UBI seminar (54th) 12/March/2020 (Thu)15:00-
 Place:Hongo, Science Building No. 1, room 413
 Speaker:Dr.Dimitri Loutchko (Univ. of Tokyo)
 Title:Information thermodynamics of the chemical nanomachine
          tryptophan synthase

Abstract: The channeling enzyme tryptophan synthase provides a paradigmatic example of a chemical nanomachine. It possesses two active centers and, as a single molecule, catalyzes a sequence of 13 different reactions with a complex pattern of allosteric regulation and with an intermediate product channeled from one active center to another. Here, the first single- molecule stochastic model of the enzyme is proposed and analyzed. Numerical simulations reveal the development of strong correlations in the states of the active centers and the emergent synchronization of intramolecular processes in tryptophan synthase. Moeover, the effects of allosteric interactions are studied using modified in silico models. The model is further analyzed within the framework of information transfer in Markov networks. In this regard, the theory by Horowitz and Esposito [1] is extended to encompass non-bipartite transitions and is thus made applicable to the presented kinetic model. Thereby, the effects of the flows of mutual information on the thermodynamics at the enzyme’s active centers are discussed and second law-like inequalities for the apparent entropy production at the centers are derived. Although the allosteric regulations in the tryptophan synthase enzyme are symmetric, we find an information theoretic asymmetry in the sense that all transitions at one active center contribute negative values to the flow of mutual information, while almost all transitions at the other center have positive contributions. We discuss ramifications and possible interpretations of this result.
[1] J. M. Horowitz and M. Esposito, Thermodynamics with continuous information flow, Phys Rev X, 4, 031015, 2014.
[2] D. Loutchko, M. Eisbach, and A. S. Mikhailov. Stochastic thermodynamics of a chemical nanomachine: The channeling enzyme tryptophan synthase. J Chem Phys, 146(2): 025101, 2017
[3] D. Loutchko, D. Gonze, and A. S. Mikhailov, Single-Molecule Stochastic Analysis of Channeling Enzyme Tryptophan Synthase. J Phys Chem B, 120(9): 2179-2186, 2016.