Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA

被引：20

作者：

Do, Trang N. ^{[2
,3
]}

Ippoliti, Emiliano ^{[1
]}

Carloni, Paolo ^{[1
]}

Varani, Gabriele ^{[4
,5
]}

Parrinello, Michele ^{[6
]}

机构：

[1] German Res Sch Simulat Sci GmbH, D-52425 Julich, Germany

[2] SISSA ISAS Int Sch Adv Studies, I-34136 Trieste, Italy

[3] Univ Sci, Dept Phys, Hochiminh City 70000, Japan

[4] Univ Washington, Dept Chem, Seattle, WA 98195 USA

[5] Univ Washington, Dept Biochem, Seattle, WA 98195 USA

[6] Swiss Fed Inst Technol, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland

来源：

JOURNAL OF CHEMICAL THEORY AND COMPUTATION | 2012年 / 8卷 / 02期

基金：

美国国家科学基金会;

关键词：

MOLECULAR-DYNAMICS SIMULATIONS; FORCE-FIELD; RECOGNITION; BULGE; ELECTROSTATICS; STEM; DNA;

D O I：

10.1021/ct2005769

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

Binding of proteins and small molecules to RNA involves many electrostatic interactions, which may alter the distribution of ions around the RNA molecule. Here, we use molecular dynamics simulations to investigate how binding of a cyclic peptide mimic of the HIV-1 Tat protein affects the ionic distribution around the HIV-1 TAR RNA element. The calculations reproduce the structural properties observed in NMR studies of TAR and its complex. They also provide insight into the rearrangement of counterions during the molecular recognition events leading to the formation of the protein/RNA complex.

引用

页码：688 / 694

页数：7

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