear myopathy (CNM) is a congenital myopathy which manifests itself as a severe neonatal (also termed myotubular myopathy), early-onset, or adult form. The histological pattern of each is marked by a considerable number of nuclei of muscle fibers being internally placed. Owing to their remote resemblance to myotubes, and their expression of developmentally regulated proteins, most authors now favor the concept that myogenesis is arrested or delayed in this disease. We here present two muscle biopsy specimens of a patient with early-onset CNM, taken at the age of 5 months and 14 years, respectively. The first biopsy sample contained internally placed nuclei in 7% of the muscle fibers, abundant minute myotubes, and hypertrophic muscle fibers. The second biopsy sample showed internally placed nuclei in 40% of the muscle fibers, and hypotrophic fibers. We suggest that the histological findings in early-onset CNM are the result of a complex dynamic process, which includes a delay in maturation.
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  • 10
    ISSN: 1432-0533
    Keywords: Key words Aging ; Blood-brain barrier ; Horseradish peroxidase ; Senescence-accelerated mouse ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract The ultrastructural features of microvessels showing increased permeability to intravenously injected horseradish peroxidase (HRP) were examined in the olfactory bulbs of senescence-accelerated prone mice (SAMP8), which showed age-related deficits in learning and memory, and senescence-accelerated resistant mice (SAMR1), which did not show the age-related deficits. HRP was visualized with tetramethyl benzidine (TMB) and diaminobenzidine (DAB) for light and electron microscopic examination, respectively. In the olfactory bulbs of 13-month-old SAMP8 mice, the staining reaction with TMB for HRP appeared in the neuropil of central area (granule cell layer and subependymal layer), in the pia mater and in the vascular wall. Some vessels located in the central area showed several changes observed at the ultrastructural level. The cytoplasm of the endothelial cells, especially in the arterioles, was segmentally thickened and contained numerous vesicles and vacuoles, some of which were HRP positive. The endothelial cell surface was occasionally undulated with microvillous protrusions. Membranous inclusions within the basal lamina, suggesting the cellular (presumably pericytal) degeneration, were frequently observed, especially in venules. The collagen deposits were occasionally observed in the subendothelial space of some vessels. Perivascular cells with vacuolated inclusions or lipid-like droplets were present around some vessels in the central area of the olfactory bulbs of aged SAMP8 mice. On the other hand, in the microvessels located in the areas negative for HRP-TMB reaction, except the vessel walls, the cytoplasm of the endothelial cells with smooth luminal surface was flattened and some vesicles located there contained HRP-DAB reaction product. Weak staining reaction with TMB for HRP appeared also in the central area of the olfactory bulbs of 3-month-old SAMP8 mice and 3- and 13-month-old SAMR1 mice. The cytoplasm of the endothelial cells in the olfactory bulbs of these mice was focally thickened and contained some cytoplasmic vesicles. Occasionally, the endothelial cell surface was moderately undulated with few microvillous protrusions. Membranous inclusions within the basal lamina were not observed in these animals. These findings indicate that the endothelial cells and pericytes in some vessels located in the central area of the olfactory bulb of aged SAMP8 mice, which show staining reaction with TMB for HRP, are ultrastructurally changed, suggesting their altered functions.
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  • 11
    ISSN: 1432-069X
    Keywords: Key words Barrier function ; pH ; Stratum corneum ; Lamellar body ; Lipid content ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Epidermal permeability barrier homeostasis requires the postsecretory processing of polar lipid precursors into nonpolar lipid products within the stratum corneum (SC) interstices by a family of lipid hydrolases. A specific requirement for β-glucocerebrosidase (β-GlcCer’ase), which exhibits a distinct acidic pH optimum, is particularly well documented. Therefore, we sought to determine whether the recovery of the barrier after acute insults requires acidification of the SC. We examined permeability barrier recovery by assessing changes in transepidermal water loss (TEWL), SC membrane ultrastructure utilizing ruthenium tetroxide (RuO 4 ) postfixation, and β-GlcCer’ase activity by in situ zymography at an acidic vs neutral pH. Barrier recovery proceeded normally when acetone-treated skin was exposed to solutions buffered to an acidic pH. In contrast, the initiation of barrier recovery was slowed when treated skin was exposed to neutral or alkaline pH, regardless of buffer composition. In addition, enhancement of the alkaline buffer-induced delay in barrier recovery occurred with Ca 2+ and K + inclusion in the buffer. Moreover, the pH-dependent alteration in barrier recovery appeared to occur through a mechanism that was independent of Ca 2+ - or K + -controlled lamellar body secretion, since both the formation and secretion of lamellar bodies proceeded comparably at pH 5.5 and pH 7.4. In contrast, exposure to pH 7.4 (but not pH 5.5) resulted in both the persistence of immature, extracellular lamellar membrane structures, and a marked decrease in the in situ activity of β-GlcCer’ase. These results suggest first that an acidic extracellular pH is necessary for the initiation of barrier recovery, and second that the delay in barrier recovery is a consequence of inhibition of postsecretory lipid processing.
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  • 12
    Electronic Resource
    Electronic Resource
    Springer
    Zeitschrift für Lebensmittel-Untersuchung und -Forschung 206 (1998), S. 38-43 
    ISSN: 1431-4630
    Keywords: Key words Starch ; Gels ; Kamaboko ; Surimi ; Gelatinization ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract  The purpose of this work was to study the changes undergone by starch during heat-induced surimi gel preparation either with or without added egg white, and their effects on the structure of gels using light and scanning electron microscopy. Gels were made from SA-grade Alaska pollack (Theragra chalcogramma) surimi with: (1) salt (3%, w/w); (2) salt and waxy corn starch (3% and 5%, respectively w/w); or (3) salt, waxy corn starch and egg white (3%, 5% and 5%, respectively, w/w). Final moisture was adjusted to 73% or 83%. The gels were prepared by prior setting (40°C, 30 min, followed by 90°C, 30 min) or cooking (90°C, 30 min). The prepared gel was frozen and stored at –20°C (±1°C) until analysis. Samples were observed by light and scanning electron microscopy. The results show that the starch granules alter according to the processing conditions, with the predominance of crystalline or amorphous morphology depending upon the availability of heat and water. Large cavities formed in the protein gel matrix during setting can trap water; as a result, water availability is limited for starch to swell and gelatinize even in the high-moisture gel.
    Type of Medium: Electronic Resource
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  • 13
    Electronic Resource
    Electronic Resource
    Springer
    Der Pathologe 19 (1998), S. 373-378 
    ISSN: 1432-1963
    Keywords: Schlüsselwörter Metaplastische Brustdrüsenkarzinome ; Plattenepithelmetaplasie ; Plattenepithelkarzinom ; Immunhistologie ; Elektronenmikroskopie ; Zytophotometrie ; Key words Pure squamous cell carcinoma ; Mammary gland ; Squamous metaplasia ; Immunohistology ; Cytophotometry ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Description / Table of Contents: Summary Squamous metaplasia can be demonstrated in about 4% of all invasive carcinomas of the breast. Primary squamous cell carcinomas of the breast are rare, since they occur in less than 1% of all primary invasive breast carcinomas. In order to classify a breast tumor as a primary squamous cell carcinoma one must exclude an epidermal origin, especially from the nipple region and the possibility of metastatic infiltration of the breast by a squamous cell carcnoma from a different location. Causative and formal pathogenesis of primary squamous cell carcinoma of the breast is not clear. A pluripotent embryonal stem cell origin is discussed, considering the phylogenetic descent of the mammary gland from skin appendages. Squamous metaplasia is also suggested to be a precursor of squamous cell carcinoma. Here endocrine stimulation and chronic inflammation may both play an inductive role. The number of published cases of squamous cell carcinomas developing years and decades after implantation of silicon prostheses has increased in recent years. These tumors probably develop on top of squamous metaplasia induced by the inflammatory pseudocapsule. Estimating the prognosis and therapeutic management in patients with squamous cell carcinoma of the breast should follow the same guidelines as for other squamous cell cancers.
    Notes: Zusammenfassung Plattenepithelmetaplasien werden bei etwa 4% aller invasiven Brustdrüsenkarzinome beschrieben. Reine Plattenepithelkarzinome der weiblichen Brustdrüse sind mit einem Anteil von wahrscheinlich unter 1% an allen invasiven epithelialen Tumoren der Mamma selten. Von einem primären Plattenepithelkarzinom der Brustdrüse darf nur gesprochen werden, wenn zum einen der Ursprung von der Epidermis, insbesondere auch im Bereich des Mamillentrichters ausgeschlossen ist und zum anderen keine metastatische Infiltration in die Brustdrüse durch ein Plattenepithelkarzinom anderer Organlokalisation vorliegt. Die kausale und formale Pathogenese der primären Plattenepithelkarzinome der Brustdrüse ist unklar. Zum einen wird ein Ursprung von pluripotenten embryonalen Stammzellen diskutiert, wobei bedacht wird, daß die Brustdrüse entwicklungsgeschichtlich ein Hautanhangsgebilde darstellt. Zum anderen werden Plattenepithelmetaplasien als Vorstufe der Plattenepithelkarzinome diskutiert, wobei neben einer endokrinen Induktion auch länger bestehende Entzündungsreize eine Rolle spielen sollen. In den letzten Jahren wird immer häufiger darüber berichtet, daß oft Jahrzehnte nach Implantation von Silikonprothesen periprothetische Plattenepithelkarzinome entstehen, die wahrscheinlich über die Stufe einer Plattenepithelmetaplasie der entzündlichen Prothesenpseudokapsel entstehen. Die Abschätzung der Prognose und therapeutische Maßnahmen bei primären Plattenepithelkarzinomen der Brustdrüse sollten an den Erfahrungen mit Plattenepithelkarzinomen anderer Organlokalisation ausgerichtet werden.
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  • 14
    ISSN: 1432-2145
    Keywords: Key words Abies ; Egg cell ; Plastid inheritance ; RFLP ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The ultrastructure of egg cells in Abies alba was examined to elucidate the lack of maternal inheritance of plastids. Before fertilization, maternal plastids are absent in the perinuclar zone containing mainly mitochondria and smooth endoplasmic reticulum. During egg cell development the maternal plastids are transformed into large inclusions which are situated mostly towards the periphery of the egg cell, and finally disintegrate. As a consequence, they do not participate in zygote formation. RFLP analysis of cpDNA of parental trees and their F1 interspecific hybrids (A. alba×A. numidica, A. alba×A. nordmanniana, A. nordmanniana×A. Alba) using HindIII and BamHI showed a paternal mode of cpDNA inheritance. Paternal inheritance has also been found with PCR/RFLP analysis of cpDNA from parental trees and their hybrids (A. alba×A. pinsapo, A. pinsapo×A. alba, A. pinsapo×A. numidica) using ApaI and HaeIII digests, as well as in the crosses of A. cephalonica×A. nordmanniana, A. nordmanniana×A. cephalonica, A. cephalonica×A. numidica using TagI digests.
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  • 15
    Electronic Resource
    Electronic Resource
    Springer
    Sexual plant reproduction 11 (1998), S. 121-130 
    ISSN: 1432-2145
    Keywords: Key words Egg cell ; Parthenogenesis ; Synergid ; Ultrastructure ; Wheat ; Zygote
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The ultrastructure of the egg apparatus of the sexual (aestivum)-Salmon line (aS) and the isogenic but alloplasmic (kotschyi)-Salmon line (kS) of the Salmon system of wheat was studied by transmission electron microscopy 3 days before and during anthesis. Additionally, the zygotic stage of aS, 17 h after pollination, was included. Metabolic activity of egg cells from the sexual line aS was low 3 days before anthesis and increased dramatically after pollination and fertilization. This timing of increased activity was evident because of changes occurring in the egg cell nucleus and nucleolus, polysomes, endoplasmic reticulum and Golgi apparatus, and the completion of the cell wall around the zygote. In contrast to the sexual line, the egg cell of the parthenogenetic line showed high activity 3 days before anthesis. The metabolic and ultrastructural characters observed in the nucleus and cytoplasm of the kS line 3 days before and during anthesis corresponded with those of the isogenic sexual line aS during anthesis and 17 h after pollination, respectively. High metabolic activity observed in the persistent synergid of kS may be connected with the occurrence of additional embryos in seeds (twins) of this line.
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  • 16
    ISSN: 1432-072X
    Keywords: Key words Magnetic bacteria ; Biomineralization ; Magnetite ; 16S rRNA ; In situ hybridization ; Ultrastructure ; Electron microscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Natural enrichments of magnetic bacteria from the Itaipu lagoon near Rio de Janeiro were dominated by coccoid-to-ovoid morphotypes that produced unusually large magnetosomes. To determine the phylogenetic position of these unusual microorganisms, 16S rRNA genes were retrieved from bacteria magnetically separated from sediment of the Itaipu lagoon by in vitro amplification and cloning of PCR products into a plasmid vector. Partial sequencing of the obtained clones revealed two clusters of closely related sequences affiliated to a distinct lineage consisting exclusively of magnetic bacteria within the α-subclass of Proteobacteria. For a detailed phylogenetic analysis, several almost complete sequences of the 16S rRNA genes were determined. One representative clone of each cluster provided a PCR template for the in vitro transcription of group-specific polynucleotide probes complementary to a variable region of the 16S rRNA molecule. At least three different morphotypes of magnetic bacteria were reliably identified by post-embedding hybridization of ultra-thin sections. Electron microscopic analyses of hybridized cells enabled for the first time a detailed description of the morphological variety and ultrastructure of phylogenetically identified, uncultured magnetic bacteria. Two distinct coccoid bacteria were identified by the transcript probe complementary to the 16S rRNA sequence mabrj12, whereas the probe complementary to the sequence mabrj58 allowed the identification of an ovoid morphotype that displayed magnetosomes with the largest volumes observed to date.
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  • 17
    Electronic Resource
    Electronic Resource
    Springer
    Cell & tissue research 292 (1998), S. 275-282 
    ISSN: 1432-0878
    Keywords: Key words Interstitial cells (Cajal) ; Large intestine ; Fluorescent dyes ; Vital staining ; Ultrastructure ; Mouse (BALB/c)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Interstitial cells of Cajal (ICCs) are believed to be a major element in generating the spontaneous rhythm of the gastrointestinal tract. A prominent problem in the study of these cells has been the difficulty in observing them in intact tissues. We used the lipophilic dye DiI to stain ICCs in the submucosal-circular muscle border of freshly dissected mouse colon. The placement of small DiI crystals in this area resulted in the labeling of ICC-like cells. Two main morphological cell types, viz., bipolar and multipolar, were noted. Bipolar cells had two primary processes emerging from the poles of an elongated soma. The mean length of these processes was 78.7 μm. These cells constituted 42.3% of the sample (n=105). Multipolar cells (54.3% of total) had a less elongated soma and extended 3–6 main processes whose mean length was 56.3 μm. These processes showed no preferred direction. The length of the primary processes of bipolar cells was 40% greater than that of multipolar cells (P〈0.02). Three cells (2.9%) had only one primary process. The DiI stain could be converted into a stable electron-opaque product. Electron-microscopic observations showed that these cells had the typical appearance of ICCs reported in previous studies. This staining method should be useful for physiological investigations of ICCs in gastrointestinal tissues.
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  • 18
    ISSN: 1432-0878
    Keywords: Key words Cutaneous scent glands ; Apocrine glands ; Myoepithelial cells ; Holocrine glands ; Ultrastructure ; Lectins ; Cytokeratins ; Impala ; Aepyceros melampus (Artiodactyla)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The cutaneous glands of the forehead and the metatarsus were studied by histological and histochemical methods and electron microscopy in adult male and female impalas in various seasons of the year. All glandular areas consist of apocrine and holocrine glands, which, however, occur in different proportions. Our findings in the apocrine gland cells suggest (1) the synthesis and exocytosis of a glycoproteinaceous secretory product stored in secretory granules, (2) typical apocrine secretion of the transformed apical cytoplasm, and (3) transepithelial fluid transport. The Golgi apparatus and apical membrane have binding sites for several lectins (PNA, HPA, RCA I, WGA). Cytokeratins 7, 14 and 19 are expressed at various intracellular localizations, suggesting an active role in the secretory mechanisms. The glands of the male forehead show marked seasonal changes in activity that are correlated with the main phases of the reproductive cycle, with the highest cellular activity occurring during the rut in April/May. The female forehead glands are only moderately developed and do not undergo seasonal changes. The metatarsal glands are of equal size in males and females and show no seasonal changes in activity. This study supports the hypothesis that (1) forehead glands in the male have a signaling role in the rut and (2) the metatarsal glands have a more general, probably social role maintaining and restoring contact between herd members.
