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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 478-485 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The three-dimensional structure of the carboxyl-terminal region of the human ras oncogenic protein (called p21) has been determined using the HDMC (High-directional Monte Carlo) method combined with MD (molecular dynamics) simulation. A truncated p21 containing residues 1-171 without the carboxyl-terminal end was analyzed using X-ray crystallography by Kim et al. It has been well documented that the carboxyl-terminal region of p21 is flexible and plays an important role in transmitting a signal from the membrane-attached domain. We have carried out the theoretical calculation for 18 undefined residues, which correspond to residues 172-189 of intact p21, in addition to seven residues (165-171) from X-ray coordinates of the C-terminal end of human C—Ha—ras protein. In this calculation, the main-chain atoms of residues 165-169 have been fitted to X-ray structure, and the remaining region has been allowed to move during the conformational analysis. We have confirmed that revised HDMC can easily alter the local minima of the polypeptide chains as the internal vibrations of molecules are allowed by MD simulation. Throughout this study, we suggest that the C-terminal end of human C—Ha—ras p21 protein has structures in the forms of an α helix for 165-172, a loop for 173-180, and an α helix for 181-187 regions, like the helical hairpin. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 97 (1992), S. 9283-9290 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new Monte Carlo sampling scheme which estimates the shape of an energy hypersurface as a covariance tensor to generate variable Monte Carlo steps, is developed. The feasibility of this method is tested on 256 Lennard-Jones particles at T*=0.719, ρ*=0.85, and 216 TIP4P water molecules at T=298 K and the results are compared with those of other methods. It is found that the Lennard-Jones solid is successfully melted to liquid by the new method while it is failed by the Metropolis algorithm and the radial distribution functions correspond well to those of other established methods. The result shows that the new method has very improved features in several respects. First, the convergence property to reach the equilibrium state is better than that of other methods. Secondly, the equilibrium distribution of ensembles are not biased.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    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: High-directional Monte Carlo (HDMC) simulations are performed to investigate the behavior of water molecules in the catalytic sites of human ras p21 proteins and the results are compared among three types of hydrated ras p21 proteins: the normal ras complexed with GDP (normal-p21/GDP), the mutant ras complexed with GDP (mutant-p21/GDP), and the normal ras complexed with GTP (normal-p21/GTP). Also, the original Metropolis Monte Carlo (MMC) simulation is performed on the normal-p21/GDP system. Comparison between HDMC and MMC shows the improved efficeincy of HDMC on this complicated system. Interaction between water molecules is represented by the TIP3P potential function. The solute-water interaction is represented by the Coulomb and van der Waals interactions from the CHARMM force field spliced with TIP3P. The mean-square displacements and dipole correlation functions are reported. We specifically examined the hydrogen-bond interactions existing near the catalytic sites, by the distribution of small water clusters connected by the hydrogen bond and by the average lengths and fluctations of hydrogen bonds between water molecules and solute atoms. Water molecules form different local structures in different types of the p21/GDP(GTP) complexes. The structure and motion of water molecules near the catalytic sites of the proteins are discussed in detail. © 1994 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A high directional Monte Carlo procedure that predicts the topology of the energy hyper-surface before it walks, is developed as a method to obtain a global energy minimum structure of polypeptides and proteins. It calculates its covariance matrix, which controls the individual trial step distribution of the next set of steps, from the second moment of the actual walk segment in the previous set. The method is successfully applied to the pentapeptide Metenkephalin system. And it is shown that some initial heating process, which provides the more flexible molecule, is necessary in order to overcome the energy barriers that can be overestimated by some biases in the empirical description of the system. The sampling efficiency, traced by an average conformational changes, is found to be at least 20 times greater than the one in the conventional Metropolis Monte Carlo methods, and it is expected that this increases in efficiency will be more prominent when the system is larger.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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