Int. J. Mol. Sci. 2013, 14(5), 10552-10569; doi:10.3390/ijms140510552
Article

Analysis of Conformational Motions and Residue Fluctuations for Escherichia coli Ribose-Binding Protein Revealed with Elastic Network Models

1,2email, 1,2email, 1,2email and 1,2,* email
Received: 18 March 2013; in revised form: 24 April 2013 / Accepted: 25 April 2013 / Published: 21 May 2013
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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.

AMA Style

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.

Chicago/Turabian Style

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.


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