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Kinetic response of a photoperturbed allosteric protein

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B. Buchli; S.A. Waldauer; R. Walser; M.L. Donten; R. Pfister; N. Blöchliger; S. Steiner; A. Caflisch; O. Zerbe; P. Hamm

Journal: Proc. Natl. Acad. Sci. U.S.A.
Year: 2013
Volume: 110
Issue: 29
Pages: 11725-11730
DOI: 10.1073/pnas.1306323110
Type of Publication: Journal Article

Allosteric Regulation; Azo Compounds; Humans; Kinetics; Lasers; Magnetic Resonance Spectroscopy; Models, Molecular; Molecular Dynamics Simulation; Photochemistry; Protein Conformation; Protein Tyrosine Phosphatase, Non-Receptor Type 13; Spectrophotometry, Infrared; Time Factors; Water


By covalently linking an azobenzene photoswitch across the binding groove of a PDZ domain, a conformational transition, similar to the one occurring upon ligand binding to the unmodified domain, can be initiated on a picosecond timescale by a laser pulse. The protein structures have been characterized in the two photoswitch states through NMR spectroscopy and the transition between them through ultrafast IR spectroscopy and molecular dynamics simulations. The binding groove opens on a 100-ns timescale in a highly nonexponential manner, and the molecular dynamics simulations suggest that the process is governed by the rearrangement of the water network on the protein surface. We propose this rearrangement of the water network to be another possible mechanism of allostery.