Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin.
Water confined in proteins exhibits dynamics distinct from the dynamics of water in the bulk or near the surface of a biomolecule. We examine the water dynamics at the interface of the two globules of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI) by molecular dynamics (MD) simulations, with focus on water-protein hydrogen bond lifetimes and rotational anisotropy of the interfacial waters. We find that relaxation of the waters at the interface of both deoxy- and oxy-HbI, which contain a cluster of 17 and 11 interfacial waters, respectively, is well described by stretched exponentials with exponents from 0.1 to 0.6 and relaxation times of tens to thousands of picoseconds. The interfacial water molecules of oxy-HbI exhibit slower rotational relaxation and hydrogen bond rearrangement than those of deoxy-HbI, consistent with an allosteric transition from unliganded to liganded conformers involving the expulsion of several water molecules from the interface. Though the interfacial waters are translationally and rotationally static on the picosecond time scale, they contribute to fast communication between the globules via vibrations. We find that the interfacial waters enhance vibrational energy transport across the interface by ≈10%.
Department of Chemistry and Chemical Physics Program, University of Nevada, Reno 89557, USA.
Ramachandran
R
Gnanasekaran
Yao
Y
Xu
David M
DM
Leitner
D000818:Animals; D019281:Dimerization; D006454:Hemoglobins / Q000737:chemistry*; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D049894:Scapharca / Q000378:metabolism; D014867:Water / Q000737:chemistry*
D006454:Hemoglobins; D014867:Water