DOI: 10.1002/bip.1979.360181008. Vibrational approach to the dynamics of an α‐helix

Vibrational approach to the dynamics of an α‐helix

10.1002/bip.1979.360181008

Crossref journal-article

Wiley

Biopolymers (311)

Abstract

AbstractThe dynamics of a finite α‐helix have been studied in the harmonic approximation by a vibrational analysis of the atomic motions about their equilibrium positions. The system were represented by an empirical potential energy function, and all degrees of freedom (bond lengths, bond angles, and torsional angles) were allowed to vary. The complete results were compared with a more restrictive model in which the peptide dihedral angle was kept rigid; also, a model potential excluding hydrogen bonds was examined. Thermal fluctuations in the backbone dihedral angles ϕ and ψ are 12° to 15°. The fluctuations of adjacent dihedral angles are highly correlated, and the correlation pattern is affected by the flexibility of the peptide dihedral angle. Time‐dependent autocorrelations in the motion of ϕ and ψ appear to decay due to dephasing in less than 1 psec, while the motions of the carbonyl oxygen and amide hydrogens out of the peptide plane are more harmonic. Length fluctuations have been evaluated and exhibit a strong end effect; the calculated elastic modulus is in agreement with other values. Rigid and adiabatic total energy surfaces corresponding to dihedral angle rotations in the middle of the helix have been obtained and compared with the quadratic approximation to those surfaces. The magnitudes and correlations between the fluctuations obtained by averaging over the adiabatic energy surface most closely resemble the vibrational results. Of particular interest is the fact that hydrogen bonds play a relatively small role in the local dihedral angle fluctuations, though the hydrogen bonds are important in the energy of overall length changes.

Bibliography

Levy, R. M., & Karplus, M. (1979). Vibrational approach to the dynamics of an Î±âhelix. Biopolymers, 18(10), 2465â2495. Portico.

Authors 2

Ronald M. Levy (first)
Martin Karplus (additional)

References 41 Referenced 71

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{'key': 'e_1_2_1_9_2', 'first-page': '436', 'volume-title': 'Peptides, Polypeptides and Proteins, Proceedings of the Rehovot Symposium on Poly‐Amino Acids', 'author': 'Torchia D. A.', 'year': '1974'} / Peptides, Polypeptides and Proteins, Proceedings of the Rehovot Symposium on Poly‐Amino Acids by Torchia D. A. (1974)
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{'key': 'e_1_2_1_23_2', 'first-page': '35', 'volume-title': 'Peptides, Polypeptides and Proteins', 'author': 'Hagler A. T.', 'year': '1974'} / Peptides, Polypeptides and Proteins by Hagler A. T. (1974)
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{'key': 'e_1_2_1_33_2', 'first-page': '311', 'volume': '15', 'author': 'Feughelman M.', 'year': '1977', 'journal-title': 'J. Polym. Sci.'} / J. Polym. Sci. by Feughelman M. (1977)
{'key': 'e_1_2_1_34_2', 'first-page': '629', 'volume': '15', 'author': 'Kotoda S.', 'year': '1972', 'journal-title': 'Rep. Prog. Polym. Phys. Jpn.'} / Rep. Prog. Polym. Phys. Jpn. by Kotoda S. (1972)
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{'key': 'e_1_2_1_40_2', 'volume-title': 'Theory of Lattice Dynamics in the Harmonic Approximation', 'author': 'Maradudin A. A.', 'year': '1971'} / Theory of Lattice Dynamics in the Harmonic Approximation by Maradudin A. A. (1971)
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10.1016/0009-2614(75)85577-1

Dates

Type	When
Created	20 years, 8 months ago (Dec. 29, 2004, 9:16 p.m.)
Deposited	1 year, 10 months ago (Oct. 19, 2023, 2:29 p.m.)
Indexed	1 year, 2 months ago (June 20, 2024, 8:34 a.m.)
Issued	45 years, 10 months ago (Oct. 1, 1979)
Published	45 years, 10 months ago (Oct. 1, 1979)
Published Online	21 years, 6 months ago (Feb. 1, 2004)
Published Print	45 years, 10 months ago (Oct. 1, 1979)

Funders 0

None

BibTeX

@article{Levy_1979, title={Vibrational approach to the dynamics of an α‐helix}, volume={18}, ISSN={1097-0282}, url={http://dx.doi.org/10.1002/bip.1979.360181008}, DOI={10.1002/bip.1979.360181008}, number={10}, journal={Biopolymers}, publisher={Wiley}, author={Levy, Ronald M. and Karplus, Martin}, year={1979}, month=oct, pages={2465–2495} }

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