Berlin 2005 – scientific programme
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AKB: Biologische Physik
AKB 200: Poster Session II
AKB 200.37: Poster
Tuesday, March 8, 2005, 17:00–19:00, Poster TU C
Simulation of Fluorescence Anisotropy Experiments: Probing Protein Flexibility — •Gunnar Schröder1, Ulrike Alexiev2, and Helmut Grubmüller1 — 1MPI biophysik. Chemie, Göttingen — 2Freie Universität, Berlin
Fluorescence anisotropy experiments in combination with site-directed fluorescent labeling offer the chance to locally probe protein conformation and dynamics. To study how information on the protein dynamics can be extracted from the fluorescence anisotropy of a bound dye, we performed molecular dynamics simulations of an Alexa488 dye covalently bound to the loop connecting the A- and B-helix of bacteriorhodopsin. The fluorescence anisotropy decay predicted by the simulation agrees well with the experimental results. The simulation revealed two depolarization processes with a rotational correlation time of about one nanosecond, which are due to the loop flexibility and slow conformational dye dynamics and which cannot be separated by experiment alone. Analysis of the correlation between the dye and the protein motions provides an atomistic description of the part of the protein dynamics, that is actually observed in the experiment. Furthermore, comparison of simulations with and without bound dye enabled us to test the inevitable assumption that in the experiment the influence of the dye on the protein dynamics is negligible. Indeed, only minor deviations in the loop flexibility were seen, thus providing solid theoretical grounds for the usual interpretation of the measurements.