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 language | English (US) |
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Pages (from-to) | 359-368 |
Number of pages | 10 |
Journal | Journal of Molecular Graphics and Modelling |
Volume | 22 |
Issue number | 5 |
DOIs | |
State | Published - May 2004 |
Externally published | Yes |
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