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

Abstract

Adenosine triphosphate (ATP) 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 (ADP), 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 molecular-dynamics 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. © 2010 The American Physical Society.