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  • Polymer and Materials Science  (4)
  • united-residue representation of a polypeptide chain  (2)
  • 1995-1999  (3)
  • 1980-1984  (3)
  • 1
    Electronic Resource
    Electronic Resource
    Helix-coil stability constants for amino acids in nonaqueous solvents. Studies of random poly(γ-benzyl-L-glutamate-co-L-alanine) and poly(γ-benzyl-L-glutamate-co-L-leucine) in a mixed solvent (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1435-1458 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The host-guest technique has been applied to the determination of the helix-coil stability constants of two naturally occurring amino acids, L-alanine and L-leucine, in a nonaqueous solvent system. Random copolymers containing L-alanine and L-leucine, respectively, as guest residues and γ-benzyl-L-glutamate as the host residue were synthesized. The polymers were fractionated and characterized for their amino acid content, molecular weight, and helix-coil transition behavior in a dichloroacetic acid (DCA)-1,2-dichloroethane (DCE) mixture. Two types of helix-coil transitions were carried out on the copolymers: solvent-induced transitions in DCA-DCE mixtures at 25°C and thermally induced transitions in a 82:18 (wt %) DCA-DCE mixture. The thermally induced transitions were analyzed by statistical mechanical methods to determine the Zimm-Bragg parameters, σ and s, of the guest residues. The experimental data indicate that, in the nonaqueous solvent, the L-alanine residue stabilizes the α-helical conformation more than the L-leucine residue does. This is in contrast to their behavior in aqueous solution, where the reverse is true. The implications of this finding for the analysis of helical structures in globular proteins are discussed.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1981.360200707
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  • 2
    Electronic Resource
    Electronic Resource
    Comparison of explicit and implicit treatments of solvation: Application to angiotensin II (1997)
    New York : Wiley-Blackwell
    Biopolymers 42 (1997), S. 363-371 
    Details
    ISSN: 0006-3525
    Keywords: surface area ; molecular dynamics ; Monte Carlo simulation ; free energy of hydration ; solvent effects ; angiotensin II ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: As a test for comparing explicit and implicit treatments of solvation, conformational analyses of the octapeptide angiotensin II have been carried out using molecular dynamics and Monte Carlo simulations. The molecular dynamics treatment uses an explicit atomic description of the solvent whereas a solvent-accessible surface-area calculation is introduced in the Monte Carlo procedure in order to mimic the effect of the solvent surrounding the solute molecule. Several hydration models proposed in the literature have been considered, and the results obtained by the Monte Carlo procedure indicate that most of these models lead to different behaviors of the peptide in water. The results obtained with each set of solvation parameters are compared with those obtained from molecular dynamics. This work demonstrates that the choice of the solvation parameters is crucial for a proper simulation of the effect of the hydration free energy on the conformations of peptides. When the appropriate parameters are used to simulate solvent effects, good agreement is obtained between molecular dynamics and Monte Carlo approaches. Considering the CPU cost of molecular dynamics simulations with explicit solvent molecules, Monte Carlo calculations using empirical solvation models appear to be more appropriate to sample conformational space of solvated chain molecules. © 1997 John Wiley & Sons, Inc. Biopoly 42: 363-371, 1997
    Additional Material: 3 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    Characterization of multiple bends in proteinsA preliminary account of this work was presented at the Sixth International Biophysics Congress, Kyoto, September 1978 [Abstract IV-30-(554)]. (1980)
    New York : Wiley-Blackwell
    Biopolymers 19 (1980), S. 1183-1210 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The concept of bends or chain reversals [nonhelical dipeptide sequences in which the distance R3 (i,i+3) between the Cα atoms of residues i and i+3 is ≦ 7.0 Å] has been extended to define double bends as tripeptide sequences, not in an α-helix, in which two successive distances R3(i,i+3) and R3 (i+1, i+4) are both ≦7.0 Å, with analogous definitions for higher-order multiple bends. A sample of 23 proteins, consisting of 4050 residues, contains 235 single, 58 double, and 11 higher-order multiple bends. Multiple bends may occur as combinations of the “standard” type I, II, and III chain reversals (as well as their mirror images), but usually they require distortions from these well-defined conformations. The frequency of occurrence of amino acids often differs significantly between single and multiple bends. The probability distribution of R3 distances does not differ in single and multiple bends. However, R4 (the distance between the Cα atoms of residues i and i+4) in multiple bends is generally shorter than in tripeptide sequences containing single bends. The value of R4 in many multiple bends is near those for α-helices. In some other multiple bends, R4 is even shorter, indicating that these structures are very compact. The signs of the dihedral angles about the virtual bonds connecting Cα atoms and the values of curvature and torsion, as defined by means of differential geometry, indicate that there is a preference for single and multiple bends to be right-handed (like an α-helical sequence, for example) and that there is a strong tendency to conserve the handedness in both single-bend components of many multiple bends. These often have a strong resemblance to distorted single turns of an α-helix and do not constitute chain reversals. Double bends, in which the signs of two successive virtual-bond dihedral angles differ, have conformations that are very different from an α-helix. They act as chain reversals occuring over three residues. These chain reversals have not been described previously. Multiple bends may play an important role in protein folding because they occur fairly frequently in proteins and cause major changes in the direction of the polypeptide chain.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1980.360190607
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  • 4
    Electronic Resource
    Electronic Resource
    Helix-coil stability constants for the naturally occurring amino acids in water. XXI. Glutamine parameters from random poly(hydroxypropylglutamine-co-L-glutamine) and poly(hydroxybutylglutamine-co-L-glutamine) (1982)
