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  • Biochemistry and Biotechnology  (7)
  • Computational Chemistry and Molecular Modeling  (5)
  • 1
    Electronic Resource
    Electronic Resource
    Continuum electrostatics and hydration phenomena (1988)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 34 (1988), S. 103-118 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A formalism for a computational treatment of the polarization of a solvent and polar solutes immersed in it is presented. The solvent is modeled as a continuum dielectric. Polarization effects are represented by a polarization charge density at the dielectric boundaries and by induced dipoles at the polarizable atoms. Applications of this formalism with nonpolarizable atoms have led to excellent agreement between the calculated and experimental hydration enthalpies of a variety of polar molecules. A problem of the choice of the charge distribution of the solute is addressed in calculations of the solution dipole moment and hydration enthalpy of polarizable molecule of water in solution. Experimental values of these properties were well reproduced in calculations starting with point charges fitted to the vacuum dipole moment of the water molecule. Tests calculations for spherical models and for a 13-residue peptide show good convergence of the computational method. It is shown in calculations on simplified models that a change in the exposure of a charged side chain can lead to large changes in the potential inside protein measured at a fixed distance from the charge and at the same depth from the protein surface. Calculations performed for the C-peptide of the ribonuclease suggest that the differential screening of partial charges can reverse the sign of the vacuum potential of the helix dipole.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560340711
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  • 2
    Electronic Resource
    Electronic Resource
    Continuum electrostatics of the C-peptide: Anatomy of the problem (1992)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 13 (1992), S. 120-131 
    Details
    ISSN: 0887-3585
    Keywords: protein folding ; α-helix ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A computational study of the role of all ionizable groups of the C-peptide in its helix-coil transition is performed within the framework of continuum electrostatics. The method employed in our computations involves a numeric solution of the Poisson equation with the Boundary Element Method. Our calculations correctly predict the experimentally observed trends in the helix-coil equilibrium of the C-peptide, and suggest that the mechanisms involved are more complex than usually presumed in the literature. Our results suggest that electrostatic interactions in the unfolded conformation are often more important than in the helix, total electrostatic contribution to the helix-coil transition due to the side chains of the C-peptide destabilizes the helix, changes in the helix stability produced by the changes in the ionization state of the side chains are dominated by side chain effects, the effect of the helix dipole on the energetics of the helix-coil transition of the C-peptide is either minor or similar to other contributions in magnitude; while the formation of a salt bridge is electrostatically favorable, formation of the hydrogen bond between a charged and a polar side chains is not. Factors limiting the accuracy of the computations are discussed. © 1992 Wiley-Liss, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340130205
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  • 3
    Electronic Resource
    Electronic Resource
    Recombinant antineuraminidase single chain antibody: Expression, characterization, and crystallization in complex with antigen (1993)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 16 (1993), S. 57-63 
    Details
    ISSN: 0887-3585
    Keywords: X-ray crystallography ; antibody domain ; recombinant DNA ; binding affinity ; antigen-antibody complex ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The variable heavy (VH) and variable light (VL) genes of NC10, a monoclonal antibody with specificity toward N9 neuraminidase (NA), were cloned and sequenced. A single chain Fv (scFv) fragment of NC10, consisting of VH and VL domains joined by a peptide linker, was designed, constructed and expressed in the E. coli expression vector pPOW. The N-terminal secretion signal PelB directed the synthesized protein into the periplasm where it was associated with the insoluble membrane fraction. An octapeptide (FLAG) tail was fused to the C-terminus of the single chain Fv to aid in its detection and remained intact throughout the protein purification process. NC10 scFv was purified by solubilization of the E. coli membrane fraction with guanidinium hydrochloride followed by column chromatography. The purified NC10 scFv showed binding affinity for its antigen, NA, 2-fold lower than that of the parent Fab. The complex between NA and the scFv has been crystallized by the vapor diffusion method. The crystals are tetragonal, space group P4212, with unit cell dimensions a = b = 141 Å, c = 218 Å. © 1993 Wiley-Liss, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340160107
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  • 4
    Electronic Resource
    Electronic Resource
    The structure of the complex between influenza virus neuraminidase and sialic acid, the viral receptor (1992)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 14 (1992), S. 327-332 
    Details
    ISSN: 0887-3585
    Keywords: crystallographic ; neuraminidase ; influenza virus ; sialic acid ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystallographic studies of neuraminidase-sialic acid complexes indicate that sialic acid is distorted on binding the enzyme. Three arginine residues on the enzyme interact with the carboxylate group of the sugar which is observed to be equatorial to the saccharide ring as a consequence of its distorted geometry. The glycosidic oxygen is positioned within hydrogen-bonding distance of Asp-151, implicating this residue in catalysis. © 1992 Wiley-Liss, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340140302
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  • 5
    Electronic Resource
    Electronic Resource
    Roughness of the globular protein surface: Analysis of high resolution X-ray data (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 28 (1997), S. 194-201 
    Details
    ISSN: 0887-3585
