DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Designing allostery-inspired response in mechanical networks

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 then 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.

Authors:
 [1];  [2];  [3];  [4];  [1];  [2]
  1. Univ. of Pennsylvania, Philadelphia, PA (United States). Dept. of Physics and Astronomy
  2. Univ. of Chicago, IL (United States). Dept. of Physics
  3. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Mechanical Engineering
  4. Harvard Univ., Cambridge, MA (United States). School of Engineering and Applied Sciences
Publication Date:
Research Org.:
Univ. of Pennsylvania, Philadelphia, PA (United States); Univ. of Chicago, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division; Inst. for Advanced Study (IAS) The Simons Center for Systems Biology, Princeton, NJ (United States); Simons Foundation; National Science Foundation (NSF); National Inst. of Standards and Technology (NIST)
OSTI Identifier:
1344433
Alternate Identifier(s):
OSTI ID: 1430120
Grant/Contract Number:  
FG02-05ER46199; FG02-03ER46088; 305547; 327939; 60NANB15D055
Resource Type:
Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 114 Journal Issue: 10; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; 97 MATHEMATICS AND COMPUTING; 74 ATOMIC AND MOLECULAR PHYSICS; 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; mechanical metamaterials; allostery; tunable response; proteins; disordered networks

Citation Formats

Rocks, Jason W., Pashine, Nidhi, Bischofberger, Irmgard, Goodrich, Carl P., Liu, Andrea J., and Nagel, Sidney R. Designing allostery-inspired response in mechanical networks. United States: N. p., 2017. Web. doi:10.1073/pnas.1612139114.
Rocks, Jason W., Pashine, Nidhi, Bischofberger, Irmgard, Goodrich, Carl P., Liu, Andrea J., & Nagel, Sidney R. Designing allostery-inspired response in mechanical networks. United States. https://doi.org/10.1073/pnas.1612139114
Rocks, Jason W., Pashine, Nidhi, Bischofberger, Irmgard, Goodrich, Carl P., Liu, Andrea J., and Nagel, Sidney R. Tue . "Designing allostery-inspired response in mechanical networks". United States. https://doi.org/10.1073/pnas.1612139114.
@article{osti_1344433,
title = {Designing allostery-inspired response in mechanical networks},
author = {Rocks, Jason W. and Pashine, Nidhi and Bischofberger, Irmgard and Goodrich, Carl P. and Liu, Andrea J. and Nagel, Sidney R.},
abstractNote = {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 then 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.},
doi = {10.1073/pnas.1612139114},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 10,
volume = 114,
place = {United States},
year = {Tue Feb 21 00:00:00 EST 2017},
month = {Tue Feb 21 00:00:00 EST 2017}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1073/pnas.1612139114

Citation Metrics:
Cited by: 104 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Jamming at zero temperature and zero applied stress: The epitome of disorder
journal, July 2003


Manipulation of Conformational Change in Proteins by Single-Residue Perturbations
journal, August 2010


Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play
journal, April 2008

  • Tsai, Chung-Jung; del Sol, Antonio; Nussinov, Ruth
  • Journal of Molecular Biology, Vol. 378, Issue 1
  • DOI: 10.1016/j.jmb.2008.02.034

Rigidity Loss in Disordered Systems: Three Scenarios
journal, April 2015


Architecture and coevolution of allosteric materials
journal, February 2017

  • Yan, Le; Ravasio, Riccardo; Brito, Carolina
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 10
  • DOI: 10.1073/pnas.1615536114

Allostery in Disease and in Drug Discovery
journal, April 2013


Strain analysis of protein structures and low dimensionality of mechanical allosteric couplings
journal, September 2016

  • Mitchell, Michael R.; Tlusty, Tsvi; Leibler, Stanislas
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 40
  • DOI: 10.1073/pnas.1609462113

The Jamming Transition and the Marginally Jammed Solid
journal, August 2010


Structural computations with the singular value decomposition of the equilibrium matrix
journal, January 1993


Global Dynamics of Proteins: Bridging Between Structure and Function
journal, April 2010


Adjustment of an Inverse Matrix Corresponding to a Change in One Element of a Given Matrix
journal, March 1950

  • Sherman, Jack; Morrison, Winifred J.
  • The Annals of Mathematical Statistics, Vol. 21, Issue 1
  • DOI: 10.1214/aoms/1177729893

Buckminster Fuller's “Tensegrity” structures and Clerk Maxwell's rules for the construction of stiff frames
journal, January 1978


Allosteric sites: remote control in regulation of protein activity
journal, April 2016


The role of rigidity in controlling material failure
journal, September 2016

  • Driscoll, Michelle M.; Chen, Bryan Gin-ge; Beuman, Thomas H.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 39
  • DOI: 10.1073/pnas.1501169113

The Principle of Independent Bond-Level Response: Tuning by Pruning to Exploit Disorder for Global Behavior
journal, June 2015


Local motions in a benchmark of allosteric proteins
journal, February 2007

  • Daily, Michael D.; Gray, Jeffrey J.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 67, Issue 2
  • DOI: 10.1002/prot.21300

Is allostery an intrinsic property of all dynamic proteins?
journal, July 2004

  • Gunasekaran, K.; Ma, Buyong; Nussinov, Ruth
  • Proteins: Structure, Function, and Bioinformatics, Vol. 57, Issue 3
  • DOI: 10.1002/prot.20232

Non-affine response: Jammed packings vs. spring networks
journal, August 2009


Tensorial elastic network model for protein dynamics: Integration of the anisotropic network model with bond-bending and twist elasticities
journal, August 2012

  • Srivastava, Amit; Halevi, Roee Ben; Veksler, Alexander
  • Proteins: Structure, Function, and Bioinformatics, Vol. 80, Issue 12
  • DOI: 10.1002/prot.24153

Protein promiscuity and its implications for biotechnology
journal, February 2009

  • Nobeli, Irene; Favia, Angelo D.; Thornton, Janet M.
  • Nature Biotechnology, Vol. 27, Issue 2
  • DOI: 10.1038/nbt1519

The ensemble nature of allostery
journal, April 2014

  • Motlagh, Hesam N.; Wrabl, James O.; Li, Jing
  • Nature, Vol. 508, Issue 7496
  • DOI: 10.1038/nature13001

New Look at Hemoglobin Allostery
journal, January 2015

  • Yuan, Yue; Tam, Ming F.; Simplaceanu, Virgil
  • Chemical Reviews, Vol. 115, Issue 4
  • DOI: 10.1021/cr500495x

Finite-Size Scaling at the Jamming Transition
journal, August 2012


Controlling Allosteric Networks in Proteins
journal, February 2016


Spatial structure of states of self stress in jammed systems
journal, January 2016

  • Sussman, Daniel M.; Goodrich, Carl P.; Liu, Andrea J.
  • Soft Matter, Vol. 12, Issue 17
  • DOI: 10.1039/C6SM00094K

A Chemical Perspective on Allostery
journal, January 2016


Origami Actuator Design and Networking Through Crease Topology Optimization
journal, July 2015

  • Fuchi, Kazuko; Buskohl, Philip R.; Bazzan, Giorgio
  • Journal of Mechanical Design, Vol. 137, Issue 9
  • DOI: 10.1115/1.4030876

Dynamic Prestress in a Globular Protein
journal, May 2012


Protein flexibility and dynamics using constraint theory
journal, February 2001