ReviewAnnual review of biophysics2017
High-Dimensional Mutant and Modular Thermodynamic Cycles, Molecular Switching, and Free Energy Transduction.
Review in Annual review of biophysics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
13 citing papers in PubMed, 27 citations in OpenAlex.
- Aminoacyl-tRNA synthetase urzymes optimized by deep learning behave as a quasispecies.Structural dynamics (Melville, N.Y.) · 2025Article
- High-throughput thermal denaturation of tryptophanyl-tRNA synthetase combinatorial mutants reveals high-order energetic coupling determinants of conformational stability.Structural dynamics (Melville, N.Y.) · 2023Article
- Microcalorimetry reveals multi-state thermal denaturation ofStructural dynamics (Melville, N.Y.) · 2023Article
- Allosteric conformational ensembles have unlimited capacity for integrating information.eLife · 2021Article
- Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis.Biomolecules · 2021Review
- Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding.International journal of molecular sciences · 2020Article
- Escapement mechanisms: Efficient free energy transduction by reciprocally-coupled gating.Proteins · 2020Article
- On the beneficent thickness of water.Interface focus · 2019Review
- Kinetic asymmetry allows macromolecular catalysts to drive an information ratchet.Nature communications · 2019Review
- Energy Transfer as A Driving Force in Nucleic Acid⁻Protein Interactions.Molecules (Basel, Switzerland) · 2019Article
- Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis.Structural dynamics (Melville, N.Y.) · 2017Article
- Augmenting the anisotropic network model with torsional potentials improves PATH performance, enabling detailed comparison with experimental rate data.Structural dynamics (Melville, N.Y.) · 2017Article
- Coding of Class I and II Aminoacyl-tRNA Synthetases.Advances in experimental medicine and biology · 2017Review
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
Understanding how distinct parts of proteins produce coordinated behavior has driven and continues to drive advances in protein science and enzymology. However, despite consensus about the conceptual basis for allostery, the idiosyncratic nature of allosteric mechanisms resists general approaches. Computational methods can identify conformational transition states from structural changes, revealing common switching mechanisms that impose multistate behavior. Thermodynamic cycles use factorial perturbations to measure coupling energies between side chains in molecular switches that mediate shear during domain motion. Such cycles have now been complemented by modular cycles that measure energetic coupling between separable domains. For one model system, energetic coupling between domains has been shown to be quantitatively equivalent to that between dynamic side chains. Linkages between domain motion, switching residues, and catalysis make nucleoside triphosphate hydrolysis conditional on domain movement, confirming an essential yet neglected aspect of free energy transduction and suggesting the potential generality of these studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.