Premium
Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates
Author(s) -
Wereszczynski Jeff,
McCammon J. Andrew
Publication year - 2012
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.2024
Subject(s) - random hexamer , molecular dynamics , atp hydrolysis , hydrolysis , chemistry , biophysics , atpase , monomer , protein structure , chemical physics , biological system , crystallography , stereochemistry , computational chemistry , biology , biochemistry , enzyme , organic chemistry , polymer
The vitally important AAA (ATPases associated with various cellular activities) protein p97 is involved in cellular functions ranging from replication to degradation of misfolded proteins and has recently been proposed as a novel chemotherapeutic target. p97 is a large molecular machine that has been shown to hexamerize in vitro , with each monomer consisting of an N domain responsible for binding to effector proteins and two AAA repeats (D1 and D2). However, structural studies are inconclusive or in disagreement with one another on several important features such as the locations of the N domains, the relative orientations of the D1 and D2 rings, and the dimensions of the central pore. Here, we present atomic‐scale simulations of the p97 hexamer in the prehydrolysis, transition, and post‐hydrolysis states. To improve the agreement between low‐ and high‐resolution experimental studies, we first use a biased simulation technique, molecular dynamics flexible fitting (MDFF), to improve the correlation between the structures described in these experiments. We follow this with extended, classical molecular dynamics simulations, which not only show that structures generated in the MDFF phase are stable, but reveal insights into the dynamics important to each state. Simulation results suggest a hybrid model for hydrolysis, in which the N and D2 domains are dynamic while the D1 domains are relatively static, salt bridges stabilize the position of the N domains in the pre‐hydrolysis state, and the rings formed by D1 and D2 rotate relative to one another.