title: Conformational state distributions and catalytically relevant dynamics of a hinge-bending enzyme studied by single-molecule FRET and a coarse-grained simulation.
abstract: Over the last few decades, a view has emerged showing that multidomain enzymes are biological machines evolved to harness stochastic kicks of solvent particles into highly directional functional motions. These intrinsic motions are structurally encoded, and Nature makes use of them to catalyze chemical reactions by means of ligand-induced conformational changes and states redistribution. Such mechanisms align reactive groups for efficient chemistry and stabilize conformers most proficient for catalysis. By combining single-molecule Förster resonance energy transfer measurements with normal mode analysis and coarse-grained mesoscopic simulations, we obtained results for a hinge-bending enzyme, namely phosphoglycerate kinase (PGK), which support and extend these ideas. From single-molecule Förster resonance energy transfer, we obtained insight into the distribution of conformational states and the dynamical properties of the domains. The simulations allowed for the characterization of interdomain motions of a compact state of PGK. The data show that PGK is intrinsically a highly dynamic system sampling a wealth of conformations on timescales ranging from nanoseconds to milliseconds and above. Functional motions encoded in the fold are performed by the PGK domains already in its ligand-free form, and substrate binding is not required to enable them. Compared to other multidomain proteins, these motions are rather fast and presumably not rate-limiting in the enzymatic reaction. Ligand binding slightly readjusts the orientation of the domains and feasibly locks the protein motions along a preferential direction. In addition, the functionally relevant compact state is stabilized by the substrates, and acts as a prestate to reach active conformations by means of Brownian motions.
authors.affiliation: Institute of Complex Systems (ICS-5) Molecular Biophysics, Forschungszentrum Jülich, Jülich, Germany. Electronic address: m.gabba@fz-juelich.de.
authors.forename: Matteo
authors.initials: M
authors.lastname: Gabba
authors.affiliation: Institute of Complex Systems (ICS-2): Theoretical Soft Matter and Biophysics, Forschungszentrum Jülich, Jülich, Germany.
authors.forename: Simón
authors.initials: S
authors.lastname: Poblete
authors.affiliation: Institute of Complex Systems (ICS-5) Molecular Biophysics, Forschungszentrum Jülich, Jülich, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Rosenkranz
authors.affiliation: Institute of Complex Systems (ICS-5) Molecular Biophysics, Forschungszentrum Jülich, Jülich, Germany.
authors.forename: Alexandros
authors.initials: A
authors.lastname: Katranidis
authors.affiliation: I. Physikalisches Institut (IA), Arbeitsgruppe Biophysik, Rheinisch-Westfaelische Technische Hochschule, Aachen, Germany.
authors.forename: Daryan
authors.initials: D
authors.lastname: Kempe
authors.affiliation: Institute of Complex Systems (ICS-5) Molecular Biophysics, Forschungszentrum Jülich, Jülich, Germany.
authors.forename: Tina
authors.initials: T
authors.lastname: Züchner
authors.affiliation: Institute of Complex Systems (ICS-2): Theoretical Soft Matter and Biophysics, Forschungszentrum Jülich, Jülich, Germany.
authors.forename: Roland G
authors.initials: RG
authors.lastname: Winkler
authors.affiliation: Institute of Complex Systems (ICS-2): Theoretical Soft Matter and Biophysics, Forschungszentrum Jülich, Jülich, Germany.
authors.forename: Gerhard
authors.initials: G
authors.lastname: Gompper
authors.affiliation: Institute of Complex Systems (ICS-5) Molecular Biophysics, Forschungszentrum Jülich, Jülich, Germany; I. Physikalisches Institut (IA), Arbeitsgruppe Biophysik, Rheinisch-Westfaelische Technische Hochschule, Aachen, Germany. Electronic address: fitter@physik.rwth-aachen.de.
authors.forename: Jörg
authors.initials: J
authors.lastname: Fitter
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D031541:Fluorescence Resonance Energy Transfer; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010735:Phosphoglycerate Kinase / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000201:enzymology; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D029701:Saccharomyces cerevisiae Proteins; D010735:Phosphoglycerate Kinase