Computing potential of the mean force profiles for ion permeation through channelrhodopsin Chimera, C1C2

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

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

Computing potential of the mean force profiles for ion permeation through channelrhodopsin Chimera, C1C2

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

Research output: Other contribution › peer-review

7 Scopus citations

Abstract

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.

Original language	English
DOIs	https://doi.org/10.1007/978-1-0716-0830-2_2
State	Published - Jan 1 2021
Externally published	Yes

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

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title = "Computing potential of the mean force profiles for ion permeation through channelrhodopsin Chimera, C1C2",

abstract = "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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T1 - Computing potential of the mean force profiles for ion permeation through channelrhodopsin Chimera, C1C2

AU - Priest, Chad

AU - VanGordon, Monika R.

AU - Rempe, Caroline

AU - Chaudhari, Mangesh I.

AU - Stevens, Mark J.

AU - Rick, Steve

AU - Rempe, Susan B.

PY - 2021/1/1

Y1 - 2021/1/1

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/85090104769

U2 - 10.1007/978-1-0716-0830-2_2

DO - 10.1007/978-1-0716-0830-2_2

M3 - Other contribution

ER -

Computing potential of the mean force profiles for ion permeation through channelrhodopsin Chimera, C1C2

Abstract

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