title: Correlated motions and residual frustration in thrombin.
abstract: Thrombin is the central protease in the cascade of blood coagulation proteases. The structure of thrombin consists of a double β-barrel core surrounded by connecting loops and helices. Compared to chymotrypsin, thrombin has more extended loops that are thought to have arisen from insertions in the serine protease that evolved to impart greater specificity. Previous experiments showed thermodynamic coupling between ligand binding at the active site and distal exosites. We present a combined approach of molecular dynamics (MD), accelerated molecular dynamics (AMD), and analysis of the residual local frustration of apo-thrombin and active-site-bound (PPACK-thrombin). Community analysis of the MD ensembles identified changes upon active site occupation in groups of residues linked through correlated motions and physical contacts. AMD simulations, calibrated on measured residual dipolar couplings, reveal that upon active site ligation, correlated loop motions are quenched, but new ones connecting the active site with distal sites where allosteric regulators bind emerge. Residual local frustration analysis reveals a striking correlation between frustrated contacts and regions undergoing slow time scale dynamics. The results elucidate a motional network that probably evolved through retention of frustrated contacts to provide facile conversion between ensembles of states.
authors.affiliation: Department of Chemistry and Biochemistry and ⊥Department of Pharmacology, University of California, San Diego , La Jolla, California, United States.
authors.forename: Brian
authors.initials: B
authors.lastname: Fuglestad
authors.forename: Paul M
authors.initials: PM
authors.lastname: Gasper
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
authors.forename: Phineus R L
authors.initials: PR
authors.lastname: Markwick
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Komives
mesh_terms: D000494:Allosteric Regulation; D000590:Amino Acid Chloromethyl Ketones / Q000737:chemistry / Q000378:metabolism; D020134:Catalytic Domain; D056004:Molecular Dynamics Simulation; D011498:Protein Precursors / Q000737:chemistry / Q000378:metabolism; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013917:Thrombin / Q000737:chemistry* / Q000378:metabolism
chemical_list: D000590:Amino Acid Chloromethyl Ketones; D011498:Protein Precursors; D013917:Thrombin; C050815:phenylalanyl-prolyl-arginine chloromethyl ketone-thrombin