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  • 1995-1999  (1,203)
  • 1970-1974
  • 1996  (1,203)
  • Biochemistry and Biotechnology  (1,203)
  • Nuclear reactions
  • 1
    Electronic Resource
    Electronic Resource
    Ion exchange purification of G6PDH from unclarified yeast cell homogenates using expanded bed adsorption (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 204-216 
    Details
    ISSN: 0006-3592
    Keywords: expanded bed adsorption ; bakers' yeast ; G6PDH ; STREAMLINE ion exchange adsorbents ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The use of expanded beds of STREAMLINE ion exchange adsorbents for the direct extraction of an intracellular enzyme glucose-6-phosphate dehydrogenase (G6PDH) from unclarified yeast cell homogenates has been investigated. It has been demonstrated that such crude feedstocks can be applied to the bed without prior clarification steps. The purification of G6PDH from an unclarified yeast homogenate was chosen as a model system containing the typical features of a direct extraction technique. Optimal conditions for the purification were determined in small scale, packed bed experiments conducted with clarified homogenates. Results from these experiments were used to develop a preparative scale separation of G6PDH in a STREAMLINE 50 EBA apparatus. The use of an on-line rotameter for measuring and controlling the height of the expanded bed when operated in highly turbid feedstocks was demonstrated. STREAMLINE DEAE has been shown to be successful in achieving isolation of G6PDH from an unclarified homogenate with a purification factor of 12 and yield of 98% in a single step process. This ion exchange adsorbent is readily cleaned using simple cleaning-in-place procedures without affecting either adsorption or the bed expansion properties of the adsorbent after many cycles of operation. The ability of combining clarification, capture, and purification in a single step will greatly simplify downstream processing flowsheets and reduce the costs of protein purification. © 1996 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    Rat hepatocyte morphology and function on lactose-derivatized polystyrene surfaces (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 259-265 
    Details
    ISSN: 0006-3592
    Keywords: hepatocytes ; lactose-derivatized polystyrene ; polystyrene ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Hepatocytes isolated from male Fisher 344VF rats were cultured on two substrates, collagen I and a lactose-derivatized polystyrene (PS-lactose), to compare morphological and functional differences. Hepatocyte morphology changed dramatically depending upon the substrate, shown through actin cytoskeletal staining and scanning electron microscopy. Functional assays performed included albumin secretion, reduced glutathione content, UDP-glucuronosyl transferase, and cytochrome P4501A1 activity. The presence of dexamethasone and dimethylsulfoxide (DMSO) in the media was required for the maintenance of several differentiated functions for cells cultured on collagen. In general, cells cultured on the PS-lactose substrate showed a much slower loss of function over the same period of time. The maintenance of differentiated function of cells on PS-lactose was enhanced with the addition of dexamethasone and DMSO. This is the first report of a culture system in which hepatocytes, cultured on a polymer substrate without additional protein coatings or media additives, have been able to maintain differentiated functions for up to 1 week. © 1996 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    Conservative chemical modification of proteins to study the effects of a single protein property on partitioning in aqueous two-phase systems (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 290-299 
    Details
    ISSN: 0006-3592
    Keywords: proteins, modified ; partitioning in aqueous system ; thaumatin ; β-lactoglobulin ; BSA ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Relatively conservative modifications of three proteins were carried out to alter their surface properties. The protein properties modified were hydrophobicity and charge. This was done by acylation of amino groups with anhydrides. For the hydrophobic modification experiments, two proteins (β-lactoglobulin and bovine serum albumin [BSA]) and four anhydrides (hexanoic, butyric, succinic, acetic) were used. For the modification of surface charge the protein thaumatin was selected and various proportions of the free amino groups were blocked with acetic anhydride to give a series of proteins with differing isoelectric points. Detailed characterization and purification of selected modified proteins was carried out including molecular weight measurements and conformational analysis. The criteria used for selecting the modified proteins for subsequent investigation of their partitioning in aqueous two-phase systems (ATPS) is described. With a judicious choice of starting material it was found that limited chemical modifications to proteins could effectively alter surface hydrophobicity or charge almost independently, with little effect on other molecular properties. It appears, however, that the method for chemical modification and the reaction conditions must also be carefully controlled. © 1996 John Wiley & Sons, Inc.
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  • 4
    Electronic Resource
    Electronic Resource
    Use of chemically modified proteins to study the effect of a single protein property on partitioning in aqueous two-phase systems: Effect of surface charge (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 309-315 
    Details
    ISSN: 0006-3592
    Keywords: surface charge ; proteins, modified ; partitioning in aqueous system ; thaumatin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A series of charge-modified thaumatins with different values of surface charge were partitioned in aqueous two-phase systems (ATPS) to study the effect of surface charge as a single property on partitioning. Electrophoretic mobility of the proteins in titration curves was used as a measure of surface charge. Four modified proteins derived from thaumatin with the following values of isoelectric point: 8.70, 8.15, 5.60, and 4.50 were used for partitioning. The resolution of the systems in terms of protein surface charge was calculated. Partitioning of modified thaumatins in PEG 4000/dextran systems with phosphate buffer, Tris buffer, NaCl, KCl, and sulfate salts was carried out. Among the sulfate salts tested, the addition of 50 mM Li2SO4 to the system buffered with phosphate gave the highest value of resolution for differences in surface protein charge (RSPC). It shows a decrease in the value of K (partition coefficient) with an increase in the protein's charge. The addition of 100 mM KCl to the system promoted the opposite effect on the RSPC value. Charge-modified proteins were partitioned in PEG/salt systems to investigate the ability of these systems for resolving differences in surface charge. The PEG/citrate system seemed to have almost no ability for resolving proteins on the basis of surface charge differences; PEG/phosphate systems had some capability for resolving differently charged proteins. The more negative proteins tended to have higher values of K than the more positively charged fractions. The use of charge-modified proteins allowed the investigation of the effect of protein surface charge on partitioning in aqueous two-phase systems independently from other protein parameters as they were prepared from a common parent protein thaumatin. This technique provides an interesting novel tool to investigate the effect of protein surface charge on partitioning in ATPS taking protein charge as an independent parameter. © 1996 John Wiley & Sons, Inc.
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  • 5
    Electronic Resource
    Electronic Resource
    A versatile oxygenator and perfusion system for magnetic resonance studies (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 348-354 
    Details
    ISSN: 0006-3592
    Keywords: oxygenator ; NMR spectroscopy ; organ perfusion ; mammalian cell culture ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A compact, reusable membrane oxygenator has been constructed for the perfusion of cultured cells and isolated organs. While the oxygenator was designed to be compatible with nuclear magnetic resonance (NMR) spectroscopy studies, it can also be used for any experiment which requires warming and oxygenation of perfusates. For the NMR studies, the oxygenator can be positioned at the opening of the magnet bore which allows oxygenation and warming of the perfusate immediately prior to delivery to the tissue, therefore eliminating problems with heat or oxygen loss which may occur with the long perfusion lines. © 1996 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/bit.260490302
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  • 6
    Electronic Resource
    Electronic Resource
    Fluid shear stress induction of the transcriptional activator c-fos in human and bovine endothelial cells, HeLa, and Chinese hamster ovary cells (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 383-390 
    Details
    ISSN: 0006-3592
    Keywords: c-fos protein ; endothelium ; hemodynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The c-fos protein belongs to a family of transcriptional cofactors that can complex with proteins of the Jun family and activate mRNA transcription from gene promoters containing an activator protein 1 (AP-1) binding element. The shear stress inducibility of the c-fos protein was studied in human and animal cell lines of vastly different origins. Primary human umbilical vein endothelial cells (HUVEC), bovine aortic endothelial cells (BAEC, passage 2-14), HeLa cells, and Chinese hamster ovary (CHO) cells were subjected to steady laminar shear stress using a parallel plate flow apparatus. After 1 h of flow exposure at 25 dyn/cm2, the c-fos levels in nuclei of shear stress HUVEC, BAEC, HeLa, and CHO were 5.4 ± 2.0 (n = 3), 2.25 ± 1.38 (n = 6), 2.14 ± 0.07 (n = 8), 1.92 ± 0.58 (n = 2) times higher, respectively, than in matched stationary controls. Flow exposure at 4 dyn/cm2 caused no enhancement of c-fos levels in any of the cell lines tested, but caused significant reduction in c-fos expression in the HeLa cells. The c-fos induction by shear stress could be blocked by pharmacological agents. For example, the flow induction of the c-fos protein levels was blocked by 50% with the preincubation of HUVEC with a protein kinase C inhibitor, H7 (10 μM) and blocked completely in HeLa cells preincubated with the phospholipase C inhibitor, neomycin (5 mM). The minimum time of shear stress exposure required to induce the c-fos protein expression in HeLa cells was found to be as low as 1 min. By Northern analysis, the c-fos mRNA levels were found to be elevated in BAEC, CHO, and HeLa cells exposed to 25 dyn/cm2 for 30 min. These studies indicate that c-fos induction is a consistent genetic response in a variety of mammalian cells that may alter cellular phenotype in mechanical environments. © 1996 John Wiley & Sons, Inc.
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  • 7
    Electronic Resource
    Electronic Resource
    Vancomycin production in batch and continuous culture (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 412-420 
    Details
    ISSN: 0006-3592
    Keywords: Amycolatopsis orientalis ; vancomycin production ; chemostat culture ; phosphate inhibition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Production of the glycopeptide antibiotic vancomycin by two Amycolatopsis orientalis strains was examined in batch shake flask culture in a semidefined medium with peptone as the nitrogen source. Different growth and production profiles were observed with the two strains; specific production (Yp/x) was threefold higher with strain ATCC 19795 than with strain NCIMB 12945. A defined medium with amino acids as the nitrogen source was developed by use of the Plackett-Burman statistical screening method. This technique identified certain amino acids (glycine, phenylalanine, tyrosine, and arginine) that gave significant increased specific production, whereas phosphate was identified as inhibitory for high specific vancomycin production. Experiments made with the improved medium and strain ATCC 19795 showed that vancomycin production kinetics were either growth dissociated or growth associated, depending on the amino acid concentration. In chemostat culture at a constant dilution rate (0.087 h-1), specific vancomycin production rate (qvancomycin) decreased linearly as the medium phosphate concentration was increased from 2 to 8 mM. In both phosphate and glucose limited chemostats, qvancomycin was a function of specific growth rate; the maximum value was observed at D = 0.087 h-1 (52% of the maximum specific growth rate). Under phosphate limited growth conditions, qvancomycin was threefold higher (0.37 mg/g dry weight/h) than under glucose limitation (0.12 mg/g dry weight/h). © 1996 John Wiley & Sons, Inc.
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  • 8
    Electronic Resource
    Electronic Resource
    On-line monitoring of respiration in recombinant-baculovirus infected and uninfected insect cell bioreactor cultures (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 36-48 
    Details
    ISSN: 0006-3592
    Keywords: insect cell culture ; Sf-9 cells ; respiration ; bioreactor ; on-line monitoring ; baculovirus expression vector system ; recombinant proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Respiration rates in Spodoptera frugiperda (Sf-9) cell bioreactor cultures were successfully measured on-line using two methods: The O2 uptake rate (OUR) was determined using gas phase pO2 values imposed by a dissolved oxygen controller and the CO2 evolution rate (CER) was measured using an infrared detector. The measurement methods were accurate, reliable, and relatively inexpensive. The CER was routinely determined in bioreactor cultures used for the production of several recombinant proteins. Simple linear relationships between viable cell densities and both OUR and CER in exponentially growing cultures were used to predict viable cell density. Respiration measurements were also used to follow the progress of baculoviral infections in Sf-9 cultures. Infection led to increases in volumetric and per-cell respiration rates. The relationships between respiration and several other culture parameters, including viable cell density, cell protein, cell volume, glucose consumption, lactate production, viral titer, and recombinant β-galactosidase accumulation, were examined. The extent of the increase in CER following infection and the time postinfection at which maximum CER was attained were negatively correlated with the multiplicity of infection (MOI) at multiplicities below the level required to infect all the cells in a culture. Delays in the respiration peak related to the MOI employed were correlated with delays in the peak in recombinant protein accumulation. DO levels in the range 5-100% did not exert any major effects on viable cell densities, CER, or product titer in cultures infected with a baculovirus expressing recombinant β-galactosidase. © 1996 John Wiley & Sons, Inc.
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  • 9
    Electronic Resource
    Electronic Resource
    Masthead (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996) 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260500101
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  • 10
    Electronic Resource
    Electronic Resource
    Aggregation of ligand-modified liposomes by specific interactions with proteins. II: Biotinylated liposomes and antibiotin antibody (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 169-183 
    Details
    ISSN: 0006-3592
    Keywords: liposomes ; biotin ; aggregation kinetics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The aggregation of biotinylated phospholipid vesicles (liposomes) cross-linked by antibiotin IgG was studied experimentally and theoretically. The liposomes were either low density liposomes that contained 0.4 mol% biotinylated phospholipid (≈100 exposed biotin molecules per liposome), or high density liposomes that contained 2.7 mol% biotinylated phospholipid (≈1000 exposed biotin molecules per liposome). The solution turbidity and mean particle size measured by quasi-elastic light scattering (QLS) were monitored throughout the aggregation. Three different lots of antibiotin antibodies, each with different association constants and binding heterogeneities, were used. The antibody binding characteristics affected the aggregation rates. The aggregation kinetics were analyzed using a model based on the Smoluchowski theory of aggregation, fractal concepts of aggregate microstructure, and Rayleigh and Mie light scattering theory. The experimental conditions of liposome concentration, protein concentration, and ligand density under which aggregation occurred correlated well with calculated sticking probabilities based on isotherms describing the adsorption of antibiotin antibody to the liposomes. These results are compared with prior observations made when avidin was used as the cross-linking protein. © 1996 John Wiley & Sons, Inc.
