Abstract
Many proteins undergo significant structural changes following the hydrolysis of a bound nucleoside triphosphate (NTP) molecule. Davydov has proposed that, in the protein myosin, vibrational excitations are taken advantage of in the energy transduction process following this hydrolysis. Using an atomistic, mixed quantum-classical molecular dynamics model, we have attempted to obtain a more detailed understanding of how this process might take place. Our results indicate that vibrational excitations may be capable of inducing transitions of protein domains from less helical to more helical states. We discuss examples of protein systems for which small changes in ??-helical structure are known to lead to biologically-significant structural effects. Evidence is reviewed supporting a model in which vibrational excitations can lead to utilization of the energy released in NTP hydrolysis through important changes in protein structure following the contraction of a protein α-helix.
Keywords: Davydov soliton, ATP hydrolysis, Protein energy transfer, α-helix, Myosin, Kinesin, nucleotide, Schrodinger equation, catalytic cycles, Polymeric actin
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