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  • 19
    Electronic Resource
    Electronic Resource
    Springer
    Cell & tissue research 293 (1998), S. 165-171 
    ISSN: 1432-0878
    Keywords: Key words Muscle injury ; Cytoskeleton ; Sarcomere organisation ; Immunohistochemistry ; Ultrastructure ; Rabbit (New Zealand White)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Immunohistochemical and electron-microscopic techniques were used to analyze the extensor digitorum longus muscles of New Zealand White rabbits 1 h, 1 day, 3, 7, and 28 days after repetitive eccentric contractions. Loss of the cytoskeletal protein desmin was the earliest manifestation of injury. Apart from 1 h post-exercise, all desmin-negative fibers stained positively with antibody to plasma fibronectin, indicating loss of cellular integrity accompanying cytoskeletal disruption. Fiber sizes were significantly increased from 1–7 days after exercise. The large (hyaline) fibers found in histological sections after repetitive eccentric contractions resulted from segmental hypercontraction of the fiber. This phenomenon occurred proximally and distally to plasma membrane lesions of the muscle fiber and necrosis and manifested itself as very short sarcomere lengths. Thus, in serial sections, staining characteristics, sizes and shapes of one and the same fiber often varied dramatically. We conclude that the following sequence of events occurs: cytoskeletal disruptions, loss of myofibrillar registry, i.e., Z-disk streaming and A-band disorganization, and loss of cell integrity as manifested by intracellular plasma fibronectin stain, hypercontracted regions, and invasion of cells. When a fiber is disrupted, the remaining intact fibers apparently take up the tension put on the muscle and later fewer fibers are subjected to eccentric contractions.
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  • 20
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    Cell & tissue research 294 (1998), S. 253-260 
    ISSN: 1432-0878
    Keywords: Key words P2X1 receptor ; Ultrastructure ; Cerebellum ; Rat (Wistar)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The distribution of the P2X1 subtype of purinoceptors associated with the extracellular activities of ATP was studied in the rat cerebellum at the electron-microscope level. Receptors were labelled with peroxidase-antiperoxidase and the avidin-biotin-peroxidase complex for immunocytochemistry. Immunoreactivity to P2X1 receptors was localized in subpopulations of synapses between varicosities of parallel fibres of granule cells and dendritic spines of Purkinje cells. Unlabelled varicosities of parallel fibres formed asymmetric synapses with labelled dendritic spines, whereas labelled varicosities of parallel fibres formed asymmetric synapses with unlabelled dendritic spines. P2X1 immunoreactivity was also localized in some astrocyte processes. The functional significance of these findings is discussed.
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  • 21
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    Cell & tissue research 294 (1998), S. 367-375 
    ISSN: 1432-0878
    Keywords: Key words Neurons ; Glia ; Tracheae ; Wing ; Ultrastructure ; Moth ; Manduca sp.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  This ultrastructural examination of sensory nerves of the Manduca wing has revealed that extensive remodeling occurs among insect sensory neurons and their associated glial cells between pupation and adult emergence. Systematic counts of axons in particular wing nerves throughout adult development have shown that a decrease in axon number per nerve occurs after day 6. The neurons and glial cells that die are believed to be cells present at pupation that have no apparent sensory function but that probably function as guidance scaffolding for neurons and glia that are born after pupation. Despite the loss of several axons from each wing nerve, these nerves continue to grow in diameter during the latter half of adult development as some of the surviving axons increase severalfold in diameter. Each growing wing nerve in turn apparently functions as a scaffold for the proximal to distal growth of adult tracheae. A correspondence exists between adult nerve pathways and adult tracheal pathways, with each trachea maintaining intimate contact with a wing nerve along its entire length.
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  • 22
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    Cell & tissue research 291 (1998), S. 549-559 
    ISSN: 1432-0878
    Keywords: Key words Endolymphatic sac ; Ultrastructure ; Fluid transport ; Otoconia ; Newt ; Cynops pyrrhogaster (Urodela)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The ultrastructure of the endolymphatic sac (ES) of the late stage larva of the Japanese red-bellied newt, Cynops pyrrhogaster (stage 57), was examined by light and transmission electron microscopy. The two endolymphatic sacs are located at the dorsal-medial side of the otic vesicle on the dorsal-lateral side of the midbrain in the cranial cavity. The wall of the sac is composed of a layer of cubical epithelial cells with loose, interposed intercellular spaces. The sac contains a large luminal cavity, in which endolymph and numerous otoconia are present. The epithelial cells of different portions of the sac have a similar structure. These cells contain an abundance of cytoplasmic organelles, including ribosomes, Golgi complexes, and numerous vesicles. Two types of vesicles are found in the epithelial cells: the “floccular” vesicle and the “granular” vesicle. The floccular vesicles are located in the supra- and lateral-nuclear cytoplasm and contain flocccular material. The granular vesicles have a fine granular substance and are usually situated apposed to the apical cell membrane. The granular vesicles are suggested to be secreted into the lumen, while the floccular vesicles are thought to be absorbed from the lumen and conveyed to the intercellular spaces by the epithelial cells. The apical surfaces of the epithelial cells bear numerous microvilli. Apparently floating cells, which bear long microvilli on the free surfaces, are observed in the lumen of the ES. Based on the fine structure, the function of the endolymphatic sac of the newt Cynops pyrrhogaster is discussed.
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  • 23
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    Cell & tissue research 293 (1998), S. 253-269 
    ISSN: 1432-0878
    Keywords: Key words Septate junctions ; Ultrastructure ; Permeability ; Ions ; Epithelium ; Photoreceptor ; Hirudo medicinalis (Hirudinea)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The leech photoreceptor forms a unicellular epithelium: every cell surrounds an extracellular “vacuole” that is connected to the remaining extracellular space via narrow clefts containing pleated septate junctions. We analyzed the complete structural layout of all septa within the junctional complex in elastic brightfield stereo electron micrographs of semithin serial sections from photoreceptors infiltrated with colloidal lanthanum. The septa form tortuous interseptal corridors that are spatially continuous, and open ended basally and apically. Individual septa seem to be impermeable to lanthanum; interseptal corridors form the only diffusional pathway for this ion. The junctions form no diffusion barrier for the electron-dense tracer Ba2+, but they hinder the diffusion of various hydrophilic fluorescent dyes as demonstrated by confocal laser scanning microscopy (CLSM) of live cells. Even those dyes that penetrate gap junctions do not diffuse beyond the septate junctions. The aqueous diffusion pathway within the septal corridors is, therefore, less permeable than the gap-junctional pore. Our morphological results combined with published electrophysiological data suggest that the septa themselves are not completely tight for small physiologically relevant ions. We also examined, by CLSM, whether the septate junctions create a permeability barrier for the lateral diffusion of fluorescent lipophilic dyes incorporated into the peripheral membrane domain. AFC16, claimed to remain in the outer membrane leaflet, does not diffuse beyond the junctional region, whereas DiIC16, claimed to flip-flop, does. Thus, pleated septate junctions, like vertebrate tight junctions, contribute to the maintenance of cell polarity.
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  • 24
    ISSN: 1432-0878
    Keywords: Key words Angiogenesis ; Capillary growth ; Prazosin ; Shear stress ; Skeletal muscle ; Ultrastructure ; Rat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Chronic vasodilatation represents a stimulus for capillary growth associated with increased luminal shear stress. We have examined the ultrastructure of more than 2000 capillaries to establish whether the sequence of angiogenesis in response to this stimulus is similar to that described during development and under pathological circumstances. Administration of the α1-blocker prazosin to rats for 2 weeks led to a greater capillary length density in extensor hallucis proprius muscles without any change in capillary tortuosity: J v(c,f)=262±54 compared with 350±17 mm–2, control compared with prazosin (P〈0.002). There were obvious signs of endothelial cell (EC) activation after prazosin treatment, including an increased proportion of capillaries with rough endoplasmic reticulum, large cytoplasmic vacuoles, thickened endothelium and an irregular luminal surface. Capillaries from control muscles had a maximum of three ECs in cross section, whereas four ECs were noted in 0.8+0.5% of capillaries after 1 week (n.s.) and 2.5±0.9% after 2 weeks (P〈0.01) of treatment. This could be due to elongation and/or migration of ECs, as cell proliferation has not been described at these time points. There was also an increase in the proportion of capillaries having a narrow, slit-like lumen (1.7±0.8% of controls; 7.1±1.9% at 1 week; 8.8±2.5% at 2 weeks; P〈0.02), some of which were smaller in size (less than 2 μm diameter) than in controls (3–5 μm) and/or “seamless”, i.e. lacking EC junctions. These may represent newly formed vessels. Focal discontinuity of the basement membrane and abluminal EC processes were rarely seen, and capillary growth by abluminal sprouting appeared to be very infrequent (less than 0.001% of profiles). Of more importance was growth starting from the luminal side. Significantly more thin cytoplasmic processes were observed protruding into the lumen of capillaries after 1 week (47.5±6.2%, P〈0.001) and 2 weeks of prazosin (34.2±5.5%, P〈0.05) than in control vessels (16.7±3.9%). Some of these traversed the entire lumen and connected with endothelium of the opposite side, probably involving membrane fusion, resulting in the appearance of a double lumen. Individual capillaries with a complete double lumen were observed after 2 weeks’ prazosin but comparatively rarely, in only four out of six muscles. These findings indicate a pattern of luminal growth which is completely different from intussusceptive growth previously described during development, and from the abluminal capillary sprouting seen under pathological circumstances.
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  • 25
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    Protoplasma 204 (1998), S. 155-169 
    ISSN: 1615-6102
    Keywords: Spores ; Ultrastructure ; Entorrhiza ; Microbotryum ; Tilletia ; Ustilago
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The concept and nomenclature for the elements of teliospore walls in smut fungi are presented and a survey of teliosporogenesis is given, as seen by light and transmission electron microscopy. Four developmental types are distinguished: the Ustilago, Microbotryum, Tilletia, and Entorrhiza type. In the Ustilago type, sporogenous hyphae are completely segmented into teliospore initials which are embedded in a hyaline matrix formed by gelatinised hyphal walls (found in species ofAnthracoidea, Cintractia, Heterotolyposporium, Kuntzeomyces, Macalpinomyces, Melanopsichium, Sporisorium, Testicularia, Tolyposporium junci, Trichocintractia, and species ofUstilago infecting members of the family Poaceae). In the Microbotryum type, septate sporogenous hyphae are also completely segmented into teliospore initials, however, they are not surrounded by a hyaline matrix (Microbotryum, Sphacelotheca, Ustilago spp. infecting dicotyledons). A yeast-like budding of teliosporogenic cells is observed for some species ofMicrobotryum, Sphacelotheca, andUstilago infecting dicotyledons. In the Tilletia type, teliospores differentiate locally in the sporogenous hyphae, in an apical or intercalary position, without a hyaline matrix (Conidiosporomyces, Doassinga, Entyloma, Erratomyces, Ingoldiomyces, Neovossia, Oberwinkleria, Rhamphospora, Tilletia). In all these types, the teliospore initials first develop a hyaline sheath under which the ornamentation, the exosporium, sometimes a middle layer, and the endosporium are successively deposited by the fungal cell. In the Entorrhiza type, the teliospores develop inside vital host cells with the wall of the sporogenous hypha included into the teliospore wall. The fungus develops a middle layer and an electron-transparent endosporium inside the hyphal wall while a layer forming the ornamentation is deposited onto the hyphal wall, probably by vesicles of dictyosomes of the host cell.
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  • 26
    ISSN: 1615-6102
    Keywords: Neck cell proliferation ; Binucleate ; Douglas fir ; Conifers ; Genetic instability ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary To study the effect of culturing on megagametophytes of Douglas fir (Pseudotsuga menziesii) and hybrid larch (Larix × eurolepis), cones were collected at the time of fertilization and the megagametophytes were removed, then placed on medium. We used a modified Murashige and Skoog medium supplemented with 5% lactose and 10% polyethylene glycol 4000. A variety of cell types proliferated including prothallial, neck, and jacket cells. Some of these multiplying cells showed a binucleate condition. The prothallial cells of the apex divided and expanded. The neck cells formed clusters composed of more cells than normally found in situ; though otherwise they showed ultrastructural similarity to neck cells in situ. These neck cells had large numbers of active Golgi complexes, numerous large and small vacuoles, coated vesicles, smooth vesicles, a well-developed endoplasmic reticulum, and thickened cell walls. These are the first reports of neck cell multiplication and induction of a binucleate state for gymnosperm megagametophyte cells in vitro.
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  • 27
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    Protoplasma 201 (1998), S. 30-37 
    ISSN: 1615-6102
    Keywords: Cell-to-cell communication ; Plasmodesmata ; Ultrastructure ; Wounding ; 2-Deoxy-D-glucose
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The transport of ions and metabolites through plasmodesmata has been thought to be controlled at the neck region where the cytoplasmic annulus is constricted and where callose has also been localised. In order to determine the possible structural and functional effects of callose, its deposition was inhibited through incubation of the plant tissue with 2-deoxy-D-glucose (DDG) for 1 h prior to fixation in 2.5% glutaraldehyde. The inhibition of callose formation was monitored through aniline blue-induced fluorescence of callose. The neck region of the plasmodesmata fromAllium cepa L. roots treated with DDG exhibited a funnel-shaped configuration. This is in contrast to the plasmodesmata from tissue not incubated with DDG, which exhibited constricted necks similar to those previously reported. Both initial dissection and glutaraldehyde fixation induced neck constriction in plasmodesmata, however, dissection of tissue increased the frequency of constrictions. The inhibition of callose formation by chemical means showed that the neck constrictions and raised collars in this area are artefacts due to physical wounding and glutaraldehyde fixation. The external electron-dense material observed when tannic acid is included in the primary fixative appears to be unrelated to the deposition of callose at the neck region.
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  • 28
    ISSN: 1615-6102
    Keywords: Chloroplast development ; Cotton ; Fluorescence induction kinetics ; Ultrastructure ; Immunocytochemistry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Many of the studies of chloroplast ontogeny in higher plants have utilized suboptimal conditions of light and growth to assess development. In this study, we utilized structural, immunological, and physiological techniques to examine the development of the chloroplast in fieldgrown cotton (Gossypium hirsutum cv. “MD 51 ne”). Our youngest leaf sample developmentally was completely folded upon itself and about 0.5 cm in length; leaves of this same plastochron were followed for three weeks to the fully expanded leaf. The chloroplasts at the earliest stage monitored had almost all of the lamellae in small, relatively electron-opaque grana, with relatively few thylakoids which were not appressed on at least one surface. During the development of the thylakoids, the membranes increase in complexity, with considerable stroma lamellae development and an increase in the number of thylakoids per granum. Besides the increase in complexity, both the size and numbers of the chloroplast increase during the development of the leaf. Developmental changes in six thylakoid proteins, five stromal proteins, and one peroxisomal protein were monitored by quantitative immunocytochemistry. Even at the earliest stages of development, the plastids are equipped with the proteins required to carry out both light and dark reactions of photosynthesis. Several of the proteins follow three phases of accumulation: a relatively high density at early stages, a linear increase to keep step with chloroplast growth, and a final accumulation in the mature chloroplast. Photosystem-II(PS II)-related proteins are present at their highest densities early in development, with an accumulation of other parts of the photosynthetic apparatus at a latter stage. The early accumulation of PS-II-related proteins correlates with the much lower ratio of chlorophylla tob in the younger leaves and with the changes in fluorescence transients. These data indicate that some of the conclusions on chloroplast development based upon studies of intercalary meristems of monocots or the greening of etiolated plants may not be adequate to explain development of chloroplasts in leaves from apical meristems grown under natural conditions.
