A structural perspective of compensatory evolution

Highlights • We identify four different approaches that are used to study compensatory evolution.• We classify different types of amino acid interactions found in protein structures.• A consensus on the importance of structural interactions in evolution is lacking.• The role of specific/general and local/allosteric compensations is required.• The study of compensatory evolution advances both structural and evolutionary biology.

• Publication year

  2014

• Venue

  Current Opinion in Structural Biology

• Publication date

  2014-06-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1016/j.sbi.2014.05.004PMID 24981969PMCID 4141909
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Structural Analysis

  2017cited by this paper
• The Gold Book

  2014cited by this paper
• Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations.

  2014cited by this paper
• A decade of riboswitches.

  2013cited by this paper
• The role of epistasis in protein evolution

  2013cited by this paper
• Mechanisms of Protein Sequence Divergence and Incompatibility

  2013cited by this paper
• What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs.

  2013cited by this paper
• Epistasis between mutations is host-dependent for an RNA virus

  2013cited by this paper
• Stability-mediated epistasis constrains the evolution of an influenza protein

  2013influential reference
• Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin

  2013cited by this paper
• Emerging methods in protein co-evolution

  2013cited by this paper
• Evolution of the Hemagglutinin Protein of the New Pandemic H1N1 Influenza Virus: Maintaining Optimal Receptor Binding by Compensatory Substitutions

  2013cited by this paper
• Molecular Insights on Pathogenic Effects of Mutations Causing Phosphoglycerate Kinase Deficiency

  2012cited by this paper
• Estimating the Rate of Irreversibility in Protein Evolution

  2012cited by this paper
• Three-dimensional structures of membrane proteins from genomic sequencing.

  2012cited by this paper
• Epistasis as the primary factor in molecular evolution

  2012cited by this paper
• The Protein-Folding Problem, 50 Years On

  2012cited by this paper
• Development and testing of PFFSol1.1, a new polarizable atomic force field for calculation of molecular interactions in implicit water environment.

  2012cited by this paper
• Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

  2012cited by this paper
• Energy landscape of knotted protein folding

  2012cited by this paper
• Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex.

  2012cited by this paper
• Altitudinal Variation at Duplicated β-Globin Genes in Deer Mice: Effects of Selection, Recombination, and Gene Conversion

  2012cited by this paper
• PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

  2012cited by this paper
• Direct-coupling analysis of residue coevolution captures native contacts across many protein families

  2011cited by this paper
• Slow protein evolutionary rates are dictated by surface–core association

  2011cited by this paper
• Correlated Evolution of Nearby Residues in Drosophilid Proteins

  2011cited by this paper
• A Highly Conserved Residue in the C-Terminal Helix of HIV-1 Matrix Is Required for Envelope Incorporation into Virus Particles

  2011cited by this paper
• Predicted residue–residue contacts can help the scoring of 3D models

  2010cited by this paper
• Transition state analogue structures of human phosphoglycerate kinase establish the importance of charge balance in catalysis.

  2010cited by this paper
• Atomic-Level Characterization of the Structural Dynamics of Proteins

  2010cited by this paper
• Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast

  2010cited by this paper
• Measurements of spontaneous rates of mutations in the recent past and the near future

  2010cited by this paper
• Compensated pathogenic deviations: analysis of structural effects.

  2010cited by this paper
• Sequence space and the ongoing expansion of the protein universe

  2010cited by this paper
• Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness

  2010cited by this paper
• Evolution of biological catalysis: ribozyme to RNP enzyme.

  2009cited by this paper
• Evolutionary and functional insights into the mechanism underlying high-altitude adaptation of deer mouse hemoglobin

  2009cited by this paper
• Compensatory mutations are repeatable and clustered within proteins

  2009cited by this paper
• An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

  2009cited by this paper
• Protein Dynamism and Evolvability

  2009cited by this paper
• Stability effects of mutations and protein evolvability.

  2009cited by this paper
• Epistatic interactions modulate the evolution of mammalian mitochondrial respiratory complex components

  2009cited by this paper
• Protein sectors: evolutionary units of three-dimensional structure.

