Monte Carlo simulations of proton pumps: On the working principles of the biological valve that controls proton pumping in cytochrome c oxidase

doi:10.1073/pnas.0510860103

Monte Carlo simulations of proton pumps: On the working principles of the biological valve that controls proton pumping in cytochrome c oxidase

Mats H. M. Olsson* and
Arieh Warshel*

Department of Chemistry, University of Southern California, 3620 McClintock Avenue, SGM418, Los Angeles, CA 90089-1062

Edited by Harry B. Gray, California Institute of Technology, Pasadena, CA, and approved March 1, 2006 (received for review December 20, 2005)

Abstract

Gaining a detailed understanding of the proton-pumping process in cytochrome c oxidase (COX) is one of the challenges of modern biophysics. Recent mutation experiments have highlighted this challenge by showing that a single mutation (the N139D mutation) blocks the overall pumping while continuing to channel protons to the binuclear center without inhibiting the oxidase activity. Rationalizing this result has been a major problem because the mutation is quite far from E286, which is believed to serve as the branching point for the proton transport in the pumping process. In the absence of a reasonable explanation for this important observation, we have developed a Monte Carlo simulation method that can convert mutation and structural information to pathways for proton translocation and simulate the pumping process in COX on a millisecond and even subsecond time scale. This tool allows us to reproduce and propose a possible explanation to the effect of the N139D mutation and to offer a consistent model for the origin of the “valve effect” in COX, which is crucial for maintaining uphill proton pumping. Furthermore, obtaining the first structure-based simulation of proton pumping in COX, or in any other protein, indicates that our approach should provide a powerful tool for verification of mechanistic hypotheses about the action of proton transport proteins.

Footnotes

*To whom correspondence may be addressed. E-mail: molsson{at}usc.edu or warshel{at}usc.edu
Author contributions: M.H.M.O. and A.W. designed research; M.H.M.O. performed research; M.H.M.O. contributed new reagents/analytic tools; M.H.M.O. and A.W. analyzed data; and M.H.M.O. and A.W. wrote the paper.
↵ † As already established in our previous work (12), the stepwise transfer involves an unrealistically large activation barrier to be consistent with experimental observations. E286 was also found to be protonated during the entire 23-μs simulation.
Conflict of interest statement: No conflicts declared.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations:

Abbreviations:

COX,

cytochrome c oxidase;

ET,

electron transfer;

PT,

proton transfer;

EVB,

empirical valence bond;

MC,

Monte Carlo;

PTR,

proton translocation.