Tools for channels

Moving towards molecular calculations of gating and permeation in ion channel biophysics

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

Research output: Contribution to journalArticle

15 Citations (Scopus)

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 - Jan 1 2004
Externally publishedYes

Fingerprint

Biophysics
biophysics
Ion Channels
Permeation
sampling
Sampling
Ions
Free energy
Voltage-Gated Potassium Channels
Importance sampling
free energy
Electric potential
Molecular structure
Potassium
electric potential
X rays
molecular structure
selectivity
profiles
x rays

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

Cite this

Tools for channels : Moving towards molecular calculations of gating and permeation in ion channel biophysics. / Woolf, Thomas B.; Zuckerman, Daniel; Lu, Nandou; Jang, Hyunbum.

In: Journal of Molecular Graphics and Modelling, Vol. 22, No. 5, 01.01.2004, p. 359-368.

Research output: Contribution to journalArticle

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