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 51-77 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Water-soluble, random copolymers containing L-glutamine and either N5-(3-hydroxypropyl)-L-glutamine or N5-(4-hydroxybutyl)-L-glutamine were synthesized, fractionated, and characterized. The thermally induced helix-coil transitions of these copolymers were studied in water. A short-range interaction theory was used to deduce the Zimm-Bragg parameters σ and s for the helix-coil transition in poly(L-glutamine) in water from an analysis of the melting curves of the copolymers in the manner described in earlier papers. The computed values of s indicate that L-glutamine is helix-indifferent at low temperature and a helix-destabilizing residue at high temperature in water. At all temperatures in the range of 0-70°C, the glutamine residue promotes helix-coil boundaries since the computed value of σ is large.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360210106
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  • 5
    Electronic Resource
    Electronic Resource
    A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 849-873 
    Details
    ISSN: 0192-8651
    Keywords: protein structure prediction ; united-residue representation of a polypeptide chain ; potential of mean force ; radial and angular distribution functions ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A two-stage procedure for the determination of a united-residue potential designed for protein simulations is outlined. In the first stage, the long-range and local-interaction energy terms of the total energy of a polypeptide chain are determined by analyzing protein-crystal data and averaging the all-atom energy surfaces. In the second stage (described in the accompanying article), the relative weights of the energy terms are optimized so as to locate the native structures of selected test proteins as the lowest energy structures. The goal of the work in the present study is to parameterize physically reasonable functional forms of the potentials of mean force for side-chain interactions. The potentials are of both radial and anisotropic type. Radial potentials include the Lennard-Jones and the shifted Lennard-Jones potential (with the shift parameter independent of orientation). To treat the angular dependence of side-chain interactions, three functional forms of the potential that were designed previously to describe anisotropic systems are evaluated: Berne-Pechukas (dilated Lennard-Jones); Gay-Berne (shifted Lennard-Jones with orientation-dependent shift parameters); and Gay-Berne-Vorobjev (the same as the preceding one, but with one more set of variable parameters). These functional forms were used to parameterize, within a short-distance range, the potentials of mean force for side-chain pair interactions that are related by the Boltzmann principle to the pair correlation functions determined from protein-crystal data. Parameter determination was formulated as a generalized nonlinear least-squares problem with the target function being the weighted sum of squares of the differences between calculated and “experimental” (i.e., estimated from protein-crystal data) angular, radial-angular, and radial pair correlation functions, as well as contact free energies. A set of 195 high-resolution nonhomologous structures from the Protein Data Bank was used to calculate the “experimental” values. The contact free energies were scaled by the slope of the correlation line between side-chain hydrophobicities, calculated from the contact free energies, and those determined by Fauchere and Pliška from the partition coefficients of amino acids between water and n-octanol. The methylene group served to define the reference contact free energy corresponding to that between the glycine methylene groups of backbone residues. Statistical analysis of the goodness of fit revealed that the Gay-Berne-Vorobjev anisotropic potential fits best to the experimental radial and angular correlation functions and contact free energies and therefore represents the free-energy surface of side-chain-side-chain interactions most accurately. Thus, its choice for simulations of protein structure is probably the most appropriate. However, the use of simpler functional forms is recommended, if the speed of computations is an issue. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 849-873, 1997
    Additional Material: 9 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 874-887 
    Details
    ISSN: 0192-8651
    Keywords: protein structure prediction ; united-residue representation of a polypeptide chain ; potential of mean force ; inverse folding ; Z-score ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Continuing our work on the determination of an off-lattice united-residue force field for protein-structure simulations, we determined and parameterized appropriate functional forms for the local-interaction terms, corresponding to the rotation about the virtual bonds (Utor), the bending of virtual-bond angles (Ub), and the energy of different rotameric states of side chains (Urot). These terms were determined by applying the Boltzmann principle to the distributions of virtual-bond torsional and virtual-bond angles and side-chain rotameric states, respectively, calculated from a data base of 195 high-resolution nonhomologous proteins. The complete energy function was constructed by combining the individual energy terms with appropriate weights. The weights were determined by optimizing the so-called Z-score value (which is the normalized difference between the energy of the native structure and the mean energy of non-native structures) of the histidine-containing phosphocarrier protein from Streptococcus faecalis (1PTF; an 88-residue α + β protein). To accomplish this, a database of Cα patterns was created using high-resolution nonhomologous protein structures from the Protein Data Bank, and the distributions of energy components of 1PTF were obtained by threading its sequence through ∼500 randomly chosen Cα-patterns from the X-ray structures in the PDB, followed by energy minimization, with the energy function incorporating initially guessed weights. The resulting minimized energies were used to optimize the Z-score value of 1PTF as a function of the weights of the various energy terms, and the new weights were used to generate new energy-component distributions. The process was iterated, until the weights used to generate the distributions and the optimized weights were self-consistent. The potential function with the weights of the various energy terms obtained by optimizing the Z-score value for 1PTF was found to locate the native structures of other test proteins (within an average RMS deviation of 3 Å): calcium-binding protein (4ICB), ubiquitin (1UBQ), α-spectrin (1SHG), major cold-shock protein (1MJC), and cytochrome b5 (3B5C) (which included α and β structures) as distinctively lowest in energy in similar threading experiments. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 874-887, 1997
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