Single-Molecule Stochastic Analysis of Channeling Enzyme 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 13 different reaction steps 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. All its transition rate constants were deduced from the experimental data available, and no fitting parameters were thus employed. Numerical simulations reveal strong correlations in the states of the active centers and the emergent synchronization of intramolecular processes in tryptophan synthase.

Stochastic thermodynamics of a chemical nanomachine: The channeling enzyme tryptophan synthase

“…We find high correlations (2.39 and 2.20 bits) between the states (G3P,indole+A-A) and (G3P,Q 3 ) after indole channeling and after the indole reaction at the β-site in the main pathway. This agrees with the previous analysis using the Pearson correlation coefficients 52 . As a result of channeling, both subunits simultaneously arrive at the state (G3P,indole+A-A) and high positive correlations are characteristic for it.…”

“…In Section III, its Markov transition network is introduced. This network is reversible and thus partially modified as compared to the previous publication 52 .…”

“…The stochastic single-molecule operation of tryptophan synthase can be seen as random wandering over a Markov network of its internal states. In this network, each binary internal state (a, b) with a = 1, ..., The kinetic Markov network for tryptophan synthase has been constructed in the previous publication 52 where all transition rates have been determined from the available experimental data. In that publication, we have modeled, however, a typical experimental situation where product concentrations remain vanishingly small.…”

“…The allosteric cross-regulations and channeling lead to the development of correlations between the internal states of the subunits. Previously, the presence of correlations has been demonstrated by computing the Pearson correlation coefficients for all possible pairs of states 52 . In this section, the concept of mutual information will be employed to further quantify the effects of allosteric cross-regulation and channeling.…”

“…Recently, a single-molecule stochastic description of tryptophan synthase has been constructed and the Markov network of this enzyme has been identified 52 . All its transition rate constants were deduced from the available experimental data and no arbitrary fitting parameters were employed.…”