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  • Articles: DFG German National Licenses  (18)
  • Biochemistry and Biotechnology  (18)
  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 616-629 
    ISSN: 0006-3592
    Keywords: cell adhesion ; radial-flow chamber ; hydrodynamic shear ; detachment kinetics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The strength of adhesion and dynamics of detachment of murine 3T3 fibroblasts from self-assembled monolayers were measured in a radial-flow chamber (RFC) by applying models for fluid mechanics, adhesion strength probability distributions, and detachment kinetics. Four models for predicting fluid mechanics in a RFC were compared to evaluate the accuracy of each model and the significance of inlet effects. Analysis of these models indicated an outer region at large radial positions consistent with creeping flow, an intermediate region influenced by inertial dampening, and an inner region dominated by entrance effects from the axially-oriented inlet. In accompanying experiments patterns of the fraction of cells resisting detachment were constructed for individual surfaces as a function of the applied shear stress and evaluated by comparison with integrals of both a normal and a log-normal distribution function. The two functions were equally appropriate, yielding similar estimates of the mean strength of adhesion. Further, varying the Reynolds number in the inlet, Red, between 630 and 1480 (corresponding to volumetric flow rates between 0.9 and 2.1 mL/s) did not affect the mean strength of adhesion. For these same experiments, analysis of the dynamics of detachment revealed three temporal phases: 1) rapid detachment of cells at the onset of flow, consistent with a first-order homogeneous kinetic model; 2) time-dependent rate of detachment during the first 30 sec. of exposure to hydrodynamic shear, consistent with the first-order heterogeneous kinetic model proposed by Dickinson and Cooper (1995); and 3) negligible detachment, indicative of pseudo-steady state after 60 sec. of flow. Our results provide rigorous guidelines for the measurement of adhesive interactions between mammalian cells and prospective biomaterial surfaces using a RFC. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 616-629, 1997.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 2
    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.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 421-433 
    ISSN: 0887-3585
    Keywords: molecular recognition ; binding energy landscapes ; recognition nucleus ; structural harmony ; minimal frustration principle ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Computational structure prediction of streptavidin-peptide complexes for known recognition sequences and a number of random di-, tri-, and tetrapeptides has been conducted, and mechanisms of peptide recognition with streptavidin have been investigated by a new computational protocol. The structural consensus criterion, which is computed from multiple docking simulations and measures the accessibility of the dominant binding mode, identifies recognition motifs from a set of random peptide sequences, whereas energetic analysis is less discriminatory. The predicted conformations of recognition tripeptide and tetrapeptide sequences are also in structural harmony and composed of peptide fragments that are individually unfrustrated in their bound conformation, resulting in a minimally frustrated energy landscape for recognition peptides. Proteins 28:421-433, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 59-67 
    ISSN: 0887-3585
    Keywords: blind trials ; CASP2 ; homology modelling ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The CASP blind trials (Critical Assessment of techniques for protein Structure Prediction) assess the accuracy of protein prediction that includes evaluation of comparative model building of protein structures. Comparative models of four proteins (T0001, T0003, T0017, and T0028) for CASP2 (held during 1996) were constructed using computer algorithms combined with visual inspection. Essentially the main-chain modelling involves construction of the target structure from rigid-body segments of homologues and loop fragments extracted from homologous and nonredundant databases. Side-chains were initially constructed by inheritance from the parent or from a rotamer library. Side-chain conformations were then refined using a novel mean field approach that includes solvation. Comparison of the models with the subsequently released X-ray structures identified the successes and limitations of our approach. The most problematic area is the quality of the sequence alignments between parent(s) and target. In this respect the overinterpretation of the conserved features within homologous families can be misleading. Several features of our approach have a positive effect on the accuracy of the models. For T0003, inspection correctly identified that a lower sequence identity parent provides the best framework for this model. Loop selection worked well where a homologous protein fragment was used, but that the use of nonredundant fragment library remains problematic for hinge movements and displacements in secondary structure elements relative to the parent. Side-chain refinement improved residue conformations relative to the initial model. Use of limited energy minimization improved the stereochemical quality of the model without increasing the RMS deviation. This study has identified methods that are effective and areas requiring further attention to improve model building by comparison. Proteins, Suppl. 1:59-67, 1997. © 1998 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 313-324 
