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  • 1
    Electronic Resource
    Electronic Resource
    Altering the Regiospecificity of Androstenedione Hydroxylase Activity in P450s 2a-4/5 by a Mutation of the Residue at Position 481 (1995)
    s.l. : American Chemical Society
    Biochemistry 34 (1995), S. 5054-5059 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00015a016
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    A Molecular Dynamics Model of HIV-1 Reverse Transcriptase Complexed with DNA: Comparison with Experimental Structures (2000)
    Springer
    Journal of molecular modeling 6 (2000), S. 575-586 
    Details
    ISSN: 0948-5023
    Keywords: HIV-1 reverse transcriptase ; Minor groove binding track ; Particle-mesh Ewald
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We have built a molecular dynamics model for human immunodeficiency virus (HIV-1) reverse transcriptase (RT) complexed with a 19/18-mer template/primer by combining the structural information of a low resolution crystal structure of a HIV-1 RT/DNA complex (1hmi) with that of a high resolution crystal structure of unliganded HIV-1 RT (1rtj). The process involved slow forcing of the α-carbons of 1rtj onto those of 1hmi using constrained MD simulations, while immersing the protein in aqueous solution. A similar technique was used to build the bent all-atom DNA duplex, which was then docked into the modeled protein. The resulting model complex was refined using molecular dynamics simulation with the Particle-mesh Ewald method employed to accommodate long-range electrostatic interactions. New parameters of the Amber force field that affect DNA twist are tested and largely validated. The model has been used successfully to explain the results of vertical scanning mutagenesis of residue 266 (Trp266). Recently, the low resolution crystal structure of the HIV-1 RT/DNA complex has been refined to a 2.8 Å resolution (2hmi) and a crystal structure of a HIV-1/RT/dTTP ternary complex has been determined at 3.2 Å resolution (1rtd). A detailed structural comparison of the prior model structure and the two experimental structures becomes possible. Overall, the three structures share many similarities. The root mean square deviations of the α-carbons for the individual subdomains among the three structures are within the same ranges. The secondary structure assignments in the three structures are nearly identical. Key protein-DNA contacts such as those in the region of the primer grip are also similar in the three structures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s0089400060575
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  • 3
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation studies of a high resolution Z-DNA crystal (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 102 (1995), S. 3830-3834 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We report two 1 ns molecular dynamic (MD) simulations on Z-DNA for which the long-range Coulomb terms are explicitly evaluated by the Particle–Mesh–Ewald method [J. Chem. Phys. 98, 10089 (1993)]. The starting structures were based on the 1 A(ring) resolution crystallographic structure of Gessner et al. [J. Bio. Chem. 264, 7921 (1989)]. The average simulation structures of the DNA compare well to the crystallographic structure; the root-mean-square position deviations for the DNA double-strand heavy atoms are approximately 0.5 A(ring). Watson–Crick hydrogen bonding patterns are preserved without invoking constraints. These results emphasize the importance of proper treatment of the long-range forces for highly ionic systems. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.468564
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  • 4
    Electronic Resource
    Electronic Resource
    MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES: Long-Range Electrostatic Effects (1999)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 28 (1999), S. 155-179 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract Current computer simulations of biomolecules typically make use of classical molecular dynamics methods, as a very large number (tens to hundreds of thousands) of atoms are involved over timescales of many nanoseconds. The methodology for treating short-range bonded and van der Waals interactions has matured. However, long-range electrostatic interactions still represent a bottleneck in simulations. In this article, we introduce the basic issues for an accurate representation of the relevant electrostatic interactions. In spite of the huge computational time demanded by most biomolecular systems, it is no longer necessary to resort to uncontrolled approximations such as the use of cutoffs. In particular, we discuss the Ewald summation methods, the fast particle mesh methods, and the fast multipole methods. We also review recent efforts to understand the role of boundary conditions in systems with long-range interactions, and conclude with a short perspective on future trends.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.28.1.155
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  • 5
    Electronic Resource
    Electronic Resource
    A minor groove binding track in reverse transcriptase (1997)
    [s.l.] : Nature Publishing Group
    Nature structural biology 4 (1997), S. 194-197 
    Details
    ISSN: 1072-8368
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Proteins that bind with high affinity to specific DNA sequences often do so through hydrogen bonding and electrostatic interactions between the DNA major groove and defined protein structural elements, such as helix-turn-helix motifs, β-ribbon recognition elements and Zn-binding domains1. ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nsb0397-194
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  • 6
    Electronic Resource
    Electronic Resource
    Some regularity results on the Ventcel-Freidlin quasi-potential function (1985)
    Springer
    Applied mathematics & optimization 13 (1985), S. 259-282 
    Details
    ISSN: 1432-0606
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract We consider regularity properties of the quasipotential function V defined by A. D. Ventcel and M. I. Freidlin in their work on asymptotically small random perturbations of stable dynamical systems. The regularity properties of V are important for the success of various asymptotic calculations carried out in the literature. Employing classical techniques from the calculus of variations and differential equations, we prove various results about the smoothness of V and its level sets. Among other things, there exists a dense connected open set, containing the stable point for the underlying dynamical system, in which V is continuously differentiable to the same degree as the Lagrangian involved in the defining variational problem.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01442211
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  • 7
    Electronic Resource
    Electronic Resource
    Charge reversal of three alkylamide ions: Free nitrenium ions (1983)
    Chichester : Wiley-Blackwell
    Biological Mass Spectrometry 18 (1983), S. 530-533 
    Details
    ISSN: 0030-493X
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The methylnitrenium, ethylnitrenium and dimethylnitrenium ions are prepared by charge reversal collisional activation (CR CA) of the corresponding negative ions; their collisional activation mass spectra are shown to support the assigned structures. MINDO/3 energies are used to evaluate relative energies of [CH4N]+ and [C2H6N]+ isomers, and to determine whether unstable forms rearrange spontaneously to stable ones. As in other examples, charge reversal here generates cations that do not exist in an energy well, but their transient existence is established because their fragmentation is more rapid than their rearrangement to a more stable form.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/oms.1210181207
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