Tools for channels: Moving towards molecular calculations of gating and permeation in ion channel biophysics

Thomas B. Woolf, Daniel M. Zuckerman, Nandou Lu, Hyunbum Jang

Research output: Contribution to journalArticle

15 Scopus citations

Abstract

Recent X-ray structures of voltage gated potassium channels provide an exciting opportunity to connect molecular structures with measured biological function. Two of the most important connections for these channels are: first, to the molecular basis behind selectivity and the associated free energy profile underlying ionic current flow and, second, to a true molecular understanding of the large-scale conformational transitions that underlie voltage dependent gating. But, existing computational tools need to be further developed to reach these goals. In this contribution to the symposia on sampling methods we outline our dynamic importance sampling method for sampling large-scale conformational transitions as well as our studies with non-equilibrium work events and equilibrium overlap sampling (OS) methods for sampling events related to the calculation of relative free energies.

Original languageEnglish (US)
Pages (from-to)359-368
Number of pages10
JournalJournal of Molecular Graphics and Modelling
Volume22
Issue number5
DOIs
StatePublished - May 2004

Keywords

  • Importance sampling
  • Ion channels
  • Kinetics
  • Molecular dynamics
  • Non-equilibrium free energy
  • Overlap sampling
  • Permeation
  • Relative free energy

ASJC Scopus subject areas

  • Spectroscopy
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Materials Chemistry

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