Short-range coherence of internal protein dynamics revealed by high-precision in silico study.
Correlated internal dynamics of proteins, which is believed to be important for their function, is analyzed at unprecedented precision using explicit-solvent submicrosecond molecular dynamics simulations of ubiquitin and calbindin D(9k). Without exception, all of the mobile dihedral angle pairs in ubiquitin with sizable dynamics correlations (R(2) >or= 0.1) are at short-range distance. In rare cases, they involve sequentially remote dihedral angles that form sparse clusters, suggesting a structural-dynamic propagation mechanism via soft torsional couplings that act over short distances with a rapid loss of coherence over longer distances.
Li
Da-Wei
DW
Chemical Sciences Laboratory, Department of Chemistry and Biochemistry, and National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, USA.
Meng
Dan
D
Brüschweiler
Rafael
R
D064026:Calbindins; D019295:Computational Biology; D056004:Molecular Dynamics Simulation; D009068:Movement; D011487:Protein Conformation; D064030:S100 Calcium Binding Protein G / Q000737:chemistry* / Q000378:metabolism*; D025801:Ubiquitin / Q000737:chemistry* / Q000378:metabolism*
D064026:Calbindins; D064030:S100 Calcium Binding Protein G; D025801:Ubiquitin