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Analysis of Conformational Motions and Residue Fluctuations for Escherichia coli Ribose-Binding Protein Revealed with Elastic Network Models
Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou University, 566 University Road West, Dezhou 253023, China
Department of Physics, Dezhou University, 566 University Road West, Dezhou 253023, China
* Author to whom correspondence should be addressed.
Received: 18 March 2013; in revised form: 24 April 2013 / Accepted: 25 April 2013 / Published: 21 May 2013
Abstract: The ribose-binding protein (RBP) is a sugar-binding bacterial periplasmic protein whose function is associated with a large allosteric conformational change from an open to a closed conformation upon binding to ribose. The open (ligand-free) and closed (ligand-bound) forms of RBP have been found. Here we investigate the conformational motions and residue fluctuations of the RBP by analyzing the modes of motion with two coarse-grained elastic network models, the Gaussian Network Model (GNM) and Anisotropic Network Model (ANM). The calculated B-factors in both the calculated models are in good agreement with the experimentally determined B-factors in X-ray crystal structures. The slowest mode analysis by GNM shows that both forms have the same motion hinge axes around residues Ser103, Gln235, Asp264 and the two domains of both structures have similar fluctuation range. The superposition of the first three dominant modes of ANM, consisting of the rotating, bending and twisting motions of the two forms, accounts for large rearrangement of domains from the ligand-free (open) to ligand-bound (closed) conformation and thus constitutes a critical component of the RBP’s functions. By analyzing cross-correlations between residue fluctuation and the difference-distance plot, it is revealed that the conformational change can be described as a rigid rotation of the two domains with respect to each other, whereas the internal structure of the two domains remains largely intact. The results directly indicate that the dominant dynamic characteristics of protein structures can be captured from their static native state using coarse-grained models.
Keywords: ribose-binding protein; elastic network model; conformational motions
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MDPI and ACS Style
Li, H.Y.; Cao, Z.X.; Zhao, L.L.; Wang, J.H. Analysis of Conformational Motions and Residue Fluctuations for Escherichia coli Ribose-Binding Protein Revealed with Elastic Network Models. Int. J. Mol. Sci. 2013, 14, 10552-10569.
Li HY, Cao ZX, Zhao LL, Wang JH. Analysis of Conformational Motions and Residue Fluctuations for Escherichia coli Ribose-Binding Protein Revealed with Elastic Network Models. International Journal of Molecular Sciences. 2013; 14(5):10552-10569.
Li, Hai Y.; Cao, Zan X.; Zhao, Li L.; Wang, Ji H. 2013. "Analysis of Conformational Motions and Residue Fluctuations for Escherichia coli Ribose-Binding Protein Revealed with Elastic Network Models." Int. J. Mol. Sci. 14, no. 5: 10552-10569.