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  • Biochemistry and Biotechnology  (28)
  • Wiley-Blackwell  (28)
  • American Institute of Physics (AIP)
  • Blackwell Science Pty
  • Macmillian Magazines Ltd.
  • 1
    ISSN: 0887-3585
    Keywords: protein structure prediction ; supersecondary structure ; genetic algorithm ; solvent accessible surface area ; hydrophobic potential ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We describe an algorithm to compute native structures of proteins from their primary sequences. The novel aspects of this method are: 1) The hydrophobic potential was set to be proportional to the nonpolar solvent accessible surface. To make computation feasible, we developed a new algorithm to compute the solvent accessible surface areas rapidly. 2) The supersecondary structures of each protein were predicted and used as restraints during the conformation searching processes. This algorithm was applied to five proteins. The overall fold of these proteins can be computed from their sequences, with deviations from crystal structures of 1.48-4.48 Å for Cα atoms. Proteins 31:247-257, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 7 Ill.
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  • 2
    ISSN: 0887-3585
    Keywords: helix stabilizing/destabilizing interactions ; helix-capping motifs ; helical boundaries ; structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A novel helix-coil transition theory has been developed. This new theory contains more types of interactions than similar theories developed earlier. The parameters of the models were obtained from a database of 351 nonhomologous proteins. No manual adjustment of the parameters was performed. The interaction parameters obtained in this manner were found to be physically meaningful, consistent with current understanding of helix stabilizing/destabilizing interactions. Novel insights into helix stabilizing/destabilizing interactions have also emerged from this analysis. The theory developed here worked well in sorting out helical residues from amino acid sequences. If the theory was forced to make prediction on every residue of a given amino acid sequence, its performance was the best among ten other secondary structural prediction algorithms in distinguishing helical residues from nonhelical ones. The theory worked even better if one only required it to make prediction on residues that were “predictable” (identifiable by the theory); 〉90% predictive reliability could be achieved. The helical residues or segments identified by the helix-coil transition theory can be used as secondary structural contraints to speed up the prediction of the three-dimensional structure of a protein by reducing the dimension of a computational protein folding problem. Possible further improvements of this helix-coil transition theory are also discussed. Proteins 28:344-359, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
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  • 3
    ISSN: 0887-3585
    Keywords: aldolase ; protein complex crystallization ; crystallization screening ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: X-ray quality crystals of class I deoxyribose-5-phosphate aldolase from Escherichia coli have been obtained for the unliganded enzyme and in complex with its substrate, 2-deoxyribose-5-phosphate. The enzyme catalyzes the reversible cleavage of 2-deoxyribose-5-phosphate to acetaldehyde and D-glyceraldehyde-3-phosphate. The unliganded and complex crystals are prismatic long rods and belong to the orthorhombic space group P212121 with cell dimensions a = 183.1 Å, b = 61.4 Å, c = 49.3 Å and a = 179.2 Å, b = 60.5, Å, c = 49.1 Å, respectively. Two molecules in the asymmetric unit are related by a noncrystallo-graphic 2-fold axis. The crystals are stable in the X-ray beam and diffract to at least 2.6 Å. A new method, reverse screening, designed to minimize protein utilization during the screening process was used to determine supersaturation and crystallization conditions. © 1995 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
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  • 4
    ISSN: 0887-3585
    Keywords: protein conformation ; protein stability ; sensitivity analysis ; avian pancreatic polypeptide (APP) ; molecular dynamics simulation ; OPLS/Amber force field ; continuum solvation model ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Computer simulations utilizing a classical force field have been widely used to study biomolecular properties. It is important to identify the key force field parameters or structural groups controlling the molecular properties. In the present paper the sensitivity analysis method is applied to study how various partial charges and solvation parameters affect the equilibrium structure and free energy of avian pancreatic polypeptide (APP). The general shape of APP is characterized by its three principal moments of inertia. A molecular dynamics simulation of APP was carried out with the OPLS/Amber force field and a continuum model of solvation energy. The analysis pinpoints the parameters which have the largest (or smallest) impact on the protein equilibrium structure (i.e., the moments of inertia) or free energy. A display of the protein with its atoms colored according to their sensitivities illustrates the patterns of the interactions responsible for the protein stability. The results suggest that the electrostatic interactions play a more dominant role in protein stability than the part of the solvation effect modeled by the atomic solvation parameters. © 1995 Wiley-Liss, Inc.
    Additional Material: 10 Ill.
