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Protein flexibility prediction by an all-atom mean-field statistical theory

¹ Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York (SUNY) at Buffalo, Buffalo, New York 14214, USA
² Surface Physics Laboratory (National Key Laboratory) and T-Center for Life Sciences, Fudan University, Shanghai 200433, China
³ School of Physics and Electronic Information, Wenzhou Normal College, Wenzhou 325027, China
⁴ T.D. Lee Physics Laboratory and Research Center for Theoretical Physics and ⁵ Department of Macromolecular Science, The Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China

(RECEIVED December 27, 2004; FINAL REVISION April 13, 2005; ACCEPTED April 22, 2005)

We extended a mean-field model to proteins with all atomic detail. The all-atom mean-field model was used to calculate the dynamic and thermodynamic properties of a three-helix bundle fragment of Staphylococcal protein A (Protein Data Bank [PDB] ID 1BDD) and -spectrin SH3 domain protein (PDB ID 1SHG). We show that a model with all-atomic detail provides a significantly more accurate prediction of flexibility of residues in proteins than does a coarse-grained residue-level model. The accuracy of flexibility prediction is further confirmed by application of the method to 18 additional proteins with the largest size of 224 residues.

Keywords: protein flexibility; mean-field statistical theory; protein thermodynamics; all-atom model

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041311005.

Reprint requests to: Yaoqi Zhou, Howard Hughes Medical Institute Center for Single Molecule Biophysics and Department of Physiology and Biophysics, State University of New York at Buffalo, 124 Sherman Hall, Buffalo, NY 14214, USA; e-mail: yqzhou{at}buffalo.edu; fax: (716) 829-2344.

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