    Keywords: accessible and molecular surfaces ; fractal and topological dimensions ; yardstick ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: In an earlier publication [Serdyuk, I.N. et al., Biofizika, in press, 1997] we demonstrated that the asymmetry extent of globular proteins does not change with increasing their sizes, and the observed nontrivial dependence of the protein accessible surface area on the molecular mass [Miller, S., J. Mol. Biol. 196:641-656, 1987] (As - M dependence) is a reflection of the protein surface relief peculiarities. To clarify these peculiarities, an analysis of the molecular surface on the basis of high-resolution x-ray data has been done for 25 globular proteins not containing prosthetic groups. The procedure was based on studying the dependence of the minimal number (N) of probe bodies (here cubes) covering the entire protein surface, both on their size (N - R dependence) and on the value of dry protein volume (N - V dependence). Two levels of protein surface organization have been detected by molecular surface analysis. On the micro scale (2-7 Å), the surface is characterized by a D = 2.1 fractal dimension which is intrinsic to surfaces with weak deformations and reflects the local atomic group packing. On the macro scale, large-scale surface defects are revealed that are interpreted as the result of secondary structure elements packing. A simple model of protein surface representation reflecting large-scale irregularities has been proposed. Proteins 28:194-201, 1997. © 1997 Wiley-Liss Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Stable isotope engineering in life studies (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 30 (1987), S. 798-798 
    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.260300615
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  • 7
    Electronic Resource
    Electronic Resource
    Influence of mass transfer and surface ligand heterogeneity on quantitative BIAcoreTM binding data. Analysis of the interaction of NC10 Fab with an anti-idiotype Fab′ (1997)
    Chicester [u.a.] : Wiley-Blackwell
    Journal of Molecular Recognition 10 (1997), S. 148-158 
    Details
    ISSN: 0952-3499
    Keywords: BIAcoreTM ; kinetics ; rate constants ; mass transfer ; ligand heterogeneity ; solution equilibrium constant ; protein-protein interaction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The interaction of monovalent Fab fragments of NC10, an antiviral neuraminidase antibody, and the anti-idiotype antibody 3-2G12 has been used as a model system to demonstrate experimentally the influence of non-ideal binding effects on BIAcoreTM binding data. Because the association rate constant for these two molecules was found to be relatively high (about 5×105 M-1 s-1), mass transfer was recognised as a potential source of error in the analysis of the interaction kinetics. By manipulation of the flow rate and the surface density of the immobilised ligand, however, the magnitude to this error was minimised. In addition, the application of site-specific immobilisation procedures was found to improve considerably the correlation of experimental binding data to the ideal 1:1 kinetic model such that the discrepancy between experimental and fitted curves was within the noise range of the instrument. Experiments performed to measure the equilibrium constant (KD) in solution resulted in a value of similar magnitude to those obtained from the ratio of the kinetic rate constants, even those measured with a heterogeneous ligand or with a significant mass transfer component. For this system, the experimental complexities introduced by covalent immobilisation did not lead to large errors in the KD values obtained using the BIAcore © 1997 John Wiley & Sons, Ltd.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Extension of MNDO to d orbitals: Parameters and results for the halogens (1992)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 44 (1992), S. 807-829 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A recently proposed extension of the MNDO formalism to d orbitals has been parameterized for the halogens CI, Br, and I. Extensive test calculations indicate slight consistent improvements for normalvalent molecules and dramatic improvements for hypervalent molecules, in comparison with established MNDO-type methods without d orbitals. The mean absolute errors in calculated heats of formation are 3.9 kcal/mol for 155 normalvalent compounds and 2.8 kcal/mol for 23 hypervalent compounds. The predicted structures of the hypervalent molecules are qualitatively correct, with a mean absolute error of 2° in 19 bond angles.
    Additional Material: 7 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560440511
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  • 9
    Electronic Resource
    Electronic Resource
    Determination of bupivacaine and three of its metabolites in rat urine by capillary electrophoresis (1998)
    Weinheim : Wiley-Blackwell
    Electrophoresis 19 (1998), S. 2997-3002 
    Details
    ISSN: 0173-0835
    Keywords: Capillary electrophoresis ; Bupivacaine ; Bupivacaine metabolites ; Drug analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: A capillary electrophoretic (CE) method for the analysis of urinary extracts of the local anesthetic, bupivacaine, and its three main metabolites, desbutylbupivacaine, 3′-hydroxybupivacaine, and 4′-hydroxybupivacaine, in rat urine has been developed. The limits of detection were 0.22 μM for desbutylbupivacaine and bupivacaine, 0.15 μM for 3′-hydroxybupivacaine, and 0.16 μM for 4′-hydroxybupivacaine. The linear range was from 0.7 μM to 16.8 μM for all four compounds. Migration time and peak height reproducibilities, and extraction efficiencies were determined for all four compounds. Peak height reproducibilities (n = 5) for the overall method were improved through the use of prilocaine as an internal standard. Peak height reproducibilities were 5.6% RSD for desbutylbupivacaine and bupivacaine, and 9.9% RSD for 3′-hydroxybupivacaine and 4′-hydroxybupivacaine. Migration time reproducibilities (n = 5) were 2.4% for all compounds. Urine samples were collected from rats administered therapeutic doses of bupivacaine and extracted using a solid-phase extraction method (SPE). Separation of bupivacaine and its metabolites was achieved in 15 min.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150191633
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  • 10
    Electronic Resource
    Electronic Resource
    Implementation of artificial intelligence for automatic drug design. I. Stepwise computation of the interactive drug-design sequence (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1393-1402 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article we represent the development of an artificial-intelligence-based method for the automatic design of valid chemical structures (AISD). The key feature of the proposed algorithm is its ability to mimic many decision-making processes carried by the human drug designer during a design session. The manual drug-design process is analyzed and transformed into a computerized form by associating a weight factor with each term. These weights enable the translation of the drug designer's intution into probabilities that control the flow of the design process. The input required to initiate a design session might be as minimal as the geometry of a previously existed pharmacophoric model, up to the three-dimensional geometry of the host receptor. A design application is demonstrated by the implementation of the proposed algorithm for the design of new potent sweeteners. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151209
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