Atomistic Characterization of Gramicidin Channel Formation

Delin Sun, Stewart He, W. F.Drew Bennett, Camille L. Bilodeau, Olaf S. Andersen, Felice C. Lightstone, Helgi I. Ingólfsson

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

We investigated gramicidin A (gA) subunit dimerization in lipid bilayers using microsecond-long replica-exchange umbrella sampling simulations, millisecond-long unbiased molecular dynamics simulations, and machine learning. Our simulations led to a dimer structure that is indistinguishable from the experimentally determined gA channel structures, with the two gA subunits joined by six hydrogen bonds (6HB). The simulations also uncovered two additional dimer structures, with different gA-gA stacking orientations that were stabilized by four or two hydrogen bonds (4HB or 2HB). When examining the temporal evolution of the dimerization, we found that two bilayer-inserted gA subunits can form the 6HB dimer directly, with no discernible intermediate states, as well as through paths that involve the 2HB and 4HB dimers.

Original languageEnglish (US)
Pages (from-to)7-12
Number of pages6
JournalJournal of Chemical Theory and Computation
Volume17
Issue number1
DOIs
StatePublished - Jan 12 2021
Externally publishedYes

ASJC Scopus subject areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry

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