Literature DB >> 28223534

Designing allostery-inspired response in mechanical networks.

Jason W Rocks1, Nidhi Pashine2, Irmgard Bischofberger3, Carl P Goodrich4, Andrea J Liu5, Sidney R Nagel2.   

Abstract

Recent advances in designing metamaterials have demonstrated that global mechanical properties of disordered spring networks can be tuned by selectively modifying only a small subset of bonds. Here, using a computationally efficient approach, we extend this idea to tune more general properties of networks. With nearly complete success, we are able to produce a strain between any two target nodes in a network in response to an applied source strain on any other pair of nodes by removing only ∼1% of the bonds. We are also able to control multiple pairs of target nodes, each with a different individual response, from a single source, and to tune multiple independent source/target responses simultaneously into a network. We have fabricated physical networks in macroscopic 2D and 3D systems that exhibit these responses. This work is inspired by the long-range coupled conformational changes that constitute allosteric function in proteins. The fact that allostery is a common means for regulation in biological molecules suggests that it is a relatively easy property to develop through evolution. In analogy, our results show that long-range coupled mechanical responses are similarly easy to achieve in disordered networks.

Entities:  

Keywords:  allostery; disordered networks; mechanical metamaterials; proteins; tunable response

Year:  2017        PMID: 28223534      PMCID: PMC5347623          DOI: 10.1073/pnas.1612139114

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


  24 in total

1.  Protein flexibility and dynamics using constraint theory.

Authors:  M F Thorpe; M Lei; A J Rader; D J Jacobs; L A Kuhn
Journal:  J Mol Graph Model       Date:  2001       Impact factor: 2.518

Review 2.  Allosteric sites: remote control in regulation of protein activity.

Authors:  Enrico Guarnera; Igor N Berezovsky
Journal:  Curr Opin Struct Biol       Date:  2015-11-10       Impact factor: 6.809

Review 3.  A Chemical Perspective on Allostery.

Authors:  Andre A S T Ribeiro; Vanessa Ortiz
Journal:  Chem Rev       Date:  2016-01-07       Impact factor: 60.622

Review 4.  Allostery: absence of a change in shape does not imply that allostery is not at play.

Authors:  Chung-Jung Tsai; Antonio del Sol; Ruth Nussinov
Journal:  J Mol Biol       Date:  2008-02-29       Impact factor: 5.469

5.  Finite-size scaling at the jamming transition.

Authors:  Carl P Goodrich; Andrea J Liu; Sidney R Nagel
Journal:  Phys Rev Lett       Date:  2012-08-27       Impact factor: 9.161

6.  Tensorial elastic network model for protein dynamics: integration of the anisotropic network model with bond-bending and twist elasticities.

Authors:  Amit Srivastava; Roee Ben Halevi; Alexander Veksler; Rony Granek
Journal:  Proteins       Date:  2012-08-21

Review 7.  Allostery in disease and in drug discovery.

Authors:  Ruth Nussinov; Chung-Jung Tsai
Journal:  Cell       Date:  2013-04-11       Impact factor: 41.582

8.  Strain analysis of protein structures and low dimensionality of mechanical allosteric couplings.

Authors:  Michael R Mitchell; Tsvi Tlusty; Stanislas Leibler
Journal:  Proc Natl Acad Sci U S A       Date:  2016-09-21       Impact factor: 11.205

Review 9.  Global dynamics of proteins: bridging between structure and function.

Authors:  Ivet Bahar; Timothy R Lezon; Lee-Wei Yang; Eran Eyal
Journal:  Annu Rev Biophys       Date:  2010       Impact factor: 12.981

10.  Spatial structure of states of self stress in jammed systems.

Authors:  Daniel M Sussman; Carl P Goodrich; Andrea J Liu
Journal:  Soft Matter       Date:  2016-03-21       Impact factor: 3.679

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  30 in total

1.  Forecasting failure locations in 2-dimensional disordered lattices.

Authors:  Estelle Berthier; Mason A Porter; Karen E Daniels
Journal:  Proc Natl Acad Sci U S A       Date:  2019-08-02       Impact factor: 11.205

2.  Rigidity percolation and geometric information in floppy origami.

Authors:  Siheng Chen; L Mahadevan
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-05       Impact factor: 11.205

3.  Structural hierarchy confers error tolerance in biological materials.

Authors:  Jonathan A Michel; Peter J Yunker
Journal:  Proc Natl Acad Sci U S A       Date:  2019-02-05       Impact factor: 11.205

4.  Periodic training of creeping solids.

Authors:  Daniel Hexner; Andrea J Liu; Sidney R Nagel
Journal:  Proc Natl Acad Sci U S A       Date:  2020-11-30       Impact factor: 11.205

5.  Principles for Optimal Cooperativity in Allosteric Materials.

Authors:  Le Yan; Riccardo Ravasio; Carolina Brito; Matthieu Wyart
Journal:  Biophys J       Date:  2018-06-19       Impact factor: 4.033

6.  Theoretical search for heterogeneously architected 2D structures.

Authors:  Weizhu Yang; Qingchang Liu; Zongzhan Gao; Zhufeng Yue; Baoxing Xu
Journal:  Proc Natl Acad Sci U S A       Date:  2018-07-16       Impact factor: 11.205

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

Authors:  Monoj Adhikari; Srikanth Sastry
Journal:  Eur Phys J E Soft Matter       Date:  2018-09-13       Impact factor: 1.890

Review 8.  Allosteric communication in molecular machines via information exchange: what can be learned from dynamical modeling.

Authors:  Dimitri Loutchko; Holger Flechsig
Journal:  Biophys Rev       Date:  2020-03-20

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

Authors:  Guido Baardink; Anton Souslov; Jayson Paulose; Vincenzo Vitelli
Journal:  Proc Natl Acad Sci U S A       Date:  2017-12-28       Impact factor: 11.205

10.  Auxetic metamaterials from disordered networks.

Authors:  Daniel R Reid; Nidhi Pashine; Justin M Wozniak; Heinrich M Jaeger; Andrea J Liu; Sidney R Nagel; Juan J de Pablo
Journal:  Proc Natl Acad Sci U S A       Date:  2018-01-30       Impact factor: 11.205

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