title: Enzymatic turnover of macromolecules generates long-lasting protein-water-coupled motions beyond reaction steady state.
abstract: The main focus of enzymology is on the enzyme rates, substrate structures, and reactivity, whereas the role of solvent dynamics in mediating the biological reaction is often left aside owing to its complex molecular behavior. We used integrated X-ray- and terahertz- based time-resolved spectroscopic tools to study protein-water dynamics during proteolysis of collagen-like substrates by a matrix metalloproteinase. We show equilibration of structural kinetic transitions in the millisecond timescale during degradation of the two model substrates collagen and gelatin, which have different supersecondary structure and flexibility. Unexpectedly, the detected changes in collective enzyme-substrate-water-coupled motions persisted well beyond steady state for both substrates while displaying substrate-specific behaviors. Molecular dynamics simulations further showed that a hydration funnel (i.e., a gradient in retardation of hydrogen bond (HB) dynamics toward the active site) is substrate-dependent, exhibiting a steeper gradient for the more complex enzyme-collagen system. The long-lasting changes in protein-water dynamics reflect a collection of local energetic equilibrium states specifically formed during substrate conversion. Thus, the observed long-lasting water dynamics contribute to the net enzyme reactivity, impacting substrate binding, positional catalysis, and product release.
authors.affiliation: Department of Physical Chemistry II, Ruhr University Bochum, Bochum 44801, Germany;
authors.forename: Jessica
authors.initials: J
authors.lastname: Dielmann-Gessner
authors.affiliation: Department of Physical Chemistry II, Ruhr University Bochum, Bochum 44801, Germany;
authors.forename: Moran
authors.initials: M
authors.lastname: Grossman
authors.affiliation: Department of Physical Chemistry II, Ruhr University Bochum, Bochum 44801, Germany;
authors.forename: Valeria
authors.initials: V
authors.lastname: Conti Nibali
authors.affiliation: Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel; and.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Born
authors.affiliation: Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel; and.
authors.forename: Inna
authors.initials: I
authors.lastname: Solomonov
authors.affiliation: Departments of Chemistry and Biology, Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL 34987-2352.
authors.forename: Gregg B
authors.initials: GB
authors.lastname: Fields
authors.affiliation: Department of Physical Chemistry II, Ruhr University Bochum, Bochum 44801, Germany; martina.havenith@rub.de Irit.sagi@weizmann.ac.il.
authors.forename: Martina
authors.initials: M
authors.lastname: Havenith
authors.affiliation: Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel; and martina.havenith@rub.de Irit.sagi@weizmann.ac.il.
authors.forename: Irit
authors.initials: I
authors.lastname: Sagi
mesh_terms: D003094:Collagen / Q000378:metabolism*; D005453:Fluorescence; D006801:Humans; D007700:Kinetics; D053511:Matrix Metalloproteinase 14 / Q000378:metabolism*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D059748:Proteolysis; D012997:Solvents / Q000378:metabolism*; D055068:Terahertz Spectroscopy; D014867:Water / Q000378:metabolism*; D056928:X-Ray Absorption Spectroscopy
chemical_list: D012997:Solvents; D014867:Water; D003094:Collagen; C507086:MMP14 protein, human; D053511:Matrix Metalloproteinase 14
keywords: enzyme catalysis; metalloenzymes; solvation dynamics