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Insights into the interactions between HIV‐1 integrase and human LEDGF/p75 by molecular dynamics simulation and free energy calculation
Author(s) -
Zhao Yaxue,
Li Weihua,
Zeng Juan,
Liu Guixia,
Tang Yun
Publication year - 2008
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21955
Subject(s) - integrase , molecular dynamics , human immunodeficiency virus (hiv) , chemistry , computational biology , biology , biophysics , virology , computational chemistry
Human cellular protein LEDGF/p75 (lens epithelium‐derived growth factor) is an important binding partner of human immunodeficiency virus type 1 (HIV‐1) integrase (IN). Without LEDGF/p75, HIV‐1 can not complete its life cycle. To study the detailed interactions between LEDGF/p75 and HIV‐1 IN, and then obtain the hotspots at the binding interface, 13 ns molecular dynamics simulations were carried out here. One‐hundred snapshots extracted from the last 4 ns trajectories were used for calculation of binding free energy and decomposition of the energy by residue. First, the structural changes and their dynamic interactions were investigated focused on the production stage. And then, the free energy was discussed. On the basis of the above results, it could be suggested that residues Gln168, Glu170, and Thr174 in chain A of IN, Thr125, and Trp131 in chain B of IN as well as Ile365, Asp366, Phe406, and Val408 in LEDGF/p75 were responsible for their binding. These results might be helpful for discovery and design of small molecules to interrupt the interaction between HIV‐1 IN and LEDGF/p75. Proteins 2008. © 2008 Wiley‐Liss, Inc.