title: Collective dynamics of periplasmic glutamine binding protein upon domain closure.
abstract: The glutamine binding protein is a vital component of the associated ATP binding cassette transport systems responsible for the uptake of glutamine into the cell. We have investigated the global movements of this protein by molecular dynamics simulations and principal component analysis (PCA). We confirm that the most dominant mode corresponds to the biological function of the protein, i.e., a hinge-type motion upon ligand binding. The closure itself was directly observed from two independent trajectories whereby PCA was used to elucidate the nature of this closing reaction. Two intermediary states are identified and described in detail. The ligand binding induces the structural change of the hinge regions from a discontinuous beta-sheet to a continuous one, which also enhances softness of the hinge and modifies the direction of hinge motion to enable closing. We also investigated the convergence behavior of PCA modes, which were found to converge rather quickly when the associated magnitudes of the eigenvalues are well separated.
authors.affiliation: Laboratory of Molecular Design, Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan. hannes.loeffler@gmail.com
authors.forename: Hannes H
authors.initials: HH
authors.lastname: Loeffler
authors.forename: Akio
authors.initials: A
authors.lastname: Kitao
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D001703:Biophysics / Q000379:methods*; D002352:Carrier Proteins / Q000737:chemistry*; D003198:Computer Simulation; D004926:Escherichia coli / Q000378:metabolism; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009038:Motion; D025341:Principal Component Analysis; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins; D008024:Ligands; C037853:glutamine transport proteins; D000255:Adenosine Triphosphate