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Redox-Promoting Protein Motions in Rubredoxin

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Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
Molecular and Structural Biochemistry Department, North Carolina State University, Raleigh, North Carolina 27695, United States
§ National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland 20899, United States
Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
Jose M. Borreguero, Oak Ridge National Laboratory, P.O. Box 2008, MS 6164, Oak Ridge, TN 37831. Phone: (865) 241-3071. Fax: (865) 576-5491. E-mail: [email protected]. Kenneth Herwig, Oak Ridge National Laboratory, P.O. Box 2008, MS 6475, Oak Ridge, TN 37831. Phone: (865) 576-5095. Fax: (865) 241-5177. E-mail: [email protected]
Cite this: J. Phys. Chem. B 2011, 115, 28, 8925–8936
Publication Date (Web):May 24, 2011
https://doi.org/10.1021/jp201346x
Copyright © 2011 American Chemical Society

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    Abstract

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    Proteins are dynamic objects, constantly undergoing conformational fluctuations, yet the linkage between internal protein motion and function is widely debated. This study reports on the characterization of temperature-activated collective and individual atomic motions of oxidized rubredoxin, a small 53 residue protein from thermophilic Pyrococcus furiosus (RdPf). Computational modeling allows detailed investigations of protein motions as a function of temperature, and neutron scattering experiments are used to compare to computational results. Just above the dynamical transition temperature which marks the onset of significant anharmonic motions of the protein, the computational simulations show both a significant reorientation of the average electrostatic force experienced by the coordinated Fe3+ ion and a dramatic rise in its strength. At higher temperatures, additional anharmonic modes become activated and dominate the electrostatic fluctuations experienced by the ion. At 360 K, close to the optimal growth temperature of P. furiosus, simulations show that three anharmonic modes including motions of two conserved residues located at the protein active site (Ile7 and Ile40) give rise to the majority of the electrostatic fluctuations experienced by the Fe3+ ion. The motions of these residues undergo displacements which may facilitate solvent access to the ion.

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    Details of sample preparation and neutron scattering measurements, computational modeling, and analysis methodology. This material is available free of charge via the Internet at http://pubs.acs.org/.

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