Tools for channels: moving towards molecular calculations of gating and permeation in ion channel biophysics
Thomas B Woolf1, Daniel M Zuckerman, Nandou Lu
1Department of Physiology, Johns Hopkins University, School of Medicine, Biophysics 206, 725 N. Wolfe Street, Baltimore, MD 21205, USA. woolf@groucho.med.jhmi.edu
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.
Related Concept Videos
Mechanically-gated Ion Channels
Mechanically-gated Ion Channels
Non-gated Ion Channels
Compared to the gated ion channels, the non-gated channels, also known as leakage or passive channels, have no gating mechanism.
Non-gated Ion Channels
Compared to the gated ion channels, the non-gated channels, also known as leakage or passive channels, have no gating mechanism.
Ion Channels
Ion channels are specialized integral membrane proteins on the plasma membrane that allow specific...
Voltage-gated Ion Channels
Generally, all voltage-gated ion channels have a 'voltage-sensing domain' that spans the lipid bilayer. The charged residues in the sensor move in response to the membrane potential changes that open the channel allowing ions movement. There are several types of...


