ArticlePLoS computational biology2016
Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Inactivation Switch for Run-up in TRPV2.Research square · 2026Article
- MAVISp: A modular structure-based framework for protein variant effects.Protein science : a publication of the Protein Society · 2026Article
- Cancer histone H2A.Z missense mutations disrupt function through distinct local and allosteric effects.Research square · 2026Article
- Physics Determines and Evolution Shapes Basic Units of Protein Function and Allosteric Regulation.Methods in molecular biology (Clifton, N.J.) · 2026Review
- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
- Second-order allosteric control as a mechanism for compensatory mutations in B-cell translocation gene 2.Protein science : a publication of the Protein Society · 2025Article
- Role of artificial intelligence in revolutionizing drug discovery.Fundamental research · 2025Review
- Temporal complexity of LVV-hemorphin-7 allosterism at the angiotensin II type 1 receptor assessed using entropy-based approaches.Computational and structural biotechnology journal · 2025Article
- Allosteric ligand-driven smart nanoconjugates for mutation-selective EGFR targeting: A precision approach to overcoming tyrosine kinase inhibitor resistance.BioImpacts : BI · 2025Review
- Elucidating the structural dynamics induced by active site mutations in 3C protease of foot-and-mouth disease virus.PloS one · 2025Article
- Protein allosteric site identification using machine learning and per amino acid residue reported internal protein nanoenvironment descriptors.Computational and structural biotechnology journal · 2024Article
- Toward the Design of Allosteric Effectors: Gaining Comprehensive Control of Drug Properties and Actions.Journal of medicinal chemistry · 2024Article
- Reconnaissance of Allostery via the Restoration of Native p53 DNA-Binding Domain Dynamics in Y220C Mutant p53 Tumor Suppressor Protein.ACS omega · 2024Article
- AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design.Nucleic acids research · 2023Article
- A Structure-Based Allosteric Modulator Design Paradigm.Health data science · 2023Review
- Article
- Direct observation of chemo-mechanical coupling in DnaK by single-molecule force experiments.Biophysical journal · 2022Article
- Emerging Methods and Applications to Decrypt Allostery in Proteins and Nucleic Acids.Journal of molecular biology · 2022Review
- Allosteric Hotspots in the Main Protease of SARS-CoV-2.Journal of molecular biology · 2022Article
- Mechanistic Understanding of the Palmitoylation of GPharmaceutics · 2022Article
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Allostery is one of the pervasive mechanisms through which proteins in living systems carry out enzymatic activity, cell signaling, and metabolism control. Effective modeling of the protein function regulation requires a synthesis of the thermodynamic and structural views of allostery. We present here a structure-based statistical mechanical model of allostery, allowing one to observe causality of communication between regulatory and functional sites, and to estimate per residue free energy changes. Based on the consideration of ligand free and ligand bound systems in the context of a harmonic model, corresponding sets of characteristic normal modes are obtained and used as inputs for an allosteric potential. This potential quantifies the mean work exerted on a residue due to the local motion of its neighbors. Subsequently, in a statistical mechanical framework the entropic contribution to allosteric free energy of a residue is directly calculated from the comparison of conformational ensembles in the ligand free and ligand bound systems. As a result, this method provides a systematic approach for analyzing the energetics of allosteric communication based on a single structure. The feasibility of the approach was tested on a variety of allosteric proteins, heterogeneous in terms of size, topology and degree of oligomerization. The allosteric free energy calculations show the diversity of ways and complexity of scenarios existing in the phenomenology of allosteric causality and communication. The presented model is a step forward in developing the computational techniques aimed at detecting allosteric sites and obtaining the discriminative power between agonistic and antagonistic effectors, which are among the major goals in allosteric drug design.
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