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Entropy 2015, 17(5), 2895-2918; doi:10.3390/e17052895

AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems

1
Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
2
HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute of Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Rick Quax
Received: 5 March 2015 / Revised: 16 April 2015 / Accepted: 30 April 2015 / Published: 7 May 2015
(This article belongs to the Special Issue Information Processing in Complex Systems)
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Abstract

In performing their biological functions, molecular machines must process and transmit information with high fidelity. Information transmission requires dynamic coupling between the conformations of discrete structural components within the protein positioned far from one another on the molecular scale. This type of biomolecular “action at a distance” is termed allostery. Although allostery is ubiquitous in biological regulation and signal transduction, its treatment in theoretical models has mostly eschewed quantitative descriptions involving the system’s underlying structural components and their interactions. Here, we show how Ising models can be used to formulate an approach to allostery in a structural context of interactions between the constitutive components by building simple allosteric constructs we termed Allosteric Ising Models (AIMs). We introduce the use of AIMs in analytical and numerical calculations that relate thermodynamic descriptions of allostery to the structural context, and then show that many fundamental properties of allostery, such as the multiplicative property of parallel allosteric channels, are revealed from the analysis of such models. The power of exploring mechanistic structural models of allosteric function in more complex systems by using AIMs is demonstrated by building a model of allosteric signaling for an experimentally well-characterized asymmetric homodimer of the dopamine D2 receptor. View Full-Text
Keywords: allostery; biophysics; Ising model; statistical mechanics; signal transduction; information theory; G protein coupled receptors (GPCRs); dopamine D2 receptor; functional selectivity allostery; biophysics; Ising model; statistical mechanics; signal transduction; information theory; G protein coupled receptors (GPCRs); dopamine D2 receptor; functional selectivity
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

LeVine, M.V.; Weinstein, H. AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems. Entropy 2015, 17, 2895-2918.

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