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  • 29
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    Protoplasma 201 (1998), S. 101-109 
    ISSN: 1615-6102
    Keywords: Kinetochore ; Kinetoplastida ; Intranuclear microtubules ; Mitosis ; Ultrastructure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The three-dimensional ultrastructural organization of the mitotic apparatus ofDimastigella mimosa was studied by computer-aided, serial-section reconstruction. The nuclear envelope remains intact during nuclear division. During mitosis, chromosomes do not condense, whereas intranuclear microtubules are found in close association with six pairs of kinetochores. No discrete microtubule-organizing centers, except kinetochore pairs, could be found within the nucleus. The intranuclear microtubules form six separate bundles oriented at different angles to each other. Each bundle contains up to 8 tightly packed microtubules which push the daughter kinetochores apart. At late anaphase only, midzones of these bundles align along an extended interzonal spindle within the narrow isthmus between segregating progeny nuclei. The nuclear division inD. mimosa can be described as closed intranuclear mitosis with acentric and separate microtubular bundles and weakly condensed chromosomes.
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  • 30
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    Plant systematics and evolution 210 (1998), S. 25-39 
    ISSN: 1615-6110
    Keywords: Cyanophyta ; Cyanobacteria ; Cyanothece ; Synechococcus ; Cyanobium ; Ultrastructure ; nucleoids ; taxonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The fine structure of the type species of the genusCyanothece Komárek 1976,C. aeruginosa, is described and compared with the main cytological characteristics of morphologically related members of the generaCyanobium, Cyanobacterium andSynechococcus. Several morphological features, such as cell walls with thick outer layers containing a special type of vesicles, position of thylakoids, “keritomy” (net-like appearance of protoplast caused by arrangement of thylakoids, net-like nucleoids and/or by tendency to form intrathylakoidal spaces) and a special structure of mucilaginous envelopes were found to be characteristic of this genus, supporting its separate position among coccal cyanoprokaryotes (cyanobacteria, cyanophytes). The taxonomic significance of ultrastructural features in all mentioned genera is discussed.
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  • 31
    ISSN: 1615-6102
    Keywords: Spore balls ; Germ areas ; Ultrastructure ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Special features of teliospores in smut fungi are described, including teliospore connections, appendages, and germ pores. Balls of teliospores in species of many different genera cohere by remnants of hyphal walls, sheaths, and sometimes interlocking ornamentation. Teliospores are connected in pairs in species ofMycosyrinx andGeminago by special local structures. Appendages can be formed locally by persistent material from the sheath (Cintractia, Anthracoidea, Sphacelotheca), thickened parts of the spore wall (e.g.,Georgefischeria, Jamesdicksonia, Rhamphospora, Tolyposporella), or persistent walls of sporogenous hyphae (Rhamphospora, genera of the Tilletia relationship). Species ofGeorgefischeria, Jamesdicksonia, andTolyposporella have teliospore walls composed of more than three layers of different electron density. “Germ areas” corresponding to thinner parts of the spore wall are known, e.g., for species ofAnthracoidea, Cintractia, andUstilago infecting members of the family Poaceae, while distinct germ pores, one per teliospore, are found in some species ofThecaphora, “Tolyposporium”, andSporisorium. Teliospores ofMycosyrinx cissi have a germination ring. Characteristics of teliospores are used to discuss the phylogeny of smut fungi. A phylogenetic tree in accordance with teliospore characteristics is compared to those obtained from ultrastructural characteristics of host-parasite interaction, of septal pores, and from sequence data. Aspects of teliospore development help to define taxa at a high systematic level (Entorrhizales, Ustilaginales, Tilletiales/Entylomatales, Microbotryaceae), while details of ornamentation ontogeny delimit groups of genera (e.g., genera related toUstilago on members of the Poaceae andSporisorium, Cintractia andAnthracoidea, Tilletia) or single genera (e.g.,Melanopsichium, Dermatosorus, Mycosyrinx, Doassinga, Rhamphospora). Types of ornamentation (warty, reticulate), middle layers, teliospore balls, and germ pores evolved repeatedly by convergence. The smut teliospore itself probably evolved independently at least twice, or perhaps three (or more) times, in the Microbotryales, in the Entorrhizales, and in a common ancestor of the remainder of the Ustilaginomycetes.
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  • 32
    ISSN: 1615-6102
    Keywords: Spores ; Ultrastructure ; Microbotryum ; Tilletia ; Tolyposporium ; Ustilago
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The walls of mature teliospores and the development of ornamentation, as seen by transmission electron microscopy, are described for 37 genera of smut fungi, based on observations of ca. 120 species and on literature. Structural diversity of mature teliospore walls is due to differences in spore wall layers forming the spore wall (endosporium, middle layer, exosporium, ornamentation) and to different elements forming the ornamentation (exosporium, ornaments, sheath, hyphal wall, adjacent fungal cells, material of the host). During teliosporogenesis the outer layers are usually deposited first. At the beginning of the formation of the ornamentation the plasma membrane may be smooth or undulated carrying the developing ornaments on its tips or in its depressions. The ornamentation of some genera appears similar when seen by scanning electron microscopy, but can be the product of different developmental patterns (e.g., warts of species ofFarysia, Tilletia, andUstilago), however, warty and reticulate ornamentation can both be produced by similar developmental processes (shown, e.g., for species ofCintractia andTilletia). Typical structures of the mature teliospore wall and developmental patterns based on homologous similarities are described for the following groups of genera or species:Macalpinomyces, Melanopsichium, Sporisorium, andUstilago infecting members of the family Poaceae;Kuntzeomyces, Testicularia, andTrichocintractia; Anthracoidea, Cintractia, Heterotolyposporium piluliforme, andTolyposporium junci; Glomosporium, Sorosporium, andThecaphora; Conidiosporomyces, Erratomyces, Ingoldiomyces, Neovossia, Oberwinkleria, andTilletia; Entyloma, and genera of the Doassansia group;Liroa, Microbotryum, Sphacelotheca, Ustilago infecting dicotyledons, andZundeliomyces; Aurantiosporium, Fulvisporium, andUstilentyloma. Special characteristics of the teliospore wall were observed for the generaDermatosorus, Doassinga, Entorrhha, Farysia, Mycosyrinx, Rhamphospora, and some species ofTolyposporium.
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  • 33
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    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 57 (1998), S. 590-599 
    ISSN: 0006-3592
    Keywords: protein refolding ; hollow-fibre membrane ; dialysis ; carbonic anhydrase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: We have used a cellulose acetate, hollow-fibre (HF) ultrafiltration membrane to refold bovine carbonic anhydrase, loaded into the lumen space, by removing the denaturant through controlled dialysis via the shell side space. When challenged with GdnHCl-denatured carbonic anhydrase, 70% of the loaded protein reptated through the membrane into the circulating dialysis buffer. Reptation occurred because the protein, in its fully unfolded configuration, was able to pass through the pores. The loss of carbonic anhydrase through the membrane was controlled by the dialysis conditions. Dialysis against 0.05 M Tris-HCl for 30 min reduced the denaturant around the protein to a concentration that allowed the return of secondary structure, increasing the hydrodynamic radius, thus preventing protein transmission. Under these conditions a maximum of 42% of carbonic anhydrase was recovered (from a starting concentration of 5 mg/mL) with 94% activity. This is an improvement over refolding carbonic anhydrase by simple batch dilution, which gave a maximum reactivation of 85% with 35% soluble protein yield. The batch refolding of carbonic anhydrase is very sensitive to temperature; however, during HF refolding between 0 and 25°C the temperature sensitivity was considerably reduced. In order to reduce the convection forces that give rise to aggregation and promote refolding the dialyzate was slowly heated from 4 to 25°C. This slow, temperature-controlled refolding gave an improved soluble protein recovery of 55% with a reactivation yield of 90%. The effect of a number of additives on the refolding system performance were tested: the presence of PEG improved both the protein recovery and the recovered activity from the membrane, while the detergents Tween 20 and IGEPAL CA-630 increased only the refolding yield. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 590-599, 1998.
    Additional Material: 8 Ill.
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  • 34
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    Biotechnology and Bioengineering 58 (1998), S. 119-120 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: No abstract.
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  • 35
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    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 58 (1998), S. 658-662 
    ISSN: 0006-3592
    Keywords: T4 lysozyme ; silica nanoparticles ; synthetic enzyme variants ; surface-induced conformational change ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Maintaining a specific molecular conformation is essential for the proper functioning of an enzyme. A substantial loss of catalytic activity can occur from the displacement caused by even a single amino acid substitution. Activity may also be lost as an enzyme undergoes a conformational change during adsorption. In this study, we investigated the effect of thermostability on the activities of three T4 lysozyme variants after adsorption to 9 nm colloidal silica particles. Less-stable T4 lysozyme variants lost more activity after adsorption than did more stable variants, apparently because they experienced more extensive structural alteration. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58: 658-662, 1998.
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  • 36
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    Biotechnology and Bioengineering 58 (1998), S. 139-148 
    ISSN: 0006-3592
    Keywords: metabolic engineering ; pathway analysis ; metabolic and energetic model ; physiological state ; Saccharomyces cerevisiae ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In this work, an integrated modeling approach based on a metabolic signal flow diagram and cellular energetics was used to model the metabolic pathway analysis for the cultivation of yeast on glucose. This approach enables us to make a clear analysis of the flow direction of the carbon fluxes in the metabolic pathways as well as of the degree of activation of a particular pathway for the synthesis of biomaterials for cell growth. The analyses demonstrate that the main metabolic pathways of Saccharomyces cerevisiae change significantly during batch culture. Carbon flow direction is toward glycolysis to satisfy the increase of requirement for precursors and energy. The enzymatic activation of TCA cycle seems to always be at normal level, which may result in the overflow of ethanol due to its limited capacity. The advantage of this approach is that it adopts both virtues of the metabolic signal flow diagram and the simple network analysis method, focusing on the investigation of the flow directions of carbon fluxes and the degree of activation of a particular pathway or reaction loop. All of the variables used in the model equations were determined on-line; the information obtained from the calculated metabolic coefficients may result in a better understanding of cell physiology and help to evaluate the state of the cell culture process. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:139-148, 1998.
    Additional Material: 9 Ill.
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  • 37
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    Biotechnology and Bioengineering 58 (1998), S. 149-153 
    ISSN: 0006-3592
    Keywords: Metabolic Control Analysis ; flux control coefficients ; top down MCA ; metabolic engineering ; Corynebacterium glutamicum ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Grouping of reactions around key metabolite branch points can facilitate the study of metabolic control of complex metabolic networks. This top-down Metabolic Control Analysis is exemplified through the introduction of group (flux, as well as concentration) control coefficients whose magnitudes provide a measure of the relative impact of each reaction group on the overall network flux, as well as on the overall network stability, following enzymatic amplification. In this article, we demonstrate the application of previously developed theory to the determination of group flux control coefficients. Experimental data for the changes in metabolic fluxes obtained in response to the introduction of six different environmental perturbations are used to determine the group flux control coefficients for three reaction groups formed around the phosphoenolpyruvate/pyruvate branch point. The consistency of the obtained group flux control coefficient estimates is systematically analyzed to ensure that all necessary conditions are satisfied. The magnitudes of the determined control coefficients suggest that the control of lysine production flux in Corynebacterium glutamicum cells at a growth base state resides within the lysine biosynthetic pathway that begins with the PEP/PYR carboxylation anaplorotic pathway. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:149-153, 1998.
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  • 38
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    Biotechnology and Bioengineering 58 (1998), S. 154-161 
    ISSN: 0006-3592
    Keywords: central carbon pathways ; metabolic optimization ; ethanol production ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Many attempts to engineer cellular metabolism have failed due to the complexity of cellular functions. Mathematical and computational methods are needed that can organize the available experimental information, and provide insight and guidance for successful metabolic engineering. Two such methods are reviewed here. Both methods employ a (log)linear kinetic model of metabolism that is constructed based on enzyme kinetics characteristics. The first method allows the description of the dynamic responses of metabolic systems subject to spatiotemporal variations in their parameters. The second method considers the product-oriented, constrained optimization of metabolic reaction networks using mixed-integer linear programming methods. The optimization framework is used in order to identify the combinations of the metabolic characteristics of the glycolytic enzymes from yeast and bacteria that will maximize ethanol production. The methods are also applied to the design of microbial ethanol production metabolism. The results of the calculations are in qualitative agreement with experimental data presented here. Experiments and calculations suggest that, in resting Escherichia coli cells, ethanol production and glucose uptake rates can be increased by 30% and 20%, respectively, by overexpression of a deregulated pyruvate kinase, while increase in phosphofructokinase expression levels has no effect on ethanol production and glucose uptake rates. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:154-161, 1998.
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  • 39
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    Biotechnology and Bioengineering 58 (1998), S. 170-174 
    ISSN: 0006-3592
    Keywords: catabolite repression ; phosphotransferase system ; inducer exclusion ; inducer expulsion ; protein kinase ; transcriptional regulation ; transport regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Catabolite repression is a universal phenomenon, found in virtually all living organisms. These organisms range from the simplest bacteria to higher fungi, plants, and animals. A mechanism involving cyclic AMP and its receptor protein (CRP) in Escherichia coli was established years ago, and this mechanism has been assumed by many to serve as the prototype for catabolite repression in all organisms. However, recent studies have shown that this mechanism is restricted to enteric bacteria and their close relatives. Cyclic AMP-independent mechanisms of catabolite repression occur in other bacteria, yeast, plants, and even E. coli. In fact, single-celled organisms such as E. coli, Bacillus subtilis, and Saccharomyces cerevisiae exhibit multiple mechanisms of catabolite repression, and most of these are cyclic AMP-independent. The mechanistic features of the best of such characterized processes are briefly reviewed, and references are provided that will allow the reader to delve more deeply into these subjects. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:170-174, 1998.
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  • 40
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    Biotechnology and Bioengineering 58 (1998), S. 162-169 
    ISSN: 0006-3592
    Keywords: bioinformatics ; metabolic engineering ; genetic engineering ; mathematical analysis ; stoichiometry ; enzyme kinetics ; modal analysis ; genetic circuits ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Ten microbial genomes have been fully sequenced to date, and the sequencing of many more genomes is expected to be completed before the end of the century. The assignment of function to open reading frames (ORFs) is progressing, and for some genomes over 70% of functional assignments have been made. The majority of the assigned ORFs relate to metabolic functions. Thus, the complete genetic and biochemical functions of a number of microbial cells may be soon available. From a metabolic engineering standpoint, these developments open a new realm of possibilities. Metabolic analysis and engineering strategies can now be built on a sound genomic basis. An important question that now arises; how should these tasks be approached? Flux-balance analysis (FBA) has the potential to play an important role. It is based on the fundamental principle of mass conservation. It requires only the stoichiometric matrix, the metabolic demands, and some strain specific parameters. Importantly, no enzymatic kinetic data is required. In this article, we show how the genomically defined microbial metabolic genotypes can be analyzed by FBA. Fundamental concepts of metabolic genotype, metabolic phenotype, metabolic redundancy and robustness are defined and examples of their use given. We discuss the advantage of this approach, and how FBA is expected to find uses in the near future. FBA is likely to become an important analysis tool for genomically based approaches to metabolic engineering, strain design, and development. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:162-169, 1998.
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  • 41
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    Biotechnology and Bioengineering 58 (1998), S. 191-195 
    ISSN: 0006-3592
    Keywords: control analysis ; Lactococcus lactis ; gene expression ; flux ; oligonucleotide ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In this article, we review some of the expression systems that are available for Metabolic Control Analysis and Metabolic Engineering, and examine their advantages and disadvantages in different contexts. In a recent approach, artificial promoters for modulating gene expression in micro-organisms were constructed using synthetic degenerated oligonucleotides. From this work, a promoter library was obtained for Lactococcus lactis, containing numerous individual promoters and covering a wide range of promoter activities. Importantly, the range of promoter activities was covered in small steps of activity change. Promoter libraries generated by this approach allow for optimization of gene expression and for experimental control analysis in a wide range of biological systems by choosing from the promoter library promoters giving, e.g., 25%, 50%, 200%, and 400% of the normal expression level of the gene in question. If the relevant variable (e.g., the flux or yield) is then measured with each of these constructs, then one can calculate the control coefficient and determine the optimal expression level. One advantage of the method is that the construct which is found to have the optimal expression level is then, in principle, ready for use in the industrial fermentation process; another advantage is that the system can be used to optimize the expression of different enzymes within the same cell. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:191-195, 1998.
