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  • 1
    Electronic Resource
    Electronic Resource
    Computational studies of ligand diffusion in globins: I. Leghemoglobin (1991)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 10 (1991), S. 70-80 
    Details
    ISSN: 0887-3585
    Keywords: locally enhanced sampling ; molecular dynamics ; ligand penetration ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The thermally assisted diffusion of a small ligand (carbon monoxide) through a protein matrix (lupine leghemoglobin) is investigated computationally. The diffusion paths are calculated by a varient of the time-dependent Hartree approximation which we call LES (locally enhanced sampling). The variant which was recently introduced by Elber and Karplus1 is based on the classical TD-SCF approximation of Gerber et al.2 The simulation enables more significant search for diffusion pathways than was possible before. This is done by increasing the number of ligand trajectories using a single trajectory for the protein. We compare qualitatively diffusion rates in leghemoglobin and in myoglobin. The calculation shows that the diffusion in leghemoglobin is much faster than the diffusion in myoglobin, in agreement with experiment. The gate in leghemoglobin is opened by fluctuations at a close contact between the B/C and the G helices. The most relevant fluctuation is the rigid shift of the C helix with respect to the G helix. This path is not observed in a comparable calculation for myoglobin.1 This finding is rationalized by the lack of the D helix in leghemoglobin and a significantly more flexible CE loop. Supporting experimental evidence for the importance of the CE loop in leghemoglobin can be found in the kinetics studies of Gibson et al.28
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340100107
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  • 2
    Electronic Resource
    Electronic Resource
    Calculations of a list of neighbors in Molecular Dynamics simulations (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 921-927 
    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: A new algorithm is proposed for the evaluation of nonbonded interactions in Molecular Dynamics simulations. The algorithm is based on a grid search and on partitioning of the atoms into boxes rather than on calculations of distances. The effort associated with the generation of the box list grows only linearly with the number of atoms. The algorithm is particularly advantageous for solvated systems. Test calculations show significant savings in CPU time and storage compared to commonly used algorithms for systems containing in excess of ca. 600 atoms.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100709
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    Paper (German National Licenses)
    Fulltext
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