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- W2912530158 abstract "Cell signaling involves a fascinatingly complex network of interacting protein molecules, where information might flow through protein-protein interactions or remote signaling within a single protein (allostery). We have used molecular dynamics simulations in conjunction with energy decomposition analysis to elucidate the thermodynamic basis of “dynamic allostery” observed in a PDZ3 domain protein present in a large number of signaling protein complexes. Allostery without structural changes has often been attributed to dynamics and/or entropic effects. Here we demonstrate that a “population shift” of highly coordinated hydrogen bonds and salt bridges might lead to the allosteric modulation in this protein. We also find that compared to structure based parameters like contact map, non-bonded interaction energy provides a more sensitive probe to subtle allosteric modulation in conformational ensemble. We propose that dynamical effects are consequences of modification in the underlying energy landscape dominated by electrostatic interactions. Comparing the features of allosteric network due to ligand binding and evidences of pH dependent dynamic allostery in this protein, we envisage presence of a universal response system. This suggests that different types of external perturbation might excite different allosteric pathways, but the overall mode of communication seems to be governed by population shift in specific interactions like hydrogen bonding and salt bridges." @default.
- W2912530158 created "2019-02-21" @default.
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- W2912530158 date "2019-02-01" @default.
- W2912530158 modified "2023-09-30" @default.
- W2912530158 title "A Thermodynamic View of Dynamic Allostery in a PDZ Domain Protein" @default.
- W2912530158 doi "https://doi.org/10.1016/j.bpj.2018.11.905" @default.
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