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  • 42
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    Biotechnology and Bioengineering 58 (1998), S. 175-190 
    ISSN: 0006-3592
    Keywords: protein-based polymers ; inverse temperature transitions ; hydrophobic-induced pKa shifts ; waters of hydrophobic hydration ; five axioms for protein engineering; microwave dielectric relaxation ; a universal mechanism for biological energy conversion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Metabolism is the conversion of available energy sources to those energy forms required for sustaining and propagating living organisms; this is simply biological energy conversion. Proteins are the machines of metabolism; they are the engines of motility and the other machines that interconvert energy forms not involving motion. Accordingly, metabolic engineering becomes the use of natural protein-based machines for the good of society. In addition, metabolic engineering can utilize the principles, whereby proteins function, to design new protein-based machines to fulfill roles for society that proteins have never been called upon throughout evolution to fulfill.This article presents arguments for a universal mechanism whereby proteins perform their diverse energy conversions; it begins with background information, and then asserts a set of five axioms for protein folding, assembly, and function and for protein engineering. The key process is the hydrophobic folding and assembly transition exhibited by properly balanced amphiphilic protein sequences. The fundamental molecular process is the competition for hydration between hydrophobic and polar, e.g., charged, residues. This competition determines Tt, the onset temperature for the hydrophobic folding and assembly transition, Nhh, the numbers of waters of hydrophobic hydration, and the pKa of ionizable functions.Reported acid-base titrations and pH dependence of microwave dielectric relaxation data simultaneously demonstrate the interdependence of Tt, Nhh and the pKa using a series of microbially prepared protein-based poly(30mers) with one glutamic acid residue per 30mer and with an increasing number of more hydrophobic phenylalanine residues replacing valine residues. Also, reduction of nicotinamides and flavins is shown to lower Tt, i.e., to increase hydrophobicity.Furthermore, the argument is presented, and related to an extended Henderson-Hasselbalch equation, wherein reduction of nicotinamides represents an increase in hydrophobicity and resulting hydrophobic-induced pKa shifts become the basis for understanding a primary energy conversion (proton transport) process of mitochondria. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:175-190, 1998.
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  • 43
    ISSN: 0006-3592
    Keywords: Escherichia coli ; Chloramphenicol Acetyltransferase (CAT) ; Culture Redox Potential (CRP) ; Dithiothreitol (DTT) ; reducing agents ; molecular chaperones ; proteases ; heat shock ; stress response ; protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The independent control of culture redox potential (CRP) by the regulated addition of a reducing agent, dithiothreitol (DTT) was demonstrated in aerated recombinant Escherichia coli fermentations. Moderate levels of DTT addition resulted in minimal changes to specific oxygen uptake, growth rate, and dissolved oxygen. Excessive levels of DTT addition were toxic to the cells resulting in cessation of growth. Chloramphenicol acetyltransferase (CAT) activity (nmoles/μg total protein min.) decreased in batch fermentation experiments with respect to increasing levels of DTT addition. To further investigate the mechanisms affecting CAT activity, experiments were performed to assay heat shock protein expression and specific CAT activity (nmoles/μg CAT min.). Expression of such molecular chaperones as GroEL and DnaK were found to increase after addition of DTT. Additionally, sigma factor 32 (σ32) and several proteases were seen to increase dramatically during addition of DTT. Specific CAT activity (nmoles/μg CAT min.) varied greatly as DTT was added, however, a minimum in activity was found at the highest level of DTT addition in E. coli strains RR1 [pBR329] and JM105 [pROEX-CAT]. In conjunction, cellular stress was found to reach a maximum at the same levels of DTT. Although DTT addition has the potential for directly affecting intracellular protein folding, the effects felt from the increased stress within the cell are likely the dominant effector. That the effects of DTT were measured within the cytoplasm of the cell suggests that the periplasmic redox potential was also altered. The changes in specific CAT activity, molecular chaperones, and other heat shock proteins, in the presence of minimal growth rate and oxygen uptake alterations, suggest that the ex vivo control of redox potential provides a new process for affecting the yield and conformation of heterologous proteins in aerated E. coli fermentations. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59: 248-259, 1998.
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  • 44
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    Biotechnology and Bioengineering 59 (1998), S. 261-272 
    ISSN: 0006-3592
    Keywords: effective diffusive permeability ; diffusion coefficient ; biofilm ; cell density ; review ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Experimental measurements of effective diffusive permeabilities and effective diffusion coefficients in biofilms are reviewed. Effective diffusive permeabilities, the parameter appropriate to the analysis of reaction-diffusion interactions, depend on solute type and biofilm density. Three categories of solute physical chemistry with distinct diffusive properties were distinguished by the present analysis. In order of descending mean relative effective diffusive permeability (De/Daq) these were inorganic anions or cations (0.56), nonpolar solutes with molecular weights of 44 or less (0.43), and organic solutes of molecular weight greater than 44 (0.29). Effective diffusive permeabilities decrease sharply with increasing biomass volume fraction suggesting a serial resistance model of diffusion in biofilms as proposed by Hinson and Kocher (1996). A conceptual model of biofilm structure is proposed in which each cell is surrounded by a restricted permeability envelope. Effective diffusion coefficients, which are appropriate to the analysis of transient penetration of nonreactive solutes, are generally similar to effective diffusive permeabilities in biofilms of similar composition. In three studies that examine diffusion of very large molecular weight solutes ( 〉 5000) in biofilms, the average ratio of the relative effective diffusion coefficient of the large solute to the relative effective diffusion coefficient of either sucrose or fluorescein was 0.64, 0.61, and 0.36. It is proposed that large solutes are effectively excluded from microbial cells, that small solutes partition into and diffuse within cells, and that ionic solutes are excluded from cells but exhibit increased diffusive permeability (but decreased effective diffusion coefficients) due to sorption to the biofilm matrix. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:261-272, 1998.
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  • 45
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    Biotechnology and Bioengineering 59 (1998), S. 281-285 
    ISSN: 0006-3592
    Keywords: protein aggregation ; RNase A ; protein formulation ; protein additives ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In the previous study (part I), heat-denatured RNase A aggregation was shown to depend on the solution pH. Interestingly, at pH 3.0, the protein did not aggregate even when exposed to 75°C for 24 h. In this study, electrostatic repulsion was shown to be responsible for the absence of aggregates at that pH. While RNase A aggregation was prevented at the extremely acidic pH, this is not an environment conducive to maintaining protein function in general. Therefore, attempts were made to confer electrostatic repulsion near neutral pH. In this study, heat-denatured RNase A was mixed with charged polymers at pH 7.8 in an attempt to provide the protein with excess surface cations or anions. At 75°C, SDS and dextran sulfate were successful in preventing RNase A aggregation, whereas their cationic, nonionic, and zwitterionic analogs did not do so. We believe that the SO3- groups present in both additives transformed the protein into polyanionic species, and this may have provided a sufficient level of electrostatic repulsion at pH 7.8 and 75°C to prevent aggregation from proceeding. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:281-285, 1998.
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  • 46
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    Biotechnology and Bioengineering 59 (1998), S. 328-343 
    ISSN: 0006-3592
    Keywords: biotrickling filters ; biotrickling filter modeling ; mono-chlorobenzene ; biodegradation kinetics of mono-chlorobenzene ; chlorinated VOC emissions ; biofiltration ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Removal of mono-chlorobenzene (m-CB) vapor from airstreams was studied in a biotrickling filter (BTF) operating under counter-current flow of the air and liquid streams. Experiments were performed under various values of inlet m-CB concentration, air and/or liquid volumetric flow rates, and pH of the recirculating liquid. Conversion of m-CB was never below 70% and at low concentrations exceeded 90%. A maximum removal rate of about 60 gm-3-reactor h-1 was observed. Conversion of m-CB was found to increase as the values of liquid and air flow rate increase and decrease, respectively. The effects of pH and frequency of medium replenishment on BTF performance were also investigated. The process was successfully described with a detailed mathematical model, which accounts for mass transfer and kinetic effects based on m-CB and oxygen availability. Solution of the model equations yielded m-CB and oxygen concentration profiles in all three phases (airstream, liquid, biofilm). It is predicted that oxygen has a controling effect on the process at high inlet m-CB concentrations. From independent, suspended culture, experiments it was found that m-CB biodegradation follows Andrews inhibitory kinetics. The kinetic constants were found to remain practically unchanged after the culture was used in BTF experiments for 8 months. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:328-343, 1998.
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  • 47
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    Biotechnology and Bioengineering 59 (1998), S. 344-350 
    ISSN: 0006-3592
    Keywords: electrodialysis ; citric acid ; pH ; temperature ; Faraday efficiency ; solute recovery efficiency ; specific energy consumption ; solute flux ; water flux ; feed solute concentration ; electric current density ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effect of pH and temperature (θ) on the overall performance indicators (i.e., solute recovery, ρ, and Faraday, η, efficiencies; specific energy consumption, ε, solute, JS, and water, JW, fluxes) of batch electrodialytic recovery of citric acid from model solutions was assessed at different values of feed solute concentration (cSf) and electric current density (j). Regardless of the initial feed concentration used, ρ and JS were found to be independent of θ; η and JW exhibited a positive trend with respect to θ, while ε a negative one. At the maximum temperature tested (33°C), as the pH of the feed solution was varied from 3 to 7, ρ increased from 0.90 ± 0.08 to 0.97 ± 0.02, η grew from 0.09 ± 0.02 to 0.50 ± 0.01, JS practically doubled, ε reduced about 8 times, but JW increased from 3 to 4 times. So, the optimal conditions for this technique are to be determined by balancing the savings in the investment and maintenance costs against the energy costs. © John Wiley & Sons, Inc. Biotechnol Bioeng 59:344-350, 1998.
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  • 48
    ISSN: 0006-3592
    Keywords: chymotrypsin ; enzyme stability ; reversed micelles ; interface ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The stability of α-chymotrypsin and δ-chymotrypsin was studied in reversed micelles of sodium bis(2-ethylhexyl)sulfosuccinate (AOT) in isooctane. α-Chymotrypsin is inactivated at the interface and at the water pool, while δ-chymotrypsin is inactivated only at the water pool. The mechanism of inactivation at the interface is related to the interaction of N-terminal group alanine 149 (absent in δ-chymotrypsin) with the negative interface. The dependence of enzyme activity on water content of these two enzymes in reversed micelles of AOT is also related with the interface interaction, since δ-chymotrypsin does not have a bell-shaped curve as observed for α-chymotrypsin. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:360-363, 1998.
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  • 49
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    Biotechnology and Bioengineering 59 (1998), S. 351-359 
    ISSN: 0006-3592
    Keywords: bioreactor ; high density ; insect cells ; perfusion ; Sf9 ; ultrasonic filter ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The baculovirus/insect cell expression system has provided a vital tool to produce a high level of active proteins for many applications. We have developed a very high-density insect cell perfusion process with an ultrasonic filter as a cell retention device. The separation efficiency of the filter was studied under various operating conditions. A cell density of over 30 million cells/mL was achieved in a controlled perfusion bioreactor and cell viability remained greater than 90%. Sf9 cells from a high-density culture and a spinner culture were infected with two recombinant baculoviruses expressing genes for the production of human chitinase and monocyte-colony inhibition factor. The protein yield on a cell basis from infecting high-density Sf9 cells was the same as or higher than that from the spinner Sf9 culture. Virus production from the high-density culture was similar to that from the spinner culture. The results show that the ultrasonic filter did not affect insect cells' ability to support protein expression and virus production following infection with baculovirus. The potential applications of the high-density perfusion culture for large-scale protein expression from Sf9 cells are also highlighted. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:351-359, 1998.
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  • 50
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    Biotechnology and Bioengineering 59 (1998), S. 374-378 
    ISSN: 0006-3592
    Keywords: conductive paint electrode ; prevention of marine biofouling ; fishing net ; alternating potential ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Conductive paint electrode was used for marine biofouling on fishing nets by electrochemical disinfection. When a potential of 1.2 V vs. a saturated calomel electrode (SCE) was applied to the conductive paint electrode, Vibrio alginolyticus cells attached on the electrode were completely killed. By applying a negative potential, the attached cells were removed from the surface of the electrode. Changes in pH and chlorine concentration were not observed at potentials in the range -0.6 ∼1.2 V vs. SCE. In a field experiment, accumulation of the bacterial cells and formation of biofilms on the electrode were prevented by application of an alternating potential, and 94% of attachment of the biofouling organisms was inhibited electrically on yarn used for fishing net coated with conductive paint. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:374-378, 1998.
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  • 51
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    Biotechnology and Bioengineering 59 (1998), S. 364-373 
    ISSN: 0006-3592
    Keywords: porous supports ; internal and external diffusion ; active site accessibility ; enzyme loading ; kinetically controlled dipeptide synthesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Mass transfer limitations were studied in enzyme preparations of α-chymotrypsin made by deposition on different porous support materials such as controlled pore glasses, Celite, and polyamides of different particle sizes. It is the onset of mass transfer limitations that determines the position of the activity optimum with respect to enzyme loading on each support. The evidence of various experiments indicates that internal diffusional limitations are the important mechanism for the observed mass transfer limitations. External diffusion was not found to play an important role under the conditions used, and it was also found that when immobilizing multilayers of enzyme the buried enzyme molecules are active to a large extent. An extreme situation is observed on Celite at very high loadings. Under these conditions, this support is expected to have its pores completely filled with packed enzyme molecules, and then it is the diffusion within the enzyme layer that determines the observed rate. As the enzyme loading increases, the area of contact between the deposited enzyme layers and the liquid solution inside the pores diminishes, causing a decrease on the observed rate of an intrinsically fast reaction which apparently is incongruous with the presence of more enzyme in the system. This work shows that mass transfer limitations can be an important factor when working with immobilized enzymes in organic media, and its study should be carried out in order to avoid undesired reduced enzyme activities and specificities. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:364-373, 1998.
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  • 52
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    Biotechnology and Bioengineering 59 (1998), S. 438-444 
    ISSN: 0006-3592
    Keywords: bioremediation ; plasma discharge ; dichlorophenol degradation ; perchloroethylene degradation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Pulsed electric discharge (PED) and bioremediation were combined to create a novel two-stage system which dechlorinates the halogenated pollutants, 2,4-dichlorophenol and perchloroethylene, with repetitive (0.1-1 kHz), short pulse (∼100 ns), low voltage (40-80 kV) discharges and then mineralizes the less chlorinated products with aerobic bacteria. A 6.1 mM aqueous dichlorophenol sample was cycled through the PED reactor (60 kV of applied pulsed voltage and 300 Hz) 6 times, resulting in the release of 55% of the initial dichlorophenol chloride ions (1 mM Cl- removed each cycle). The respective average specific efficiency is 0.4-0.6 keV/(Cl- molecule). Pseudomonas mendocina KR1, which grows in minimal medium supplemented with phenol but not with dichlorophenol, increased in cell density in all cultures supplemented with the PED-treated DCP samples and yielded a maximum of two-fold additional Cl- released compared to the PED-related alone. The number of PED-treatment cycles, voltage, and frequency were also varied, showing that both cell densities and overall dichlorophenol dechlorination were highly dependent upon the number of PED-treatment cycles, rather than the tested voltages and frequencies. Using this two-stage treatment system, PED released 31% of the initial chloride ions from dichlorophenol (after three cycles at 40-45 kV and 1.2 kHz) while P. mendocina KR1 in the second stage increased dechlorination to 90%. These results were corroborated by the 35% additional chloride release found with activated sludge cultures. Perchloroethylene (0.6 mM) was similarly treated in a first-stage PED reactor (80% chloride removal after four cycles) followed by biodegradation of the dechlorinated products with a recombinant toluene o-monooxygenase-expressing Pseudomonas fluorescens strain. Gas chromatographic analysis showed that the PED reactor created less-chlorinated byproducts (i.e., trichloroethylene) that were removed (74%) upon exposure to the recombinant bacterium. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:438-444, 1998.
