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  • 1
    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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  • 2
    Electronic Resource
    Electronic Resource
    DNA REPLICATION FIDELITY1 (2000)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 69 (2000), S. 497-529 
    Details
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract DNA replication fidelity is a key determinant of genome stability and is central to the evolution of species and to the origins of human diseases. Here we review our current understanding of replication fidelity, with emphasis on structural and biochemical studies of DNA polymerases that provide new insights into the importance of hydrogen bonding, base pair geometry, and substrate-induced conformational changes to fidelity. These studies also reveal polymerase interactions with the DNA minor groove at and upstream of the active site that influence nucleotide selectivity, the efficiency of exonucleolytic proofreading, and the rate of forming errors via strand misalignments. We highlight common features that are relevant to the fidelity of any DNA synthesis reaction, and consider why fidelity varies depending on the enzymes, the error, and the local sequence environment.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biochem.69.1.497
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  • 3
    Electronic Resource
    Electronic Resource
    Preferential cis – syn thymine dimer bypass by DNA polymerase η occurs with biased fidelity (2004)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 428 (2004), S. 97-100 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Human DNA polymerase η (Pol η) modulates susceptibility to skin cancer by promoting DNA synthesis past sunlight-induced cyclobutane pyrimidine dimers that escape nucleotide excision repair (NER). Here we have determined the efficiency and fidelity of dimer bypass. We show that Pol η ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature02352
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  • 4
    Electronic Resource
    Electronic Resource
    Low fidelity DNA synthesis by human DNA polymerase-η (2000)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 404 (2000), S. 1011-1013 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] A superfamily of DNA polymerases that bypass lesions in DNA has been described. Some family members are described as error-prone because mutations that inactivate the polymerase reduce damage-induced mutagenesis. In contrast, mutations in the skin cancer susceptibility gene XPV, which ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/35010014
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  • 5
    Electronic Resource
    Electronic Resource
    Passing the baton in base excision repair (2000)
    [s.l.] : Nature America Inc.
    Nature structural biology 7 (2000), S. 176-178 
    Details
    ISSN: 1072-8368
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Many different substances produce DNA base damage. Such an onslaught would be ultimately lethal were it not for the ability of mammalian cells to remove much of this damage through base excision repair (BER). The importance of this system is illustrated by the fact that a BER deficiency leads ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/73260
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  • 6
    Electronic Resource
    Electronic Resource
    Cadmium is a mutagen that acts by inhibiting mismatch repair (2003)
    [s.l.] : Nature Publishing Group
    Nature genetics 34 (2003), S. 326-329 
    Details
    ISSN: 1546-1718
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Most errors that arise during DNA replication can be corrected by DNA polymerase proofreading or by post-replication mismatch repair (MMR). Inactivation of both mutation-avoidance systems results in extremely high mutability that can lead to error catastrophe. High mutability and the likelihood of ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/ng1172
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