Elements of Coevolution in Biological Sequences

Abstract

Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure, and sectors, which are larger groups of structurally connected amino acids that underlie the biochemical properties of proteins. By reconciling two approaches for analyzing correlations in multiple sequence alignments, we link these two findings together and with coevolving units of intermediate size, called `sectons', which are shown to provide additional information. By extending the analysis to the co-occurrence of orthologous genes in bacterial genomes, we also show that the methods and results are general and relevant beyond protein structures.

References in corpus (1)

• Identification of direct residue contacts in protein-protein interaction by message passing

Cited by in corpus (10)

• Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences
• Protein sectors: statistical coupling analysis versus conservation
• Improving contact prediction along three dimensions
• Phylogenetic correlations can suffice to infer protein partners from sequences
• Beyond position weight matrices: nucleotide correlations in transcription factor binding sites and their description
• The network of stabilizing contacts in proteins studied by coevolutionary data
• Revealing evolutionary constraints on proteins through sequence analysis
• Parsimonious evolutionary scenario for the origin of allostery and coevolution patterns in proteins
• Identifying relevant positions in proteins by Critical Variable Selection
• Progress and open problems in evolutionary dynamics