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  • 1
    Electronic Resource
    Electronic Resource
    Hybrid immunoglobulin isotypes of identical specificity produced by genetic recombination in Escherichia coli and expression in lymphoid cellsThis work was performed at the Department of Biological Sciences, Stanford University and Becton Dickinson Immunocytometry Systems, Mountain View, CA. (1987)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 2 (1987), S. 81-89 
    Details
    ISSN: 0887-3585
    Keywords: hybrid immunologlobulin ; compatible plasmids ; transfection ; mouse IgG1 ; mouse IgG2a ; dansyl ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We have produced a series of hybrid IgG1-IgG2a mouse immunoglobulins with identical light chains (L) and variable regions to facilitate the identification of structural features associated with functional differnces between immunoglobulin isotypes. Hybrid heavy chain (H) constant region gene segments were generated by genetic recombination in Escherichia coli between plasmids carrying mouse γ1 and γ2a gene segments. Crossovers occured through out these segments although the frequency was highest in regions of high nucleotide sequence homology. Eleven variant immunoglobulins produced by transfected hybridoma cell lines are assembled into H2L2 tetramers and properly glycosylated. In addition, all 11 immunoglbulins have identical antigen combining sites specific for the fluorescent hapten ε-dansyll-L-lysine. Protein A binding was used as probe of the structural integrity of the Fc portion of the variant antibodies. Differeneces in protein A binding between IgG1 and IgG2a appear to be due to amino acid differances at postions 252 (Thr→Met) and 254 (Thr→Ser) of the heavy chain (EU numbering).
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340020203
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  • 2
    Electronic Resource
    Electronic Resource
    Correlated mutations and residue contacts in proteins (1994)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 18 (1994), S. 309-317 
    Details
    ISSN: 0887-3585
    Keywords: protein structure prediction ; predicted contact maps ; correlated mutations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The maintenance of protein function and structure constrains the evolution of amino acid sequences. This fact can be exploited to interpret correlated mutations observed in a sequence family as an indication of probable physical contact in three dimensions. Here we present a simple and general method to analyze correlations in mutational behavior between different positions in a multiple sequence alignment. We then use these correlations to predict contact maps for each of 11 protein families and compare the result with the contacts determined by crystallography. For the most strongly correlated residue pairs predicted to be in contact, the prediction accuracy ranges from 37 to 68% and the improvement ratio relative to a random prediction from 1.4 to 5.1. Predicted contact maps can be used as input for the calculation of protein tertiary structure, either from sequence information alone or in combination with experimental information. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340180402
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  • 3
    Electronic Resource
    Electronic Resource
    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.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Database of homology-derived protein structures and the structural meaning of sequence alignment (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 9 (1991), S. 56-68 
    Details
    ISSN: 0887-3585
    Keywords: secondary structure ; tertiary structure ; residue conservation ; sequence variability ; sequence profile ; folding units ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The database of known protein three-dimensional structures can be significantly increased by the use of sequence homology, based on the following observations. (1) The database of known sequences, currently at more than 12,000 proteins, is two orders of magnitude larger than the database of known structures. (2) The currently most powerful method of predicting protein structures is model building by homology. (3) Structural homology can be inferred from the level of sequence similarity. (4) The threshold of sequence similarity sufficient for structural homology depends strongly on the length of the alignment. Here, we first quantify the relation between sequence similarity, structure similarity, and alignment length by an exhaustive survey of alignments between proteins of known structure and report a homology threshold curve as a function of alignment length. We then produce a database of homology-derived secondary structure of proteins (HSSP) by aligning to each protein of known structure all sequences deemed homologous on the basis of the threshold curve. For each known protein structure, the derived database contains the aligned sequences, secondary structure, sequence variability, and sequence profile. Tertiary structures of the aligned sequences are implied, but not modeled explicity. The database effectively increases the number of known protein structures by a factor of five to more than 1800. The results may be useful in assessing the structural significance of matches in sequence database searches, in deriving preferences and patterns for structure prediction, in elucidating the structural role of conserved residues, and in modeling three-dimensional detail by homology.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340090107
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  • 5
    Electronic Resource
    Electronic Resource
    Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 49-60 
    Details
    ISSN: 0887-3585
    Keywords: kohonen network ; mitochondrial processing peptidase (MPP) ; mitochondrial intermediate peptidase (MIP) ; neural network ; protein import ; sequence motif ; mitochondrial targeting ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Cleavage sites in nuclear-encoded mitochondrial protein targeting peptides (mTPs) from mammals, yeast, and plants have been analysed for characteristic physicochemical features using statistical methods, perceptrons, multilayer neural networks, and self-organizing feature maps. Three different sequence motifs were found, revealing loosely defined arginine motifs with Arg in positions -10, -3, and -2. A self-organizing feature map was able to cluster these three types of endopeptidase target sites but did not identify any species-specific characteristics in mTPs. Neural networks were used to define local sequence features around precursor cleavage sites. Proteins 30:49-60, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Electrostatic fields at the active site of ribulose-1,5-bisphosphate carboxylase (1992)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 12 (1992), S. 117-127 
    Details
    ISSN: 0887-3585