    ISSN: 0887-3585
    Keywords: molecular docking ; receptor-specific binding ; binding energy landscapes ; structural water molecules ; minimal frustration principle ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Mean field analysis of FKBP12 complexes with FK506 and rapamycin has been performed by using structures obtained from molecular docking simulations on a simple, yet robust molecular recognition energy landscape. When crystallographic water molecules are included in the simulations as an extension of the FKBP12 protein surface, there is an appreciable stability gap between the energy of the native FKBP12-FK506 complex and energies of conformations with the “native-like” binding mode. By contrast, the energy spectrum of the FKBP12-rapamycin complex is dense regardless of the presence of the water molecules. The stability gap in the FKBP12-FK506 system is determined by two critical water molecules from the effector region that participate in a network of specific hydrogen bond interactions. This interaction pattern protects the integrity and precision of the composite ligand-protein effector surface in the binary FKBP12-FK506 complex and is preserved in the crystal structure of the FKBP12-FK506-calcineurin ternary complex. These features of the binding energy landscapes provide useful insights into specific and nonspecific aspects of FK506 and rapamycin recognition. Proteins 28:313-324, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 19 (1977), S. 1417-1417 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: NO Abstract.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 19 (1977), S. 365-375 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Invertase from Candida utilis was immobilized on porous cellulose beads by an ionic-quanidino bond. The immobilized invertase showed optimum activity between pH 4.0 and 5.4, while the free enzyme had a sharp optimum at pH 4.1. Both temperature profiles were fairly similar up to 55°C. However, above this temperature the immobilized enzyme was more stable than the free enzyme. From the temperature data, the activation energies were found to be 7,322 and 4,052 cal/g mol for the free and the immobilized enzyme, respectively.Candida invertase shows characteristics of substrate inhibition. Both the Km and Ki for the free and the immobilized enzymes were determined. The apparent Ki for the immobilized invertase was much higher than the Ki of the free enzyme, suggesting a diffusion effect. Immobilized invertase molecules deep in the pores only see sucrose concentrations much less than the bulk concentrations. Immobilization, thus, offers certain processing advantages in this regard.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 23 (1981), S. 1067-1078 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The conversion of the enzymatic hydrolysate of shellfish chitin waste to single-cell protein was investigated as part of a comprehensive waste treatment program. Forty-two yeasts were screened for ability to assimilate the monomer of chitin, N-acetylglucosamine, which has been shown to be the sole product of enzymatic hydrolysis of chitin. The Yeast Pichia Kudriavzevii was selected for study, based on ability to grow at high temperature (37°C and above), low pH (4.0 ± 0.5), and in a nutritionally simple medium. Growth rates of P. kudriavzevii were similar on N-acetylglucosamine and on the chitin hydrolysate. Dependencies of specific growth rate on temperature, pH, medium composition, and oxygen tension were studied. The variations of yield, protein content, and total nucleic acid content with the specific growth rate were evaluated. The amino acid distribution of the protein of P. kudriavzevii was obtained.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 27 (1985), S. 769-775 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: As part of the development of a comprehensive mathematical model for chitinase production by Serratia marcescens QMB 1466 growing on chitin, the different mass transport and kinetic steps involved during chitin hydrolysis were studied. The experimental results for the hydrolysis of chitin by a crude preparation of chitinase show a system kinetically limited by the overall rate of chitin hydrolysis. This rate is linearly related to the concentration of enzyme adsorbed on the chitin particle. Adsorbed and bulk enzyme concentration were found to be related through a Langmuir type of isotherm.
    Additional Material: 6 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 40 (1992), S. 735-742 
    ISSN: 0006-3592
    Keywords: subtilisin ; computer modeling ; enantioselectivity ; enzymes ; organic solvents ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: In order to rationalize our discovery of a marked dependence of subtilisin's enantioselectivity on the organic solvent used as the reaction medium, we empolyed the X-ray crystal structure of the enzyme and the means of interactive computer modeling to construct the structures of the reactive enzyme-substrate complexes. For subtilisin-catalyzed transesterifications between vinyl butyrate and S and R enantiomers of chiral secondary alcohols XCH(OH)Y, the computer simulation data clearly explain a higher reactivity of the former enantiomer on the basis of severe steric hindrances experienced by the latter enantiomer in the active site of subtilisin. The models of binding derived by computer modeling also successfully predicted changes in subtilisin enantioselectivity as a function of the sizes of the X and Y substituents in the nucleophile and upon addition of certain inhibitors. © 1992 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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