IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v603y2022ics0378437122004861.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437122004861
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000
    File URL: https://libkey.io/10.1016/j.physa.2022.127735?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. 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.
    2. 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.
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Vishal Maingi & Zhao Zhang & Chris Thachuk & Namita Sarraf & Edwin R. Chapman & Paul W. K. Rothemund, 2023. "Digital nanoreactors to control absolute stoichiometry and spatiotemporal behavior of DNA receptors within lipid bilayers," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    2. Agnese I. Curatolo & Ofer Kimchi & Carl P. Goodrich & Ryan K. Krueger & Michael P. Brenner, 2023. "A computational toolbox for the assembly yield of complex and heterogeneous structures," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Jeroen F. Dyck & Jonathan R. Burns & Kyle I. P. Huray & Albert Konijnenberg & Stefan Howorka & Frank Sobott, 2022. "Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    4. Hong Kang & Yuexuan Yang & Bryan Wei, 2024. "Synthetic molecular switches driven by DNA-modifying enzymes," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    5. Yahong Chen & Chaoyong Yang & Zhi Zhu & Wei Sun, 2022. "Suppressing high-dimensional crystallographic defects for ultra-scaled DNA arrays," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    6. Sungwook Woo & Sinem K. Saka & Feng Xuan & Peng Yin, 2024. "Molecular robotic agents that survey molecular landscapes for information retrieval," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:phsmap:v:603:y:2022:i:c:s0378437122004861. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.