Premium
Reaction path and free energy calculations of the transition between alternate conformations of HIV‐1 protease
Author(s) -
Rick Steven W.,
Erickson John W.,
Burt Stanley K.
Publication year - 1998
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/(sici)1097-0134(19980701)32:1<7::aid-prot3>3.0.co;2-k
Subject(s) - chemistry , crystallography , ligand (biochemistry) , conformational entropy , active site , energy landscape , reaction coordinate , stereochemistry , enzyme , computational chemistry , molecule , biochemistry , receptor , organic chemistry
Two different structures of ligand‐free HIV protease have been determined by X‐ray crystallography. These structures differ in the position of two 12 residue, β‐hairpin regions (or “flaps”) which cap the active site. The movements of the flaps must be involved in the binding of substrates since, in either conformation, the flaps block the binding site. One of these structures is similar to structures of the ligand‐bound enzyme; however, the importance of both structures to enzyme function is unclear. This transformation takes place on a time scale too long for conventional molecular dynamics simulations, so the process was studied by first identifying a reaction path between the two structures and then calculating the free energy along this path using umbrella sampling. For the ligand‐free enzyme, it is found that the two structures are nearly equally stable, with the ligand‐bound‐type structure being less stable, consistent with X‐ray crystallography data. The more stable open structure does not have a lower potential energy, but is stabilized by entropy. The transition occurs through a collapse and reformation of the β‐sheet structure of the conformationally flexible, glycine‐rich flap ends. Additionally, some problems in studying conformational changes in proteins through the use of a single reaction path are addressed. Proteins 32:7–16, 1998. © 1998 Wiley‐Liss, Inc.