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. 1988 Mar;53(3):297–309. doi: 10.1016/S0006-3495(88)83107-2

The normal modes of the gramicidin-A dimer channel.

B Roux 1, M Karplus 1
PMCID: PMC1330198  PMID: 2450595

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.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

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