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  • 11
    Electronic Resource
    Electronic Resource
    Masthead (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996) 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260500201
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  • 12
    Electronic Resource
    Electronic Resource
    Collagenase digestion of bone fragments in microgravity (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 211-216 
    Details
    ISSN: 0006-3592
    Keywords: microgravity ; bioprocessing ; sedimentation ; turbulence ; collagenase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effect of a quiescent microgravity fluid environment on the activity of collagenase directed at demineralized bone fragments was investigated over a period of 10 days. Enzyme treatment resulted in greater mass loss in microgravity, with nearly three times the loss of mass during Space Shuttle mission STS-62 compared to the stationary ground control. Clinorotation enhanced the loss of mass relative to a stationary control, but this increase was still significantly less than the increase with exposure to microgravity. This suggests the detrimental influence of turbulence on the enzyme function and the benefit of using microgravity to provide both low turbulence and uniformity of unequally dense materials within the reaction chamber. The results are considered for their general applicability to a variety of bioprocessing applications that may be enhanced in microgravity. © 1996 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/bit.260500203
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  • 13
    Electronic Resource
    Electronic Resource
    Mini-review: Mechanical factors affecting cartilage regeneration in vitro (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 430-437 
    Details
    ISSN: 0006-3592
    Keywords: cartilage ; tissue regeneration ; chondrocytes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In the last 5 to 10 years, tissue engineering has revolutionized the way in which medical researchers and clinicians are thinking of and, in some cases, actually treating diseases involving tissue damage and destruction. One such disease, osteoarthritis, results from progressive degeneration of articular cartilage, which has a limited ability to repair itself. With tissue engineering, scientists are now able to regenerate cartilage in vitro from isolated mature chondrocytes. While the regeneration process is still not fully understood, enough has been learned that physicians are already implanting cultured chondrocytes into humans and other animals in the hopes of effecting joint repair. One aspect which has not been fully explored is the effect of mechanical stress on developing and implanted cartilage, especially over the long term. This article will review in brief what is now known about the mechanical factors affecting cartilage regeneration in vitro and what still remains to be determined for optimum tissue engineering of cartilage constructs. © 1996 John Wiley & Sons, Inc.
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  • 14
    Electronic Resource
    Electronic Resource
    Osteoblast migration on poly(α-hydroxy esters) (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 443-451 
    Details
    ISSN: 0006-3592
    Keywords: osteoblast ; migration ; poly(αhydroxy esters) ; poly(DL-lactic-co-glycolic acid) ; PLGA ; biodegradable polymers ; tissue engineering ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: We investigated the migration of rat calvaria osteoblast populations on poly(α-hydroxy ester) films for up to 14 days to determine effects of substrate composition and culture conditions on the migratory characteristics of osteoblasts. Initial osteoblast culture conditions included cell colonies formed by seeding a high (84,000 cells/cm2) or low (42,000 cells/cm2) density of isolated osteoblasts on the polymer films, and bone tissue cultures formed by plating bone chips directly on the substrates. High density osteoblast colonies cultured and allowed to migrate and proliferate radially on 85:15 poly(DL-lactic-co-glycolic acid) (PLGA) films, 75:25 PLGA films, and tissue culture polystyrene controls demonstrated that the copolymer ratio in the polymer films did not affect the rate of increase in substrate surface area (or culture area) covered by the growing cell colony. However, the rate of increase in culture area was dependent on the initial osteoblast seeding density. Initial cell colonies formed with a lower osteoblast seeding density on 75:25 PLGA resulted in a lower rate of increase in culture area, specifically 4.9 ± 0.3 mm2/day, versus 14.1 ± 0.7 mm2/day for colonies seeded with a higher density of cells on the same polymer films. The proliferation rate for osteoblasts in the high and low density seeded osteoblast colonies did not differ, whereas the proliferation rate for the osteoblasts arising from the bone chips was lower than either of these isolated cell colonies. Confocal and light microscopy revealed that the osteoblast migration occurred as a monolayer of individual osteoblasts and not a calcified tissue front. These results demonstrated that cell seeding conditions strongly affect the rates of osteoblast migration and proliferation on biodegradable poly(α-hydroxy esters). © 1996 John Wiley & Sons, Inc.
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  • 15
    Electronic Resource
    Electronic Resource
    Different measures of human hematopoietic cell culture performance are optimized under vastly different conditions (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996), S. 505-513 
    Details
    ISSN: 0006-3592
    Keywords: bone marrow ; hematopoiesis ; perfusion ; culture optimization ; stroma ; stem cells ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Hematopoiesis, the formation of mature blood cells from stem (LTC-IC) and progenitor (CFU-GM) cells in the bone marrow, is a complex tissue-forming process that leads to many important physiological functionalities. Consequently, a functioning ex vivo hematopoietic system has a variety of basic scientific and clinical uses. The design and operation of such a system presents the tissue engineer with challenges and choices. In this study, three culture variables were used to control ex vivo human hematopoiesis. Systematic variation of inoculum density (ID), medium exchange interval (MEI), and the use of preformed stroma (PFS) showed that (1) all three variables significantly influenced culture performance, (2) the three variables interacted strongly, and (3) the variables could be manipulated to achieve the optimization of different performance criteria. Donor-to-donor variability in culture performance was great at low ID but was minimized at higher ID. PFS had a large positive effect on cell and CFU-GM output at low ID, but had minimal effect at higher ID. In fact, PFS caused a decrease in LTC-IC output at high ID. The effects of PFS indicated that stromal cell elements became more limiting than proliferative cell elements as ID was reduced.In cultures without PFS, maximum cell output was obtained with high ID using a short MEI, whereas the greatest cell expansion ratio was obtained at low ID with an intermediate MEI. Maximum CFU-GM output was obtained from cultures with high ID using a short to intermediate MEI, whereas the greatest CFU-GM expansion ratio was obtained at intermediate ID with an intermediate MEI. The addition of PFS altered the locations of these maxima. In general, PFS moved the maxima to lower ID, and culture output became more sensitive to MEI. Therefore, the optimization of one performance criterion always resulted in a decline of the others. This study demonstrates that ex vivo tissue function is sensitive to many culture variables in an interactive fashion and that systematic multivariable studies are required to characterize tissue function. Once the effects of individual variables and their interactions are known, this knowledge can be used to optimize tissue performance with respect to desired criteria. © 1996 John Wiley & Sons, Inc.
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  • 16
    Electronic Resource
    Electronic Resource
    Masthead (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 50 (1996) 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260500501
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  • 17
    Electronic Resource
    Electronic Resource
    Thermal stability studies of a globular protein in aqueous poly(ethylene glycol) by 1H NMR (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 51 (1996), S. 410-421 
    Details
    ISSN: 0006-3592
    Keywords: lysozyme ; thermal stability ; 1H NMR ; conformational flexibility ; melting temperature ; PEG ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The reversible folding destabilization of hen lysozyme has been confirmed by a melting temperature (Tm) decrease in aqueous poly(ethylene glycol) (PEG). The percent denatured, extracted from the histidine 15 C2H (H15 C2H) native and denatured peak areas from 500-MHz one-dimensional proton nuclear magnetic resonance (1D 1H NMR) spectra in D2O, was analyzed through denaturation temperatures at 0% and 20% (w/w) PEG 1000. The lysozyme (3.5 mM) Tm decreased by 4.2°C and 7.1°C in 20% (w/w) PEG 1000 at pH 3.8 and 3.0, respectively. The Tm decreased with increasing lysozyme concentration. Additionally, the temperature-induced resonance migrations of 17 protons from 8 residues indicate that the native lysozyme structure undergoes temperature-induced conformational changes. The changes were essentially identical in both 0% and 20% (w/w) PEG 1000 at both pH 3.0 and 3.8. This small, local restructuring of the hydrophobic box region may be a manifestation of temperature-dependent solution hydrophobicity, whereas active-site cleft fluctuations may be due to the inherent active-site flexibility. The lysozyme structure in PEG at 35°C was determined to be essentially native from the 1H nuclear Overhauser effect spectroscopy (NOESY) fingerprint regions. Additionally, lysozyme chemical shifts, from 1D spectra, in PEG 200, 300, and 1000 at 35°C and various concentrations were essentially identical, further confirming that the conformation remains native in various PEG solutions. © 1996 John Wiley & Sons, Inc.
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  • 18
    Electronic Resource
    Electronic Resource
    Factors affecting cellulose hydrolysis and the potential of enzyme recycle to enhance the efficiency of an integrated wood to ethanol process (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 51 (1996), S. 375-383 
    Details
    ISSN: 0006-3592
    Keywords: cellulase ; enzyme recycling ; enzyme adsorption ; lignocellulosic hydrolysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Past technoeconomic modeling work has identified the relatively large contribution that enzymatic hydrolysis adds to the total cost of producing ethanol from lignocellulosic substrates. This cost was primarily due to the high concentration of enzyme and long incubation time that was required to obtain complete hydrolysis. Although enzyme and substrate concentration and end-product inhibition influenced the rate of hydrolysis, the effect was less pronounced during the initial stages of hydrolysis. During this time most of the cellulases were adsorbed onto the unhydrolyzed residue. By recycling the cellulases adsorbed to the residual substrate remaining after an initial 24 h, a high rate of hydrolysis, with low overall residence time and minimal cellulase input, could be achieved for several rounds of enzyme recycle. A comparison of the front end (pretreatment, fractionation, and hydrolysis) of a softwood/hardwood to ethanol process indicated that the lignin associated with the softwood-derived cellulose stream limited the number of times the cellulose containing residue could be recycled. © 1996 John Wiley & Sons, Inc.
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  • 19
    Electronic Resource
    Electronic Resource
    Sparging and agitation-induced injury of cultured animals cells: Do cell-to-bubble interactions in the bulk liquid injure cells? (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 51 (1996), S. 399-409 
    Details
    ISSN: 0006-3592
    Keywords: cell damage ; cell culture ; bubble aeration ; agitation ; bubble coalescence and breakup ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: It has been established that the forces resulting from bubbles rupturing at the free air (gas)/liquid surface injure animal cells in agitated and/or sparged bioreactors. Although it has been suggested that bubble coalescence and breakup within agitated and sparged bioreactors (i.e., away from the free liquid surface) can be a source of cell injury as well, the evidence has been indirect. We have carried out experiments to examine this issue. The free air/liquid surface in a sparged and agitated bioractor was eliminated by completely filling the 2-L reactor and allowing sparged bubbles to escape through an outlet tube. Two identical bioreactors were run in parallel to make comparisons between cultures that were oxygenated via direct air sparging and the control culture in which silicone tubing was used for bubble-free oxygenation. Thus, cell damage from cell-to-bubble interactions due to processes (bubble coalescence and breakup) occurring in the bulk liquid could be isolated by eliminating damage due to bubbles rupturing at the free air/liquid surface of the bioreactor. We found that Chinese hamster ovary (CHO) cells grown in medium that does not contain shear-protecting additives can be agitated at rates up to 600 rpm without being damaged extensively by cell-to bubble interactions in the bulk of the bioreactor. We verified this using both batch and high-density perfusion cultures. We tested two impeller designs (pitched blade and Rushton) and found them not to affect cell damage under similar operational conditions. Sparger location (above vs. below the impeller) had no effect on cell damage at higher agitation rates but may affect the injury process at lower agitation intensities (here, below 250 rpm). In the absence of a headspace, we found less cell damage at higher agitation intensities (400 and 600 rpm), and we suggest that this nonintuitive finding derives from the important effect of bubble size and foam stability on the cell damage process. © 1996 John Wiley & Sons, Inc.
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    Modulation of the phosphate-starvation response in Escherichia coli by genetic manipulation of the polyphosphate pathways (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 51 (1996), S. 434-438 
    Details
    ISSN: 0006-3592
    Keywords: polyphosphate ; Escherichia coli ; phosphate starvation ; gene expression ; heterologous ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effect of intracellular polyphosphate on the phosphate-starvation response in Escherichia coli was studied by genetically manipulating the intracellular polyphosphate levels and by performing phosphate shifts on the genetically engineered strains. Strains that produced large quantities of polyphosphate and were able to degrade it induced the phosphate-starvation response to a lesser extent than wild-type strains, whereas strains that were unable to degrade a large intracellular polyphosphate pool induced the phosphate-starvation response to a greater extent than wild-type strains. These results have important implications for expression of heterologous genes under control of the phoA promoter. © 1996 John Wiley & Sons, Inc.
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    Effect of high shear on proteins (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 51 (1996), S. 458-465 
    Details
    ISSN: 0006-3592
    Keywords: concentric-cylinder shear device ; rotor/stator homogenization ; shear ; shear rate ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Shear is present in almost all bioprocesses and high shear is associated with processes involving agitation and emulsification. The purpose of this study is to investigate the effect of high shear and high shear rate on proteins. Two concentric cylinder-based shear systems were used. One was a closed concentric-cylinder shear device (CCSD) and the other was a homogenizer with a rotor/stator assembly. Mathematical modeling of these systems allowed calculation of the shear rate and shear. The CCSD generated low shear rates (a few hundred s-1), whereas the homogenizer could generate very high shear rates (〉 105 s-1). High shear could be achieved in both systems by increasing the processing time. Recombinant human growth hormone (rhGH) and recombinant human deoxyribonuclease (rhDNase) were used as the model proteins in this study. It was found that neither high shear nor high shear rate had a significant effect on protein aggregation. However, a lower melting temperature and enthalpy were detected for highly sheared rhGH by using scanning microcalorimetry, presumably due to some changes in protein's conformation. Also, SDS-PAGE indicated the presence of low molecular-weight fragments, suggesting that peptide bond breakage occurred due to high shear. rhDNase was relatively more stable than rhGH under high shear. No conformational changes and protein fragments were observed. © 1996 John Wiley & Sons, Inc.
