Allocating dissipation across a molecular machine cycle to maximize flux

Proceedings of the National Academy of Sciences of the United States of America
Aidan I Brown, David A Sivak

Abstract

Biomolecular machines consume free energy to break symmetry and make directed progress. Nonequilibrium ATP concentrations are the typical free energy source, with one cycle of a molecular machine consuming a certain number of ATP, providing a fixed free energy budget. Since evolution is expected to favor rapid-turnover machines that operate efficiently, we investigate how this free energy budget can be allocated to maximize flux. Unconstrained optimization eliminates intermediate metastable states, indicating that flux is enhanced in molecular machines with fewer states. When maintaining a set number of states, we show that-in contrast to previous findings-the flux-maximizing allocation of dissipation is not even. This result is consistent with the coexistence of both "irreversible" and reversible transitions in molecular machine models that successfully describe experimental data, which suggests that, in evolved machines, different transitions differ significantly in their dissipation.

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Citations

Mar 10, 2018·Chemistry, an Asian Journal·Katsuhiko ArigaWaka Nakanishi
Sep 8, 2019·The Journal of Chemical Physics·Julian LeeSteve Pressé
Jul 25, 2019·Physical Review. E·Arshia ZarrinAidan I Brown
Feb 20, 2019·Physical Review. E·Joseph N E LuceroDavid A Sivak
Mar 10, 2019·Proceedings of the National Academy of Sciences of the United States of America·Jason A Wagoner, Ken A Dill
Aug 8, 2019·Nature Communications·Ignacio A MartínezJuan M R Parrondo
Mar 15, 2020·Physical Review. E·Steven Blaber, David A Sivak
Feb 6, 2020·Proceedings of the National Academy of Sciences of the United States of America·Samuel J Bryant, Benjamin B Machta
Aug 23, 2019·Molecular Biology and Evolution·Jason A Wagoner, Ken A Dill
Dec 25, 2019·Physical Review. E·Daniel Jacobson, Stephen Whitelam
Apr 12, 2019·Nature Communications·Junang LiNikta Fakhri
Jul 15, 2020·Physical Biology·Saurabh S MogreElena F Koslover
Oct 13, 2020·Biological cybernetics·Abhishek Deshpande, Thomas E Ouldridge
Mar 20, 2021·Physical Review. E·Steven J LargeDavid A Sivak
May 13, 2021·Proceedings of the National Academy of Sciences of the United States of America·Jason A Wagoner, Ken A Dill
Jan 2, 2018·The Journal of Physical Chemistry. B·Aidan I Brown, David A Sivak
Jan 14, 2018·The Journal of Physical Chemistry Letters·Wonseok Hwang, Changbong Hyeon
Aug 15, 2019·Chemical Reviews·Aidan I Brown, David A Sivak
Nov 30, 2019·The Journal of Physical Chemistry. B·Vahe Galstyan, Rob Phillips

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