Collective Dynamics of Periplasmic Glutamine Binding Protein upon Domain Closure Export

@article{citeulike:6066145, 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 ²-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.}, author = {Loeffler, Hannes H. and Kitao, Akio}, citeulike-article-id = {6066145}, citeulike-linkout-0 = {http://www.cell.com/biophysj/abstract/S0006-3495(09)01375-7}, day = {4}, keywords = {pca}, month = {November}, number = {9}, pages = {2541--2549}, posted-at = {2009-11-04 02:00:22}, priority = {2}, title = {Collective Dynamics of Periplasmic Glutamine Binding Protein upon Domain Closure}, url = {http://www.cell.com/biophysj/abstract/S0006-3495(09)01375-7}, volume = {97}, year = {2009} }

TY - JOUR ID - citeulike:6066145 L3 - citeulike-article-id:6066145 N2 - 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 ²-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. IS - 9 EP - 2549 TI - Collective Dynamics of Periplasmic Glutamine Binding Protein upon Domain Closure VL - 97 SP - 2541 KW - pca AU - Loeffler, Hannes AU - Kitao, Akio PY - 2009/11/04/ UR - http://www.cell.com/biophysj/abstract/S0006-3495(09)01375-7 ER -