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Interplay of energy, dissipation, and error in kinetic proofreading: Control via concentration and binding energy

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  • Kumar, Premashis
  • Banerjee, Kinshuk
  • Gangopadhyay, Gautam

Abstract

Kinetic proofreading mechanisms explain the extraordinary accuracy observed in central biological events in terms of the enhanced specificity of substrate selection networks under a nonequilibrium environment. The nonequilibrium steady state theory incorporated with a chemical thermodynamic framework is implemented to execute a systematic investigation of dynamic and thermodynamic features of the proofreading network under continuous fuel consumption. We have identified that the dissipation-error trade-off domain of the network has a one-to-one correspondence with the deeper portion of the basin-like error rate profile depicted here. Further, quantifying the energy cost through concentration control of the chemical fuel aids in unveiling the association of the energy and chemical work with the optimal operating region of the biological error-correcting mechanism. It is shown that the proper energy content of the system, the semigrand Gibbs free energy, approaches a nominal value in the trade-off regime, whereas it gets considerably minimized in the domain with a lack of trade-off. We have also introduced a performance measuring entity corresponding to different magnitudes of energetic discrimination as a product of average dissipation and coefficient of variation for the whole range of chemical fuel. The numerical illustration for an error-correcting scheme is provided for tRNA selection and DNA replication as a typical biological scenario.

Suggested Citation

  • Kumar, Premashis & Banerjee, Kinshuk & Gangopadhyay, Gautam, 2022. "Interplay of energy, dissipation, and error in kinetic proofreading: Control via concentration and binding energy," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 603(C).
    • Handle: RePEc:eee:phsmap:v:603:y:2022:i:c:s0378437122004861
    DOI: 10.1016/j.physa.2022.127735
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    References listed on IDEAS

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    1. Bryan Wei & Mingjie Dai & Peng Yin, 2012. "Complex shapes self-assembled from single-stranded DNA tiles," Nature, Nature, vol. 485(7400), pages 623-626, May.
    2. Sebastian Pilsl & Charles Morgan & Moujab Choukeife & Andreas Möglich & Günter Mayer, 2020. "Optoribogenetic control of regulatory RNA molecules," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    3. Dennis Della Corte & Hugo L. Beek & Falk Syberg & Marcus Schallmey & Felix Tobola & Kai U. Cormann & Christine Schlicker & Philipp T. Baumann & Karin Krumbach & Sascha Sokolowsky & Connor J. Morris & , 2020. "Engineering and application of a biosensor with focused ligand specificity," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
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