Theory of nonequilibrium free energy transduction by molecular machines

AI Brown, DA Sivak - Chemical reviews, 2019 - ACS Publications
Biomolecular machines are protein complexes that convert between different forms of free
energy. They are utilized in nature to accomplish many cellular tasks. As isothermal …

The divergence of mutation rates and spectra across the Tree of Life

M Lynch, F Ali, T Lin, Y Wang, J Ni, H Long - EMBO reports, 2023 - embopress.org
Owing to advances in genome sequencing, genome stability has become one of the most
scrutinized cellular traits across the Tree of Life. Despite its centrality to all things biological …

[HTML][HTML] A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus

WJ Fitzsimmons, RJ Woods, JT McCrone… - PLoS …, 2018 - journals.plos.org
Mutation rates can evolve through genetic drift, indirect selection due to genetic hitchhiking,
or direct selection on the physicochemical cost of high fidelity. However, for many systems, it …

[HTML][HTML] Systematic detection of amino acid substitutions in proteomes reveals mechanistic basis of ribosome errors and selection for translation fidelity

E Mordret, O Dahan, O Asraf, R Rak, A Yehonadav… - Molecular Cell, 2019 - cell.com
The translation machinery and the genes it decodes co-evolved to achieve production
throughput and accuracy. Nonetheless, translation errors are frequent, and they affect …

Theoretical perspectives on biological machines

ML Mugnai, C Hyeon, M Hinczewski… - Reviews of Modern Physics, 2020 - APS
Many biological functions are executed by molecular machines, which like man-made
motors are powered by chemical energy, released by adenosine triphosphate hydrolysis …

[HTML][HTML] Antibiotic-induced population fluctuations and stochastic clearance of bacteria

J Coates, BR Park, D Le, E Şimşek, W Chaudhry… - Elife, 2018 - elifesciences.org
Effective antibiotic use that minimizes treatment failures remains a challenge. A better
understanding of how bacterial populations respond to antibiotics is necessary. Previous …

Energetic costs, precision, and transport efficiency of molecular motors

W Hwang, C Hyeon - The journal of physical chemistry letters, 2018 - ACS Publications
An efficient molecular motor would deliver cargo to the target site at a high speed and in a
punctual manner while consuming a minimal amount of energy. According to a recently …

Mutual linearity of nonequilibrium network currents

PE Harunari, S Dal Cengio, V Lecomte, M Polettini - Physical Review Letters, 2024 - APS
For continuous-time Markov chains and open unimolecular chemical reaction networks, we
prove that any two stationary currents are linearly related upon perturbations of a single …

Kinetic proofreading

H Boeger - Annual Review of Biochemistry, 2022 - annualreviews.org
Biochemistry and molecular biology rely on the recognition of structural complementarity
between molecules. Molecular interactions must be both quickly reversible, ie, tenuous, and …

Proofreading does not result in more reliable ligand discrimination in receptor signaling due to its inherent stochasticity

D Kirby, A Zilman - Proceedings of the National Academy of …, 2023 - National Acad Sciences
Kinetic proofreading (KPR) has been used as a paradigmatic explanation for the high
specificity of ligand discrimination by cellular receptors. KPR enhances the difference in the …