Computing Potential of the Mean Force Profiles for Ion Permeation Through Channelrhodopsin Chimera, C1C2

Priest, Chad; VanGordon, Monika R.; Rempe, Caroline; Chaudhari, Mangesh I.; Stevens, Mark J.; Rick, Steve; Rempe, Susan B.

doi:10.1007/978-1-0716-0830-2_2

Title: Computing Potential of the Mean Force Profiles for Ion Permeation Through Channelrhodopsin Chimera, C1C2

Journal Article · Tue Sep 01 00:00:00 EDT 2020 · Methods in Molecular Biology

DOI:https://doi.org/10.1007/978-1-0716-0830-2_2· OSTI ID:1770350

Priest, Chad ^[1]; VanGordon, Monika R. ^[2]; Rempe, Caroline ^[1]; Chaudhari, Mangesh I. ^[1]; Stevens, Mark J. ^[1]; Rick, Steve ^[2]; Rempe, Susan B. ^[1]

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.

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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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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Umbrella sampling (US)
Molecular dynamics
Potential of mean force (PMF)
Statistical mechanics
Free energies
Reaction coordinate (RC)
Weighted histogram method (WHAM)
Nanotechnology Optogenetics

Title: Computing Potential of the Mean Force Profiles for Ion Permeation Through Channelrhodopsin Chimera, C1C2

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