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Interdomain dynamics and ligand binding: molecular dynamics simulations of glutamine binding protein
Author(s) -
Pang Andrew,
Arinaminpathy Yalini,
Sansom Mark S.P.,
Biggin Philip C.
Publication year - 2003
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/s0014-5793(03)00866-4
Subject(s) - dynamics (music) , molecular dynamics , protein dynamics , chemistry , glutamine , biophysics , ligand (biochemistry) , biochemistry , computational chemistry , physics , biology , amino acid , receptor , acoustics
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.