Biophysical Journal 70: 2043-2051 (1996)
© 1996 the Biophysical Society

This Article Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Sagnella, D E Articles by Voth, G A Search for Related Content PubMed PubMed Citation Articles by Sagnella, D E Articles by Voth, G A

Structure and dynamics of hydronium in the ion channel gramicidin A.

Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323, USA.

ABSTRACT

The effects of the hydronium ion, H(3)0+, on the structure of the ion channel gramicidin A and the hydrogen-bonded network of waters within the channel were studied to help elucidate a possible mechanism for proton transport through the channel. Several classical molecular dynamics studies were carried out with the hydronium in either the center of a gramicidin monomer or in the dimer junction. Structural reorganization of the channel backbone was observed for different hydronium positions, which were most apparent when the hydronium was within the monomer. In both cases the average O-O distance between the hydronium ion and its nearest neighbor water molecule was found to be approximately 2.55 A, indicating a rather strong hydrogen bond. Importantly, a subsequent break in the hydrogen-bonded network between the nearest neighbor and the next-nearest neighbor(approximately 2.7 -3.0 A) was repeatedly observed. Moreover, the carbonyl groups of gramicidin A were found to interact with the charge on the hydronium ion, helping in its stabilization. These facts may have significant implications for the proton hopping mechanism. The presence of the hydronium ion in the channel also inhibits to some degree the reorientational motions of the channel water molecules.

This article has been cited by other articles:

				S. Narayan, D. L. Wyatt, D. S. Crumrine, and S. Cukierman Proton Transfer in Water Wires in Proteins: Modulation by Local Constraint and Polarity in Gramicidin A Channels Biophys. J., September 1, 2007; 93(5): 1571 - 1579. [Abstract] [Full Text] [PDF]

				V. Vijayvergiya, R. Wilson, A. Chorak, P. F. Gao, T. A. Cross, and D. D. Busath Proton Conductance of Influenza Virus M2 Protein in Planar Lipid Bilayers Biophys. J., September 1, 2004; 87(3): 1697 - 1704. [Abstract] [Full Text] [PDF]

				T. Chou Water Alignment, Dipolar Interactions, and Multiple Proton Occupancy during Water-Wire Proton Transport Biophys. J., May 1, 2004; 86(5): 2827 - 2836. [Abstract] [Full Text] [PDF]

				Y. Wu and G. A. Voth A Computer Simulation Study of the Hydrated Proton in a Synthetic Proton Channel Biophys. J., August 1, 2003; 85(2): 864 - 875. [Abstract] [Full Text] [PDF]