Biomolecular coevolution and its applications: Going from structure prediction toward signaling, epistasis, and function
- 20 October 2017
- journal article
- review article
- Published by Portland Press Ltd. in Biochemical Society Transactions
- Vol. 45 (6), 1253-1261
- https://doi.org/10.1042/bst20170063
Abstract
Evolution leads to considerable changes in the sequence of biomolecules, while their overall structure and function remain quite conserved. The wealth of genomic sequences, the ‘Biological Big Data’, modern sequencing techniques provide allows us to investigate biomolecular evolution with unprecedented detail. Sophisticated statistical models can infer residue pair mutations resulting from spatial proximity. The introduction of predicted spatial adjacencies as constraints in biomolecular structure prediction workflows has transformed the field of protein and RNA structure prediction toward accuracies approaching the experimental resolution limit. Going beyond structure prediction, the same mathematical framework allows mimicking evolutionary fitness landscapes to infer signaling interactions, epistasis, or mutational landscapes.This publication has 72 references indexed in Scilit:
- Three-Dimensional Structures of Membrane Proteins from Genomic SequencingCell, 2012
- Genomics-aided structure predictionProceedings of the National Academy of Sciences of the United States of America, 2012
- Structural basis of histidine kinase autophosphorylation deduced by integrating genomics, molecular dynamics, and mutagenesisProceedings of the National Academy of Sciences of the United States of America, 2012
- Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysisProceedings of the National Academy of Sciences of the United States of America, 2012
- Direct-coupling analysis of residue coevolution captures native contacts across many protein familiesProceedings of the National Academy of Sciences of the United States of America, 2011
- Accessory Mutations Maintain Stability in Drug-Resistant HIV-1 ProteaseJournal of Molecular Biology, 2011
- High-resolution protein complexes from integrating genomic information with molecular simulationProceedings of the National Academy of Sciences of the United States of America, 2009
- Structure is three to ten times more conserved than sequence—A study of structural response in protein coresProteins, 2009
- Identification of direct residue contacts in protein–protein interaction by message passingProceedings of the National Academy of Sciences of the United States of America, 2009
- Weak pairwise correlations imply strongly correlated network states in a neural populationNature, 2006