    Keywords: photosynthesis ; photorespiration ; Rubisco ; protein engineering ; protein electrostatics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A macroscopic approach has been employed to calculate the electrostatic potential field of nonactivated ribulose-1,5-bis-phosphate carboxylase and of some complexes of the enzyme with activator and substrate. The overall electrostatic field of the L2-type enzyme from the photosynthetic bacterium Rhodospirillum rubrum shows that the core of the dimer, consisting of the two C-terminal domains, has a predominantly positive potential. These domains provide the binding sites for the negatively charged phosphate groups of the substrate. The two N-terminal domains have mainly negative potential. At the active site situated between the C-terminal domain of one subunit and the N-terminal domain of the second subunit, a large potential gradient at the substrate binding site is found. This might be important for polarization of chemical bonds of the substrate and the movement of protons during catalysis. The immediate surroundings of the activator lysine, K191, provide a positive potential area which might cause the pK value for this residue to be lowered. This observation suggests that the electrostatic field at the active site is responsible for the specific carbamylation of the ε-amino group of this lysine side chain during activation. Activation causes a shift in the electrostatic potential at the position of K166 to more positive values, which is reflected in the unusually low pK of K166 in the activated enzyme species. The overall shape of the electrostatic potential field in the L2 building block of the L8S8-type Rubisco from spinach is, despite only 30% amino acid homology for the L-chains, strikingly similar to that of the L2-type Rubisco from Rhodospirillum rubrum. A significant difference between the two species is that the potential is in general more positive in the higher plant Rubisco. In particular, the second phosphate binding site has a considerably more positive potential, which might be responsible for the higher affinity for the substrate of L8S8-type enzymes. The higher potential at this site might be due to two remote histidine residues, which are conserved in the plant enzymes.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340120205
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  • 7
    Electronic Resource
    Electronic Resource
    Controlled pH and oxidation-Reduction potential with a new glass tissue-culture fermentor (1965)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 7 (1965), S. 529-553 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A 1-l. fermentor was designed and tested for use as a tissue-culture vessel. It features a temperature control device, impeller agitation without the necessity of a shaft seal, and a means of measuring, recording, and controlling both pH and oxidation-reduction potential (ORP). Tests have shown the ORP to change fairly rapidly with impeller speed variations under conditions of a continuous carbon dioxide-air overlay. Working with strain L mouse fibroblasts (Earle), cell counts of more than 1.25 ×106 ml., without centrifugation and medium renewal, were achieved, and cell counts were maintained above 1 ×106 for more than 30 hr. With the vessel studied, pH control was ±0.05, the ORP control was ±10 mV. Controlled environments for tissue-cell metabolic studies are entirely feasible with this system.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260070408
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  • 8
    Electronic Resource
    Electronic Resource
    A model for enzymatic isomerization of D-glucose to D-fructose in a batch reactor (1976)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 18 (1976), S. 633-648 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Using whole cells containing glucose isomerase, mathematical models for the enzymatic conversion of D-glucose to D-fructose and for the inactivation of the enzyme catalyst have been postulated and verified experimentally. The heat of reaction, the equilibrium constant, and the individual rate constants and their activation energies have been estimated. The model can be used to predict the time course for the enzymatic production of fructose in a batch reactor within the tested experimental range of 40-80°C.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260180504
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  • 9
    Electronic Resource
    Electronic Resource
    Stabilization of soluble and immobilized horse liver alcohol dehydrogenase by adenosine 5′-monophosphate (1984)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 26 (1984), S. 998-1002 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Horse liver alcohol dehydrogenase, which catalyzes oxidoreductions for a broad spectrum of substrates of organic chemical interest, was immobilized on CNBr-activated Sepharose and on decylamine-substituted agarose. The specific activities of the immobilized enzyme preparations were compared with the free enzyme, and the apparent Km values of the preparations were determined for a selection of substrates. At pH 9 and 60°C, soluble liver alcohol dehydrogenase was rapidly inactivated, while the enzyme immobilized on CNBr-activated Sepharose was more stable. Adenosine monophosphate (AMP), adenosine diphosphate, and adenosine diphosphoribose protected the free and immobilized alcohol dehydrogenase against heat inactivation. On storage under a variety of conditions, AMP effectively stabilized free horse liver alcohol dehydrogenase and the immobilized preparations.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260260827
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  • 10
    Electronic Resource
    Electronic Resource
    A three-dimensional solubility parameter approach to nonaqueous enzymology (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 37 (1991), S. 627-638 
    Details
    ISSN: 0006-3592
    Keywords: solubility parameters ; hydrophobicity index ; Hansen parameter ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Widespread commercial application of enzymes as catalysts for specialty or commodity chemical synthesis will require their use in nonaqueous systems. While a number of non-aqueous enzyme applications have been demonstrated, the lack of useful rules for predicting enzyme-solvent interactions has hindered the development of this technology. Both Hildebrand and solvent hydrophobicity (octanol-water partition coefficient) parameters have been used previously to correlate and predict enzyme activity in nonaqueous systems, with some success, but any single-parameter approach is inherently limited in its ability to reflect the spectrum of possible enzyme-solvent interactions. Therefore, this study evaluates the three-dimensional solubility parameter space, as proposed by Hansen, to correlate and predict enzyme activity in microaqueous, miscible, and biphasic nonaqueous systems. Preliminary results suggest that Hansen parameters may be useful for correlating nonaqueous enzyme activity, and that the dispersive and polar parameters may be disproportionately important in single-phase microaqueous systems. The Hansen hydrogen-bonding parameter appears to be the only parameter yet evaluated capable of correlating the water requirement for enzyme activity in microaqueous systems, suggesting that water affects protein structure through enthalpic rather than entropic processes in nonaqueous systems. Insufficient data are available for miscible and biphasic systems, but it is proposed that enzyme activity may correlate with the average solubility parameters of miscible systems and of the aqueous phase in biphasic systems.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260370705
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