Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein.
Periplasmic binding proteins from Gram-negative bacteria possess a common architecture, comprised of two domains linked by a hinge region, a fold which they share with the neurotransmitter-binding domains of ionotropic glutamate receptors (GluRs). Glutamine-binding protein (GlnBP) is one such protein, whose crystal structure has been solved in both open and closed forms. Multi-nanosecond molecular dynamics simulations have been used to explore motions about the hinge region and how they are altered by ligand binding. Glutamine binding is seen to significantly reduce inter-domain motions about the hinge region. Essential dynamics analysis of inter-domain motion revealed the presence of both hinge-bending and twisting motions, as has been reported for a related sugar-binding protein. Significantly, the influence of the ligand on GlnBP dynamics is similar to that previously observed in simulations of rat glutamate receptor (GluR2) ligand-binding domain. The essential dynamics analysis of GlnBP also revealed a third class of motion which suggests a mechanism for signal transmission in GluRs.
Pang
Andrew
A
Laboratory of Molecular Biophysics, Department of Biochemistry, The University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
Arinaminpathy
Yalini
Y
Sansom
Mark S P
MS
Biggin
Philip C
PC
D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism*; D003198:Computer Simulation; D004926:Escherichia coli; D005973:Glutamine / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding / Q000502:physiology; D011487:Protein Conformation; D017434:Protein Structure, Tertiary
D002352:Carrier Proteins; D008024:Ligands; C037853:glutamine transport proteins; D005973:Glutamine