title: Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin.
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.
authors.affiliation: Fachbereich Physik und Forschungszentrum OPTIMAS, Universität Kaiserslautern, Erwin-Schrödinger-Strasse, 67663, Kaiserslautern, Germany.
authors.forename: Saravana Prakash
authors.initials: SP
authors.lastname: Thirumuruganandham
authors.forename: Herbert M
authors.initials: HM
authors.lastname: Urbassek
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D006801:Humans; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017299:Rod Opsins / Q000737:chemistry*; D013055:Spectrophotometry, Infrared / Q000379:methods*; D014732:Vibration; D014867:Water / Q000737:chemistry
chemical_list: D017299:Rod Opsins; C095855:long-wavelength opsin; C095854:middle-wavelength opsin; C095853:short-wavelength opsin; D014867:Water