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The VES Hypothesis and Protein Conformational Changes

Leonor Cruzeiro

Abstract

This work started as a (biased) review of the state of the art of the Davydov/Scott model for energy transfer in proteins via the propagation of amide I excitations and of how this initial quantum stage may lead to protein conformational changes. It is not a traditional review because certain results reported in the literature have been complemented by extra simulations which revealed, for instance, a new class of possible states for the amide I excitation, here designated as double discrete breathers. The issue of the thermal stability of the Davydov soliton is discussed, as well as the deeper question of how to simulate the non-equilibrium regime of a mixed quantum-classical system at finite temperature. While an exact answer to the latter question is not yet available, a specific formalism that is able to reproduce the correct canonical ensemble is described. Finally, the question of how a quantum amide I excitation can generate of the specific protein conformational changes known to be associated with function is also explored. Indeed, computer simulations indicate that a local action can lead to reproducible conformational changes. The paper ends with a discussion of some of the open questions that plague/stimulate this field and with a suggestion for an experiment to test the basic assumption of the Davydov/Scott model.

Acknowledgement

This work received national funds from FCT – Foundation for Science and Technology, Portugal, through the project UID/Multi/04326/2013. The author also acknowledges the Laboratory for Advanced Computing at University of Coimbra (http://www.lca.uc.pt) for providing HPC computing resources that have contributed to the research results reported within this paper.

This article is dedicated to Professor Michael Springborg on the occasion of his 60th birthday. With best wishes for a long and happy scientific and personal life.

Received: 2015-10-15
Accepted: 2016-1-14
Published Online: 2016-2-8
Published in Print: 2016-5-28

©2016 Walter de Gruyter Berlin/Boston