ArticleMethods in molecular biology (Clifton, N.J.)2021
Disclosing Allostery Through Protein Contact Networks.
Article in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- In silico study of cytochrome-C binding to a cardiolipin-containing membrane.European biophysics journal : EBJ · 2026Article
- Chemophysical Characterization of Carotenoproteins From Crustacean Shell Waste for Pharmaceutical Applications.International journal of food science · 2026Article
- Evaluating the Topological Features of Monomeric and Trimeric TRAF2-C: A Multi-Disciplinary Approach.Biomolecules · 2025Article
- The Dynamical Asymmetry in SARS-CoV2 Protease Reveals the Exchange Between Catalytic Activity and Stability in Homodimers.Molecules (Basel, Switzerland) · 2025Article
- Temperature sensitive contact modes allosterically gate TRPV3.PLoS computational biology · 2023Article
- Computational analysis of the sequence-structure relation in SARS-CoV-2 spike protein using protein contact networks.Scientific reports · 2023Article
- SARS-CoV-2 protein structure and sequence mutations: Evolutionary analysis and effects on virus variants.PloS one · 2023Article
- A Statistical Journey through the Topological Determinants of the β2 Adrenergic Receptor Dynamics.Entropy (Basel, Switzerland) · 2022Article
- Biophysical Insight into the SARS-CoV2 Spike-ACE2 Interaction and Its Modulation by Hepcidin through a Multifaceted Computational Approach.ACS omega · 2022Article
- The Odd Faces of Oligomers: The Case of TRAF2-C, A Trimeric C-Terminal Domain of TNF Receptor-Associated Factor.International journal of molecular sciences · 2021Article
- Polymorphism on human aromatase affects protein dynamics and substrate binding: spectroscopic evidence.Biology direct · 2021Article
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4 authors.
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Abstract
Proteins are located in the twilight zone between chemistry and biology, where a peculiar kind of complexity starts. Proteins are the smallest 'devices' showing a sensible adaptation to their environment by the production of appropriate behavior when facing a specific stimulus. This fact qualifies (from the 'effector' side) proteins as nanomachines working as catalysts, motors, or switches. However (from the sensor side), the need to single out the 'specific stimulus' out of thermal noise qualifies proteins as information processing devices. Allostery corresponds to the modification of the configuration (in a broad sense) of the protein molecule in response to a specific stimulus in a non-strictly local way, thereby connecting the sensor and effector sides of the nanomachine. This is why the 'disclosing' of allostery phenomenon is at the very heart of protein function; in this chapter, we will demonstrate how a network-based representation of protein structure in terms of nodes (aminoacid residues) and edges (effective contacts between residues) is the natural language for getting rid of allosteric phenomena and, more in general, of protein structure/function relationships.
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