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Solvation influences flap collapse in HIV‐1 protease
Author(s) -
Meagher Kristin L.,
Carlson Heather A.
Publication year - 2004
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.20274
Subject(s) - solvation , nanosecond , molecular dynamics , flexibility (engineering) , hiv 1 protease , human immunodeficiency virus (hiv) , ligand (biochemistry) , conformational change , chemistry , protease , chemical physics , computational chemistry , stereochemistry , physics , molecule , biology , optics , receptor , organic chemistry , laser , biochemistry , statistics , mathematics , immunology , enzyme
HIV‐1 protease (HIVp) is an important target for the development of therapies to treat AIDS and is one of the classic examples of structure‐based drug design. The flap region of HIVp is known to be highly flexible and undergoes a large conformational change upon binding a ligand. Accurately modeling the inherent flexibility of the HIVp system is critical for developing new methods for structure‐based drug design. We report several 3‐ns molecular dynamics simulations investigating the role of solvation in HIVp flap rearrangement. Using an unliganded crystal structure of HIVp, other groups have observed flap reorganization on the nanosecond timescale. We have also observed rapid, initial flap movement, but we propose that it may be caused by system setup. The initial solvation of the system creates vacuum regions around the protein that may encourage large conformational deformities. By reducing the vacuum space created by the solvation routine, the observed flap collapse is attenuated. Also, a more thorough equilibration procedure preserves a more stable protein conformation over the course of the simulation. Proteins 2005. © 2004 Wiley‐Liss, Inc.