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  • 5
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The reliability of the process of Ramanathan and Gaudy (Biotechnol Bioeng., 13, 125 (1971)) for the completely mixed activated-sludge process holding the recycle cell concentration, XR, as a system constant with respect to step changes in hydraulic retention time was investigated. The experiments were run at initial dilution rates of ⅛, ⅙, ¼, and ½ hr-1 treating a soft drink bottling wastewater. The influent substrate concentration was maintained at 1000 mg/liter chemical oxygen demand and the hydraulic recycle ratio at 0.3. The recycle sludge concentration was maintained at about 7000 mg/liter.It was found that the system could accommodate hydraulic shock loads up to 200% positive changes and down to 50%negative changes without disruption of the effluent quality. Shorter retention time of the range studied, from 2 to 8 hr, has the advantage of shorter response time with respect to the response of the concentration of biological solids in the reactor.
    Additional Material: 8 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 12 (1970), S. 1103-1109 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Enzymes subjected to shearing in a viscometer are partially inactivated. It is possible with viscometry to calculate the degree of inactivation that occura when an enzyme solution flows through a capillary tube. When shear rate × exposure time is less than 104, there is little or no inactivation.The masa average shear-rate × time or shear, for laminar flow in a cylindrical tube is simply 16L/3D. It is surprising that for a single pass through a tube, the masa average shear is independent of flow rate and shear rate.
    Additional Material: 5 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 20 (1978), S. 917-920 
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Additional Material: 1 Tab.
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  • 8
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Steam explosion after sulphur dioxide impregnation of wood chips is an effective method for improving the enzymatic digestibility of cellulose in the softwood Pinus radiata. Digestibility of pretreated fiber was progressively increased by altering the conditions of steam explosion. With increasing digestibility, there was an observed increase in fiber porosity as measured by the solute exclusion technique. Accessible pore volume and accessible surface area to a 5-nm dextran probe positively correlated with both 2- and 24-h digestion yields from pretreated fiber. The increase in accessibility was probably the result of hemicellulose extraction and lignin redistribution. A subsequent loss in accessibility, brought about by structural collapse or further lignin redistribution, resulted in a corresponding loss in digestibility. It appears that steam explosion increases cellulose digestibility in P. radiata by increasing fiber porosity.
    Additional Material: 5 Ill.
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  • 9
    ISSN: 0006-3592
    Keywords: xylanase ; kraft pulp ; peroxide bleaching ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The effects of multiple xylanase treatments were assessed during the peroxide bleaching of three pulps: Douglas-fir (kraft); Western hemlock (oxygen delignified kraft); and trembling Aspen (kraft). The addition of a xylanase treatment stage, either before or after the peroxide bleaching stage(s), resulted in the enhanced brightening of all pulps. A higher brightness was achieved using two enzyme treatments, one before and one after the peroxide stage(s). Both bleach boosting and direct brightening seemed to contribute to the enhancement of the peroxide bleaching. Compared to xylanase prebleaching, xylanase posttreatment of peroxide bleached pulps solubilized less lignin and chromophores and made smaller amounts of these materials alkaline soluble. Nevertheless, the final brightness achieved by xylanase posttreatment was similar or superior to that achieved with xylanase prebleaching of the corresponding unbleached pulps. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 54: 312-318, 1997.
    Additional Material: 5 Ill.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 55 (1997), S. 556-564 
    ISSN: 0006-3592
    Keywords: cumulative sedimentation analysis ; cell debris size ; Escherichia coli ; homogenization ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A new method to measure Escherichia coli cell debris size after homogenization is presented. It is based on cumulative sedimentation analysis under centrifugal force, coupled with Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) analysis of sedimented proteins. The effects that fermentation and homogenization conditions have on the resulting debris distributions were investigated using this method. Median debris size decreased significantly from approximately 0.5 μm to 0.3 μm as the number of homogenization passes increased from 2 to 10. Under identical homogenization conditions, uninduced host cells in stationary phase had a larger debris size than exponential cells after 5 homogenizer passes. This difference was not evident after 2 or 10 passes, possibly because of confounding intact cells and the existence of a minimum debris size for the conditions investigated. Recombinant cells containing protein inclusion bodies had the smallest debris size following homogenization. The method was also used to measure the size distribution of inclusion bodies. This result compared extremely well with an independent determination using centrifugal disc photosedimentation (CDS), thus validating the method. This is the first method that provides accurate size distributions of E. coli debris without the need for sample pretreatment, theoretical approximations (e.g. extinction coefficients), or the separation of debris and inclusion bodies prior to analysis. © 1997 John Wiley & Sons, Inc. Biotechnol Bioang 55: 556-564, 1997.
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