Seminar: A Practically Complete Set of Lysozyme Statistical Substates Derived from Molecular Dynamics Simulations
Title: A Practically Complete Set of Lysozyme Statistical Substates Derived from Molecular Dynamics Simulations
Speaker: Pu Tian
PhD,Materials Sci. & Eng.
Univ. of Utah, Salt Lake City, UT
Host: CHEN Fei
Time: 10:00-12:00AM, Wednesday , May 23nd, 2012
Location: Conference room 202 Beijing Institute of Genomics，CAS
Abstract: During last two decades, we have witnessed great progress in characterization of protein conformational substates and their transition. However, distribution and organization of statistical substates, which are of great importance in protein-protein and protein-ligand interactions, in conformational space remains a mystery. Using extensive molecular dynamics simulations, we constructed a large set of statistical substates for Hen Egg White Lysozyme. This set includes all 122 high resolution crystal structures in the Protein Data Bank as its most important subset. A few statistical states occupied by many crystal structures exhibit frequent mutual transitions, and they serve as the hub for the whole conformational space. The overall topology is fractal, with each local cluster of states has a heavily populated central hub state and many sparsely populated satellite states.The simulation derived statistical substates satisfies available NOE distance, hydrogen bonds and dihedral restraints reasonably well. These findings demonstrate that modern molecular mechanics force fields provide a decent description of both organization and individual identities for statistical substates that are of practical significance.
