ArticleBMC bioinformatics2015
Capturing coevolutionary signals inrepeat proteins.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Membrane platform protein PulF of themBio · 2024Article
- Digging into the 3D Structure Predictions of AlphaFold2 with Low Confidence: Disorder and Beyond.Biomolecules · 2022Article
- The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database.Molecular biology and evolution · 2022Article
- Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families.PLoS computational biology · 2021Article
- Size and structure of the sequence space of repeat proteins.PLoS computational biology · 2019Article
- Characterization of C-ring component assembly in flagellar motors from amino acid coevolution.Royal Society open science · 2018Article
- Patterns of coevolving amino acids unveil structural and dynamical domains.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Origins of coevolution between residues distant in protein 3D structures.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Inferring repeat-protein energetics from evolutionary information.PLoS computational biology · 2017Article
- Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness.Current opinion in structural biology · 2017Review
- RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures.Nucleic acids research · 2017Article
- New Techniques for Ancient Proteins: Direct Coupling Analysis Applied on Proteins Involved in Iron Sulfur Cluster Biogenesis.Frontiers in molecular biosciences · 2017Article
- Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes.Molecular biology and evolution · 2016Article
- Protein Repeats from First Principles.Scientific reports · 2016Article
- Structural and Energetic Characterization of the Ankyrin Repeat Protein Family.PLoS computational biology · 2015Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe analysis of correlations of amino acid occurrences in globular domains has led to the development of statistical tools that can identify native contacts - portions of the chains that come to close distance in folded structural ensembles. Here we introduce a direct coupling analysis for repeat proteins - natural systems for which the identification of folding domains remains challenging.
resultsWe show that the inherent translational symmetry of repeat protein sequences introduces a strong bias in the pair correlations at precisely the length scale of the repeat-unit. Equalizing for this bias in an objective way reveals true co-evolutionary signals from which local native contacts can be identified. Importantly, parameter values obtained for all other interactions are not significantly affected by the equalization. We quantify the robustness of the procedure and assign confidence levels to the interactions, identifying the minimum number of sequences needed to extract evolutionary information in several repeat protein families.
conclusionsThe overall procedure can be used to reconstruct the interactions at distances larger than repeat-pairs, identifying the characteristics of the strongest couplings in each family, and can be applied to any system that appears translationally symmetric.
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