Title: The conformational changes analysis of Maltodextrin binding protein based on elastic network model

Authors: Haiyan Li; Jihua Wang

Addresses: Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou University, Physics Department, Dezhou University, Dezhou, Shandong 253023, China ' Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Dezhou University, Physics Department, Dezhou University, Dezhou, Shandong 253023, China

Abstract: Maltodextrin Binding Protein (MBP) has provided a model system for investigating open-closed conformation transition based on two coarse-grained elastic network models. GNM results show that the open and closed forms have the same motion hinge axes and the open-closed conformational transition mainly exhibits as a large movement of the N-domain. ANM calculation shows a transition from open/closed to closed/open, which is helpful for ligand binding or release. During the open-closed transition, the residues within the domains move in a highly coupled way, and this indicates that the hinge connecting the domains is flexible, while the domains themselves are rigid.

Keywords: conformational changes; GNM; Gaussian network model; ANM; anisotropy network model; MBP; maltodextrin binding protein; elastic network models; bioinformatics.

DOI: 10.1504/IJDMB.2013.054227

International Journal of Data Mining and Bioinformatics, 2013 Vol.7 No.4, pp.436 - 449

Accepted: 11 Oct 2011
Published online: 20 Oct 2014 *

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