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  • 53
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    Biotechnology and Bioengineering 59 (1998), S. 445-450 
    ISSN: 0006-3592
    Keywords: CHO cells ; glycosylation engineering ; antisense ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Novel glycoproteins, inaccessible by other techniques, can be obtained by metabolic engineering of the oligosaccharide biosynthesis pathway. Furthermore, alteration of cell-surface oligosaccharides can change the properties of receptors involved in cell-cell adhesion. Sialyl Lewis X (sLex) is a cell-surface oligosaccharide determinant which is specifically expressed on granulocytes and monocytes and which interacts with selectins to influence leukocyte trafficking, thrombosis, inflammation, and cancer. Antisense technology targeting fucosyltransferase VI (Fuc-TVI), an enzyme necessary for the synthesis of the sLex in engineered Chinese hamster ovary (CHO) cells, has reduced Fuc-TVI activity, sLex synthesis, and adhesion to endothelial cells. Antisense methodology to reduce targeted activity in oligosaccharide biosynthesis or other pathways is an important addition to CHO cell metabolic engineering capabilities. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:445-450, 1998.
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  • 54
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    Biotechnology and Bioengineering 59 (1998), S. 451-460 
    ISSN: 0006-3592
    Keywords: protein fouling ; membrane transport ; ultrafiltration ; adsorption ; filtration ; composite membrane ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Protein fouling can significantly alter both the flux and retention characteristics of ultrafiltration membranes. There has, however, been considerable controversy over the nature of this fouling layer. In this study, hydraulic permeability and dextran sieving data were obtained both before and after albumin adsorption and/or filtration using polyethersulfone ultrafiltration membranes. The dextran molecular weight distributions were analyzed by gel permeation chromatography to evaluate the sieving characteristics over a broad range of solute size. Protein fouling caused a significant reduction in the dextran sieving coefficients, with very different effects seen for the diffusive and convective contributions to dextran transport. The changes in dextran sieving coefficients and diffusive permeabilities were analyzed using a two-layer membrane model in which a distinct protein layer is assumed to form on the upstream surface of the membrane. The data suggest that the protein layer formed during filtration was more tightly packed than that formed by simple static adsorption. Hydrodynamic calculations indicated that the pore size of the protein layer remained relatively constant throughout the adsorption or filtration, but the thickness of this layer increased with increasing exposure time. These results provide important insights into the nature of protein fouling during ultrafiltration and its effects on membrane transport. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:451-460, 1998.
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  • 55
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    Biotechnology and Bioengineering 59 (1998), S. 461-470 
    ISSN: 0006-3592
    Keywords: aqueous two-phase separation ; protein partitioning ; T4 lysozyme ; electrochemical partitioning ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Protein partitioning in aqueous two-phase systems based on phase-forming polymers is strongly affected by the net charge of the protein, but a thermodynamic description of the charge effects has been hindered by conflicting results. Many of the difficulties could be because of problems in isolating electrochemical effects from other interactions of phase components.We explored charge effects on protein partitioning in poly(ethylene glycol)-dextran two-phase systems by using two series of genetically engineered charge modifications of bacteriophage T4 lysozyme produced in Escherichia coli. The two series, one in the form of charged-fusion tails and the other in the form of charge-change point mutations, provided matching net charges but very different polarity. Partition coefficients of both series were obtained and interfacial potential differences of the phase systems were measured. Multi-angle laser light scattering measurements were also performed to determine second virial coefficients. A semi-empirical model accounting for the roles of both charge and non-charge effects on protein partitioning behavior is proposed, and the results predicted from the model are compared to the results from the experiments. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 59:461-470, 1998.
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  • 56
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    Biotechnology and Bioengineering 57 (1998), S. 518-528 
    ISSN: 0006-3592
    Keywords: ammonium ; UDP-GlcNAc ; N -glycosylation ; BHK-21 cells ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effect of different ammonium concentrations and glucosamine on baby hamster kidney (BHK)-21 cell cultures grown in continuously perfused double membrane bioreactors was investigated with respect to the final carbohydrate structures of a secretory recombinant glycoprotein. The human interleukin-2 (IL-2) mutant glycoprotein variant IL-Mu6, which bears a novel N-glycosylation site (created by a single amino acid exchange of Gln100 to Asn), was produced under different defined protein-free culture conditions in the presence or absence of either glutamine, NH4Cl, or glucosamine. Recombinant glycoprotein products were purified and characterized by amino acid sequencing and carbohydrate structural analysis using matrix-assisted laser desorption ionization time of flight mass spectrometry, high-pH anion-exchange chromatography with pulsed amperometric detection, and methylation analysis. In the absence of glutamine, cells secreted glycoprotein forms with preponderantly biantennary, proximal fucosylated carbohydrate chains (85%) with a higher NeuAc content (58%). Under standard conditions in the presence of 7.5 mM glutamine, complex-type N-glycans were found to be mainly biantennary (68%) and triantennary structures (33%) with about 50% containing proximal α1-6-linked fucose; 37% of the antenna were found to be substituted with terminal α2-3-linked N-acetylneuraminic acid. In the presence of 15 mM exogenously added NH4Cl, a significant and reproducible increase in tri- and tetraantennary oligosaccharides (45% of total) was detected in the secretion product. In glutamin-free cultures supplemented with glucosamine, an intermediate amount of high antennary glycans was detected. The increase in complexity of N-linked oligosaccharides is considered to be brought about by the increased levels of intracellular uridine diphosphate-GlcNAc/GalNAc. These nucleotide sugar pools were found to be significantly elevated in the presence of high NH3/NH4+ and glucosamine concentrations. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 518-528, 1998.
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  • 57
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    Biotechnology and Bioengineering 57 (1998), S. 557-570 
    ISSN: 0006-3592
    Keywords: Alcaligenes eutrophus ; polyhydroxyalkanoates ; metabolic engineering ; mathematical modeling ; enzyme kinetics ; regulation of metabolism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A mathematical model describing intracellular polyhydroxybutyrate (PHB) synthesis in Alcaligenes eutrophus has been constructed. The model allows investigation of issues such as the existence of rate-limiting enzymatic steps, possible regulatory mechanisms in PHB synthesis, and the effects different types of rate expressions have on model behavior. Simulations with the model indicate that activities of all PHB pathway enzymes influence overall PHB flux and that no single enzymatic step can easily be identified as rate limiting. Simulations also support regulatory roles for both thiolase and reductase, mediated through AcCoA/CoASH and NADPH/NADP+ ratios, respectively. To make the model more realistic, complex rate expressions for enzyme-catalyzed reactions were used which reflect both the reversibility of the reactions and the reaction mechanisms. Use of the complex kinetic expressions dramatically changed the behavior of the system compared to a simple model containing only Michaelis-Menten kinetic expressions; the more complicated model displayed different responses to changes in enzyme activities as well as inhibition of flux by the reaction products CoASH and NADP+. These effects can be attributed to reversible rate expressions, which allow prediction of reaction rates under conditions both near and far from equilibrium. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 557-570, 1998.
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  • 58
    ISSN: 0006-3592
    Keywords: rhG-CSF ; fusion protein ; secretion efficiency ; glycosylation ; multimer ; conformation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The synthesis and secretion of recombinant human granulocyte colony-stimulating factor (rhG-CSF) are investigated in fed-batch cultures at high cell concentration of recombinant Saccharomyces cerevisiae, and some important characteristics of the secreted rhG-CSF are demonstrated. Transcription of the recombinant gene is regulated by a GAL1-10 upstream activating sequence (UASG), and the rhG-CSF is expressed in a hybrid fusion protein consisting of signal sequence of Kluyveromyces lactis killer toxin and N-terminal 24 amino acids of human interleukin 1β. The intracellular KEX2 cleavage leads to excretion of mature rhG-CSF into extracellular culture broth, and the cleavage process seems to be highly efficient. In spite of relatively low copy number the plasmid propagation is stably maintained even at nonselective culture conditions. The rhG-CSF synthesis does not depend on galactose level, whereas the production of extracellular rhG-CSF was significantly enhanced by increasing the inducer concentration above a certain level and also by supplementing the nonionic surfactant to the culture medium, which is notably due to the enhanced secretion efficiency. Various immunoblotting analyses demonstrate that none of the rhG-CSF is accumulated in the cell wall fraction and that a significant amount of intracellular rhG-CSF antibody-specific immunoreactive proteins is located in the ER. A core N-glycosylation at fused IL-1β fragment is likely to play a critical role in directing the high-level secretion of rhG-CSF, and the O-glycosylation of secreted rhG-CSF seems nearly negligible. Also the extracellular rhG-CSF is observed to exist as various multimers, and the nature of molecular interaction is evidently not the covalent disulfide bridges. The CD spectra of purified rhG-CSF and Escherichia coli-derived standard show that the conformations of both are similar and are almost identical to that reported for natural hG-CSF. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 600-609, 1998.
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  • 59
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    Biotechnology and Bioengineering 57 (1998), S. 620-623 
    ISSN: 0006-3592
    Keywords: protein refolding ; reversed micelles ; solid-liquid extraction ; RNase A ; DNA ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: This article reports that a reversed micellar solution is useful for refolding proteins directly from a solid source. The solubilization of denatured RNase A, which had been prepared by reprecipitation from the denaturant protein solution, into reversed micelles formulated with sodium di-2-ethylhexyl sulfosuccinate (AOT) has been investigated by a solid-liquid extraction system. This method is an alternative to the ordinary protein extraction in reversed micelles based on the liquid-liquid extraction. The solid-liquid extraction method was found to facilitate the solubilization of denatured proteins more efficiently in the reversed micellar media than the ordinary phase transfer method of liquid extraction. The refolding of denatured RNase A entrapped in reversed micelles was attained by adding a redox reagent (reduced and oxidized glutathion). Enzymatic activity of RNase A was gradually recovered with time in the reversed micelles. The denatured RNase A was completely refolded within 30 h. In addition, the efficiency of protein refolding was enhanced when reversed micelles were applied to denatured RNase A containing a higher protein concentration that, in the case of aqueous media, would lead to protein aggregation. The solid-liquid extraction technique using reversed micelles affords better scale-up advantages in the direct refolding process of insoluble protein aggregates. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 620-623, 1998.
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  • 60
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    Biotechnology and Bioengineering 57 (1998), S. 610-619 
    ISSN: 0006-3592
    Keywords: dynamic model ; Saccharomyces cerevisiae ; oxidative capacity ; feedback control ; calorimetry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The objective of this study was to characterize the dynamic adaptation of the oxidative capacity of Saccharomyces cerevisiae to an increase in the glucose supply rate and its implications for the control of a continuous culture designed to produce biomass without allowing glucose to be diverted into the reductive metabolism. Continuous cultures subjected to a sudden shift-up in the dilution rate showed that the glucose uptake rate increased immediately to the new feeding rate but that the oxygen consumption could not follow fast enough to ensure a completely oxidative metabolism. Thus, part of the glucose assimilated was degraded by the reductive metabolism, resulting in a temporary decrease of biomass concentration, even if the final dilution rate was below Dcrit. The dynamic increase of the specific oxygen consumption rate, qO2, was characterized by an initial immediate jump followed by a first-order increase to the maximum value. It could be modeled using three parameters denoted qjumpO2, qmaxO2, and a time constant τ. The values for the first two of the parameters varied considerably from one shift to another, even when they were performed under identical conditions. On the basis of this model, a time-dependent feed flow rate function was derived that should permit an increase in the dilution rate from one value to another without provoking the appearance of reductive metabolism. The idea was to increase the glucose supply in parallel with the dynamic increase of the oxidative capacity of the culture, so that all of the assimilated glucose could always be oxidized. Nevertheless, corresponding feed-profile experiments showed that deviations in the reductive metabolism could not be completely suppressed due to variability in the model parameters. Therefore, a proportional feedback controller using heat evolution rate measurements was implemented. Calorimetry provides an excellent and rapid estimate of the metabolic activity. Satisfactory control was achieved and led to constant biomass yields. Ethanol accumulated only up to 0.49 g L-1 as compared to an accumulation of 1.82 g L-1 without on-line control in the shift-up experiment to the same final dilution rate. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 610-619, 1998.
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  • 61
    ISSN: 0006-3592
    Keywords: c-jun ; cell cycle ; apoptosis ; antisense ; growth deprivation ; F-MEL ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: F-MEL cells were transfected with the c-jun antisense gene located downstream of a glucocorticoid-inducible MMTV promoter, and the obtained cells were named c-jun AS cells. When the c-jun AS cells were treated with dexamethasone (DEX) in DMEM supplemented with 10% serum, the growth of the cells was completely suppressed for a duration of 16 days with a high cell viability exceeding 86%. The c-jun expression in the c-jun AS cells was suppressed moderately in the absence of DEX and strongly in the presence of DEX. The c-jun AS cells grew well and reached a density of 106 cells/mL without supplementation of any serum components. Viability was greater than 80% after the cells had been cultured for 8 days in the absence of DEX. The c-jun AS cells stayed at a constant cell density and high viability above 80% for 8 days when they were cultured in the presence of DEX under serum deprivation. In contrast, the wild type F-MEL cells were unable to grow and died by apoptosis in 3 days under serum deprivation. Internucleosomal cleavage of DNA, a landmark of apoptosis, was clearly detectable. Thus the c-jun AS cell line that is resistant to apoptosis induced by serum deprivation and can reversibly and viably be growth-arrested was established. A dual-signal model was proposed to explain the experimental result, the interlinked regulation of apoptosis, and growth by c-jun.© 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:65-72, 1998.
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  • 62
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    Biotechnology and Bioengineering 58 (1998), S. 380-386 
    ISSN: 0006-3592
    Keywords: reverse micelles ; cutinase ; deactivation ; conformational changes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Deactivation data and fluorescence intensity changes were used to probe functional and structural stability of cutinase in reverse micelles. A fast deactivation of cutinase in anionic (AOT) reverse micelles occurs due to a reversible denaturation process. The deactivation and denaturation of cutinase is slower in small cationic (CTAB/1-hexanol) reverse micelles and does not occur when the size of the cationic reverse micellar water-pool is larger than cutinase. In both systems, activity loss and denaturation are coupled processes showing the same trend with time. Denaturation is probably caused by the interaction between the enzyme and the surfactant interface of the reversed micelle. When the size of the empty reversed micelle water-pool is smaller than cutinase (at W0 5, with W0 being the water:surfactant concentration ratio) a three-state model describes denaturation and deactivation with an intermediate conformational state existing on the path from native to denaturated cutinase. This intermediate was clearly detected by an increase in activity and shows only minor conformational changes relative to the native state. At W0 20, the size of the empty water-pool was larger than cutinase and the data was well described by a two-state model for both anionic and cationic reverse micelles. For AOT reverse micelles at W0 20, the intermediate state became a transient state and the deactivation and denaturation were described by a two-state model in which only native and denaturated cutinase were present. For CTAB/1-hexanol reverse micelles at W0 20, the native cutinase was in equilibrium with an intermediate state, which did not suffer denaturation. 1-Hexanol showed a stabilizing effect on cutinase in reverse micelles, contributing to the higher stabilities observed in the cationic CTAB/1-hexanol reverse micelles. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 58:380-386, 1998.
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  • 63
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    Proteins: Structure, Function, and Genetics 30 (1998), S. 34-42 
    ISSN: 0887-3585
    Keywords: allostery ; buried water molecules ; molecular recognition ; Na+ site ; thrombin ; trypsin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Conservation of clusters of buried water molecules is a structural motif present throughout the serine protease family. Frequently, these clusters are shaped as water channels forming extensive hydrogen-bonding networks linked to the protein backbone. The most conspicuous example is the water channel present in the specificity pocket of trypsin and thrombin. In thrombin, other vitamin K-dependent proteases, and some complement factors, Na+ binds in this water channel and enhances allosterically the catalytic activity of the enzyme, whereas digestive and fibrinolytic proteases are devoid of such regulation. A comparative analysis of proteases with and without Na+ binding capability reveals the role of the water channel in maintaining the structural organization of the specificity pocket and in Na+ coordination. This enables the formulation of a molecular mechanism for Na+ binding in thrombin and leads to the identification of the structural changes necessary to engineer a functional Na+ site and enhanced catalytic activity in trypsin and other proteases. Proteins 30:34-42, 1998. © 1998 Wiley-Liss, Inc.
