Regensburg 2025 – scientific programme
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BP: Fachverband Biologische Physik
BP 29: Focus Session: Innovations in Research Software Engineering (joint session BP/DY)
BP 29.6: Talk
Thursday, March 20, 2025, 16:30–16:45, H44
Estimation of kinetic rates by constrained optimization — •Federico Marotta1, Maria Zimmermann-Kogadeeva1, Peer Bork1, Julia Mahamid1, and Sophia Rudorf2 — 1European Molecular Biology Laboratory — 2Leibniz Universität Hannover
Biological systems often rely on molecular motors to perform useful work. The kinetics of the reactions in a motor’s cycle can be easily investigated in vitro or in model organisms, but it is difficult to generalize them to a different system. We present a method to estimate the transition kinetics in an uncharacterized system, where minimal data are available, by leveraging a reference system where the kinetics have been elucidated. The motor’s activity is represented as a continuous-time Markov chain, characterized by an infinitesimal generator matrix Q whose entries are functions of the transition rates of the cycle (the vector ω) and possibly of the concentrations of external molecules. In the uncharacterized system, the available data induce a constraint on the admissible rates. By employing an extremum principle, we estimate the rates ωunc that minimize the kinetic distance with respect to the reference rates ωref while respecting such constraint. As an application of this strategy, we describe a model of the translation elongation cycle, where reference data are available for E. coli in vitro, and estimate the rates either in vivo or in a different organism, under constraints on the total elongation time or the steady-state occupancies, respectively.
Keywords: ribosome; optimization; markov chain