Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels.

Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Research Abstract Details 

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Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Abstract Text:

Toby W Allen,Olaf S Andersen,Benoit Roux,

Ion channels catalyze the permeation of charged molecules across cell membranes and are essential for many vital physiological functions, including nerve and muscle activity. To understand better the mechanisms underlying ion conduction and valence selectivity of narrow ion channels, we have employed free energy techniques to calculate the potential of mean force (PMF) for ion movement through the prototypical gramicidin A channel. Employing modern all-atom molecular dynamics (MD) force fields with umbrella sampling methods that incorporate one hundred 1-2 ns trajectories, we find that it is possible to achieve semi-quantitative agreement with experimental binding and conductance measurements. We also examine the sensitivity of the MD-PMF results to the choice of MD force field and compare PMFs for potassium, calcium and chloride ions to explore the basis for the valence selectivity of this narrow and uncharged ion channel. A large central barrier is observed for both anions and divalent ions, consistent with lack of experimental conductance. Neither anion or divalent cation is seen to be stabilized inside the channel relative to the bulk electrolyte and each leads to large disruptions to the protein and membrane structure when held deep inside the channel. Weak binding of calcium ions outside the channel corresponds to a free energy well that is too shallow to demonstrate channel blocking. Our findings emphasize the success of the MD-PMF approach and the sensitivity of ion energetics to the choice of biomolecular force field.

Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Publishing Authors By Initials

TW Allen,OS Andersen,B Roux,

For similar inorganic chemicals: elements: metals, alkali: potassium research abstracts see: inorganic chemicals: elements: metals, alkali: potassium research

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MEDLINE DATE:

Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Biophysical chemistry

VOLUME: 124

Page Numbers: 251-67

Journal Abbreviation: Biophys. Chem.

ISSN: 0301-4622

DAY: 9

MONTH: 05

YEAR: 2006

Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 403171

Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Keywords Mesh Terms:

KEYWORDS: Potassium

MESH TERMS: chemistry

Chemical & Substance for Abstract: Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels. Information

Substance Name: Chlorine

Registry Number: 7782-50-5

Grant and Affiliation Information for Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels.

AFFILIATION: Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA. twallen@ucdavis.edu

Country: Netherlands

AGENCY: United States NIGMS

GRANT: GM70791

ACRONYM: GM

MEDLINETA: Biophys Chem

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