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  • 64
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    Proteins: Structure, Function, and Genetics 30 (1998), S. 43-48 
    ISSN: 0887-3585
    Keywords: molten globule ; α-lactalbumin ; calorimetry ; viscosimetry ; derivative spectroscopy ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Thermal and denaturant-induced transitions of the acid molten globule state of bovine α-lactalbumin (acid [A] state) are analyzed by scanning calorimetry, titration calorimetry, viscosimetry, and derivative spectroscopy. A denaturant-induced heat effect of the A state is shown by a calorimetric difference titration of the A-state versus unfolded (reduced) α-lactalbumin. However, changes of viscosity and derivative spectra do not parallel the heat effect. At thermal denaturation monitored by derivative spectroscopy and scanning microcalorimetry the presence of a gradual transition in α-lactalbumin A state is shown. The results are consistent with the existence of tertiary interactions in the A state and the absence of a cooperative unfolding transition of the molten globule. The results do not support the idea that the molten globule is a third thermodynamic state. Proteins 30:43-48, 1998. © 1998 Wiley-Liss, Inc.
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  • 65
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    Proteins: Structure, Function, and Genetics 30 (1998), S. 61-73 
    ISSN: 0887-3585
    Keywords: xenon ; krypton ; hydrophobic cavity ; protein-ligand binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: X-ray diffraction is used to study the binding of xenon and krypton to a variety of crystallised proteins: porcine pancreatic elastase; subtilisin Carlsberg from Bacillus licheniformis; cutinase from Fusarium solani; collagenase from Hypoderma lineatum; hen egg lysozyme, the lipoamide dehydrogenase domain from the outer membrane protein P64k from Neisseria meningitidis; urate-oxidase from Aspergillus flavus, mosquitocidal δ-endotoxin CytB from Bacillus thuringiensis and the ligand-binding domain of the human nuclear retinoid-X receptor RXR-α. Under gas pressures ranging from 8 to 20 bar, xenon is able to bind to discrete sites in hydrophobic cavities, ligand and substrate binding pockets, and into the pore of channel-like structures. These xenon complexes can be used to map hydrophobic sites in proteins, or as heavy-atom derivatives in the isomorphous replacement method of structure determination. Proteins 30:61-73, 1998. © 1998 Wiley-Liss, Inc.
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  • 66
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    Proteins: Structure, Function, and Genetics 30 (1998), S. 74-85 
    ISSN: 0887-3585
    Keywords: folding and binding ; kinetics ; pepstatin A ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The prediction of binding affinities from structure is a necessary requirement in the development of structure-based molecular design strategies. In this paper, a structural parameterization of the energetics previously developed in this laboratory has been incorporated into a molecular design algorithm aimed at identifying peptide conformations that minimize the Gibbs energy. This approach has been employed in the design of mutants of the aspartic protease inhibitor pepstatin A. The simplest design strategy involves mutation and/or chain length modification of the wild-type peptide inhibitor. The structural parameterization allows evaluation of the contribution of different amino acids to the Gibbs energy in the wild-type structure, and therefore the identification of potential targets for mutation in the original peptide. The structure of the wild-type complex is used as a template to generate families of conformational structures in which specific residues have been mutated. The most probable conformations of the mutated peptides are identified by systematically rotating around the side-chain and backbone torsional angles and calculating the Gibbs potential function of each conformation according to the structural parametrization. The accuracy of this approach has been tested by chemically synthesizing two different mutants of pepstatin A. In one mutant, the alanine at position five has been replaced by a phenylalanine, and in the second one a glutamate has been added at the carboxy terminus of pepstatin A. The thermodynamics of association of pepstatin A and the two mutants have been measured experimentally and the results compared with the predictions. The difference between experimental and predicted Gibbs energies for pepstatin A and the two mutants is 0.23 ± 0.06 kcal/mol. The excellent agreement between experimental and predicted values demonstrates that this approach can be used in the optimization of peptide ligands. Proteins 30:74-85, 1998. © 1998 Wiley-Liss, Inc.
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  • 67
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    Proteins: Structure, Function, and Genetics 30 (1998), S. 100-107 
    ISSN: 0887-3585
    Keywords: cytochrome c oxidase ; proton pump ; oxygen diffusion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cytochrome c oxidase is a redox-driven proton pump, which couples the reduction of oxygen to water to the translocation of protons across the membrane. The recently solved x-ray structures of cytochrome c oxidase permit molecular dynamics simulations of the underlying transport processes. To eventually establish the proton pump mechanism, we investigate the transport of the substrates, oxygen and protons, through the enzyme.   Molecular dynamics simulations of oxygen diffusion through the protein reveal a well-defined pathway to the oxygen-binding site starting at a hydrophobic cavity near the membrane-exposed surface of subunit I, close to the interface to subunit III.   A large number of water sites are predicted within the protein, which could play an essential role for the transfer of protons in cytochrome c oxidase. The water molecules form two channels along which protons can enter from the cytoplasmic (matrix) side of the protein and reach the binuclear center. A possible pumping mechanism is proposed that involves a shuttling motion of a glutamic acid side chain, which could then transfer a proton to a propionate group of heme α3. Proteins 30:100-107, 1998. © 1998 Wiley-Liss, Inc.
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  • 68
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    Proteins: Structure, Function, and Genetics 30 (1998), S. 183-192 
    ISSN: 0887-3585
    Keywords: chemical modification ; fluorescent probe ; site-directed mutagenesis ; cysteine-free protein ; alanine scanning ; enzyme reconstitution ; protein-DNA interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A monomercury derivative of fluoresceine acetate (FMMA) was previously suggested as a specific reagent reacting with only one of four cysteine (Cys) residues in the α subunit of Escherichia coli RNA polymerase. Here, we analyzed the reactivity against FMMA of both isolated α subunit and α subunit assembled in the holoenzyme. In both cases, the highest reactivity was identified for Cys-269 positioned in the regulatory helix of C-terminal domain (CTD) which includes the contact sites for both class-I transcription factors and DNA UP elements. Substitution of Ala for both Cys-269 and Cys-176 completely eliminates the reactivity of α subunit against the fluorescent dye, supporting the prediction that another reactive amino acid under native conformation is Cys-176, which is positioned within or near the region important for α dimerization and its binding of β' subunit. In the isolated α subunit, the reactivity against FMMA is different between these two Cys residues and the order is from Cys-269 to Cys-176. Mutant α-subunits, bearing only one Cys residue at either 269 or 176, could be reconstituted into locally modified and active enzymes. This FMMA modification system may provide a tool suitable for studies of intra- and intermolecular interactions of this subunit. Proteins 30:183-192, 1998. © 1998 Wiley-Liss, Inc.
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  • 69
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    Proteins: Structure, Function, and Genetics 30 (1998), S. 155-167 
    ISSN: 0887-3585
    Keywords: X-ray diffraction ; protein folding ; genetic engineering ; circular permutation ; 1,3-1,4-β-glucanase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The 1,3-1,4-β-glucanases from Bacillus macerans and Bacillus licheniformis, as well as related hybrid enzymes, are stable proteins comprised of one compact jellyroll domain. Their structures are studied in an effort to reveal the degree of redundancy to which the three-dimensional structure of protein domains is encoded by the amino acid sequence. For the hybrid 1,3-1,4-β-glucanase H(A16-M), it could be shown recently that a circular permutation of the sequence giving rise to the variant cpA16M-59 is compatible with wildtype-like enzymatic activity and tertiary structure (Hahn et al., Proc. Natl. Acad. Sci. USA 91:10417-10421, 1994). Since the circular permutation yielding cpA16M-59 mimicks that found in the homologous enzyme from Fibrobacter succinogenes, the question arose whether de novo circular permutations, not guided by molecular evolution of the 1,3-1,4-β-glucanases, could also produce proteins with native-like fold. The circularly permuted variants cpA16M-84, cpA16M-127, and cpA16M-154 were generated by PCR mutagenesis of the gene encoding H(A16-M), synthesized in Escherichia coli and shown to be active in β-glucan hydrolysis. CpA16M-84 and cpA16M-127 were crystallized in space groups P21 and P1, respectively, and their crystal structures were determined at 1.80 and 2.07 Å resolution. In both proteins the main parts of the β-sheet structure remain unaffected by the circular permutation as is evident from a root-mean-square deviation of main chain atoms from the reference structure within the experimental error. The only major structural perturbation occurs near the novel chain termini in a surface loop of cpA16M-84, which becomes destabilized and rearranged. The results of this study are interpreted to show that: (1) several circular permutations in the compact jellyroll domain of the 1,3-1,4-β-glucanases are tolerated without radical change of enzymatic activity or tertiary structure, (2) the three-dimensional structures of simple domains are encoded by the amino acid sequence with sufficient redundancy to tolerate a change in the sequential order of secondary structure elements along the sequence, and (3) the native N-terminal region is not needed to guide the folding polypeptide chain toward its native conformation. Proteins 30:155-167, 1998. © 1998 Wiley-Liss, Inc.
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  • 70
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    Proteins: Structure, Function, and Genetics 30 (1998), S. 193-212 
    ISSN: 0887-3585
    Keywords: secondary structure arrangements ; protein structure database ; left/right topology ; knowledge-based structure prediction ; intrinsic stability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present a fully automatic structural classification of supersecondary structure units, consisting of two hydrogen-bonded β strands, preceded or followed by an α helix. The classification is performed on the spatial arrangement of the secondary structure elements, irrespective of the length and conformation of the intervening loops. The similarity of the arrangements is estimated by a structure alignment procedure that uses as similarity measure the root mean square deviation of superimposed backbone atoms. Applied to a set of 141 well-resolved nonhomologous protein structures, the classification yields 11 families of recurrent arrangements. In addition, fragments that are structurally intermediate between the families are found; they reveal the continuity of the classification. The analysis of the families shows that the α helix and β hairpin axes can adopt virtually all relative orientations, with, however, some preferable orientations; moreover, according to the orientation, preferences in the left/right handedness of the α-β connection are observed. These preferences can be explained by favorable side by side packing of the α helix and the β hairpin, local interactions in the region of the α-β connection or stabilizing environments in the parent protein. Furthermore, fold recognition procedures and structure prediction algorithms coupled to database-derived potentials suggest that the preferable nature of these arrangements does not imply their intrinsic stability. They usually accommodate a large number of sequences, of which only a subset is predicted to stabilize the motif. The motifs predicted as stable could correspond to nuclei formed at the very beginning of the folding process. Proteins 30:193-212, 1998. © 1998 Wiley-Liss, Inc.
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  • 71
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    Proteins: Structure, Function, and Genetics 30 (1998), S. 244-248 
    ISSN: 0887-3585
    Keywords: quasi-chemical ; cost function ; HP model ; Boltzmann statistics ; contact hamiltonian ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We outline a general strategy for determining the effective coarse-grained interactions between the amino acids of a protein from the experimentally derived native-state structures. The method is, in principle, free from any adjustable or empirically determined parameters, and it is tested on simple models and compared with other existing approaches. Proteins 30:244-248, 1998. © 1998 Wiley-Liss, Inc.
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  • 72
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    Proteins: Structure, Function, and Genetics 30 (1998), S. 275-286 
    ISSN: 0887-3585
    Keywords: nucleotide-binding domain ; CFTR ; multidrug resistance ; structure prediction ; P-glycoprotein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: ABC transporters are a large superfamily of integral membrane proteins involved in ATP-dependent transport across biological membranes. Members of this superfamily play roles in a number of phenomena of biomedical interest, including cystic fibrosis (CFTR) and multidrug resistance (P-glycoprotein, MRP). Most ABC transporters are predicted to consist of four domains, two membrane-spanning domains and two cytoplasmic domains. The latter contain conserved nucleotide-binding motifs. Attempts to determine the structure of ABC transporters and of their separate domains are in progress but have not yet been successful.   To aid structure determination and possibly learn more about the domain boundaries, we set out to model nucleotide-binding domains (NBDs) of ABC transporters based on a known structure. Previous attempts to predict the 3D structure of NBDs were based solely on sequence similarity with known nucleotide-binding folds. We have analyzed the sequences of a number of nucleotide-binding domains with the algorithm THREADER, developed by D.T. Jones, and a possible fold was found in the structure of aspartate aminotransferase. We present a model for the N-terminal NBD of CFTR, based on the large domain of the A chain of aspartate aminotransferase. The model is refined using multiple sequence alignment, secondary structure prediction, and 3D-1D profiles. Our model seems to be in good agreement with known properties of nucleotide-binding domains and has some appealing characteristics compared with the previous models. Proteins 30:275-286, 1998. © 1998 Wiley-Liss, Inc.
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  • 73
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    Proteins: Structure, Function, and Genetics 30 (1998), S. 295-308 
    ISSN: 0887-3585
    Keywords: hydrogen exchange mechanism ; denaturants ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Equilibrium amide hydrogen exchange studies of barstar have been carried out at pH 6.7, 32° SDC using one- and two-dimensional nuclear magnetic resonance. An unusually large fraction of the backbone amide hydrogens of barstar exchange too fast to be measured, and the exchange rates of only fifteen slow-exchanging amide sites including indole amides of two tryptophans could be measured in the presence of 0 to 1.8 M guanidine hydrochloride (GdnHCl). Measurement of exchange occurring in tens of seconds in the unfolding transition region was possible by the use of a fast stopped-flow mixing method. The observed exchange rates have been simulated in the EX2 limit according to a two-process model that incorporates two exchange-competent states: a transiently unfolded state (U*) in which many amide hydrogens are completely accessible to solvent-exchange, and a near-native locally unfolded state (N*), in which only one or a few amide hydrogens are completely accessible to solvent-exchange. The two-process model appears to account for the observed exchange behavior over the entire range of GdnHCl concentrations studied. For several measurable slow-exchanging amide hydrogens, the free energies of production of exchange-competent states from the exchange-incompetent native state are significantly higher than the free-energy of production of the equilibrium unfolded state from the native state, when the latter is determined from circular dichroism- or fluorescence-monitored equilibrium unfolding curves. The result implies that U*, which forms transiently in the strongly native-like conditions used for the hydrogen exchange studies, is higher in energy than the equilibrium-unfolded state. The higher energy of this transiently unfolded exchange-competent state can be attributed to either proline isomerization or to the presence of residual structure. On the basis of the free energies of production of exchange-competent states, the measured amide sites of barstar appear to define two structural subdomains - a three-helix unit and a two-β-strand unit in the core of the protein. Proteins 30:295-308, 1998. © 1998 Wiley-Liss, Inc.
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  • 74
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    Proteins: Structure, Function, and Genetics 30 (1998), S. 321-336 
    ISSN: 0887-3585
    Keywords: surface characterization ; DOCK ; structure-based molecular design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The characterization of receptor binding sites is an important aspect of molecular docking, molecular recognition, and the structure-based design process. This characterization can take several forms: the receptor surface itself can be delineated or described, the space adjacent to the surface can be chemically mapped, or a negative image of the protein binding region can be generated. In this report, we describe a new method of constructing a negative image through generation of a set of spheres. These spheres lie along the receptor surface, and their centers represent possible ligand atom positions. By the method in which they are constructed, these spheres carry a limited amount of energetic and chemical information in addition to their primary geometric information. We test the accuracy of the image by comparing sphere positions to the positions of bound ligand atoms and propose a figure of merit for such tests. Then, we use the spheres to orient ligands in enzyme active sites and show how they can be used to generate low scoring configurations more efficiently than other approaches that search orientation space. In addition, two novel applications of these spheres are described: they are used to help identify structural differences among families of enzymes and to suggest points for ligand modification in analog design. Proteins 30:321-336, 1998. © 1998 Wiley-Liss, Inc.