  2009cited by this paper
• Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites

  2008cited by this paper
• HEMOGLOBIN FUNCTION AND PHYSIOLOGICAL ADAPTATION TO HYPOXIA IN HIGH-ALTITUDE MAMMALS

  2007cited by this paper
• A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures

  2007cited by this paper
• Compensatory Evolution of a WW Domain Variant Lacking the Strictly Conserved Trp Residue

  2007cited by this paper
• Characterization of compensated mutations in terms of structural and physico-chemical properties.

  2007cited by this paper
• The Molecular Basis of High-Altitude Adaptation in Deer Mice

  2007influential reference
• FUNCTIONAL ORIGINS OF FITNESS EFFECT‐SIZES OF COMPENSATORY MUTATIONS IN THE DNA BACTERIOPHAGE ØX174

  2006cited by this paper
• An enhanced MITOMAP with a global mtDNA mutational phylogeny

  2006cited by this paper
• Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins

  2006cited by this paper
• Identification of Diverse Archaeal Proteins with Class III Signal Peptides Cleaved by Distinct Archaeal Prepilin Peptidases

  2006cited by this paper
• Evolution of Hormone-Receptor Complexity by Molecular Exploitation

  2006cited by this paper
• FUNCTIONAL ORIGINS OF FITNESS EFFECT-SIZES OF COMPENSATORY MUTATIONS IN THE DNA BACTERIOPHAGE ϕX174

  2006influential reference
• Mitochondrial DNA mutations in human disease

  2006cited by this paper
• Missense meanderings in sequence space: a biophysical view of protein evolution

  2005cited by this paper
• The Rate of Compensatory Mutation in the DNA Bacteriophage φX174

  2005cited by this paper
• Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis

  2005cited by this paper
• Mitochondrial DNA mutations in human disease

  2005cited by this paper
• Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs

  2004cited by this paper
• Evolution of interacting proteins in the mitochondrial electron transport system in a marine copepod.

  2004cited by this paper
• NMR studies of structure and function of biological macromolecules (Nobel Lecture)*

  2003cited by this paper
• Impact of disease-related mitochondrial mutations on tRNA structure and function.

  2003cited by this paper
• Dobzhansky–Muller incompatibilities in protein evolution

  2002influential reference
• Theoretical study of a landscape of protein folding-unfolding pathways. Folding rates at midtransition.

  2001cited by this paper
• Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water

  2001cited by this paper
• Salt bridge stability in monomeric proteins.

  1999cited by this paper
• The population genetics of speciation: the evolution of hybrid incompatibilities.

  1995cited by this paper
• Correlated Mutations and Residue Contacts

  1994cited by this paper
• Correlated mutations and residue contacts in proteins

  1994cited by this paper
• Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?

  1994cited by this paper
• Compensating changes in protein multiple sequence alignments.

  1994cited by this paper
• How frequent are correlated changes in families of protein sequences?

  1994cited by this paper
• Compendium of chemical terminology

  1987cited by this paper
• The role of compensatory neutral mutations in molecular evolution

  1985cited by this paper
• Principles that govern the folding of protein chains.

  1973cited by this paper
• An introduction to population genetics theory

  1971cited by this paper

• Beyond additivity: zero-shot methods cannot predict impact of epistasis on protein properties and function

  2026cites this paper
• Community and functional shifts in sediment microbiomes driven by coral-algal proximity in the Northern Red Sea

  2026cites this paper
• Epistasis-mediated compensatory evolution in a fitness landscape with adaptational tradeoffs

  2025cites this paper
• Assessing nonlinearities in the GFP random mutagenesis landscape using the Power Transform

  2025cites this paper
• Sign Epistasis Can be Absent in Multi-peaked Landscapes With Neutral Mutations

  2025cites this paper
• Compensatory Evolution Following Deleterious Episodes of GC-biased Gene Conversion in Rodents

  2025influential citation
• Addressing epistasis in the design of protein function

  2024cites this paper
• How proteins manage to fold and how chaperones manage to assist the folding.

