Molecular dynamics of HIV-1 reverse transcriptase indicates increased flexibility upon DNA binding
文献类型：期刊论文
| 作者 | Madrid, M; Lukin, JA; Madura, JD; Ding, JP; Arnold, E |
| 刊名 | PROTEINS-STRUCTURE FUNCTION AND GENETICS
 |
| 出版日期 | 2001 |
| 卷号 | 45期号:3页码:176-182 |
| 关键词 | molecular modeling concerted correlated collective motions B-factors refinement HIV-1 RT |
| 通讯作者 | Madrid, M (reprint author), Pittsburgh Supercomp Ctr, 4400 5th Ave, Pittsburgh, PA 15213 USA., |
| 英文摘要 | HIV-1 reverse transcriptase (RT) is one of the main targets for drugs used in the treatment of AIDS, among them, the non-nucleoside RT inhibitors (NNRTIs). The flexibility of RT unliganded and complexed to double-stranded DNA (RT/dsDNA), in water, has been studied by means of molecular dynamics. The simulations show that RT flexibility depends on its ligation state. The RT/dsDNA trajectories show larger fluctuations in the atomic positions than uncomplexed RT, particularly at the tips of the p66 fingers and thumb subdomains. This increased flexibility is consistent with the ability of the p66 fingers of the RT/dsDNA complex to close down after the binding of a deoxynucleoside triphosphate (dNTP) molecule, as observed in the crystal structures of RT/dsDNA bound to dNTP. The two complexation states present different patterns of concerted motions, indicating that the bound dsDNA alters RT flexibility. The motions of amino acid residues that form the non-nucleoside RT inhibitor binding pocket upon complexation with a NNRTI are anticorrelated with the p66 fingers (in RT/dsDNA) and correlated to the RNase H subdomain (unliganded RT). These concerted motions indicate that binding of a NNRTI could alter the flexibility of the subdomains whose motions are correlated to those of the binding pocket. (C) 2001 Wiley-Liss,Inc. |
| 学科主题 | Biochemistry & Molecular Biology; Biophysics |
| 类目[WOS] | Biochemistry & Molecular Biology ; Biophysics |
| 关键词[WOS] | IMMUNODEFICIENCY-VIRUS TYPE-1 ; PARTICLE MESH EWALD ; DOUBLE-STRANDED DNA ; ANGSTROM RESOLUTION ; COLLECTIVE MOTIONS ; CRYSTAL-STRUCTURE ; DRUG-RESISTANCE ; ACTIVE-SITE ; INHIBITION ; COMPLEX |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000171699800002 |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.143/handle/331003/2615]  |
| 专题 | 上海生化细胞研究所_上海生科院生化细胞研究所 |
| 推荐引用方式 GB/T 7714 | Madrid, M,Lukin, JA,Madura, JD,et al. Molecular dynamics of HIV-1 reverse transcriptase indicates increased flexibility upon DNA binding[J]. PROTEINS-STRUCTURE FUNCTION AND GENETICS,2001,45(3):176-182. |
| APA | Madrid, M,Lukin, JA,Madura, JD,Ding, JP,&Arnold, E.(2001).Molecular dynamics of HIV-1 reverse transcriptase indicates increased flexibility upon DNA binding.PROTEINS-STRUCTURE FUNCTION AND GENETICS,45(3),176-182. |
| MLA | Madrid, M,et al."Molecular dynamics of HIV-1 reverse transcriptase indicates increased flexibility upon DNA binding".PROTEINS-STRUCTURE FUNCTION AND GENETICS 45.3(2001):176-182. |
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