ArticlePloS one2012
Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Motifs in SARS-CoV-2 evolution.RNA (New York, N.Y.) · 2023Article
- Co-evolutionary landscape at the interface and non-interface regions of protein-protein interaction complexes.Computational and structural biotechnology journal · 2021Article
- Integrated Computational Approaches and Tools forAllosteric Drug Discovery.International journal of molecular sciences · 2020Review
- Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning.Frontiers in molecular biosciences · 2020Review
- A Single Mutation Increases the Thermostability and Activity ofMolecules (Basel, Switzerland) · 2019Article
- MISTIC2: comprehensive server to study coevolution in protein families.Nucleic acids research · 2018Article
- Dissecting Structure-Encoded Determinants of Allosteric Cross-Talk between Post-Translational Modification Sites in the Hsp90 Chaperones.Scientific reports · 2018Article
- Applications of sequence coevolution in membrane protein biochemistry.Biochimica et biophysica acta. Biomembranes · 2018Review
- Protein-protein interactions leave evolutionary footprints: High molecular coevolution at the core of interfaces.Protein science : a publication of the Protein Society · 2017Article
- Article
- Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.PLoS computational biology · 2017Article
- UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.Nucleic acids research · 2016Article
- Article
- Article
- The role of the N-terminal tail for the oligomerization, folding and stability of human frataxin.FEBS open bio · 2013Article
- Recent advances in functional region prediction by using structural and evolutionary information - Remaining problems and future extensions.Computational and structural biotechnology journal · 2013Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Amino acids committed to a particular function correlate tightly along evolution and tend to form clusters in the 3D structure of the protein. Consequently, a protein can be seen as a network of co-evolving clusters of residues. The goal of this work is two-fold: first, we have combined mutual information and structural data to describe the amino acid networks within a protein and their interactions. Second, we have investigated how this information can be used to improve methods of prediction of functional residues by reducing the search space. As a main result, we found that clusters of co-evolving residues related to the catalytic site of an enzyme have distinguishable topological properties in the network. We also observed that these clusters usually evolve independently, which could be related to a fail-safe mechanism. Finally, we discovered a significant enrichment of functional residues (e.g. metal binding, susceptibility to detrimental mutations) in the clusters, which could be the foundation of new prediction tools.
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