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    Properties of two insect cell lines useful for the baculovirus expression system in serum-free culture (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 51 (1996), S. 494-499 
    Details
    ISSN: 0006-3592
    Keywords: cell metabolism ; baculovirus ; insect cells ; recombinant protein OSF-2 ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The properties of Sf9 and Tn5 insect cells were analyzed comparatively under serum-free culture conditions. Sf9 cells in SF900II medium apparently utilized sucrose as a primary nutrient both before and after virus infection, yielding small amounts of lactate and ammonia. Tn5 cells in Excell 401 medium consumed all the nutrients examined, including sucrose. The productivity of a recombinant glycoprotein, OSF-2, by Tn5 cells, was moderate in both monolayer and spinner cultures, but the ability to secrete it was compromised in the former case. Relative to the Tn5 cultures, Sf9 produced 30-fold more OSF-2 in either culture mode. © 1996 John Wiley & Sons, Inc.
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    NMR imaging of heavy metal absorption in alginate, immobilized cells, and kombu algal biosorbents (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 51 (1996), S. 538-543 
    Details
    ISSN: 0006-3592
    Keywords: NMR imaging ; biosorption ; alginate ; shrinking core model ; Laminaria ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In this contribution, an NMR imaging study of heavy metal absorption in alginate, immobilized-cell biosorbents, and kombu (Laminaria japonica) algal biomass is presented. This method provides the good possibility of directly monitoring the time evolution of the spatial distribution of the ions in the materials. From these results, we demonstrate that rare earth ions are absorbed with a steep reaction front that can be described very well with a modified shrinking core model, while copper ions are absorbed with a more diffuse front.
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    Enzymatic resolution of 1-phenyl-1,2-ethanediol by enantioselective oxidation: Overcoming product inhibition by continuous extraction (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 51 (1996), S. 544-550 
    Details
    ISSN: 0006-3592
    Keywords: oxidoreductase ; chiral alcohol ; racemic resolution ; membrane reactor ; continuous extraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Oxidations of alcohols by alcohol dehydrogenases often suffer from low conversions and slow reaction rates due to severe product inhibition. This can be overcome by continuous product extraction, because only the concentrations, but not the kinetic parameters, can be changed. As a consequence, it is favorable to apply a differential circulation reactor with continuous product extraction, where only a small amount of product is formed per cycle. The product is then directly extracted using a microporous hydrophobic hollow fiber membrane. This results in an increase of the relative activity of the dehydrogenase at a given conversion. The reaction investigated is the kinetic resolution of racemic 1-phenyl-1,2-ethanediol by glycerol dehydrogenase (GDH). The resulting oxidation product, 2-hydroxyacetophenone, causes a strong product inhibition. Additionally, it reacts in a chemical reaction with the cofactor lowering its active concentration. Because the GDH needs β-nicotinamide adenine dinucleotide (NAD+) as a cofactor, lactate dehydrogenase is used to regenerate NAD+ from NADH by reducing pyruvate to (L)-lactate. A conversion of 50% with respect to the racemate and an enantiomeric excess 〉99% of the (S)-enantiomer was reached.
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    Immobilization of DNA onto a polymer support and its potentiality as immunoadsorbent (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 51 (1996), S. 581-590 
    Details
    ISSN: 0006-3592
    Keywords: microfiber ; graft polymerization ; DNA immobilization ; immunoadsorbent ; DNA ; anti-DNA antibody ; systemic lupus erythematosus ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Immobilization of DNA to the surface of poly(ethylene terephthalate) (PET) microfibers with a high specific surface area of 0.83 m2/g was carried out to give the fiber surface an affinity for anti-DNA antibody. Following ozone oxidation, the microfibers were subjected to graft polymerization of monomers including acrylic acid, methacryloyloxyethyl phosphate, N,N-dimethylaminoethyl methacrylate, N-vinylformamide, and glycidyl methacrylate. Calf thymus DNA was immobilized to the grafted fiber surface through either covalent binding or polyion complexation with the grafted polymer chains. The highest surface density of DNA immobilized (0.6 μg/cm2) was obtained when DNA was immobilized through formation of phosphodiester linkage between the hydroxyl group of DNA and the phosphate group in grafted poly(methacryloyloxyethyl phosphate) using 1,1-carbonyldiimidazole, or through polyion complexation between the anionic DNA and the cationic grafted poly(N,N-dimethylaminoethyl methacrylate) chains. Batch adsorption of anti-DNA antibody to the grafted PET fibers with and without DNA immobilized on their surface was conducted with serum obtained from systemic lupus erythematosus model mice. The DNA-immobilized PET fibers exhibited a higher adsorption capacity and specificity than the others. In addition, the DNA-immobilized fibers effectively adsorbed human anti-DNA antibody.
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    Comparing folding codes for proteins and polymers (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 335-344 
    Details
    ISSN: 0887-3585
    Keywords: protein design ; synthetic heteropolymer design ; energy matrix ; sequence degeneracy ; structural encodability ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Proteins fold to unique compact native structures. Perhaps other polymers could be designed to fold in similar ways. The chemical nature of the monomer “alphabet” determines the “energy matrix” of monomer interactions - which defines the folding code, the relationship between sequence and structure. We study two properties of energy matrices using two-dimensional lattice models: uniqueness, the number of sequences that fold to only one structure, and encodability, the number of folds that are unique lowest-energy structures of certain monomer sequences. For the simplest model folding code, involving binary sequences of H (hydrophobic) and P (polar) monomers, only a small fraction of sequences fold uniquely, and not all structures can be encoded. Adding strong repulsive interactions results in a folding code with more sequences folding uniquely and more designable folds. Some theories suggest that the quality of a folding code depends only on the number of letters in the monomer alphabet, but we find that the energy matrix itself can be at least as important as the size of the alphabet. Certain multi-letter codes, including some with 20 letters, may be less physical or protein-like than codes with smaller numbers of letters because they neglect correlations among inter-residue interactions, treat only maximally compact conformations, or add arbitrary energies to the energy matrix.
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    A simple model of chaperonin-mediated protein folding (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 345-351 
    Details
    ISSN: 0887-3585
    Keywords: energy landscape ; kinetic traps ; hydrophobic interaction ; multiple folding pathways ; chaperone action ; lattice models ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Chaperonins are oligomeric proteins that help other proteins fold. They act, according to the “Anfinsen cage” or “box of infinite dilution” model, to provide private space, protected from aggregation, where a protein can fold. Recent evidence indicates, however, that proteins are often ejected from the GroEL chaperonin in nonnative conformations, and repeated cycles of binding and ejection are needed for successful folding. Some experimental evidence suggests that GroEL chaperonins can act as folding “catalysts” in an ATP-dependent manner even when no aggregation takes place. This implies that chaperonins must somehow recognize the kinetically trapped intermediate states of a protein. A central puzzle is how a chaperonin can catalyze the folding reaction of a broad spectrum of different proteins. We propose a physical mechanism by which chaperonins can flatten the energy barriers to folding in a nonspecific way. Using a lattice model, we illustrate how a chaperonin could provide a sticky surface that helps pull apart an incorrectly folded protein so it can try again to fold. Depending on the relative sizes of the protein and the chaperonin cavity, folding can proceed both inside and outside the chaperonin. Consistent with experiments, we find that the folding rate and amount of native protein can be considerably enhanced, or sometimes reduced, depending on the amino acid sequence, the chaperonin size, and the binding and ejection rates from the chaperonin.
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    Solution structure of P01, a natural scorpion peptide structurally analogous to scorpion toxins specific for apamin-sensitive potassium channel (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 359-369 
    Details
    ISSN: 0887-3585
    Keywords: scorpion venom ; neurotoxin ; NMR ; structure-activity relationships ; calcium activated-potassium channel ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The venom of the North African scorpion Androctonus mauretanicus mauretanicus possesses numerous highly active neurotoxins that specifically bind to various ion channels. One of these, P05, has been found to bind specifically to calcium-activated potassium channels and also to compete with apamin, a toxin extracted from bee venom. Besides the highly potent ones, several of these peptides (including that of P01) have been purified and been found to possess only a very weak, although significant, activity in competition with apamin. The amino acid sequence of P01 shows that it is shorter than P05 by two residues. This deletion occurs within an α-helix stretch (residues 5-12). This α-helix has been shown to be involved in the interaction of P05 with its receptor via two arginine residues. These two arginines are absent in the P01 sequence. Furthermore, a proline residue in position 7 of the P01 sequence may act as an α-helix breaker. We have determined the solution structure of P01 by conventional two-dimensional 1H nuclear magnetic resonance and show that 1) the proline residue does not disturb the α-helix running from residues 5 to 12; 2) the two arginines are topologically replaced by two acidic residues, which explains the drop in activity; 3) the residual binding activity may be due to the histidine residue in position 9; and 4) the overall secondary structure is conserved, i.e., an α-helix running from residues 5 to 12, two antiparallel stretches of β-sheet (residues 15-20 and 23-27) connected by a type I′ β-turn, and three disulfide bridges connecting the α-helix to the β-sheet.
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    Thermally induced hydrogen exchange processes in small proteins as seen by FTIR spectroscopy (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 379-387 
    Details
    ISSN: 0887-3585
    Keywords: infrared spectroscopy ; protein structure ; unfolding ; RNase T1 ; RNase A ; histone-like protein HBsu ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Fourier-transform infrared (FTIR) spectroscopy has been used to study the thermally induced exchange characteristics of those backbone amide protons which persist H-D exchange at ambient conditions in ribonuclease A, in wild type ribonuclease T1 and some of its variants, and in the histone-like protein HBsu. The H-D exchange processes were induced by increasing the thermal energy of the protein solutions in two ways: (i) by linearly increasing the temperature, and (ii) by a temperature jump. To trace the H-D exchange in the proteins, various infrared absorption bands known to be sensitive to H-D exchange were used as specific monitors. Characteristic H-D exchange curves were obtained from which the endpoints (TH/D) of H-D exchange could be determined. The H-D exchange curves, the TH/D-values and the phase transition temperatures Tm were used to estimate the structural flexibility and stability of the given proteins. It is suggested that time-resolved FTIR spectroscopy can be used to determine global stability parameters of proteins.
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    A partial model of the erythropoietin receptor complex (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 394-401 
    Details
    ISSN: 0887-3585
    Keywords: cytokines ; homology modeling ; erythropoietin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model of the structure of erythropoietin (Epo) is presented based on structural homology to other hemopoietic cytokines. A model of the erythropoietin receptor complex was made based on evidence that this includes a homodimer of the receptor chain with known sequence. Key interactions are noted which explain data from mutation experiments, although at not all residues believed to be important to binding of Epo are at the interface. This is consistent with the hypothesis that the Epo receptor complex includes proteins in addition to the cloned receptor chain that have been cross-linked to Epo (Todokoro et al., Proc. Natl. Acad. Sci. USA 84:4126-4130, 1987; Mayeux et al., J. Biol. Chem. 266:23380-23385, 1991) but not isolated.
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    Crystallization and preliminary X-ray analysis of the Escherichia coli replication terminator protein complexed with DNA (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 402-403 
    Details
    ISSN: 0887-3585
    Keywords: Tus ; terminus site ; protein-DNA interaction ; replication arrest ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of the Escherichia coli replication terminator protein (Tus) complexed with its binding site DNA were obtained by a microdialysis method using PEG 4000. They belong to the tetragonal space group P41212 or P43212 with the unit cell parameter: a = 68.1 Å, c = 230.7 Å and contain one protein-DNA complex in an asymmetric unit. The native data set has been collected to 2.7 Å resolution.
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    Purification, crystallization, and preliminary crystallographic analysis of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from Escherichia coli (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 404-406 
    Details
    ISSN: 0887-3585
    Keywords: DAHP synthase ; metalloenzyme ; shikimate pathway ; KDOP synthase ; affinity chromatography ; protein crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The phenylalanine-regulated isozyme of 3-deoxy-D-arabino-heptulosonate-7-phosphate- synthase (DAHPS) from Escherichia coli, its binary complexes with either substrate, phosphoenolpyruvate (PEP), or feedback inhibitor, Phe, and its ternary complexes with either PEP or Phe plus metal cofactor (either Mn2+, Cd2+, or Pb2+) were crystallized from polyethylglycol (PEG) solutions. All crystals of the DAHPS without Phe belong to space group C2, with cell parameters a = 213.5 Å, b = 54.3 Å, c = 149.0 Å, β = 116.6°. All crystals of the enzyme with Phe also belong to space group C2, but with cell parameters a = 297.1 Å, b = 91.4 Å, c = 256.5 Å, and β = 148.2°.
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    Masthead (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240301
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    Federal support for protein engineering (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 1-1 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240302
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    Current protocols in protein science, edited by J.E. Coligan, B.M. Dunn, H.L. Ploegh, D.W. Speicher, and P.T. Wingfield. New York: Wiley, 1995, 864 pages (core) + 576 pages (4 supplements)/year (updated looseleaf), print and CD-ROM (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 409-409 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240303
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    Errata (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 410-410 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240304
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    The role of helix formation in the folding of a fully α-helical coiled coil (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 427-432 
    Details
    ISSN: 0887-3585
    Keywords: GCN4 ; protein folding ; folding kinetics ; helix formation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To determine when secondary structure forms as two chains coalesce to form an α-helical dimer, the folding rates of variants of the coiled coil region of GCN4 were compared. Residues at non-perturbing positions along the exterior length of the helices were substituted one at a time with alanine and glycine to vary helix propensity and therefore dimer stability. For all variants, the bimolecular folding rate remains largely unchanged; the unfolding rate changes to largely account for the change in stability. Thus, contrary to most folding models, widespread helix is not yet formed at the rate-limiting step in the folding pathway. The high-energy transition state is a collapsed form that contains little if any secondary structure, as suggested for the globular protein cytochrome c (Sosnick et al., Proteins 24:413-426, 1996).
