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Principles for Optimal Cooperativity in Allosteric Materials.

Le Yan1, Riccardo Ravasio2, Carolina Brito3

  • 1Kavli Institute for Theoretical Physics, University of California, Santa Barbara, Santa Barbara, California.

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|June 21, 2018
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Summary
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Optimized allosteric proteins efficiently propagate energy through a cooperative mechanism, differing from strain-propagating materials. Their design principle, an extended soft mode, shows frequency dependent on system size and dimension, offering insights into protein function.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Allosteric proteins transmit mechanical signals upon ligand binding.
  • Understanding the transmitted information and optimal architectures for allosteric transmission is challenging.

Purpose of the Study:

  • To investigate the nature of information transmission in allosteric proteins.
  • To identify architectural principles that optimize cooperative energy propagation.

Main Methods:

  • In silico evolution scheme.
  • Theoretical arguments and analysis of cooperative architectures.
  • Investigation of energy propagation versus strain propagation.

Main Results:

  • Cooperative architectures optimized for energy propagation differ from those optimized for strain propagation.
  • A universal principle of a mechanism (extended soft mode) characterizes functioning cooperative architectures.
  • Optimal frequency of the soft mode scales with system size (L) and dimension (d) as L-d/2.
  • Cooperativity decay is logarithmic in 2D and absent in 3D for optimal designs.

Conclusions:

  • The study reveals key design principles for efficient energy propagation in allosteric proteins.
  • Findings provide a natural explanation for observed phenomena in allosteric proteins.
  • Suggests an experimental approach to assess the optimality of allosteric protein designs.