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Low‐frequency vibrations in α‐helices: Helicoidal analysis of polyalanine and deoxymyoglobin molecular dynamics trajectories
Author(s) -
FuroisCorbin S.,
Smith J. C.,
Lavery R.
Publication year - 1995
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360350602
Subject(s) - myoglobin , helix (gastropod) , molecular dynamics , vibration , curvature , chemistry , bending , position (finance) , crystallography , molecular vibration , spectral line , physics , molecule , computational chemistry , thermodynamics , geometry , mathematics , acoustics , biochemistry , quantum mechanics , biology , ecology , organic chemistry , snail , finance , economics
We present an approach to the analysis of low‐frequency (0‐200 cm −1 ) α‐helix vibrations in molecular dynamics simulation. The approach employs the P‐Curves algorithm [H. Sklenar, C. Etchebest, and R. Lavery, (1989) Proteins: Structure, Function and Genetics, Vol. 6. pp. 46–60] to determine the helical axis and a set of helicoidal parameters describing the axis curvature and the position of the repealing units with respect to the axis and each other. The vibrations are analyzed in terms of time correlation functions of the fluctuations of P‐Curves parameters and their Fourier transforms. Simulations of polyalanine and myoglobin are analyzed. For polyalanine, global twisting, bending, and stretching vibrations are found at 11, 20, and 40 cm −1 , respectively. In myoglobin, the spectra of the global helix vibrations are qualitatively different from those of polyalanine and considerably more complicated. Local vibrations of individual amino acid units in the helix backbones are also analyzed with P‐Curves and compared. © 1995 John Wiley & Sons, Inc.