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  • 75
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 33-41 
    ISSN: 0887-3585
    Keywords: ricin structure ; inhibitor design ; energy minimization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Ricin A-chain is an N-glucosidase that attacks ribosomal RNA at a highly conserved adenine residue. Our recent crystallographic studies show that not only adenine and formycin, but also pterin-based rings can bind in the active site of ricin. For a better understanding of the means by which ricin recognizes adenine rings, the geometries and interaction energies were calculated for a number of complexes between ricin and tautomeric modifications of formycin, adenine, pterin, and guanine. These were studied by molecular mechanics, semi-empirical quantum mechanics, and ab initio quantum mechanical methods. The calculations indicate that the formycin ring binds better than adenine and pterin better than formycin, a result that is consistent with the crystallographic data. A tautomer of pterin that is not in the low energy form in either the gas phase or in aqueous solution has the best interaction with the enzyme. The net interaction energy, defined as the interaction energy calculated in vacuo between the receptor and an inhibitor minus the solvation energy of the inhibitor, provides a good prediction of the ability of the inhibitor to bind to the receptor. The results from experimental and molecular modeling work suggest that the ricin binding site is not flexible and may only recognize a limited range of adenine-like rings. Proteins 31:33-41, 1998. Published 1998 Wiley-Liss, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
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  • 76
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 42-60 
    ISSN: 0887-3585
    Keywords: quantum chemistry ; molecular mechanics ; inhibitor ; metalloenzyme complexes ; selectivity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We investigated the binding properties of the metalloprotease inhibitors hydroxamate, methanethiolate, and methylphosphoramidate to a model coordination site occurring in several Zn2+ metalloproteases, including thermolysin. This was carried out using both the SIBFA (sum of interactions between fragments ab initio-computed) molecular mechanics and the SCF/MP2 procedures for the purpose of evaluating SIBFA as a metalloenzyme modeling tool. The energy-minimized structures were closely similar to the X-ray crystallographic structures of related thermolysin-inhibitor complexes. We found that selectivity between alternative geometries and between inhibitors usually stemmed from multiple interaction components included in SIBFA. The binding strength sequence is hydroxamate 〉 methanethiolate ≥ methylphosphoramidate from multiple interaction components included in SIBFA. The trends in interaction energy components, rankings, and preferences for mono- or bidentate binding were consistent in both computational procedures. We also compared the Zn2+ vs. Mg2+ selectivities in several other polycoordinated sites having various “hard” and “soft” qualities. This included a hexahydrate, a model representing Mg2+/Ca2+ binding sites, a chlorophyll-like structure, and a zinc finger model. The latter three favor Zn2+ over Mg2+ by a greater degree than the hydrated state, but the selectivity varies widely according to the ligand “softness.” SIBFA was able to match the ab initio binding energies by 〈2%, with the SIBFA terms representing dispersion and charge-transfer contributing the most to Zn2+/Mg2+ selectivity. These results showed this procedure to be a very capable modeling tool for metalloenzyme problems, in this case giving valuable information about details and limitations of “hard” and “soft” selectivity trends. Proteins 31:42-60, 1998. © 1998 Wiley-Liss, Inc.
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  • 77
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 61-73 
    ISSN: 0887-3585
    Keywords: mutagenesis ; protein stability ; salt bridge ; protein folding ; malic enzyme ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A double mutant (R9E/M17K) of pigeon liver malic enzyme with glutamate and lysine replaced for arginine and methionine at positions 9 and 17, respectively, was found to be much more stable in urea and thermal denaturation, but was enzymatically less active than the wild-type enzyme (WT). Unfolding of the enzyme by urea produced a large red shifting of the protein fluorescence maximum from 320 to 360 nm, which was completely reversible upon dilution. Analysis of the denaturation curves monitored by enzyme activity lost suggested that a putative intermediate was involved in the denaturation process. The half unfolding urea concentration, measured by fluorescence spectral changes, increased from 2.24 M for WT to 3.13 M for R9E/M17K. The melting temperature increased by approximately 10°C for R9E/M17K compared with that for WT. Kinetic analysis of the thermal inactivation at 58°C also conformed to a three-state model with the rate constant for the intermediate state of R9E/M17K (k2 = 0.03 min-1) being much smaller than the WT value (k2= 2.39 min-1). Results obtained from single mutants indicated that the decreasing enzyme activity of R9E/M17K was exclusively due to R9 mutation, which increased the KmMn and KmMal by at least one order of magnitude compared with WT. Consequently, a decrease occurred in the specificity constant [kcat/(KmMnKmNADPKmMal)] for the R9 mutants at least four orders of magnitude smaller than the WT. M17K has similar properties to the WT, while R9E is more labile than the WT enzyme. The above results indicate that the extra stability gained by the double mutant possibly occurs through the introduction of an extra ion-pair between E9 and K17, which freezes the double mutant in the putative intermediate state. Examination of the N-terminal amino acid sequence of pigeon liver malic enzyme reveals that position 15 is also a lysine residue. Since the R9E mutant, which has an extra Glu9-Lys15 ion-pair, is less stable than the WT, we conclude that the contribution to malic enzyme stability is specific for the Glu9-Lys17 ion-pair. Proteins 31:61-73, 1998. © 1998 Wiley-Liss, Inc.
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  • 78
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 74-96 
    ISSN: 0887-3585
    Keywords: Monte Carlo minimizations in torsion space ; prediction of secondary structure ; protein folding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We describe a method for predicting the three-dimensional (3-D) structure of proteins from their sequence alone. The method is based on the electrostatic screening model for the stability of the protein main-chain conformation. The free energy of a protein as a function of its conformation is obtained from the potentials of mean force analysis of high-resolution x-ray protein structures. The free energy function is simple and contains only 44 fitted coefficients. The minimization of the free energy is performed by the torsion space Monte Carlo procedure using the concept of hierarchic condensation. The Monte Carlo minimization procedure is applied to predict the secondary, super-secondary, and native 3-D structures of 12 proteins with 28-110 amino acids. The 3-D structures of the majority of local secondary and super-secondary structures are predicted accurately. This result suggests that control in forming the native-like local structure is distributed along the entire protein sequence. The native 3-D structure is predicted correctly for 3 of 12 proteins composed mainly from the α-helices. The method fails to predict the native 3-D structure of proteins with a predominantly β secondary structure. We suggest that the hierarchic condensation is not an appropriate procedure for simulating the folding of proteins made up primarily from β-strands. The method has been proved accurate in predicting the local secondary and super-secondary structures in the blind ab initio 3-D prediction experiment. Proteins 31:74-96, 1998. © 1998 Wiley-Liss, Inc.
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  • 79
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 104-104 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Buchwald, P., Bodor, N. Octanol-Water Partition of Nonzwitterionic Peptides: Predictive Power of a Molecular Size-Based Model. Proteins 30:86-99, 1998.Equation 2 should read: P = (Cin - Cfin) Vw/Cfin Vo.In the printed version, the volume ratio (Vw/Vo) incorrectly divides, and not multiplies, the concentration ratio.The publisher apologizes for this error.
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  • 80
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 97-103 
    ISSN: 0887-3585
    Keywords: α domains ; β domains ; α/β domains ; α+β domains ; resubstitution ; jackknife ; SCOP database ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Can the coupling effect among different amino acid components be used to improve the prediction of protein structural classes? The answer is yes according to the study by Chou and Zhang (Crit. Rev. Biochem. Mol. Biol. 30:275-349, 1995), but a completely opposite conclusion was drawn by Eisenhaber et al. when using a different dataset constructed by themselves (Proteins 25:169-179, 1996). To resolve such a perplexing problem, predictions were performed by various approaches for the datasets from an objective database, the SCOP database (Murzin, Brenner, Hubbard, and Chothia. J. Mol. Biol. 247:536-540, 1995). According to SCOP, the classification of structural classes for protein domains is based on the evolutionary relationship and on the principles that govern the 3D structure of proteins, and hence is more natural and reliable. The results from both resubstitution tests and jackknife tests indicate that the overall rates of correct prediction by the algorithm incorporated with the coupling effect among different amino acid components are significantly higher than those by the algorithms without using such an effect. It is elucidated through an analysis that the main reasons for Eisenhaber et al. to have reached an opposite conclusion are the result of (1) misusing the component-coupled algorithm, and (2) using a conceptually incorrect rule to classify protein structural classes. The formulation and analysis presented in this article are conducive to clarify these problems, helping correctly to apply the prediction algorithm and interpret the results. Proteins 31:97-103, 1998. © 1998 Wiley-Liss, Inc.
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  • 81
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 107-115 
    ISSN: 0887-3585
    Keywords: calorimetry ; desolvation ; linear extrapolation model ; binding ; denaturation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The effects of urea on protein stability have been studied using a model system in which we have determined the energetics of dissolution of a homologous series of cyclic dipeptides into aqueous urea solutions of varying concentration at 25°C using calorimetry. The data support a model in which urea denatures proteins by decreasing the hydrophobic effect and by directly binding to the amide units via hydrogen bonds. The data indicate also that the enthalpy of amide hydrogen bond formation in water is considerably higher than previously estimated. Previous estimates included the contribution of hydrophobic transfer of the α-carbon resulting in an overestimate of the binding between urea and the amide unit of the backbone and an underestimate of the binding enthalpy. Proteins 31:107-115, 1998. © 1998 Wiley-Liss, Inc.
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  • 82
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 116-127 
    ISSN: 0887-3585
    Keywords: molecular dynamics ; X-ray crystallography ; essential dynamics ; lysozyme ; hinge bending ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A comparison of a series of extended molecular dynamics (MD) simulations of bacteriophage T4 lysozyme in solvent with X-ray data is presented. Essential dynamics analyses were used to derive collective fluctuations from both the simulated trajectories and a distribution of crystallographic conformations. In both cases the main collective fluctuations describe domain motions. The protein consists of an N- and C-terminal domain connected by a long helix. The analysis of the distribution of crystallographic conformations reveals that the N-terminal helix rotates together with either of these two domains. The main domain fluctuation describes a closure mode of the two domains in which the N-terminal helix rotates concertedly with the C-terminal domain, while the domain fluctuation with second largest amplitude corresponds to a twisting mode of the two domains, with the N-terminal helix rotating concertedly with the N-terminal domain. For the closure mode, the difference in hinge-bending angle between the most open and most closed X-ray structure along this mode is 49 degrees. In the MD simulation that shows the largest fluctuation along this mode, a rotation of 45 degrees was observed. Although the twisting mode has much less freedom than the closure mode in the distribution of crystallographic conformations, experimental results suggest that it might be functionally important. Interestingly, the twisting mode is sampled more extensively in all MD simulations than it is in the distribution of X-ray conformations. Proteins 31:116-127, 1998. © 1998 Wiley-Liss, Inc.
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  • 83
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 172-185 
    ISSN: 0887-3585
    Keywords: sequence-to-structure correlation ; contact environment ; contact prediction ; Bayesian classification ; cluster analysis ; nearest-neighbor classification ; decision tree classification ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The identification of correlations between sequence patterns and structural motifs is a prerequisite in the development of protein structure prediction methods. The prediction accuracy indicates whether these correlations are discerned. We present an approach to identify long-range relationships between sequence patterns and structural motifs by varying the granulation of the structure description. Since interaction among residues is a major determinant in protein folding, we consider contact environments formed by two triplets of three sequentially neighboring residues and described by vectors whose components express contact strengths on an atomic level. Through testing various classification schemes, including their resolution and optimizing parameters, discernible relationships between sequences and folds are explored. About ten structural contact states, together with information from noncontacting regions, could improve the accuracy of contact prediction. Proteins 31:172-185, 1998. © 1998 Wiley-Liss, Inc.
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  • 84
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    Keywords: lipid binding ; lipid transfer protein ; maize ; molecular modeling ; NMR ; X-ray ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The three-dimensional solution structure of maize nonspecific lipid transfer protein (nsLTP) obtained by nuclear magnetic resonance (NMR) is compared to the X-ray structure. Although both structures are very similar, some local structural differences are observed in the first and the fourth helices and in several side-chain conformations. These discrepancies arise partly from intermolecular contacts in the crystal lattice. The main characteristic of nsLTP structures is the presence of an internal hydrophobic cavity whose volume was found to vary from 237 to 513 Å3 without major variations in the 15 solution structures. Comparison of crystal and NMR structures shows the existence of another small hollow at the periphery of the protein containing a water molecule in the X-ray structure, which could play an important structural role. A model of the complexed form of maize nsLTP by α-lysopalmitoylphosphatidylcholine was built by docking the lipid inside the protein cavity of the NMR structure. The main structural feature is a hydrogen bond found also in the X-ray structure of the complex maize nsLTP/palmitate between the hydroxyl of Tyr81 and the carbonyl of the lipid. Comparison of 12 primary sequences of nsLTPs emphasizes that all residues delineating the cavities calculated on solution and X-ray structures are conserved, which suggests that this large cavity is a common feature of all compared plant nsLTPs. Furthermore several conserved basic residues seem to be involved in the stabilization of the protein architecture. Proteins 31:160-171, 1998. © 1998 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 33 (1998), S. 38-49 
    ISSN: 0887-3585
    Keywords: MS/MS electrospray mass spectrometry ; CD ; human immunodeficiency virus (HIV) ; glycoprotein 41,000 (gp41) ; N-terminal domain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The N-terminal domain of human immunodeficiency virus (HIV)-1 glycoprotein 41,000 (FP; residues 1-23; NH2-AVGIGALFLGFLGAAGSTMGARS-CONH2) is involved in the fusion and cytolytic processes underlying viral-cell infection. Here, we use circular dichroism (CD) spectroscopy, along with electrospray ionization (ESI) mass spectrometry and tandem (MS/MS) mass spectrometry during the course of hydrogen/deuterium exchange, to probe the local conformations of this synthetic peptide in two membrane mimics. Since amino acids that participate in defined secondary structure (i.e., α-helix or β-sheet) exchange amido hydrogens more slowly than residues in random structures, deuterium exchange was combined with CD spectroscopy to map conformations to specific residues. For FP suspended in the highly structure-promoting solvent hexafluoroisopropanol (HFIP), CD spectra indicated high α-helix and disordered structures, whereas ESI and MS/MS mass spectrometry indicated that residues 5-15 were α-helical and 16-23 were disordered. For FP suspended in the less structure-promoting solvent trifluoroethanol (TFE), CD spectra showed lower α-helix, with ESI and MS/MS mass spectrometry indicating that only residues 9-15 participated in the α-helix. These results compare favorably with previous two-dimensional nuclear magnetic resonance studies on the same peptide. Proteins Suppl. 2:38-49, 1998. © 1998 Wiley-Liss, Inc.
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  • 86
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    Keywords: MALDI mass spectrometric peptide mapping ; membrane proteins ; in situ gel digestion ; porin ; permeability transition ; noncovalent complexes ; protein interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Mass spectrometric peptide mapping, particularly by matrix-assisted laser desorption-ionization (MALDI-MS), has recently been shown to be an efficient tool for the primary structure characterization of proteins. In combination with in situ proteolytic digestion of proteins separated by one- and two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), mass spectrometric peptide mapping permits identification of proteins from complex mixtures such as cell lysates. In this study we have investigated several ion channel membrane proteins (porins) and their supramolecular assembly in mitochondrial membranes by peptide mapping in solution and upon digestion in the gel matrix. Porins are integral membrane proteins serving as nonspecific diffusion pores or as specific systems for the transport of substrates through bacterial and mitochondrial membranes. The well-characterized porin from Rhodobacter capsulatus (R.c.-porin) has been found to be a native trimeric complex by the crystal structure and was used as a model system in this study. R.c.-porin was characterized by MALDI-MS peptide mapping in solution, and by direct in situ-gel digestion of the trimer. Furthermore, in this study we demonstrate the direct identification of the noncovalent complex between a mitochondrial porin and the adenine nucleotide translocator from rat liver, by MALDI-MS determination of the specific peptides due to both protein sequences in the SDS-PAGE gel band. The combination of native gel electrophoresis and mass spectrometric peptide mapping of the specific gel bands should be developed as a powerful tool for the molecular identification of protein interactions. Proteins Suppl. 2:63-73, 1998. © 1998 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 282-298 
    ISSN: 0887-3585
    Keywords: diphtheria toxin ; docking ; ligand design ; molecular recognition ; NAD ; pertussis toxin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We describe a novel application of a fragment-based ligand docking technique; similar methods are commonly applied to the de novo design of ligands for target protein binding sites. We have used several new flexible docking and superposition tools, as well as a more conventional rigid-body (fragment) docking method, to examine NAD binding to the catalytic subunits of diphtheria (DT) and pertussis (PT) toxins, and to propose a model of the NAD-PT complex. Docking simulations with the rigid NAD fragments adenine and nicotinamide revealed that the low-energy dockings clustered in three distinct sites on the two proteins. Two of the sites were common to both fragments and were related to the structure of NAD bound to DT in an obvious way; however, the adenine subsite of PT was shifted relative to that of DT. We chose adenine/nicotinamide pairs of PT dockings from these clusters and flexibly superimposed NAD onto these pairs. A Monte Carlo-based flexible docking procedure and energy minimization were used to refine the modeled NAD-PT complexes. The modeled complex accounts for the sequence and structural similarities between PT and DT and is consistent with many results that suggest the catalytic importance of certain residues. A possible functional role for the structural difference between the two complexes is discussed. Proteins 31:282-298, 1998. © 1998 Wiley-Liss, Inc.