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    Hydrophilicity of cavities in proteins (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 433-438 
    Details
    ISSN: 0887-3585
    Keywords: structure refinement ; buried water ; free energy calculation ; molecular dynamics simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Water molecules inside cavities in proteins constitute integral parts of the structure. We have sought a quantitative measure of the hydrophilicity of the cavities by calculating energies and free energies of introducing a water molecule into these cavities. A threshold value of the water-protein interaction energy at -12 kcal/mol was found to be able to distinguish hydrated from empty cavities. It follows that buried waters have entropy comparable to that of liquid water or ice. A simple consistent picture of the energetics of the buried waters provided by this study enabled us to address the reliability of buried waters assigned in experiments.
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    Molecular collapse: The rate-limiting step in two-state cytochrome c folding (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 413-426 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; folding kinetics ; folding barriers ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Experiments with cytochrome c (cyt c) show that an initial folding event, molecular collapse, is not an energetically downhill continuum as commonly presumed but represents a large-scale, time-consuming, cooperative barrier-crossing process. In the absence of later misfold-reorganization barriers, the early collapse barrier limits cyt c folding to a time scale of milliseconds. The collapse process itself appears to be limited by an uphill search for some coarsely determined transition state structure that can nucleate subsequent energetically downhill folding events. An earlier “burst phase” event at strongly native conditions appears to be a non-specific response of the unfolded chain to reduced denaturant concentration. The molecular collapse process may or may not require the co-formation of the amino- and carboxyl-terminal helices, which are present in an initial metastable intermediate directly following the rate-limiting collapse. After the collapse-nucleation event, folding can proceed rapidly in an apparent two-state manner, probably by way of a predetermined sequence of metastable intermediates that leads to the native protein structure (Bai et al., Science 269:192-197, 1995).
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    Patterns in ionizable side chain interactions in protein structures (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 439-449 
    Details
    ISSN: 0887-3585
    Keywords: salt bridges ; hydrogen bonds ; secondary structure ; ionizable side chains ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In a selected set of 44 high-resolution, non-homologous protein structures, the intramolecular hydrogen bonds or salt bridges formed by ionizable amino acid side chains were identified and analyzed. The analysis was based on the investigation of several properties of the involved residues such as their solvent exposure, their belonging to a certain secondary structural element, and their position relative to the N- and C-termini of their respective structural element. It was observed that two-thirds of the interactions made by basic or acidic side chains are hydrogen bonds to polar uncharged groups. In particular, the majority (78%) of the hydrogen bonds between ionizable side chains and main chain polar groups (sch:mch bonds) involved at least one buried atom, and in 42% of the cases both interacting atoms were buried. In α-helices, the sch:mch bonds observed in the proximity of the C- and N-termini show a clear preference for acidic and basic side chains, respectively. This appears to be due to the partial charges of peptide group atoms at the termini of α-helices, which establish energetically favorable electrostatic interactions with side chain carrying opposite charge, at distances even greater than 4.5 Å. The sch:mch interactions involving ionizable side chains that belong either to β-strands or to the central part of α-helices are based almost exclusively on basic residues. This results from the presence of main chain carbonyl oxygen atoms in the protein core which have unsatisfied hydrogen bonding capabilities.
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    Phylogenetic occurrence of coiled coil proteins: Implications for tissue structure in metazoa via a coiled coil tissue matrix (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 467-484 
    Details
    ISSN: 0887-3585
    Keywords: heptad repeat ; alpha helix ; intermediate filament ; nuclear matrix ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We examined GenBank sequence files with a heptad repeat analysis program to assess the phylogenetic occurrence of coiled coil proteins, how heptad repeat domains are organized within them, and what structural/functional categories they comprise. Of 102,007 proteins analyzed, 5.95% (6,074) contained coiled coil domains; 1.26% (1,289) contained “extended” (〉 75 amino acid) domains. While the frequency of proteins containing coiled coils was surprisingly constant among all biota, extended coiled coil proteins were fourfold more frequent in the animal kingdom and may reflect early events in the divergence of plants and animals. Structure/function categories of extended coils also revealed phylogenetic differences. In pathogens and parasites, many extended coiled coil proteins are external and bind host proteins. In animals, the majority of extended coiled coil proteins were identified as constituents of two protein categories: 1) myosins and motors; or 2) components of the nuclear matrix-intermediate filament scaffold. This scaffold, produced by sequential extraction of epithelial monolayers in situ, contains only 1-2% of the cell mass while accurately retaining morphological features of living epithelium and is greatly enriched in proteins with extensive, interrupted coiled coil forming domains. The increased occurrence of this type of protein in Metazoa compared with plants or protists leads us to hypothesize a tissue-wide matrix of coiled coil interactions underlying metazoan differentiated cell and tissue structure.
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    Ion pair formation of phosphorylated amino acids and lysine and arginine side chains: A theoretical study (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 495-501 
    Details
    ISSN: 0887-3585
    Keywords: ab initio calculations ; density functional theory ; semiempirical calculations ; solvent reaction field ; phosphoserine ; phosphothreonine ; phosphotyrosine ; hydrogen bonding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Protein phosphorylation is one of the major signal transduction mechanisms for controlling and regulating intracellular processes. Phosphorylation of specific hydroxylated amino acid side chains (Ser, Thr, Tyr) by protein kinases can activate numerous enzymes; this effect can be reversed by the action of protein phosphatases. Here we report ab initio (HF/6-31G* and Becke3LYP/6-31G*) and semiempirical (PM3) molecular orbital calculations pertinent to the ion pair formation of the phosphorylated amino acids with the basic side chains of Lys and Arg. Methyl-, ethyl-, and phenylphosphate, as well as methylamine and methylguanidinium were used as model compounds for the phosphorylated and basic amino acids, respectively. Phosphorylated amino acids were calculated as mono- and divalent anions. Our results indicate that the PSer/PThr ion pair interaction energies are stronger than those with PTyr. Moreover, the interaction energies with the amino group of Lys are generally more favorable than with the guanidinium group of Arg. The Lys amino groups form stable bifurcated hydrogen bonded structures; while the Arg guanidinium group can form a bidentate hydrogen bonded structure. Reasonable values for the interaction free energies in aqueous solution were obtained for some complexes by the inclusion of a solvent reaction field in the computation (PM3-SM3).
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    Towards meeting the paracelsus challenge: The design, synthesis, and characterization of paracelsin-43, an α-helical protein with over 50% sequence identity to an all-β protein (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 502-513 
    Details
    ISSN: 0887-3585
    Keywords: de novo design ; protein structure ; inverse folding ; genetic algorithms ; 1H NMR ; CD ; peptide ; protein folding ; methanol ; ethylene glycol ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In response to the Paracelsus Challenge (Rose and Creamer, Proteins, 19:1-3, 1994), we present here the design, synthesis, and characterization of a helical protein, whose sequence is 50% identical to that of an all-β protein. The new sequence was derived by applying an inverse protein folding approach, in which the sequence was optimized to “fit” the new helical structure, but constrained to retain 50% of the original amino acid residues. The program utilizes a genetic algorithm to optimize the sequence, together with empirical potentials of mean force to evaluate the sequence-structure compatibility. Although the designed sequence has little ordered (secondary) structure in water, circular dichroism and nuclear magnetic resonance data show clear evidence for significant helical content in water/ethylene glycol and in water/methanol mixtures at low temperatures, as well as melting behavior indicative of cooperative folding. We believe that this represents a significant step toward meeting the Paracelsus Challenge.
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    Crystallization and preliminary X-ray crystallographic studies of L-2-haloacid dehalogenase from Pseudomonas sp. YL (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 520-522 
    Details
    ISSN: 0887-3585
    Keywords: dehalogenase ; hydrolase ; Pseudomonas ; crystallization ; X-ray diffraction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The dimeric L-2-haloacid dehalogenase from Pseudomonas sp. YL, (subunit mass, 26179 Da), has been crystallized by vapor diffusion, supplemented by repetitive seeding, against a 50 mM potassium dihydrogenphosphate solution (pH 4.5) containing 15% (w/v) polyethylene glycol 8,000 and 1% (v/v) n-propanol. The crystals belong to the monoclinic space group C2 with unit cell dimensions of a = 92.21 Å, b = 62.78 Angst; c = 50.84 Å, and β = 122.4°, and contain two dehalogenase dimers in the unit cell. They are of good quality and diffract up to 1.5 Å resolution.
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    Masthead (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240401
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  • 46
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    Crystallization and preliminary X-ray diffraction study of 1,3,8-trihydroxynaphthalene reductase from Magnaporthe grisea (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 525-527 
    Details
    ISSN: 0887-3585
    Keywords: naphtol reductase ; melanin synthesis ; rice blast disease ; fungicide ; rational drug design ; crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: 1,3,8-Trihydroxynaphthalene reductase was crystallized in the presence of NADPH and the inhibitor tricyclazole. The crystals are trigonal, space group P3121 or its enantiomorph P3221. Two crystal forms with slightly different cell dimensions were obtained. Form A has unit cell dimensions a = b = 142.6 Å, c = 70.1 Å and form B cell dimensions a = b = 142.6 Å, c = 72.9 Å. The diffraction pattern of the latter crystal form extends to 2.5 Å resolution.
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    Prediction of the secondary structure of HIV-1 gp120 (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 1-11 
    Details
    ISSN: 0887-3585
    Keywords: HIV-1 gp120 ; secondary structure ; prediction ; multiple alignment ; CD4-binding site ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The secondary structure of HIV-1 gp120 was predicted using multiple alignment and a combination of two independent methods based on neural network and nearest-neighbor algorithms. The methods agreed on the secondary structure for 80% of the residues in BH10 gp120. Six helices were predicted in HIV strain BH10 gp120, as well as in 27 other HIV-1 strains examined. Two helical segments were predicted in regions displaying profound sequence variation, one in a region suggested to be critical for CD4 binding. The predicted content of helix, β-strand, and coil was consistent with estimates from Fourier transform infrared spectroscopy. The predicted secondary structure of gp120 compared well with data from NMR analysis of synthetic peptides from the V3 loop and the C4 region. As a first step towards modeling the tertiary structure of gp120, the predicted secondary structure may guide the design of future HIV sub-unit vaccine candidates. © 1996 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.1
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  • 48
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    Constructing amino acid residue substitution classes maximally indicative of local protein structure (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 28-37 
    Details
    ISSN: 0887-3585
    Keywords: protein evolution ; structure prediction ; information theory ; amino acid substitution ; multiple sequence alignment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Using an information theoretic formalism, we optimize classes of amino acid substitution to be maximally indicative of local protein structure. Our statistically-derived classes are loosely identifiable with the heuristic constructions found in previously published work. However, while these other methods provide a more rigid idealization of physicochemically constrained residue substitution, our classes provide substantially more structural information with many fewer parameters. Moreover, these substitution classes are consistent with the paradigmatic view of the sequence-to-structure relationship in globular proteins which holds that the three-dimensional architecture is predominantly determined by the arrangement of hydrophobic and polar side chains with weak constraints on the actual amino acid identities. More specific constraints are imposed on the placement of prolines, glycines, and the charged residues. These substitution classes have been used in highly accurate predictions of residue solvent accessibility. They could also be used in the identification of homologous proteins, the construction and refinement of multiple sequence alignments, and as a means of condensing and codifying the information in multiple sequence alignments for secondary structure prediction and tertiary fold recognition. © 1996 Wiley-Liss, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.3
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    Study of global motions in proteins by weighted masses molecular dynamics: Adenylate kinase as a test case (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 79-88 
    Details
    ISSN: 0887-3585
    Keywords: weighted masses ; molecular dynamics ; adenylate kinase ; domain movement ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The weighted masses molecular dynamics (WMMD) technique is applied to the protein adenylate kinase. A novel set of restraints has been developed to allow the use of this technique with proteins. The WMMD simulation is successful in predicting the flexibility of the two mobile domains of the protein. The end product of the simulation is similar to the known open and AMP bound forms of the enzyme. The biological relevance of the restraints used and potential methods of improving the technique are discussed. © 1996 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.6
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  • 50
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    The rate-limiting step in the folding of the cis-Pro167Thr mutant of TEM-1 β-lactamase is the trans to cis isomerization of a non-proline peptide bond (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 104-111 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; guanidine hydrochloride denaturation ; folding/unfolding kinetics ; cis-trans isomerization ; cis-proline mutant ; cis-non-proline amino acid ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The stability and kinetics of unfolding and refolding of the P167T mutant of the TEM-1 β-lactamase have been investigated as a function of guanidine hydrochloride concentration. The activity of the mutant enzyme was not significantly modified, which strongly suggests that the Glu166-Thr167 peptide bond, like the Glu166-Pro167, is cis. The mutation, however, led to a significant decrease in the stability of the native state relative to both the thermodynamically stable intermediate and the fully unfolded state of the protein. In contrast to the two slower phases seen in the refolding of the wild-type enzyme, only one phase was detected in the refolding of the mutant, indicating a determining role of proline 167 in the kinetics of folding of the wild-type enzyme. The former phases are replaced by rapid refolding when the enzyme is unfolded for short periods of time, but the latter is independent of the time of unfolding. The monophasic refolding reaction of the mutant is proposed to reflect mainly the trans→cis isomerization of the Glu166-Thr167 peptide bond. © 1996 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.8
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    The three-dimensional structure of Escherichia coli porphobilinogen deaminase at 1.76-Å resolution (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 48-78 
    Details
    ISSN: 0887-3585
    Keywords: prophobilinogen deaminase ; E. coli ; selenomethionine ; X-ray analysis ; tetrapyrrole biosynthesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Porphobilinogen deaminase (PBGD) catalyses the polymerization of four molecules of porphobilinogen to form the 1-hydroxymethylbilane, preuroporphyrinogen, a key intermediate in the biosynthesis of tetrapyrroles. The three-dimensional structure of wild-type PBGD from Escherichia coli has been determined by multiple isomorphous replacement and refined to a crystallographic R-factor of 0.188 at 1.76 Å resolution. The polypeptide chain of PBGD is folded into three α/β domains. Domains 1 and 2 have a similar overall topology, based on a five-stranded, mixed β-sheet. These two domains, which are linked by two hinge segments but otherwise make few direct interactions, form an extensive active site cleft at their interface. Domain 3, an open-faced, anti-parallel sheet of three strands, interacts approximately equally with the other two domains. The dipyrromethane cofactor is covalently attached to a cysteine side-chain borne on a flexible loop of domain 3. The cofactor serves as a primer for the assembly of the tetrapyrrole product and is held within the active site cleft by hydrogen-bonds and salt-bridges that are formed between its acetate and propionate side-groups and the polypeptide chain. The structure of a variant of PBGD, in which the methionines have been replaced with selenomethionines, has also been determined. The cofactor, in the native and functional form of the enzyme, adopts a conformation in which the second pyrrole ring (C2) occupies an internal position in the active site cleft. On oxidation, however, this C2 ring of the cofactor adopts a more external position that may correspond approximately to the site of substrate binding and polypyrrole chain elongation. The side-chain of Asp84 hydrogen-bonds the hydrogen atoms of both cofactor pyrrole nitrogens and also potentially the hydrogen atom of the pyrrole nitrogen of the porphobilinogen molecule bound to the proposed substrate binding site. This group has a key catalytic role, possibly in stabilizing the positive charges that develop on the pyrrole nitrogens during the ring-coupling reactions. Possible mechanisms for the processive elongation of the polypyrrole chain involve: accommodation of the elongating chain within the active site cleft, coupled with shifts in the relative positions of domains 1 and 2 to carry the terminal ring into the appropriate position at the catalytic site; or sequential translocation of the elongating polypyrrole chain, attached to the cofactor on domain 3, through the active site cleft by the progressive movement of domain 3 with respect to domains 1 and 2. Other mechanisms are considered although the amino acid sequence comparisons between PBGDs from all species suggest they share the same three-dimensional structure and mechanism of activity. © 1996 Wiley-Liss, Inc.
