Determination of thermal intermediate state ensemble of box 5 with restrained molecular dynamics simulations

Article ID	Journal	Published Year	Pages	File Type
5394921	Computational and Theoretical Chemistry	2011	8 Pages	PDF

Abstract

âº The “invisible” intermediate state was predicted with ensemble-averaged simulations. âº Distance and angle restraints from experiments were imposed on the simulations. âº The structural characters of intermediate state ensemble were depicted in detail. âº The ensemble was high heterogeneity and L-shaped topology was vanished. âº Helix 3 was more native-like and the hydrophobic core was unformed completely.

Keywords

PDB RCS Hmg NOE HUBF nuclear magnetic resonance Cluster analysis paramagnetic relaxation enhancement NMR nuclear Overhauser enhancement intermediate state Molecular dynamics Molecular dynamics simulation pre Protein Data Bank high mobility group