ArticleMolecular biology and evolution2019
Ligand-Binding-Site Structure Shapes Allosteric Signal Transduction and the Evolution of Allostery in Protein Complexes.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 36 citations in OpenAlex.
- Origins of allostery in vertebrate hemoglobin evolution.bioRxiv : the preprint server for biology · 2026Article
- Cellular location shapes quaternary structure of enzymes.Nature communications · 2024Article
- Unusual Evolution of Cephalopod Tryptophan Indole-Lyases.Journal of molecular evolution · 2023Article
- Binding Affinity and Mechanisms of Potential Antidepressants Targeting Human NMDA Receptors.Molecules (Basel, Switzerland) · 2023Article
- An Assessment of Quaternary Structure Functionality in Homomer Protein Complexes.Molecular biology and evolution · 2023Article
- It's ok to be outnumbered - sub-stoichiometric modulation of homomeric protein complexes.RSC medicinal chemistry · 2023Review
- Calculation of centralities in protein kinase A.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- How gene duplication diversifies the landscape of protein oligomeric state and function.Current opinion in genetics & development · 2022Review
- Known allosteric proteins have central roles in genetic disease.PLoS computational biology · 2022Article
- Towards the Idea of Molecular Brains.International journal of molecular sciences · 2021Review
- CoeViz 2: Protein Graphs Derived from Amino Acid Covariance.Frontiers in bioinformatics · 2021Article
- Selective Modulation of Dynamic Protein Complexes.Cell chemical biology · 2020Review
- Determining the interaction status and evolutionary fate of duplicated homomeric proteins.PLoS computational biology · 2020Article
- Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.Current opinion in structural biology · 2020Review
- Recent advances suggest increased influence of selective pressure in allostery.Current opinion in structural biology · 2020Review
- AnalyzingFrontiers in molecular biosciences · 2020Article
- Ligands and Receptors with Broad Binding Capabilities Have Common Structural Characteristics: An Antibiotic Design Perspective.Journal of medicinal chemistry · 2019Review
- Ligand Binding Site Structure Shapes Folding, Assembly and Degradation of Homomeric Protein Complexes.Journal of molecular biology · 2019Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The structure of ligand-binding sites has been shown to profoundly influence the evolution of function in homomeric protein complexes. Complexes with multichain binding sites (MBSs) have more conserved quaternary structure, more similar binding sites and ligands between homologs, and evolve new functions slower than homomers with single-chain binding sites (SBSs). Here, using in silico analyses of protein dynamics, we investigate whether ligand-binding-site structure shapes allosteric signal transduction pathways, and whether the structural similarity of binding sites influences the evolution of allostery. Our analyses show that: 1) allostery is more frequent among MBS complexes than in SBS complexes, particularly in homomers; 2) in MBS homomers, semirigid communities and critical residues frequently connect interfaces and thus they are characterized by signal transduction pathways that cross protein-protein interfaces, whereas SBS homomers usually not; 3) ligand binding alters community structure differently in MBS and SBS homomers; and 4) except MBS homomers, allosteric proteins are more likely to have homologs with similar binding site than nonallosteric proteins, suggesting that binding site similarity is an important factor driving the evolution of allostery.
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