Journal of Molecular Modeling

, Volume 15, Issue 8, pp 959–969 | Cite as

Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin

  • Saravana Prakash Thirumuruganandham
  • Herbert M. Urbassek
Original Paper

Abstract

Vibrational excitations of low-frequency collective modes are essential for functionally important conformational transitions in proteins. We carried out an analysis of the low-frequency modes in the G protein coupled receptors (GPCR) family of cone opsins based on both normal-mode analysis and molecular dynamics (MD) simulations. Power spectra obtained by MD can be compared directly with normal modes. In agreement with existing experimental evidence related to transmembrane proteins, cone opsins have functionally important transitions that correspond to approximately 950 modes and are found below 80 cm−1. This is in contrast to bacteriorhodopsin and rhodopsin, where the important low-frequency transition modes are below 50 cm−1. We find that the density of states (DOS) profile of blue opsin in a solvent (e.g. water) has increased populations in the very lowest frequency modes (<15 cm−1); this is indicative of the increased thermostability of blue opsin. From our work we found that, although light absorption behaves differently in blue, green and red opsins, their low-frequency vibrational motions are similar. The similarities and differences in the domain motions of blue, red and green opsins are discussed for several representative modes. In addition, the influence of the presence of a solvent is reported and compared with vacuum spectra. 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.

Keywords

Normal modes Molecular dynamics Vibrational modes Proteins Infrared absorbance 

PACS numbers

36.20.Ng 87.15.M- 87.14.ep 87.15.hp 

Notes

Acknowledgements

The authors acknowledge financial support by the Deutsche Forschungsgemeinschaft via the Graduiertenkolleg 792, and thank R. Diller for valuable discussions on the subject.

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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Saravana Prakash Thirumuruganandham
    • 1
  • Herbert M. Urbassek
    • 1
  1. 1.Fachbereich Physik und Forschungszentrum OPTIMASUniversität KaiserslauternKaiserslauternGermany

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