Science · 2015 · 410 citations · 93 references
Natural SciencesBiophysicsPhysicsMolecular BiophysicsStructural BiologyStructural BiophysicsConformational DynamicsMolecular DynamicsProtein DynamicsProtein StructureProtein-ligand BindingCollective Response MechanismsHybrid Quantum MechanicsLigand DissociationMolecular Vibrational ModesProtein Conformational DynamicsProtein Structural ChangesTime-resolved CrystallographyVibrational Modes
The hemoprotein myoglobin is a model system for the study of protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray free-electron laser to resolve the ultrafast structural changes in the carbonmonoxy myoglobin complex upon photolysis of the Fe-CO bond. Structural changes appear throughout the protein within 500 femtoseconds, with the C, F, and H helices moving away from the heme cofactor and the E and A helices moving toward it. These collective movements are predicted by hybrid quantum mechanics/molecular mechanics simulations. Together with the observed oscillations of residues contacting the heme, our calculations support the prediction that an immediate collective response of the protein occurs upon ligand dissociation, as a result of heme vibrational modes coupling to global modes of the protein.
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Density-functional thermochemistry. III. The role of exact exchange
Axel D. Becke · The Journal of Chemical Physics · 1993 · 102.8K citations
Natural Sciences, Chemistry, Physics +13
Molecular dynamics with coupling to an external bath
Herman J. C. Berendsen, Johan P. M. Postma, Wilfred F. van Gunsteren et al. · The Journal of Chemical Physics · 1984 · 31K citations · Full text
Natural Sciences, Chemistry, Physics +17