  2024cites this paper
• Inferring the Selective History of CNVs Using a Maximum Likelihood Model

  2024cites this paper
• In Silico Simulations Reveal Molecular Mechanism of Uranyl Ion Toxicity towards DNA-Binding Domain of PARP-1 Protein

  2023cites this paper
• Distinguishing features of fold‐switching proteins

  2023cites this paper
• Intragenic compensation through the lens of deep mutational scanning

  2022cites this paper
• Gene loss and compensatory evolution promotes the emergence of morphological novelties in budding yeast

  2022cites this paper
• Local fitness and epistatic effects lead to distinct patterns of linkage disequilibrium in protein-coding genes

  2022cites this paper
• Using metagenomic data to boost protein structure prediction and discovery

  2022cites this paper
• Asymmetrical dose responses shape the evolutionary trade-off between antifungal resistance and nutrient use

  2022cites this paper
• Octopaminergic/tyraminergic Tdc2 neurons regulate biased sperm usage in female Drosophila melanogaster.

  2022cites this paper
• Conservation and coevolution determine evolvability of different classes of disordered residues in human intrinsically disordered proteins

  2021cites this paper
• Evolutionary pathways to SARS-CoV-2 resistance are opened and closed by epistasis acting on ACE2

  2021cites this paper
• The Structural Determinants of Intra-Protein Compensatory Substitutions

  2021cites this paper
• Coevolution of interacting proteins through non-contacting and non-specific mutations

  2021cites this paper
• Can we distinguish modes of selective interactions using linkage disequilibrium?

  2021cites this paper
• Diversification of DNA-Binding Specificity by Permissive and Specificity-Switching Mutations in the ParB/Noc Protein Family

  2020cites this paper
• Incongruences Between Sequence and Secondary Structure Alignments of Nucleic Acids

  2020influential citation
• Limits to compensatory mutations: Insights from temperature-sensitive alleles.

  2019cites this paper
• Shedding light on the dark matter of the biomolecular structural universe: Progress in RNA 3D structure prediction.

  2019cites this paper
• Adenine·cytosine substitutions are an alternative pathway of compensatory mutation in angiosperm ITS2

  2019cites this paper
• Compensatory mutation can drive gene regulatory network evolution

  2019cites this paper
• Evolving a new protein-DNA interface via sequential introduction of permissive and specificity-switching mutations

  2019cites this paper
• Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision

  2018cites this paper
• Detecting Amino Acid Coevolution with Bayesian Graphical Models.

  2018cites this paper
• Compensatory mutations and epistasis for protein function.

  2018cites this paper
• Interactome evolution: insights from genome-wide analyses of protein-protein interactions.

  2018cites this paper
• Coevolutionary Signals and Structure-Based Models for the Prediction of Protein Native Conformations.

  2018cites this paper
• Evolution of complex adaptations in molecular systems

  2017cites this paper
• Applications of sequence coevolution in membrane protein biochemistry.

  2017cites this paper
• Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System

  2017cites this paper
• The genomic landscape of evolutionary convergence in mammals, birds and reptiles

  2017cites this paper
• Causes of molecular convergence and parallelism in protein evolution

  2016cites this paper
• The Molecular Basis of Human Brain Evolution.

  2016cites this paper
• Protein structural robustness to mutations: an in silico investigation.

  2016cites this paper
• Evolutionary analysis of Slc11 mechanism of proton-coupled metal-ion transmembrane import

  2016cites this paper
• Compensatory Evolution in Disease‐Associated Genes

  2015cites this paper
• Topological features of rugged fitness landscapes in sequence space.

  2015cites this paper
• Evolutionary Innovations and Dynamics in Wagner's Model of Genetic Regulatory Networks

  2015cites this paper
• Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins

  2015cites this paper
• biophysicsof protein evolution and evolutionary protein

  2014cites this paper
• Biophysics of protein evolution and evolutionary protein biophysics

  2014cites this paper