Paul Grayson, Emad Tajkhorshid, and Klaus Schulten.
Mechanisms of selectivity in channels and enzymes studied with
interactive molecular dynamics.
Biophysical Journal, 85:36-48, 2003.
(PMC: 1303063)
GRAY2003
Interactive molecular dynamics, a new modeling tool for rapid investigation of the physical mechanisms of
biological processes at the atomic level, is applied to study selectivity and regulation of the membrane channel protein GlpF and
the enzyme glycerol kinase. These proteins facilitate the first two steps of Escherichia coli glycerol metabolism. Despite their different function and architecture the proteins are found to employ common mechanisms for substrate selectivity: an induced
geometrical fit by structurally homologous binding sites and an induced rapid dipole moment reversal. Competition for hydrogen
bonding sites with water in both proteins is critical for substrate motion. In glycerol kinase, it is shown that the proposed domain
motion prevents competition with water, in turn regulating the binding of glycerol.
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