    Additional Material: 16 Ill.
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    URL: http://dx.doi.org/10.1002/prot.5
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    Crystallization of a family 8 cellulase from Clostridium thermocellum (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 134-136 
    Details
    ISSN: 0887-3585
    Keywords: family 8 glycohydrolase ; Clostridium thermocellum ; endoglucanase CelA ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The catalytic domain of cellulase CelA, a family 8 glycohydrolase from C. thermocellum, has been crystallized in the orthorhombic space group P212121 with unit cell dimensions a = 50.12 Å, b = 63.52 Å, c = 104.97 Å. The diffraction pattern extends beyond 1.5 Å resolution. © 1996 Wiley-Liss, Inc.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.12
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    Accessing the Kabat antibody sequence database by computer (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 130-133 
    Details
    ISSN: 0887-3585
    Keywords: immunoglobulin ; sequence comparison ; cloning ; complementarity determining regions ; alignment ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Kabat antibody sequence database has for many years been the primary site for depositing sequence information on antibodies and other proteins of immunological interest. The chief drawback of this database has been that it has only been available in the form of a printed book (Kabat et al., Sequences of Proteins of Immunological Interest, 1991). These data have recently become available on the global computer Internet, but no method of searching the data has, as yet, been provided. Here, the development of a specialized database program for accessing the antibody data is described. This database software has been made accessible over the World Wide Web, together with a program which allows a novel antibody sequence to be tested against the Kabat sequence database, to identify unusual features of an antibody sequence which may represent cloning artifacts or sequencing errors. © 1996 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.11
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  • 54
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    Crystallization and preliminary crystallographic analysis of RepA1, a replication control protein of the RepFIC replicon of enterotoxin plasmid EntP307 (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 137-138 
    Details
    ISSN: 0887-3585
    Keywords: antisense RNA ; macroseeding ; cryocrystallography ; DNA replication ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: RepA1 protein is essential for replication of the RepFIC replicon of enterotoxin plasmid EntP307 and is thought to interact directly with the origin of replication. We have purified RepA1 from an over-producing expression system and have prepared single crystals using a macroseeding technique. The crystals belong to space group P212121 or P21212, with cell dimensions a = 61 Å, b = 67 Å, and c = 243 Å. They diffract X-rays to 3.3 Å resolution and probably contain two 40,000 molecular weight RepA1 molecules per asymmetric unit. © 1996 Wiley-Liss, Inc.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.13
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    The surface of β-sheet proteins contains amphiphilic regions which may provide clues about protein folding (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 253-260 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; protein folding ; chaperone ; folding path ; amphiphilic sequences ; β-sheet proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A major bottleneck in the field of biochemistry is our limited understanding of the processes by which a protein folds into its native conformation. Much of the work on this issue has focused on the conserved core of the folded protein. However, one might imagine that a ubiquitous motif for unaided folding or for the recognition of chaperones may involve regions on the surface of the native structure. We explore this possibility by an analysis of the spatial distribution of regions with amphiphilic α-helical potential on the surface of β-sheet proteins.All proteins, Including β-sheet proteins, contain regions with amphiphilic α-helical potential. That is, any α-helix formed by that region would be amphiphilic, having both hydrophobic and hydrophilic surfaces. In the three-dimensional structure of all β-sheet proteins analyzed, we have found a distinct pattern in the spatial distribution of sequences with amphiphilic α-helical potential. The amphiphilic regions occur in ring shaped clusters approximately 20 to 30 Å in diameter on the surface of the protein. In addition, these regions have a strong preference for positively charged amino acids and a lower preference for residues not favorable to α-helix formation. Although the purpose of these amphiphilic regions which are not associated with naturally occurring α-helix is unknown, they may play a critical role in highly conserved processes such as protein folding. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.10
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  • 56
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    The native state of apomyoglobin described by proton NMR spectroscopy: The A-B-G-H interface of wild-type sperm whale apomyoglobin (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 267-285 
    Details
    ISSN: 0887-3585
    Keywords: myoglobin ; histidine ; hydrophobic core ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Proton nuclear magnetic resonance spectroscopy was applied to sperm whale apomyoglobin to describe the conformation adopted by the protein under native conditions. The study focused on the A-B-G-H interface, a region known to form a compact subdomain in the apoprotein (Hughson and Baldwin, Biochemistry 28:4415-4422, 1989). Two histidine residues located in this subdomain, His24 and His119, interact and are thought to play a role in the acid denaturation process (Barrick et al., J. Mol. Biol. 237:588-601, 1994). A stable double mutant at these positions (His24Va1/His119Phe sperm whale apomyoglobin) was compared with wild-type apomyoglobin. The amino acid replacements result in chemical shift perturbations near the mutations, in particular in the AB interhelical region, and in a deceleration of backbone amide hydrogen exchange in the B helix from position 27 to position 33. The double mutant data were used to expand and confirm the wild-type spectral analysis. Signals from the D helix were identified that demonstrate the formation of holoprotein-like structure. The assigned wild-type nuclear Overhauser effects, although in small number, were sufficient to construct a model of the compact subdomain of the apoprotein. This was achieved by using the structure of the holoprotein and restraining it with the geometrical information on the apoprotein in a simulated annealing procedure. The experimental restraints define a low-resolution model of the A-B-G-H interface in apomyoglobin. © 1996 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.1
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    Identification and analysis of long-range electrostatic effects in proteins by computer modeling:Aspartate transcarbamylase (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 300-314 
    Details
    ISSN: 0887-3585
    Keywords: electrostatic modeling ; Poisson-Boltzmann equation ; finite difference ; multigrid ; allosteric regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: While ion pairs are readily identified in crystal structures, longer range electrostatic interactions cannot be identified from the three-dimensional structure alone. These interactions are likely to be important in large, multisubunit proteins that are regulated by allosteric interactions. In this paper, we show that these interactions are readily detected by electrostatic modeling, using, as an example, unliganded Escherichia coli aspartate transcarbamylase, a widely studied allosteric enzyme with 12 subunits and a molecular weight of 310 kD. The Born, dipolar, and site-site interaction terms of the free energy of protonation of the 810 titratable sites in the holoenzyme were calculated using the multigrid solution of the nonlinear Poisson-Boltzmann equation. Calculated titration curves are in good agreement with experimental titration curves, and the structural asymmetry observed in the crystal structure is readily apparent in the calculated free energies and pK1/2 values. Most of the residues with pK1/2 values that differ substantially from those of model compounds are buried in the low dielectric medium of the protein, particularly at the intersubunit interfaces. The dependence of the site-site interaction free energies on distance is complex, with a steep dependence at distances less than 5 Å and a more shallow dependence at longer distances. Interactions over distances of 6 to 15 Å require a bridging residue and are often not apparent in the structure. The network of interactions between ionizable groups extends across and between subunits and provides a potential mechanism for transmitting long-range structural effects and allosteric signals. © 1996 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.3
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    The linker of calmodulin lacking Glu84 is elongated in solution, although it is bent in the crystal (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 335-341 
    Details
    ISSN: 0887-3585
    Keywords: solution X-ray scattering ; calcium-dependent conformational change ; calmodulin-melittin complex ; deviation from crystal structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The solution structure of a mutant calmodulin (des84) lacking Glu84 in the central helix linking the two calmodulin lobes is substantially different from its crystal structure. As determined by small-angle X-ray scattering, the radius of gyration and the maximum linear dimension of des84 in the presence of 0.1 mM calcium are 20.8 Å and 62.5 Å, respectively. These respective dimensions are larger than those expected from the crystal structure of des84, 18.5 Å and 55.0 Å, and smaller than those expected from the crystal structure of wild type, 22.8 Å and 67.5 Å. The distance distribution function of des84 indicates that it assumes an elongated, dumbbell shape in solution. The solution scattering profile of des84 is indistinguishable from that of wild-type calmodulin. The calcium-dependent binding of melittin to des84 causes a change in its shape from elongated to spherical, as seen with other calmodulins. In comparison with calcium-saturated des84, calcium-free des84 is slightly elongated; a slight compaction is observed with native calmodulin. The observed differences between the averaged solution structure and the crystal structure of des84 suggests that an ensemble of structures is available to calmodulin in solution and that its target need not induce a change in its conformation. These results support the theory that the linker region of the central helix of calmodulin functions as a flexible tether. © 1996 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
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    Chemical cross-linking between lysine groups in vimentin oligomers is dependent on local peptide conformations (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 215-224 
    Details
    ISSN: 0887-3585
    Keywords: α-helix ; β-helix ; β-strand ; coiled coil ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Previous studies have shown that cytoplasmic intermediate filaments, other than the keratins, are each constructed from a single type of polypeptide chain. Studies involving chemical crosslinking between lysine groups have shown that assembly of the filaments begins with the formation of dimers in which the peptide chains are parallel and in exact register, and that these dimers further associate in antiparallel patterns having specific degrees of overlap. In the present study, molecular modeling of the conformations of vimentin molecules indicated that lysine side chains in identical positions in regions of α-helix in parallel chains might be unable to be linked because they are on opposite sides of the coiled coil hydrophobic core. Examination of published data on chemical crosslinking of lysines in vimentin confirmed that there were no instances of linkage within dimers between the nine pairs of identical lysines that lie more than one position within α-helical regions in parallel chains. Even among linkages that apparently were between dimers, only one of the 11 linkage products identified involved lysines that were both within an α-helical region. In 10 of the 11 identified linkages between dimers, one or both of the linked lysines were in regions of random coil conformation. These results of molecular modeling indicate that relative motion between polypeptide chains in oligomers of intermediate filament proteins is not sufficient to overcome an orientation of lysine groups that is unfavorable for their chemical linkage. This finding supports the interpretations of keratin cross-linking data indicating that parallel homodimers are the basis for keratin intermediate filament assembly. © 1996 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.7
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    Protein structure and the sequential structure of mRNA: α-Helix and β-sheet signals at the nucleotide level (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 237-252 
    Details
    ISSN: 0887-3585
    Keywords: cotranslational folding ; protein secondary structure ; ribosome ; reading frame ; neural network ; computer-prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A direct comparison of experimentally determined protein structures and their corresponding protein coding mRNA sequences has been performed. We examine whether real world data support the hypothesis that clusters of rare codons correlate with the location of structural units in the resulting protein. The degeneracy of the genetic code allows for a biased selection of codons which may control the translational rate of the ribosome, and may thus in vivo have a catalyzing effect on the folding of the polypeptide chain. A complete search for GenBank nucleotide sequences coding for structural entries in the Brookhaven Protein Data Bank produced 719 protein chains with matching mRNA sequence, amino acid sequence, and secondary structure assignment. By neural network analysis, we found strong signals in mRNA sequence regions surrounding helices and sheets. These signals do not originate from the clustering of rare codons, but from the similarity of codons coding for very abundant amino acid residues at the N- and C-termini of helices and sheets. No correlation between the positioning of rare codons and the location of structural units was found. The mRNA signals were also compared with conserved nucleotide features of 16S-like ribosomal RNA sequences and related to mechanisms for maintaining the correct reading frame by the ribosome. © 1996 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/prot.9
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    Masthead (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340250201
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    Crystallization and preliminary x-ray crystallographic studies of recombinant bovine neurocalcin δ (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 261-264 
    Details
    ISSN: 0887-3585
    Keywords: X-ray diffraction ; calcium-binding myristoylation ; noncrystallographic symmetry ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Neurocalcins are novel brain-specific proteins that belong to a new subclass of the EF-hand super-family of calcium binding proteins, defined by the photoreceptor cell-specific protein recoverin (Terasawa et al., J. Biol. Chem. 267:19596-19599, 1992). Here we report the purification and crystallization of unmyristoylated recombinant bovine neurocalcin δ from Escherichia coli. Crystals of a bovine neurocalcin δ have been grown by macro-seeding at room temperature through vapor phase equilibration using the hanging drop technique with ammonium sulfate as the precipitating agent. The crystals diffract to at least 2.5 Å resolution and belong to monoclinic space group P2I with unit cell dimensions a = 42.734 Å, b = 94.343 Å, c = 50.696 Å, and β = 98.37°. The asymmetric unit contains two molecules, with corresponding crystal volume per protein mass (Vm) of 2.29 Å3/Da and solvent fraction of 45% by volume, exhibiting an approximate 222 point symmetry. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.11
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    Folding simulations and computer redesign of protein A three-helix bundle motifs (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 286-299 
    Details
    ISSN: 0887-3585
    Keywords: lattice model of proteins ; Monte Carlo method ; mirror image fold ; multiple mutations ; hydrophobic core repacking ; turn handedness modification ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In solution, the B domain of protein A from Staphylococcus aureus (B domain) possesses a three-helix bundle structure. This simple motif has been previously reproduced by Kolinski and Skolnick (Proteins 18: 353-366, 1994) using a reduced representation lattice model of proteins with a statistical interaction scheme. In this paper, an improved version of the potential has been used, and the robustness of this result has been tested by folding from the random state a set of three-helix bundle proteins that are highly homologous to the B domain of protein A. Furthermore, an attempt to redesign the B domain native structure to its topological mirror image fold has been made by multiple mutations of the hydrophobic core and the turn region between helices I and II. A sieve method for scanning a large set of mutations to search for this desired property has been proposed. It has been shown that mutations of native B domain hydrophobic core do not introduce significant changes in the protein motif. Mutations in the turn region were also very conservative; nevertheless, a few mutants acquired the desired topological mirror image motif. A set of all atom models of the most probable mutant was reconstructed from the reduced models and refined using a molecular dynamics algorithm in the presence of water. The packing of all atom structures obtained corroborates the lattice model results. We conclude that the change in the handedness of the turn induced by the mutations, augmented by the repacking of hydrophobic core and the additional burial of the second helix N-cap side chain, are responsible for the predicted preferential adoption of the mirror image structure. © 1996 Wiley-Liss, Inc.
