Mixed quantum-classical dynamics of an amide-I vibrational excitation in a protein a-helix

Freedman, Holly; Martel, Paulo; Cruzeiro, Leonor

http://hdl.handle.net/10400.1/3550

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Authors

Freedman, Holly

Martel, Paulo

Cruzeiro, Leonor

Abstract(s)

Adenosine triphosphate sATPd is known to be the main energy currency of the living cell, and is used as a coenzyme to generate energy for many cellular processes through hydrolysis to adenosine diphosphate sADPd,although the mechanism of energy transfer is not well understood. It has been proposed that following hydrolysis of the ATP cofactor bound to a protein, up to two quanta of amide-I vibrational energy are excited and utilized to bring about important structural changes in the protein. To study whether, and how, amide-I vibrational excitations are capable of leading to protein structural changes, we have added components arising from quantum-mechanical amide-I vibrational excitations to the total energy and force terms within a moleculardynamics simulation. This model is applied to helical deca-alanine as a test case to investigate how its dynamics differs in the presence or absence of an amide-I excitation. We find that the presence of an amide-I excitation can bias the structure toward a more helical state.

URI

http://hdl.handle.net/10400.1/3550

Citation

Freedman, Holly; Martel, Paulo; Cruzeiro, Leonor. Mixed quantum-classical dynamics of an amide-I vibrational excitation in a protein a-helix, Physical Review B, 82, 17, 1-8, 2010.