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Tryptophan Rotamers as Evidenced by X-Ray, Fluorescence Lifetimes, and Molecular Dynamics Modeling

Samuel L. C. Moors ^*, Mario Hellings , Marc De Maeyer , Yves Engelborghs  and Arnout Ceulemans ^*

^* Laboratory of Quantum Chemistry, Laboratory for Bio-Molecular Dynamics, and Laboratory for Bio-Molecular Modeling, University of Leuven, Leuven, Belgium

Correspondence: Address reprint requests to Arnout Ceulemans, Laboratory of Quantum Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium. Tel.: 32-1632-7363; Fax: 32-1632-7992; E-mail: Arnout.Ceulemans{at}chem.kuleuven.be.

We investigated the native-state dynamics of the Bacillus caldolyticus cold-shock protein mutant Bc-Csp L66E, using fluorescence and appropriate molecular dynamics methods. Two fluorescence lifetimes were found, the amplitudes of which agree very well with tryptophan rotamer populations, obtained from parallel tempering calculations. Rotamer lifetimes were predicted by transition-state theory from high-temperature simulations. Transition pathways were extracted from the transition rates between individual rotameric states. The molecular dynamics also reveal the loop fluctuations in the native state.

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