The conformational changes analysis of maltodextrin binding protein based on elastic network model

Int J Data Min Bioinform. 2013;7(4):436-49. doi: 10.1504/ijdmb.2013.054227.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Carrier Proteins / chemistry*
  • Carrier Proteins / metabolism
  • Computer Simulation
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism
  • Ligands
  • Models, Molecular
  • Periplasmic Binding Proteins
  • Protein Conformation

Substances

  • Carrier Proteins
  • Escherichia coli Proteins
  • Ligands
  • MalE protein, E coli
  • Periplasmic Binding Proteins