Literature DB >> 28223497

Architecture and coevolution of allosteric materials.

Le Yan1, Riccardo Ravasio2, Carolina Brito3, Matthieu Wyart2.   

Abstract

We introduce a numerical scheme to evolve functional elastic materials that can accomplish a specified mechanical task. In this scheme, the number of solutions, their spatial architectures, and the correlations among them can be computed. As an example, we consider an "allosteric" task, which requires the material to respond specifically to a stimulus at a distant active site. We find that functioning materials evolve a less-constrained trumpet-shaped region connecting the stimulus and active sites, and that the amplitude of the elastic response varies nonmonotonically along the trumpet. As previously shown for some proteins, we find that correlations appearing during evolution alone are sufficient to identify key aspects of this design. Finally, we show that the success of this architecture stems from the emergence of soft edge modes recently found to appear near the surface of marginally connected materials. Overall, our in silico evolution experiment offers a window to study the relationship between structure, function, and correlations emerging during evolution.

Keywords:  disordered materials; evolution; proteins

Year:  2017        PMID: 28223497      PMCID: PMC5347607          DOI: 10.1073/pnas.1615536114

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  26 in total

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Authors:  Le Yan; Matthieu Wyart
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3.  Functional dynamics of PDZ binding domains: a normal-mode analysis.

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4.  Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations.

Authors:  Wenjun Zheng; Bernard R Brooks; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2006-05-08       Impact factor: 11.205

5.  Structural identification of the pathway of long-range communication in an allosteric enzyme.

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Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-04       Impact factor: 11.205

Review 6.  Allostery in disease and in drug discovery.

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8.  Stereochemistry of cooperative effects in haemoglobin.

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9.  The spatial architecture of protein function and adaptation.

Authors:  Richard N McLaughlin; Frank J Poelwijk; Arjun Raman; Walraj S Gosal; Rama Ranganathan
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Authors:  Tiberiu Teşileanu; Lucy J Colwell; Stanislas Leibler
Journal:  PLoS Comput Biol       Date:  2015-02-27       Impact factor: 4.475

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  22 in total

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3.  Designing allostery-inspired response in mechanical networks.

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Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-21       Impact factor: 11.205

4.  Principles for Optimal Cooperativity in Allosteric Materials.

Authors:  Le Yan; Riccardo Ravasio; Carolina Brito; Matthieu Wyart
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5.  Theoretical search for heterogeneously architected 2D structures.

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6.  Memory formation in cyclically deformed amorphous solids and sphere assemblies.

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Review 7.  Allosteric communication in molecular machines via information exchange: what can be learned from dynamical modeling.

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Journal:  Biophys Rev       Date:  2020-03-20

8.  Localizing softness and stress along loops in 3D topological metamaterials.

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Journal:  Proc Natl Acad Sci U S A       Date:  2017-12-28       Impact factor: 11.205

Review 9.  Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins.

Authors:  D Thirumalai; Changbong Hyeon
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2018-06-19       Impact factor: 6.237

10.  Deterministic and stochastic control of kirigami topology.

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