Computing Potential of the Mean Force Profiles for Ion Permeation Through Channelrhodopsin Chimera, C1C2
Journal Article
·
· Methods in Molecular Biology
- Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
- University of New Orleans, LA (United States)
Umbrella sampling, coupled with a weighted histogram analysis method (US-WHAM), can be used to construct potentials of mean force (PMFs) for studying the complex ion permeation pathways of membrane transport proteins. Despite the widespread use of US-WHAM, obtaining a physically meaningful PMF can be challenging. Here, we provide a protocol to resolve that issue. Then, we apply that protocol to compute a meaningful PMF for sodium ion permeation through channelrhodopsin chimera, C1C2, for illustration.
- Research Organization:
- Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
- Sponsoring Organization:
- USDOE National Nuclear Security Administration (NNSA)
- Grant/Contract Number:
- AC04-94AL85000
- OSTI ID:
- 1770350
- Report Number(s):
- SAND-2021-2338J; 694346
- Journal Information:
- Methods in Molecular Biology, Vol. 2191; ISSN 1064-3745
- Publisher:
- SpringerCopyright Statement
- Country of Publication:
- United States
- Language:
- English
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