    Additional Material: 15 Ill.
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    URL: http://dx.doi.org/10.1002/prot.2
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    The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: How well is the x-ray structure “maintained”? (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 315-334 
    Details
    ISSN: 0887-3585
    Keywords: particle mesh Ewald ; cutoff ; periodic box ; shell ; root mean square deviation ; atomic fluctuation ; order parameters ; force field ; aqueous solution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present molecular dynamics simulations on ubiquitin with explicit solvent molecules and investigate the influence of different force fields [Weiner et al. (J. Am. Chem. Soc. 106:765-784, 1984; J. Comput. Chem. 7:230-252, 1986) vs. Cornell et al. (J. Am. Chem. Soc. 117:5179-5197, 1995)], different treatments of the long-range electrostatic interaction (8 Å cutoff vs. particle mesh Ewald), and different solvation models (periodic box vs. small shell of water molecules) on the structure and the dynamics of the protein. Structural data are monitored by atomic root mean square deviations (RMSDs) from the crystal structure, the radius of gyration, the solvent-accessible surface area, and the pattern of the backbone hydrogen bonds. The dynamic behavior is assessed by the atomic fluctuations and the order parameters of the N-H backbone vectors.With the Cornell et al. force field and a periodic box model, the simulated structures stay much closer to the experimental X-ray structure than with the older Weiner et al. force field. A further improvement of the simulation is found when the electrostatic interaction is evaluated with the particle mesh Ewald method; after 1.2 ns of simulation the backbone RMSD amounts to only 1.13 Å. The analysis of the dynamic parameters shows that this good structural agreement is not due to a damping of internal motion in the protein.For a given length of simulation time, the shell models achieve an agreement between simulated and experimental structures that is comparable to the best models that employ a periodic box of solvent models. However, compared with the box models, the fluctuations of the protein atoms in the shell models are smaller, and only with simulation times as long as 2 ns do they become of comparable size to the experimental ones. © 1996 Wiley-Liss, Inc.
    Additional Material: 12 Ill.
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    URL: http://dx.doi.org/10.1002/prot.4
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    Exploring the energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 342-353 
    Details
    ISSN: 0887-3585
    Keywords: structure-based drug design ; ligand-protein recognition ; binding landscapes ; docking funnels ; stochastic search ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Energy landscapes of molecular recognition are explored by performing “semi-rigid” docking of FK-506 and rapamycin with the Fukisawa binding protein (FKBP-12), and flexible docking simulations of the Ro-31-8959 and AG-1284 inhibitors with HIV-1 protease by a genetic algorithm. The requirements of a molecular recognition model to meet thermodynamic and kinetic criteria of ligand-protein docking simultaneously are investigated using a family of simple molecular recognition energy functions. The critical factor that determines the success rate in predicting the structure of ligand-protein complexes is found to be the roughness of the binding energy landscape, in accordance with a minimal frustration principle. The results suggest that further progress in structure prediction of ligand-protein complexes can be achieved by designing molecular recognition energy functions that generate binding landscapes with reduced frustration. © 1996 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/prot.6
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    The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 366-378 
    Details
    ISSN: 0887-3585
    Keywords: hydration/solvation ; Kohlrausch-Williams-Watts relaxation ; diffusion ; residence time ; Voronoi polyhedra ; ubiquitin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A system containing the globular protein ubiquitin and 4,197 water molecules has been used for the analysis of the influence exerted by a protein on solvent dynamics in its vicinity. Using Voronoi polyhedra, the solvent has been divided into three subsets, i.e., the first and second hydration shell, and the remaining bulk, which is hardly affected by the protein. Translational motion in the first shell is retarded by a factor of 3 in comparison to bulk. Several molecules in the first shell do not reach the diffusive regime within 100 ps. Shell-averaged orientational autocorrelation functions, which are also subject to a retardation effect, cannot be modeled by a single exponential time law, but are instead well-described by a Kohlrausch-Williams-Watts (KWW) function. The underlying distribution of single-molecule rotational correlation times is both obtained directly from the simulation and derived theoretically. The temperature dependence of reorientation is characterized by a strongly varying correlation time, but a virtually temperature-independent KWW exponent. Thus, the coupling of water structure relaxation with the respective environment, which is characteristic of each solvation shell, is hardly affected by temperature. In other words, the functional form of the distributions of single-molecule rotational correlation times is not subject to a temperature effect. On average, a correlation between reorientation and lifetimes of neighborhood relations is observed. © 1996 Wiley-Liss, Inc.
    Additional Material: 13 Ill.
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    URL: http://dx.doi.org/10.1002/prot.8
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    Adjusting potential energy functions for lattice models of chain molecules (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 379-388 
    Details
    ISSN: 0887-3585
    Keywords: protein modeling ; lattice approximation error ; adjusting of energy functions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Lattice models of proteins can approximate off-lattice structures to arbitrary precision with RMS (root mean squared) deviations roughly equal to half the lattice spacing (Rykunov et al., Proteins 22:100-109, 1995; Reva et al., J. Comp. Biol., 1996). However, even small distortions in the positions of chain links lead to significant errors in lattice-based energy calculations (Reva et al., J. Comp. Chem., 1996). These errors arise mainly from rigid interactions (such as steric repulsion) which change their energies considerably at a range which is much smaller than the usual accuracy of lattice modeling (〉1.0 Å). To reduce this error, we suggest a procedure of adjusting energy functions to a given lattice. The general approach is illustrated with energy calculations based on pairwise potentials by Kolinski et al. (J. Chem. Phys. 98:1-14, 1993). At all the lattice spacings, from 0.5-3.8 Å, the lattice-adjusted potentials improve the accuracy of lattice-based energy calculations and Increase the correlations between off-lattice and lattice energies. © 1996 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.9
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    Building self-avoiding lattice models of proteins using a self-consistent field optimization (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 1-8 
    Details
    ISSN: 0887-3585
    Keywords: lattice models of proteins ; self-consistent field optimization ; self-avoiding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We present an algorithm to build self-avoiding lattice models of chain molecules with low RMS deviation from their actual 3D structures. To find the optimal coordinates for the lattice chain model, we minimize a function that consists of three terms: (1) the sum of squared deviations of link coordinates on a lattice from their off-lattice values, (2) the sum of “short-range” terms, penalizing violation of chain connectivity, and (3) the sum of “long-range” repulsive terms, penalizing chain self-intersections. We treat this function as a chain molecule “energy” and minimize it using self-consistent field (SCF) theory to represent the pairwise link repulsions as 3D fields acting on the links. The statistical mechanics of chain molecules enables computation of the chain distribution in this field on the lattice. The field is refined by iteration to become self-consistent with the chain distribution, then dynamic programming is used to find the optimal lattice model as the “lowest-energy” chain pathway in this SCF. We have tested the method on one of the coarsest (and most difficult) lattices used for model building on proteins of all structural types and show that the method is adequate for building self-avoiding models of proteins with low RMS deviations from the actual structures. © 1996 Wiley-Liss, Inc.
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    Computational simulations of stem-cell factor/c-Kit receptor interaction (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 42-54 
    Details
    ISSN: 0887-3585
    Keywords: cell surface receptors ; hematopoietic factors ; cytokines ; structure prediction ; homology modeling ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Stem-cell factor (SCF) is a noncovalent homodimeric cytokine that exhibits profound biological function in the early stages of hematopoiesis by binding to a cell surface tyrosine kinase receptor that is encoded by the c-Kit proto-oncogene. The results obtained from a combined implementation of homology-based molecular modeling and computational simulations in the study of species-specific SCF/c-Kit interactions are reported. The structural models of the human and rat SCF ligands are based on the close structural similarity to the cytokine M-CSF, whose Cα structure has recently become available. The constant domains of the human Fc fragment are used as a template for the ligand binding domains of the c-Kit receptor. The factors responsible for the stabilization of the SCF quaternary structure and the molecular determinants for ligand recognition and ligand specificity have been identified by assessing the conformational, topographical, and dynamic features of the isolated ligands and of the ligand-receptor complexes. © 1996 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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    Electrostatic properties deduced from refined structures of NADH-cytochrome b5 reductase and the other flavin-dependent reductases: Pyridine nucleotide-binding and interaction with an electron-transfer partner (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 32-41 
    Details
    ISSN: 0887-3585
    Keywords: α/β structure ; β barrel ; electrostatic potential ; flavin adenine dinucleotide ; flavin mononucleotide ; pyridine nucleotide ; structure refinement ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Electrostatic properties on the protein surface were examined on the basis of the crystal structure of NADH-cytochrome b5 reductase refined to a crystallographic R factor of 0.223 at 2.1 Å resolution and of the other three flavin-dependent reductases. A structural comparison of NADH-cytochrome b5 reductase with the other flavin-dependent reductases, ferredoxin-NADP+ reductase, phthalate dioxygenase reductase, and nitrate reductase, showed that the α/β structure is the common motif for binding pyridine nucleotide. Although the amino acid residues associated with pyridine nucleotide-binding are not conserved, the electrostatic properties and the location of the pyridine nucleotide-binding pockets of NADH-requiring reductases were similar to each other. The electrostatic potential of the surface near the flavin-protruding side (dimethylbenzene end of the flavin ring) of NADH-cytochrome b5 reductase was positive over a wide area while that of the surface near the heme-binding site of cytochrome b5 was negative. This implied that the flavin-protruding side of NADH-cytochrome b5 reductase is suitable for interacting with its electron-transfer partner, cytochrome b5. This positive potential area is conserved among four flavin-dependent reductases. A comparison of the electron-transfer partners of four flavin-dependent reductases showed that there are significant differences in the distribution of electrostatic potential between inter-molecular and inter-domain electron-transfer reactions. © 1996 Wiley-Liss, Inc.
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    Structural stability of disulfide mutants of basic pancreatic trypsin inhibitor: A molecular dynamics study (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 66-71 
    Details
    ISSN: 0887-3585
    Keywords: BPTI ; folding ; unfolding ; disulfide ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure and folding of basic pancreatic trypsin inhibitor (BPTI) has been studied extensively by experimental means. We report a computer simulation study of the structural stability of various disulfide mutants of BPTI, involving eight 250-psec molecular dynamics simulations of the proteins in water, with and without a phosphate counterion. The presence of the latter alters the relative stability of the single disulfide species [5-55] and [30-51]. This conclusion can explain results of mutational studies and the conservation of residues in homologues of BPTI, and suggests a possible role of ions in stabilizing one intermediate over another in unfolding or folding processes. © 1996 Wiley-Liss, Inc.
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    Masthead (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340260101
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    No crystals no grant (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No Abstracts.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340260102
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    Patent history (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: No abstract.
