AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems
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 sc...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2015-05-01
|
| Series: | Entropy |
| Subjects: | |
| Online Access: | http://www.mdpi.com/1099-4300/17/5/2895 |
| _version_ | 1797999499708203008 |
|---|---|
| author | Michael V. LeVine Harel Weinstein |
| author_facet | Michael V. LeVine Harel Weinstein |
| author_sort | Michael V. LeVine |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T11:04:23Z |
| format | Article |
| id | doaj.art-c3a64b34c2644c3089227a5b941b8c9f |
| institution | Directory Open Access Journal |
| issn | 1099-4300 |
| language | English |
| last_indexed | 2024-04-11T11:04:23Z |
| publishDate | 2015-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Entropy |
| spelling | doaj.art-c3a64b34c2644c3089227a5b941b8c9f2022-12-22T04:28:24ZengMDPI AGEntropy1099-43002015-05-011752895291810.3390/e17052895e17052895AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular SystemsMichael V. LeVine0Harel Weinstein1Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065, USADepartment of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, New York, NY 10065, USAIn 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.http://www.mdpi.com/1099-4300/17/5/2895allosterybiophysicsIsing modelstatistical mechanicssignal transductioninformation theoryG protein coupled receptors (GPCRs)dopamine D2 receptorfunctional selectivity |
| spellingShingle | Michael V. LeVine Harel Weinstein AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems Entropy allostery biophysics Ising model statistical mechanics signal transduction information theory G protein coupled receptors (GPCRs) dopamine D2 receptor functional selectivity |
| title | AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems |
| title_full | AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems |
| title_fullStr | AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems |
| title_full_unstemmed | AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems |
| title_short | AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems |
| title_sort | aim for allostery using the ising model to understand information processing and transmission in allosteric biomolecular systems |
| topic | allostery biophysics Ising model statistical mechanics signal transduction information theory G protein coupled receptors (GPCRs) dopamine D2 receptor functional selectivity |
| url | http://www.mdpi.com/1099-4300/17/5/2895 |
| work_keys_str_mv | AT michaelvlevine aimforallosteryusingtheisingmodeltounderstandinformationprocessingandtransmissioninallostericbiomolecularsystems AT harelweinstein aimforallosteryusingtheisingmodeltounderstandinformationprocessingandtransmissioninallostericbiomolecularsystems |