title: Stochastic thermodynamics of a chemical nanomachine: The channeling enzyme tryptophan synthase.
abstract: The enzyme tryptophan synthase is characterized by a complex pattern of allosteric interactions that regulate the catalytic activity of its two subunits and opening or closing of their ligand gates. As a single macromolecule, it implements 13 different reaction steps, with an intermediate product directly channeled from one subunit to another. Based on experimental data, a stochastic model for the operation of tryptophan synthase has been earlier constructed [D. Loutchko, D. Gonze, and A. S. Mikhailov, J. Phys. Chem. B 120, 2179 (2016)]. Here, this model is used to consider stochastic thermodynamics of such a chemical nanomachine. The Gibbs energy landscape of the internal molecular states is determined, the production of entropy and its flow within the enzyme are analyzed, and the information exchange between the subunits resulting from allosteric cross-regulations and channeling is discussed.
authors.affiliation: Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.
authors.forename: Dimitri
authors.initials: D
authors.lastname: Loutchko
authors.affiliation: Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstraße 36, 10623 Berlin, Germany.
authors.forename: Maximilian
authors.initials: M
authors.lastname: Eisbach
authors.affiliation: Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Mikhailov
mesh_terms: D000494:Allosteric Regulation; D019277:Entropy; D005994:Glycerophosphates / Q000138:chemical synthesis / Q000737:chemistry; D008954:Models, Biological; D015394:Molecular Structure; D049329:Nanostructures; D021122:Protein Subunits / Q000737:chemistry; D012694:Serine / Q000737:chemistry; D013269:Stochastic Processes; D013816:Thermodynamics; D014364:Tryptophan / Q000138:chemical synthesis; D014367:Tryptophan Synthase / Q000737:chemistry*
chemical_list: D005994:Glycerophosphates; D021122:Protein Subunits; C008117:indoleglycerol phosphate; D012694:Serine; D014364:Tryptophan; C029620:alpha-glycerophosphoric acid; D014367:Tryptophan Synthase