Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein
Copyright policy )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.
- Laboratory of Molecular Biophysics Department of Biochemistry University of Oxford United Kingdom
- University of Oxford United Kingdom
- University of Oxford United Kingdom
- Laboratory of Molecular Biophysics Department of Biochemistry University of Oxford United Kingdom
Models, Molecular, Binding Sites, Protein Conformation, Glutamine, Hydrogen Bonding, Ligands, Protein Structure, Tertiary, Molecular simulation, Escherichia coli, Periplasmic binding protein, Computer Simulation, Essential dynamics, Carrier Proteins, Protein Binding
Models, Molecular, Binding Sites, Protein Conformation, Glutamine, Hydrogen Bonding, Ligands, Protein Structure, Tertiary, Molecular simulation, Escherichia coli, Periplasmic binding protein, Computer Simulation, Essential dynamics, Carrier Proteins, Protein Binding
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