2014/07/25 by Rocío Espada, Espada, Rocío, R. Gonzalo Parra +8
Biochemistry, Genetics and Molecular Biology · Neuroscience · #Algorithm #Biological system #Biology #Biomolecules (q-bio.BM) #Computational biology #Computer science #FOS: Biological sciences #Gene #Genetic Neurodegenerative Diseases #Genetics #Globular protein #Identification (biology) #Protein Structure and Dynamics #RNA and protein synthesis mechanisms #Robustness (evolution) #q-bio.BM
paper · pdf · doi:10.48550/arxiv.1407.6903
arxiv created 2014/07/25 · openalex publication_date 2014/07/25 · arxiv updated 2014/07/28 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The analysis of correlations of amino acid occurrences in globular proteins 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 statistical coupling analysis for repeat proteins -- natural systems for which the identification of domains remains challenging. We 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 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. The overall procedure can be used to reconstruct the interactions at long distances, identifying the characteristics of the strongest couplings in each family, and can be applied to any system that appears translationally symmetric.