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    Heptad breaks in α-helical coiled coils: Stutters and stammers (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 26 (1996), S. 134-145 
    Details
    ISSN: 0887-3585
    Keywords: α-fibrous proteins ; supercoiling ; structure prediction ; hemagglutinin ; mannose-binding protein ; protein engineering ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The discontinuities found in heptad repeats of α-helical coiled-coil proteins have been characterized. A survey of 40 α-fibrous proteins reveals that only two classes of heptad breaks are prevalent: the stutter, corresponding to a deletion of three residues, and the newly identified “stammer,” corresponding to a deletion of four residues. This restriction on the variety of insertions/deletions encountered gives support to a unifying structural model, where different degrees of supercoiling accommodate the observed breaks. Stutters in the hemagglutinin coiled-coil region have previously been shown to produce an underwinding of the supercoil, and we show here how, in other cases, stammers would lead to overwinding. An analysis of main-chain structure also indicates that the mannose-binding protein, as well as hemagglutinin, contains an underwound coiled-coil region. In contrast to knobs-into-holes packing, these models give rise to non-close-packed cores at the sites of the heptad phase shifts. We suggest that such non-close-packed cores may function to terminate certain coiled-coil regions, and may also account for the flexibility observed in such long α-fibrous molecules as myosin. The local underwinding or overwinding caused by these specific breaks in the heptad repeat has a global effect on the structure and can modify both the assembly of the protein and its interaction properties. © 1996 Wiley-Liss, Inc.
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    Identification of a decapeptide with the binding reactivity for tumor-associated TAG72 antigen from a phage displayed library (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 352-358 
    Details
    ISSN: 0887-3585
    Keywords: peptide ; phage displayed library ; tumor-associated antigen ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Peptide ligands for tumor-associated TAG72 antigen were identified by screening a large, diverse decapeptide library expressed on the surface of filamentous phages. Fifty-eight clones of phages were selected from the eluates after the third round of biopanning and their DNA inserts were sequenced. A dominant decapeptide HYVSIELPDH (14/58) was found with the binding reactivity for TAG72 antigen in the TAG72-binding ELISA and Western dot blotting. It also showed a preferential binding to colonic adenocarcinomatous cells expressing the TAG72 antigen in the histochemical study. Therefore, this anti-TAG72 decapeptide may be useful in serving as the starting point with regard to further designing peptidomimetics for potential pharmaceuticals.
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    Fitting an inhibitor into the active site of thermolysin: A molecular dynamics case study (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 227-237 
    Details
    ISSN: 0887-3585
    Keywords: computer simulation ; metalloenzymes ; protein/ligand interactions ; rational drug design ; substrate docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We used molecular dynamics computer simulation to “fly” a small flexible ligand, L-leucine hydroxamic acid, into the active site of thermolysin. The potential, which imposed no constraints between protein and ligand, produced conformations close to the crystallographically determined one. The calculations made use of the combined molecular mechanics/grid method of Luty et al. (J. Comp. Chem. 16:454-464, 1995), in which atoms of the active site are free to move whereas the rest of the protein, assumed to be rigid, is represented as points of a grid, and which also includes an implicit solvation model. The method is sufficiently fast that large sets of simulations could be carried out, enabling statistical sampling and exploration of the effect of initial position and conformation of the ligand on the probability of successful docking. In a charged catalytic Glu/uncharged ligand regime, when the initial position of the ligand was determined by random translations and rotations that kept the center of mass within 8.0 Å of the crystal one, none of the 20 runs placed the ligand correctly. In a second set with uncharged Glu and zwitterionic ligand, 3 of 24 similarly placed random structures flew the ligand in successfully. In a third set with the same protonation scheme as the second the starting positions had randomly determined conformations but kept the hydroxyamate oxygens within 4.0 Å of the zinc; in this case 22 of 25 runs reoriented correctly. A diverse set of energetic, structural, and dynamic criteria was used for evaluation of the calculations. The results indicate the method to be a promising tool for the rational drug design process.
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  • 78
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    Overexpression of Bacillus subtilis phosphoribosylpyrophosphate synthetase and crystallization and preliminary X-ray characterization of the free enzyme and its substrate-effector complexes (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 238-246 
    Details
    ISSN: 0887-3585
    Keywords: nucleotide dependent enzymes ; pyrophosphotransferase ; allostery ; substrate-effector complexes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Bacillus subtilis phosphoribosylpyrophosphate (PRPP) synthetase has been expressed to high levels in an Escherichia coli host strain devoid of endogenous PRPP synthetase. A rapid and efficient purification protocol has been developed allowing production of enzyme preparations with purity conforming to the stringent criteria required for crystallization. Crystallization experiments, in combination with dynamic light scattering studies, have led to the production of three crystal forms of the enzyme. These forms include the free enzyme, the enzyme in a binary complex with the substrate adenosine triphosphate (ATP), and the enzyme in a quaternary complex with the substrate analog α, β-methylene adenosine triphosphate (mATP), the substrate ribose-5-phosphate (Rib-5-P), and the allosteric inhibitor adenosine diphosphate (ADP). Diffraction data showed that all three crystal forms are suitable for structure determination. They crystallize in the same hexagonal space group, P63, with virtually identical unit cell dimensions of a = b = 115.6 Å c = 107.8 Å, and with two molecules in the asymmetric unit. The self-rotation function showed the existence of a non-crystallographic twofold axis perpendicular to the c axis. The availability of the different complexes should allow questions regarding the molecular mechanisms of catalysis and allostery in PRPP synthetase to be addressed.
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  • 79
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    Incorporation of microcrystals by growing protein and virus crystals (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 247-252 
    Details
    ISSN: 0887-3585
    Keywords: atomic force microscopy ; canavalin ; satellite tobacco mosaic virus ; dislocation ; two-dimensional nuclei ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In the course of time-lapse video and atomic force microscopy (AFM) investigations of macromolecular crystal growth, we frequently observed the sedimentation of microcrystals and three-dimensional nuclei onto the surfaces of much larger, growing protein or virus crystals. This was followed by the direct incorporation over time of the smaller crystals into the bulk of the larger crystals. In some cases, clear indications were present that upon absorption of the small crystal onto the surface of the larger, there was proper alignment of the respective lattices, and consolidation proceeded without observable defect formation, i.e., the two lattices knitted together without discontinuity. In the case of at least one virus crystal, cubic satellite tobacco mosaic virus (STMV), addition of three-dimensional nuclei and subsequent expansion provided the principal growth mechanism at high supersaturation. This process has not been reported for growth from solution of conventional crystals. In numerous other instances, the lattices of the small and larger crystals were obviously misaligned, and incorporation occurred with the formation of some defect. This phenomenon of small crystals physically embedded in larger crystals could only degrade the overall diffraction and materials properties of macromolecular crystals.
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  • 80
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    Large-scale purification and preliminary X-ray diffraction studies of human aspartylglucosaminidase (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 253-258 
    Details
    ISSN: 0887-3585
    Keywords: glycosylasparaginase ; crystallization ; protein purification ; lysosomes ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Aspartylglucosaminidase (AGA) is a lysosomal asparaginase that takes part in the ordered degradation of glycoproteins and a deficiency of which results in a lysosomal accumulation disease aspartylglucosaminuria in human. The mature enzyme consists of 24-kDa and 17-kDa subunits, which are both heterogeneously glycosylated. Activation of the enzyme from a single precursor polypeptide into two subunits is accomplished in the endoplasmic reticulum (ER). The relative lack of this proteolytic capacity in several tested high-producing expression systems has complicated the production of active recombinant enzyme in high quantities, which would be an alternative for purification of this molecule for crystallization. Consequently, the AGA enzyme has to be purified directly from cellular or tissue sources for crystallographic analysis. Here we describe a large-scale purification method to produce milligram amounts of homogeneous AGA from human leukocytes. The purified AGA enzyme represents a heterogeneous pool of molecules not only due to glycosylation, but also heterogeneity at the polypeptide level, as demonstrated here. We were able to isolate a homogeneous polypeptide pool that was successfully crystallized and preliminary X-ray data collected from the crystals. The crystals diffract well to 2.0 Å and are thus suitable for determination of the crystal structure of AGA.
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  • 81
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    Crystallization and preliminary X-ray analysis of Pit-1 POU domain complexed to a 28 base pair DNA element (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 263-265 
    Details
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; POU-domain ; transcription factor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The POU domain, representing an approximately 150 amino acid conserved region, serves as the DNA-recognition domain for a large number of eukaryotic transcription factors. Bipartite in nature, the POU domain is comprised of a N-terminal POU-specific domain connected by a linker of variable length to a C-terminal homeodomain. We report here co-crystals of pituitary-specific factor Pit-1 POU domain bound as a dimer to a 28 bp DNA fragment. The crystals diffract to at least 2.3 Å in resolution and belong to space group P1 with unit cell dimensions of a = 42.5 Å, b = 50.1 Å, c = 55.8 Å, α = 76.7°, β = 79.3°, and γ = 67.2°.
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  • 82
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    Crystallization and preliminary crystallographic study of the pentamerizing domain from cartilage oligomeric matrix protein: A five-stranded α-helical bundle (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 259-262 
    Details
    ISSN: 0887-3585
    Keywords: coiled-coil ; extracellular matrix ; thrombospondin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cartilage oligomeric matrix protein (COMP) is a pentameric glycoprotein of the thrombospondin family found in cartilage and tendon. Self-association of COMP is achieved through the formation of a five-stranded α-helical bundle that involves 64 N-terminal residues (from 20 to 83). The complex is further stabilized by the interchain disulfide bonds between cysteines 68 and 71. We have prepared, by expression in Escherichia coli, several peptides of different lengths from the N-terminal region of COMP and studied their amenability to crystallization. Crystals of the best quality were obtained with a peptide spanning COMP residues 28-72. This peptide forms disulfide linked pentamers with 87% of α-helical structure. Crystals were grown by the hanging drop vapor diffusion method, using polyethylene glycol 1500 as a precipitant. The crystals belong to space group P21 with unit cell dimensions a = 38.47 Å, b = 49.47 Å, c = 54.98 Å, β = 103.84° and contain one pentamer per asymmetric unit. They diffract strongly to at least 1.8 Å resolution.
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  • 83
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    Crystallization of a mammalian ornithine decarboxylase (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 266-268 
    Details
    ISSN: 0887-3585
    Keywords: polyamines ; group IV decarboxylases ; pyridoxal phosphate ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of truncated (Δ425-461) pyridoxal-5′-phosphate (PLP)-dependent mouse ornithine decarboxylase (mOrnDC′) have been obtained that diffract to 2.2 Å resolution (P21212, a = 119.5 Å, b = 74.3 Å, c = 46.1 Å). OrnDC produces putrescine, which is the precursor for the synthesis of polyamines in eukaryotes. Regulation of activity and understanding of the mechanism of action of this enzyme may aid in the development of compounds against cancer. mOrnDC is a member of group IV PLP-dependent decarboxylases, for which there are no known representative structures.
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  • 84
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    Crystallization and preliminary X-ray characterization of the Methanothermus fervidus histones HMfA and HMfB (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 269-271 
    Details
    ISSN: 0887-3585
    Keywords: Archaea ; hyperthermophiles ; histone fold ; X-ray diffraction ; anomalous dispersion ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: HMfA and HMfB are histone proteins from the thermophilic archaeon Methanothermus fervidus. They wrap DNA into nucleosome-like structures and appear to represent the basic core histone fold. HMfA was crystallized in space groups P42212 and P212121. HMfB crystallized in space group P21212, while a selenomethionine-substituted variant, SeMet-HMfB, yielded crystals in C2221. In all crystal forms HMfA, HMfB, or SeMet-HMfB may be present as homodimers.
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  • 85
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    Masthead (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240201
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  • 86
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    Happy birthday michael rossmann (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340240202
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  • 87
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    Crystallization and preliminary X-ray studies of ornithine decarboxylase from Trypanosoma brucei (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 272-273 
    Details
    ISSN: 0887-3585
    Keywords: polyamines ; pyridoxal phosphate ; drug design ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Trypanosoma brucei ornithine decarboxylase, expressed and purified from E. coli, has been crystallized by the vapor diffusion method using PEG 3350 as a precipitant. The crystals belong to the monoclinic space group P21 and have cell constants of a = 66.3 Å, b = 151.8 Å, c = 83.7 Å, and β = 101.2°. While larger crystals are twinned, smaller crystals (0.4 × 0.3 × 0.05 mm3) are single.
    Additional Material: 1 Tab.
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  • 88
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    Structure conservation in lipoxygenases: Structural analysis of soybean lipoxygenase-1 and modeling of human lipoxygenases (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 275-291 
    Details
    ISSN: 0887-3585
    Keywords: homology modeling ; 5-lipoxygenases ; 12-lipoxygenases ; 15-lipoxygenases ; side chain placement ; arachidonic acid metabolism ; leukotrienes ; lipoxins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Lipoxygenases are a class of non-heme iron dioxygenases which catalyze the hydroperoxidation of fatty acids for the biosynthesis of leukotrienes and lipoxins. The structure of the 839-residue soybean lipoxygenase-1 was used as a template to model human 5-, 12-, and 15-lipoxygenases. A distance-based algorithm for placing side chains in a low homology environment (only the four iron ligands were fixed during side chain placement) was devised. Twenty-six of the 56 conserved lipoxygenase residues were grouped in four distinct regions of the enzyme. These regions were analyzed to discern whether the side chain interactions could be duplicated in the models or whether alternate conformers should be considered. The effects of site directed mutagenesis variants were rationalized using the models of the human lipoxygenases. In particular, variants which shifted positional specificity between 12- and 15-lipoxygenase activity were analyzed. Analysis of active site residues produced a model which accounts for observed lipoxygenase positional specificity and stereospecificity.
