Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A

Diane E. Sagnella, Kari Laasonen, Michael L. Klein*

*Corresponding author for this work

Research output: Contribution to journalArticleScientificpeer-review

97 Citations (Scopus)

Abstract

Proton transfer in biological systems is thought to often proceed through hydrogen-bonded chains of water molecules. The ion channel, gramicidin A (gA), houses within its helical structure just such a chain. Using the density functional theory based ab initio molecular dynamics Car- Parrinello method, the structure and dynamics of proton diffusion through a polyglycine analog of the gA ion channel has been investigated. In the channel, a proton, which is initially present as hydronium (H3O+), rapidly forms a strong hydrogen bond with a nearest neighbor water, yielding a transient H5O2/+ complex. As in bulk water, strong hydrogen bonding of this complex to a second neighbor solvation shell is required for proton transfer to occur. Within gA, this second neighbor shell included not only a channel water molecule but also a carbonyl of the channel backbone. The present calculations suggest a transport mechanism in which a priori carbonyl solvation is a requirement for proton transfer.

Original languageEnglish
Pages (from-to)1172-1178
Number of pages7
JournalBiophysical Journal
Volume71
Issue number3
Publication statusPublished - Sep 1996
MoE publication typeA1 Journal article-refereed

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