Dynamical heterogeneity of specific amino acids in bacteriorhodopsin.
Components of biological macromolecules, complexes and membranes are animated by motions occurring over a wide range of time and length scales, the synergy of which is at the basis of biological activity. Understanding biological function thus requires a detailed analysis of the underlying dynamical heterogeneity. Neutron scattering, using specific isotope labeling, and molecular dynamics simulations were combined in order to study the dynamics of specific amino acid types in bacteriorhodopsin within the purple membrane (PM) of Halobacterium salinarum. Motions of leucine, isoleucine and tyrosine residues on the pico- to nanosecond time scale were examined separately as a function of temperature from 20 to 300 K. The dynamics of the three residue types displayed different temperature dependence: isoleucine residues have larger displacements compared to the global PM above 120 K; leucine residues have displacements similar to that of PM in the entire temperature range studied; and tyrosine residues have displacements smaller than that of the average membrane in an intermediate temperature range. Experimental features were mostly well reproduced by molecular dynamics simulations performed at five temperatures, which allowed the dynamical characterisation of the amino acids under study as a function of local environment. The resulting dynamical map of bacteriorhodopsin revealed that movements of a specific residue are determined by both its environment and its residue type.
Institut Laue-Langevin, 6 rue Jules Horowitz, B.P. 156, 38042 Grenoble Cedex 9, France.
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Wood
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Grudinin
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Kessler
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Weik
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Johnson
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Kneller
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Oesterhelt
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Zaccai
D000596:Amino Acids / Q000737:chemistry*; D001436:Bacteriorhodopsins / Q000737:chemistry* / Q000528:radiation effects; D003198:Computer Simulation; D003903:Deuterium; D019617:Halobacterium salinarum / Q000737:chemistry; D007553:Isotope Labeling; D008958:Models, Molecular; D009502:Neutrons; D017433:Protein Structure, Secondary; D018717:Purple Membrane / Q000737:chemistry; D012542:Scattering, Radiation; D013057:Spectrum Analysis; D013696:Temperature; D014867:Water / Q000737:chemistry
D000596:Amino Acids; D014867:Water; D001436:Bacteriorhodopsins; D003903:Deuterium