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  • 89
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    Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 304-313 
    Details
    ISSN: 0887-3585
    Keywords: protein structure determination by NMR ; distance geometry ; structure calculation with DIANA ; molecular dynamics simulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The NMR solution structure of bovine pancreatic trypsin inhibitor (BPTI) obtained by distance geometry calculations with the program DIANA is compared with groups of conformers generated by molecular dynamics (MD) simulations in explicit water at ambient temperature and pressure. The MD simulations started from a single conformer and were free or restrained either by the experimental NOE distance restraints or by time-averaged restraints; the groups of conformers were collected either in 10 ps intervals during 200 ps periods of simulation, or in 50 ps intervals during a 1 ns period of simulation. Overall, these comparisons show that the standard protein structure determination protocol with the program DIANA provides a picture of the protein structure that is in agreement with MD simulations using “realistic” potential functions over a nanosecond timescale. For well-constrained molecular regions there is a trend in the free MD simulation of duration 1 ns that the sampling of the conformation space is slightly increased relative to the DIANA calculations. In contrast, for surface-exposed side-chains that are less extensively constrained by the NMR data, the DIANA conformers tend to sample larger regions of conformational space than conformers selected from any of the MD trajectories. Additional insights into the behavior of surface side-chains come from comparison of the MD runs of 200 ps or 1 ns duration. In this time range the sampling of conformation space by the protein surface depends strongly on the length of the simulation, which indicates that significant side-chain transitions occur on the nanosecond timescale and that much longer simulations will be needed to obtain statistically significant data on side-chain dynamics.
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  • 90
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    2.0 Å resolution structure of a ternary complex of pig muscle phosphoglycerate kinase containing 3-phospho-D-glycerate and the nucleotide Mn adenylylimidodiphosphate (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 292-303 
    Details
    ISSN: 0887-3585
    Keywords: catalysis ; mechanism ; phosphotransfer ; X-ray diffraction ; crystal ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of a ternary complex of pig muscle phosphoglycerate kinase (PGK) containing 3-phosphoglycerate (3-PG) and manganese adenylylimidodiphosphate (Mn AMP-PNP) has been determined and refined at 2.0 A resolution. The complex differs from the true substrate ternary complex only in the presence of an imido- rather than an oxylink between β- and γ-phosphates of the bound nucleotide. The 3-PG is bound in a similar manner to that observed in binary complexes. The nucleotide is bound in a similar manner to Mg ADP except that the metal ion is coordinated by all three α-, β-, and γ-phosphates, but not by the protein. The γ-phosphate, which is transferred in the reaction, is not bound by the protein. One further characteristic of the ternary complex is that Arg-38 moves to a position where its guanidinium group makes a triple interaction with the N-terminal domain, the C-terminal domain, and the 1-carboxyl group of the bound 3-PG.Although a hinge-bending conformation change is seen in the ternary complex, it is no larger than that observed in the 3-PG binary complex. To reduce that distance between two bound substrates to a value consistent with the direct in-line transfer known to occur in PGK, we modeled the closure of a pronounced cleft in the protein structure situated between the bound substrates. This closure suggested a mechanism of catalysis that involves the “capture” of the γ-phosphate by Arg-38 and the N-terminus of helix-14, which has a conserved Gly-Gly-Gly phosphate binding motif. We propose that nucleophilic attack by the 1-carboxyl group of the 3-PG on the γ-phosphorus follows the capture of the γ-phosphate, leading to a pentacoordinate transition state that may be stabilized by hydrogen bonds donated by the NH groups in the N-terminus of helix 14 and the guanidinium group of Arg-38. During the course of the reaction the metal ion is proposed to migrate to a position coordinating the α- and β-phosphates and the carboxyl group of Asp-374. The mechanism is consistent with the structural information from binary and ternary substrate complexes and much solution data, and gives a major catalytic role to Arg-38, as indicated by site-directed mutagenesis.
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  • 91
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    Structural investigation of the complexation properties between horse spleen apoferritin and metalloporphyrins (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 314-321 
    Details
    ISSN: 0887-3585
    Keywords: X-ray protein crystallography ; structure determination ; anomalous scattering ; protein-porphyrin interaction ; metalloporphyrin demetalation ; multiple alignment ; structural comparison ; ferritin and bacterioferritin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystallographic studies of L-chain horse spleen apoferritin (HSF) co-crystallized with Pt-hematoporphyrin IX and Sn-protoporphyrin IX have brought significant new insights into structure-function relationships in ferritins. Interactions of HSF with porphyrins are discussed. Structural results show that the nestling properties into HSF are dependent on the porphyrin moiety. (Only protoporphyrin IX significantly interacts with the protein, whereas hematoporphyrin IX does not.) These studies additionally point out the L-chain HSF ability to demetalate metalloporphyrins, a result which is of importance in looking at the iron storage properties of ferritins. In both compound investigated (whether the porphyrin reaches the binding site or not), the complexation appears to be concomitant with the extraction of the metal from the porphyrin.To analyze further the previous results, a three-dimensional alignment of ferritin sequences based on available crystallographic coordinates, including the present structures, is given. It confirms a high degree of homology between these members of the ferritin family and thus allows us to emphasize observed structural differences: 1) unlike L-chain HSF, H-chain human ferritin presents no preformed binding site; and 2) despite the absence of axial ligands, and due to the demetalation, L-chain HSF is able to host protoporphyrin at a similar location to that naturally found in bacterioferritin.
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  • 92
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    A theoretical study of torsional flexibility in the active site of aspartic proteinases: Implications for catalysis (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 24 (1996), S. 322-334 
    Details
    ISSN: 0887-3585
    Keywords: aspartic proteinases ; catalysis ; Hartree-Fock calculations ; substrate binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have performed ab initio Hartree-Fock self-consistent field calculations on the active site of endothiapepsin. The active site was modeled as a formic acid/formate anion moiety (representing the catalytic aspartates, Asp-32 and -215) and a bound water molecule. Residues Gly-34, Ser-35, Gly-217, and Thr-218, which all form hydrogen bonds to the active site, were modeled using formamide and methanol molecules. The water molecule, which is generally believed to function as the attacking nucleophile in catalysis, was allowed to bind to the active site in four distinct configurations. The geometry of each configuration was optimized using two basis sets (4-31G and 4-31G*). The results indicate that in the native enzyme the nucleophilic water is bound in a catalytically inert configuration. However, by rotating the carboxyl group of Asp-32 by about 90° the water molecule can be reorientated to attack the scissile bond of the substrate. A model of the bound enzyme-substrate complex was constructed from the crystal structure of a difluorostatone inhibitor complexed with endothiapepsin. This model suggests that the substrate itself initiates the reorientation of the nucleophilic water immediately prior to catalysis by forcing the carboxyl group of Asp-32 to rotate. The theoretical results predict that the active site of endothiapepsin undergoes a large distortion during substrate binding and this observation has been used to explain some of the kinetics results which have been reported for mutant aspartic proteinases.
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    Production and crystallization of a selenomethionyl variant of UmuD′, an Echerichia coli SOS response protein (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 506-509 
    Details
    ISSN: 0887-3585
    Keywords: MAD phasing ; mutagenesis ; auto-digestion ; replication ; dimerization ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of both native and mutant Escherichia coli UmuD′ protein were obtained using the hanging drop method. Soaking the native crystals in solutions of heavy metal ions failed to produce good isomorphous derivatives, and selenomethionine substituted wild-type protein did not crystallize under conditions that gave native crystals. Site-directed mutagenesis was used to change the penultimate residue, a methionine amino acid, to either a valine or a threonine amino acid. Crystals were subsequently obtained from these mutant proteins with and without selenomethionine Incorporation. Crystals of the native, the mutant, and the selenomethionine Incorporated protein were all similar, crystallizing in the P41212 space group. © 1996 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.10
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  • 94
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    Expression, purification, and crystallization of meso-diaminopimelate dehydrogenase from Corynebacterium glutamicum (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 514-516 
    Details
    ISSN: 0887-3585
    Keywords: D-amino acid ; x-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The gene encoding the meso-diaminopimelate dehydrogenase (DAPDH) from Corynebacterium glutamicum was overexpressed and purified to homogeneity. Crystals of the binary DAPDH-NADP+ complex were obtained from solutions of polyethylene glycol 8000, 100 mM sodium cacodylate, pH 6.5, and 150-300 mM Mg(OAc)2. The crystals diffract to 2.2 Å, belong to the orthorhombic space group P21, and contain two molecules per asymmetric unit. © 1996 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.12
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  • 95
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    1996 Johns Hopkins protein folding meeting (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340250402
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  • 96
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    Masthead (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340250301
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  • 97
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    Is the binding of β-amyloid protein to antichymotrypsin in Alzheimer plaques mediated by a β-strand insertion? (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 420-424 
    Details
    ISSN: 0887-3585
    Keywords: serpin ; β-sheet rearrangement ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A growing body of experimental evidence demonstrates that the serpin antichymotrypsin plays a regulatory role in Alzheimer plaque physiology by interacting with the 42 residue β-amyloid protein, and we have used molecular modeling and energy minimization techniques to study this interaction. Based on the unique plasticity of β-sheet elements in antichymotrypsin (as well as other serpins), we conclude that the interaction of the two proteins is mediated by insertion of the N-terminus of β-amyloid into β-sheet C of antichymotrypsin as a pseudo-strand s1C. This β-strand insertion requires the displacement of native antichymotrypsin strand s1C, which is known to occur partially or completely at different stages of serpin function. Thus, the association of the two proteins in vivo may be facilitated by a particular functional state of the serpin, e.g., the native or protease-complexed state. © 1996 Wiley-Liss, Inc.
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    URL: http://dx.doi.org/10.1002/prot.2
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  • 98
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    Electronic Resource
    Quantifying biological specificity: The statistical mechanics of molecular recognition (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 438-445 
    Details
    ISSN: 0887-3585
    Keywords: random energy model ; protein-ligand complexes ; docking ; specific recognition ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Random Energy Model of statistical physics is applied to the problem of the specificity of recognition between two biological (macro)molecules forming a non-covalent complex. In this model, the native mode of association is separated by an energy gap from a large body of non-native modes. Whereas the native mode is unique, the non-native modes form an energy spectrum which is approximated by a gaussian distribution. Specificity can then be estimated by writing the partition function and calculating the ratio r of non-native to native modes at thermodynamic equilibrium. We examine three situations: (i) recognition in the absence of a competitor; (ii) recognition in the presence of a competing ligand; (iii) recognition in a heterogeneous mixture. We derive the dependence of the ratio r on temperature and on the concentration of competing ligands, and we estimate the effect of a local perturbation such as can result from a point mutation. Cases (i) and (iii) are modeled by docking experiments in the computer. In case (iii), which is representative of a wide variety of biological situations, we show that Increasing the heterogeneity of a mixture affects the specificity of recognition, even when the concentration of competing species is kept constant. © 1996 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.4
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  • 99
    Electronic Resource
    Electronic Resource
    Molecular mechanisms of pressure induced conformational changes in BPTI (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 446-455 
    Details
    ISSN: 0887-3585
    Keywords: molecular dynamics ; GROMOS ; high pressure ; unfolding ; denaturation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have performed a 800 ps molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI) in water coupled to a pressure bath at 1, 10,000, 15,000, and 20,000 bar. The simulation reproduces quite well the experimental behavior of the protein under high pressure. The protein keeps its globular form, but adopts a different conformation with a very small reduction in volume. Some residues in the hydrophobic core become exposed to water and a large part of the secondary structure of the protein, (60% of the sheet structure and 40% of the helical structure) is denatured between 10 and 15 kbar. This is in good agreement with experimental data (Goossens, K., et al. Eur. J. Biochem, 236:254-262, 1996) that show denaturation of BPTI between 8 and 14 kbar. A further Increase of the pressure results in a freezing of the protein as deduced from the large decrease of the mobility of the residues. During the simulation, the normal structure of water changes from an ice Ih-like to an ice VI-like structure, while keeping the liquid state. The driving force of the high pressure induced conformational transition seems be the higher compressibility of the water compared with the protein. This produces a change in the solvent properties and leads to penetration of the solvent into the hydrophobic core. © 1996 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.5
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  • 100
    Electronic Resource
    Electronic Resource
    The roles of residues Tyr150, Glu272, and His314 in class C β-lactamases (1996)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 25 (1996), S. 473-485 
    Details
    ISSN: 0887-3585
    Keywords: site-directed mutagenesis ; active-site serine ; tyrosine ; glutamic acid ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Serine β-lactamases contribute widely to the β-lactam resistance phenomena. Unfortunately, the intimate details of their catalytic mechanism remain elusive and subject to some controversy even though many “natural” and “artificial” mutants of these different enzymes have been isolated.This paper is essentially focused on class C β-lactamases, which contain a Tyr (Tyr150) as the first residue of the second conserved element, in contrast to their class A counterparts, in which a Ser is found in the corresponding position. We have modified this Tyr residue by site-directed mutagenesis. On the basis of the three-dimensional structure of the Enterobacter cloacae P99 enzyme, it seemed that residues Glu272 and His314 might also be important. They were similarly substituted. The modified enzymes were isolated and their catalytic properties determined.Our results indicated that His314 was not required for catalysis and that Glu272 did not play an important role in acylation but was involved to a small extent in the deacylation process. Conversely, Tyr150 was confirmed to be central for catalysis, at least with the best substrates.On the basis of a comparison of data obtained for several class C enzyme mutants and in agreement with recent structural data, we propose that the phenolate anion of Tyr150, in conjunction with the alkyl ammonium of Lys315, acts as the general base responsible for the activation of the active-site Ser64 during the acylation step and for the subsequent activation of a water molecule in the deacylation process.The evolution of the important superfamily of penicillin-recognizing enzymes is further discussed in the light of this proposed mechanism. © 1996 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.7
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