Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effects.
The nature of proton transduction (PTR) through a file of water molecules, along the gramicidin A (gA) channel, has long been considered as being highly relevant to PTR in biological systems. Previous attempts to model this process implied that the so-called Grotthuss mechanism and the corresponding orientation of the water file plays a major role. The present work reexamines the PTR in gA by combining a fully microscopic empirical valence bond (EVB) model and a recently developed simplified EVB-based model with Langevin dynamics (LD) simulations. The full model is used first to evaluate the free energy profile for a stepwise PTR process. The corresponding results are then used to construct the effective potential of the simplified EVB. This later model is then used in Langevin dynamics simulations, taking into account the correct physics of possible concerted motions and the effect of the solvent reorganization. The simulations reproduce the observed experimental trend and lead to a picture that is quite different from that assumed previously. It is found that the PTR in gA is controlled by the change in solvation energy of the transferred proton along the channel axis. Although the time dependent electrostatic fluctuations of the channel and water dipoles play their usual role in modulating the proton-transfer process (Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 444), the PTR rate is mainly determined by the free energy profile. Furthermore, the energetics of the reorientation of the unprotonated water file do not appear to provide a consistent way of assessing the activation barrier for the PTR process. It seems to us that in the case of gA, and probably other systems with significant electrostatic barriers for the transfer of the proton charge, the PTR rate is controlled by the electrostatic barrier. This finding has clear consequences with regards to PTR processes in biological systems.
Braun-Sand
Sonja
S
University of Southern California, Los Angeles, California 90089, USA.
Burykin
Anton
A
Chu
Zhen Tao
ZT
Warshel
Arieh
A
D003198:Computer Simulation; D006096:Gramicidin / Q000737:chemistry*; D007473:Ion Channels / Q000737:chemistry*; D008956:Models, Chemical; D011522:Protons; D012997:Solvents / Q000737:chemistry; D013997:Time Factors; D014867:Water / Q000737:chemistry
D007473:Ion Channels; D011522:Protons; D012997:Solvents; D014867:Water; D006096:Gramicidin