ArticleBiophysical journal2017
Design of Elastic Networks with Evolutionary Optimized Long-Range Communication as Mechanical Models of Allosteric Proteins.
Article in Biophysical journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Evolutionary pathways in epistatic mechanical networks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- Discrete protein dynamics enable long-range communication.bioRxiv : the preprint server for biology · 2025Article
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Learning to learn by using nonequilibrium training protocols for adaptable materials.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Evolutionary coupling range varies widely among enzymes depending on selection pressure.Biophysical journal · 2021Article
- Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.Current opinion in structural biology · 2020Review
- Allosteric communication in molecular machines via information exchange: what can be learned from dynamical modeling.Biophysical reviews · 2020Review
- Direct coupling analysis of epistasis in allosteric materials.PLoS computational biology · 2020Article
- Identification of Alternative Allosteric Sites in Glycolytic Enzymes for Potential Use as Species-Specific Drug Targets.Frontiers in molecular biosciences · 2020Article
- Mechanics of Allostery: Contrasting the Induced Fit and Population Shift Scenarios.Biophysical journal · 2019Article
- Simple mechanics of protein machines.Journal of the Royal Society, Interface · 2019Article
- Chokepoints in Mechanical Coupling Associated with Allosteric Proteins: The Pyruvate Kinase Example.Biophysical journal · 2019Article
- Allostery in Its Many Disguises: From Theory to Applications.Structure (London, England : 1993) · 2019Review
- Revealing evolutionary constraints on proteins through sequence analysis.PLoS computational biology · 2019Article
- Limits of multifunctionality in tunable networks.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Coarse-Grained Protein Dynamics Studies Using Elastic Network Models.International journal of molecular sciences · 2018Review
- Designed Elastic Networks: Models of Complex Protein Machinery.International journal of molecular sciences · 2018Review
- Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- Principles for Optimal Cooperativity in Allosteric Materials.Biophysical journal · 2018Article
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1 author.
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Abstract
Allosteric effects often underlie the activity of proteins, and elucidating generic design aspects and functional principles unique to allosteric phenomena represent a major challenge. Here an approach consisting of the in silico design of synthetic structures, which, as the principal element of allostery, encode dynamical long-range coupling among two sites, is presented. The structures are represented by elastic networks, similar to coarse-grained models of real proteins. A strategy of evolutionary optimization was implemented to iteratively improve allosteric coupling. In the designed structures, allosteric interactions were analyzed in terms of strain propagation, and simple pathways that emerged during evolution were identified as signatures through which long-range communication was established. Moreover, robustness of allosteric performance with respect to mutations was demonstrated. As it turned out, the designed prototype structures reveal dynamical properties resembling those found in real allosteric proteins. Hence, they may serve as toy models of complex allosteric systems, such as proteins. Application of the developed modeling scheme to the allosteric transition in the myosin V molecular motor was also demonstrated.
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