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Low‐frequency vibrational modes in blue opsin: A computational study
Author(s) -
Thirumuruganandham Saravana Prakash,
Urbassek Herbert M.
Publication year - 2010
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.21908
Subject(s) - opsin , molecular physics , physics , chemistry , rhodopsin , retinal , biochemistry
Vibrational excitations of low‐frequency collective modes are essential for functionally important conformational transitions in proteins. We have carried out an analysis of the low‐frequency modes in blue opsin based on both normal‐mode analysis and molecular dynamics simulations. Power spectra obtained by molecular dynamics agree well with the normal modes. A representative set of low‐frequency modes is discussed with the help of vector‐field representation. We thus demonstrate that terahertz spectroscopy of low‐frequency modes might be relevant for identifying those vibrational degrees of freedom that correlate to known conformational changes in opsins. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2010