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PMID: 2450595 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

The normal modes of the gramicidin-A dimer channel.

Biophysical journal ·Vol. 53 ·No. 3 ·1988-03-00 ·Pages 297-309

Roux B, Karplus M

Abstract

The dynamics of the gramicidin-A dimer channel is studied in the harmonic approximation by a vibrational analysis of the atomic motions relative to their equilibrium positions. The system is represented by an empirical potential energy function, and all degrees of freedom (bonds lengths, bond angles, and torsional angles) are allowed to vary. The thermal fluctuations in the backbone dihedral angles phi and psi, atomic root mean square displacements, and the correlations between the different amide planes are computed. It is found that only adjacent dihedral psi i and phi i+1 are strongly correlated, while different hydrogen-bonded amide planes are only weakly correlated. Modes with relatively low vibrational frequencies (75-175 cm-1) make the dominant contributions to the carbonyl librations. The general flexibility of the structure and the role of carbonyl librations in the ion transport mechanism are discussed.

MeSH Terms
Biophysical Phenomena Biophysics Gramicidin Ion Channels Models, Molecular Motion Protein Conformation Thermodynamics
Chemicals
Ion Channels Gramicidin
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Roux B
Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138.
Karplus M
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40 references, click to expand
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Article Info
Journal
Biophysical journal
Abbr.
Biophys J
ISSN
0006-3495
DOI
10.1016/S0006-3495(88)83107-2
Published
1988-03-00
Pages
297-309
Language
English
Region
United States
NLM ID
0370626
PMCID
PMC1330198
Subset
IM
External Links
PubMed source DOI: 10.1016/S0006-3495(88)83107-2 PMC Full Text View journal details
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