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Low-frequency vibrational modes in blue opsin: A computational study

Abstract:

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.