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  • 88
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 299-308 
    ISSN: 0887-3585
    Keywords: quasi-chemical approximation ; statistical potential ; energy landscape ; glass transition ; threading ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In this study, we exploited an elementary 2-dimensional square lattice model of HP polymers to test the premise of extracting contact energies from protein structures. Given a set of prespecified energies for H-H, H-P, and P-P contacts, all possible sequences of various lengths were exhaustively enumerated to find sequences that have unique lowest-energy conformations. The lowest-energy structures (or native structures) of such (native) sequences were used to extract contact energies using the Miyazawa-Jernigan procedure and here-defined reference state. The relative magnitudes of the original energies were restored reasonably well, but the extracted contact energies were independent of the absolute magnitudes of the initial energies. We turned to a more detailed characterization of the energy landscapes of the native sequences in light of a new theoretical framework on protein folding. Foldability of such sequences imposes two limits on the absolute value of the prespecified energies: a lower bound entailed by the minimum requirement for thermodynamic stability and an upper bound associated with the entrapment of the chain to local minima. We found that these two limits confine the prespecified energy values to a rather narrow range which, surprisingly, also contains the extracted energies in all the cases examined. These results indicate that the quasi-chemical approximation can be used to connect quantitatively the occurrence of various residue-residue contacts in an ensemble of native structures with the energies of the contacts. More importantly, they suggest that the extracted contact energies do contain information on structural stability and can be used to estimate actual structural energetics. This study also encourages the use of structure-derived contact energies in threading. The finding that there is a rather narrow range of energies that are optimal for folding a sequence also cautions the use of arbitrary energy Hamiltonion in minimal folding models. Proteins 31:299-308, 1998. © 1998 Wiley-Liss, Inc.
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 309-319 
    ISSN: 0887-3585
    Keywords: tyrosine kinase ; protein stability ; differential scanning calorimetry ; CD-spectroscopy ; Sso7d ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The thermal unfolding of three SH3 domains of the Tec family of tyrosine kinases was studied by differential scanning calorimetry and CD spectroscopy. The unfolding transition of the three protein domains in the acidic pH region can be described as a reversible two-state process. For all three SH3 domains maximum stability was observed in the pH region 4.5 〈 pH 〈 7.0 where these domains unfold at temperatures of 353K (Btk), 342K (Itk), and 344K (Tec). At these temperatures an enthalpy change of 196 kJ/mol, 178 kJ/mol, and 169 kJ/mol was measured for Btk-, Itk-, and Tec-SH3 domains, respectively. The determined changes in heat capacity between the native and the denatured state are in an usual range expected for small proteins. Our analysis revealed that all SH3 domains studied are only weakly stabilized and have free energies of unfolding which do not exceed 12-16 kJ/mol but show quite high melting temperatures.Comparing unfolding free energies measured for eukaryotic SH3 domains with those of the topologically identical Sso7d protein from the hyperthermophile Sulfolobus solfataricus, the increased melting temperature of the thermostable protein is due to a broadening as well as a significant lifting of its stability curve. However, at their physiological temperatures, 310K for mesophilic SH3 domains and 350K for Sso7d, eukaryotic SH3 domains and Sso7d show very similar stabilities. Proteins 31:309-319, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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  • 90
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 320-333 
    ISSN: 0887-3585
    Keywords: cutinase ; crystal polymorphism ; packing contacts ; hydrophobicity ; electrostatic and hydrophobic interactions ; protein-accessible surface ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: During the characterization of mutants and covalently inhibited complexes of Fusarium solani cutinase, nine different crystal forms have been obtained so far. Protein mutants with a different surface charge distribution form new intermolecular salt bridges or long-range electrostatic interactions that are accompanied by a change in the crystal packing. The whole protein surface is involved in the packing contacts and the hydrophobicities of the protein surfaces in mutual contact turned out to be noncorrelated, which indicates that the packing interactions are nonspecific. In the case of the hydrophobic variants, the packing contacts showed some specificity, as the protein in the crystal tends to form either crystallographic or noncrystallographic dimers, which shield the hydrophobic surface from the solvent. The likelihood of surface atoms to be involved in a crystal contact is the same for both polar and nonpolar atoms. However, when taking areas in the 200-600 Å2 range, instead of individual atoms, the either highly hydrophobic or highly polar surface regions were found to have an increased probability of establishing crystal lattice contacts. The protein surface surrounding the active-site crevice of cutinase constitutes a large hydrophobic area that is involved in packing contacts in all the various crystalline contexts. Proteins 31:320-333, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
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  • 91
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 335-344 
    ISSN: 0887-3585
    Keywords: conformational transition ; protein folding ; lattice simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: This study focuses on the phenomenon of kinetic partitioning when a polypeptide chain has two ground-state conformations, one of which is kinetically more reachable than the other. We designed sequences for lattice model proteins with two different conformations of equal energy corresponding to the global energy minimum. Folding simulations revealed that one of these conformations was indeed much more kinetically accessible than the other. We found that the number and strength of local contacts in the ground-state conformation are the major factors that determine which conformation is reached faster; the greater the number of local contacts, the more kinetically reachable a conformation is. We present simple statistical-mechanical arguments to explain these findings. Our results may be relevant in explaining the phenomenology of such proteins as human plasminogen activator inhibitor-1 (PAI-1), photosystem II, and prions. Proteins 31:335-344, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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  • 92
    ISSN: 0887-3585
    Keywords: DEX gene ; dextranase ; protein threading ; structure prediction ; circular dichroism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The DEX gene encodes an extracellular dextranase (EC 3.2.1.11); this enzyme hydrolyzes the α(1,6) glucosidic bond contained in dextran to release small isomaltosaccharides. Sequence analysis has revealed only one homologous sequence, CB-8 protein, from Arthrobacter sp., with 30% sequence identity. The secondary structure prediction for Dex was corroborated by circular dichroism measurements. To explore the possibility that Dex protein might adopt a fold similar to any known structure, we conducted a threading search of a three-dimensional structure database. This search revealed that the Dex sequence is compatible with the galactose oxidase/methanol dehydrogenase/sialidase fold. A structural model of Dex based on these results is physically and biologically plausible and leads to testable predictions, including the prediction that Asp246 and Glu299 might be catalytic residues. Also, according to this model the Dex enzyme has a mechanism of hydrolysis with net inversion of anomeric configuration. Proteins 31:345-354, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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  • 93
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 355-369 
    ISSN: 0887-3585
    Keywords: homology modeling ; database searching ; conserved torsional angles ; prediction of sidechain conformations ; homologous families of proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We investigated the conservation of sidechain conformation for each residue within a homologous family of proteins in the Protein Data Bank (PDB) and performed sidechain modeling using this information. The information was represented by the probability of conserved sidechain torsional angles obtained from many families of proteins, and these were calculated for a pair of residues at topologically equivalent positions as a result of structural alignment. Probabilities were obtained for a pair of same amino acids and for a pair of different amino acids. The correlation between environmental residues and the fluctuation of probability was examined for the pair of same amino acid residues, and the simple probability was calculated for the pair of different amino acids. From the results on the same amino acid pairs, 17 amino acids, except for Ala, Gly, and Pro, were divided into two types: those that were influenced and those that were not influenced by the environmental residues. From results on different amino acid pairs, a replacement between large residues, such as Trp, Phe, and Tyr, was performed assuming conservation of their torsional angles within a homologous family of proteins. We performed sidechain modeling for 11 known proteins from their native and modeled backbones, respectively. With the native backbones, the percentage of the χ1 angle correct within 30° was found to be 67% and 80% for all and core residues, respectively. With the modeled backbones, the percentage of the correct χ1 angle was found to be 60% and 72% for all and core residues, respectively. To estimate an upper limit on the accuracy for predicting sidechain conformations, we investigated the probability of conserved sidechain torsional angles for highly similar proteins having 〉 90% sequence identity and 〈2.5-Å X-ray resolution. In those proteins, 83% of the sidechain conformations were conserved for the χ1 angle. Proteins 31:355-369, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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  • 94
    ISSN: 0887-3585
    Keywords: complement control protein ; protein modeling ; blood coagulation ; C4b-binding protein ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: C4b-binding protein (C4BP) contributes to the regulation of the classical pathway of the complement system and plays an important role in blood coagulation. The main human C4BP isoform is composed of one β-chain and seven α-chains essentially built from three and eight complement control protein (CCP) modules, respectively, followed by a nonrepeat carboxy-terminal region involved in polymerization of the chains. C4BP is known to interact with heparin, C4b, complement factor I, serum amyloid P component, streptococcal Arp and Sir proteins, and factor VIII/VIIIa via its α-chains and with protein S through its β-chain. The principal aim of the present study was to localize regions of C4BP involved in the interaction with C4b, Arp, and heparin. For this purpose, a computer model of the 8 CCP modules of C4BP α-chain was constructed, taking into account data from previous electron microscopy (EM) studies. This structure was investigated in the context of known and/or new experimental data. Analysis of the α-chain model, together with monoclonal antibody studies and heparin binding experiments, suggests that a patch of positively charged residues, at the interface between the first and second CCP modules, plays an important role in the interaction between C4BP and C4b/Arp/Sir/heparin. Putative binding sites, secondary-structure prediction for the central core, and an overall reevaluation of the size of the C4BP molecule are also presented. An understanding of these intermolecular interactions should contribute to the rational design of potential therapeutic agents aiming at interfering specifically some of these protein-protein interactions. Proteins 31:391-405, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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  • 95
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 406-416 
    ISSN: 0887-3585
    Keywords: electrostatics ; Brownian dynamics ; triose phosphate isomerase ; diffusion-control ; similarity index ; rate enhancement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Triose phosphate isomerase (TIM) is a diffusion-controlled enzyme whose rate is limited by the diffusional encounter of the negatively charged substrate glyceraldehyde 3-phosphate (GAP) with the homodimeric enzyme's active sites. Translational and orientational steering of GAP toward the active sites by the electrostatic field of chicken muscle TIM has been observed in previous Brownian dynamics (BD) simulations. Here we report simulations of the association of GAP with TIMs from four species with net charges at pH 7 varying from -12e to +12e. Computed second-order rate constants are in good agreement with experimental data. The BD simulations and computation of average Boltzmann factors of substrate-protein interaction energies show that the protein electrostatic potential enhances the rates for all the enzymes. There is much less variation in the computed rates than might be expected on the basis of the net charges. Comparison of the electrostatic potentials by means of similarity indices shows that this is due to conservation of the local electrostatic potentials around the active sites which are the primary determinants of electrostatic steering of the substrate. Proteins 31:406-416, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
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  • 96
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 434-444 
    ISSN: 0887-3585
    Keywords: hinge ; structural change ; xylose ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Recent crystallographic studies have revealed a range of structural changes in the three-dimensional structure of endo-1,4-xylanase (XYNII) from Trichoderma reesei. The observed conformational changes can be described as snapshots of an open-close movement of the active site of XYNII. These structures were further analyzed in this study. In addition, a total of four 1 ns molecular dynamics (MD) simulations were performed representing different states of the enzyme. A comparison of the global and local changes found in the X-ray structures and the MD runs suggested that the simulations reproduced a similar kind of active site opening and closing as predicted by the crystal structures. The open-close movement was characterized by the use of distance difference matrixes and the Hingefind program (Wriggers and Schulten, Proteins 29:1-14, 1997) to be a ‘hinge-bending’ motion involving two large rigidly-moving regions and an extended hinge. This conformational feature is probably inherent to this molecular architecture and probably plays a role in the function of XYNII. Proteins 31:434-444, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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  • 97
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 417-433 
    ISSN: 0887-3585
    Keywords: molecular dynamics ; sex-determining region Y (SRY) protein ; high mobility group (HMG) box ; DNA-binding proteins ; DNA bending ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular dynamics simulations have been conducted to study the interaction of human sex-determining region Y (hSRY) protein with DNA. For this purpose, simulations of the hSRY high mobility group (HMG) domain (hSRY-HMG) with and without its DNA target site, a DNA octamer, and the DNA octamer alone have been carried out, employing the NMR solution structure of hSRY-HMG-DNA complex as a starting model. Analyses of the simulation results demonstrated that the interaction between hSRY and DNA was hydrophobic, just a few hydrogen bonds and only one water molecule as hydrogen-bonding bridge were observed at the protein-DNA interface. These two hydrophobic cores in the hSRY-HMG domain were the physical basis of hSRY-HMG-DNA specific interaction. They not only maintained the stability of the complex, but also primarily caused the DNA deformation. The salt bridges formed between the positive-charged residues of hSRY and phosphate groups of DNA made the phosphate electroneutral, which was advantageous for the deformation of DNA and the formation of a stable complex. We predicted the structure of hSRY-HMG domain in the free state and found that both hSRY and DNA changed their conformations to achieve greater complementarity of geometries and properties during the binding process; that is, the protein increased the angle between its long and short arms to accommodate the DNA, and the DNA became bent severely to adapt to the protein, although the conformational change of DNA was more severe than that of the hSRY-HMG domain. The sequence specificity and the role of residue Met9 are also discussed. Proteins 31:417-433, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 12 Ill.
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  • 98
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 453-459 
    ISSN: 0887-3585
    Keywords: quantum mechanical calculations ; substrate-enzyme interactions ; mutants ; functional role of amino acids ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The enzyme herpes simplex virus type 1 thymidine kinase (HSV1 TK) salvages thymidine into the DNA metabolism of the virus. In the active site, the thymine ring of the nucleoside binds in a pocket, formed by two residues, Tyr-172 and Met-128, in a sandwich-type orientation. To investigate the nature of the thymine-enzyme pocket interactions, we have carried out density functional theory calculations with gradient-corrected exchange-correlation functionals of models of the thymine-HSV1 TK adduct. Our calculations indicate that the role of Met-128 in the substrate fixation is purely steric and hydrophobic, while the substrate-Tyr-172 interaction is essentially electrostatic in nature. These findings are completely consistent with the available catalytic properties of mutants on the 128 position. Proteins 31:453-459, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
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  • 99
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    Proteins: Structure, Function, and Genetics 31 (1998), S. 445-452 
    ISSN: 0887-3585
    Keywords: chorismate mutase ; activity ; allosteric ; electrostatics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The predicted active site of chorismate mutase of baker's yeast Saccharomyces cerevisiae has been studied by continuum electrostatics, molecular surface/volume calculations, and molecular modeling. Our study shows that despite being subject to an allosteric transition, the enzyme's active-site pocket neither decreased in volume nor deformed significantly in shape between the active R state and the inactive T state. We find that the polar atmosphere in the pocket is responsible for the enzyme's affinity. A single amino acid, Glu23, can adequately account for the atmospheric variation. This residue swings into the active-site pocket from the R state to the T state. In the R state, Glu23 on helix H2 doubly pairs with Arg204 and Lys208 of H11, which is packed against H2. In the T state, a slide occurs between H11 and H2 such that Glu23 can no longer interact with Lys208 and competes with Asp24 for interacting with Arg204. Consequently, Glu23 is found in the T state to couple with Arg157, an active-site residue critical to substrate binding. The tandem sliding of H11 in both monomers profoundly changes the interactions in the dimer interface. The loop between H11 and H12 demonstrates the largest conformational change. Hence, we establish a connection between the allosteric transition and the activity of the enzyme. The conformational change in the transition is suggested to propagate into the active-site pocket via a series of polar interactions that result in polarity reversal in the active-site pocket, which regulates the enzyme's activity. Proteins 31:445-452, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
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  • 100
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    Proteins: Structure, Function, and Genetics 32 (1998), S. 1-2 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
    Type of Medium: Electronic Resource
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