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Emerging methods in protein co-evolution

Key Points

  • Co-evolution is an essential component of evolution that contributes to maintain the structure of ecological and molecular networks while allowing species, and proteins and genes, to change and adapt over time.

  • The signatures of co-evolution detected by computational methods in multiple sequence alignments of protein families are intimately related with physical and functional interactions.

  • Co-evolutionary methods are applied to two different levels: inter-residue correlations in single proteins and correlations between evolutionary patterns of protein pairs or protein collections. Some hybrid methods combine both levels.

  • A new generation of methods able to single-out direct interactions, by efficiently dealing with complex networks of correlations, has been successfully applied to the detection of protein interaction partners and to the construction of protein structure models.

  • Co-evolutionary methodology has been applied and in many cases combined with experimental approaches to: protein modelling, detection of binding sites, deciphering protein mechanisms of action, prediction of protein–protein interaction partners and reconstruction of protein complexes and interaction networks.

  • Co-evolution-based methods have been independently developed and up to now have been considered unrelated. This general Review of the field prompts us to think that unifying co-evolutionary methods under a common framework would be an important step forward in the understanding of the molecular basis of co-evolution.

Abstract

Co-evolution is a fundamental component of the theory of evolution and is essential for understanding the relationships between species in complex ecological networks. A wide range of co-evolution-inspired computational methods has been designed to predict molecular interactions, but it is only recently that important advances have been made. Breakthroughs in the handling of phylogenetic information and in disentangling indirect relationships have resulted in an improved capacity to predict interactions between proteins and contacts between different protein residues. Here, we review the main co-evolution-based computational approaches, their theoretical basis, potential applications and foreseeable developments.

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Figure 1: Co-evolutionary features extracted from protein multiple sequence alignments.
Figure 2: Influence of phylogenetic history in the association of co-evolution and different types of molecular interactions.

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Acknowledgements

We thank J. Onuchic from the University of California, San Diego, USA, D. Jones from the University College London, UK, C. Sander from the Computational Biology Center at the Memorial Sloan–Kettering Cancer Center, New York, USA, E. van Nimwegen from Biozentrum at the University of Basel, Switzerland, F. Gervasio and S. Marsili from the Computational Biophysics Group at CNIO, A. Rausell from the Swiss Institute of Bioinformatics Vital-IT & Institute of Microbiology of the University of Lausanne and D. Ochoa from the Computational Systems Biology Group at CNB–CSIC for interesting discussions, as well as the many authors and collaborators with important contributions to the field of molecular co-evolution in the past 20 years, many of which could not be included in this Review.

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Correspondence to Alfonso Valencia.

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Glossary

Molecular phylogenetics

The study of evolutionary phenomena using biomolecular data, generally in the form of sequences of nucleic acids or proteins.

Covarion model

A phylogenetic model in which the evolutionary rate of different codons are interdependent.

Protein family

A set of homologous proteins defined according to a given threshold of sequence similarity.

Homologues

Genes and proteins arisen from a common ancestor. In most cases, this common origin is traceable at the sequence level, albeit the sequence similarity can be very low and difficult to detect.

Correlated mutations

Relationship between two positions of a multiple sequence alignment in which the amino acid changes in one of the positions (mutational pattern) parallels that in the other.

Phylogenetic trees

Representations of the evolutionary relationships between a set of biological entities (such as proteins, genes or organisms).

Protein interfaces

Regions of the surface of a protein involved in the interaction with others.

Amino acid substitution matrix

A matrix containing, for every possible pair between the 20 canonical amino acids, a quantification of the 'interchangeability' of one by the other in the same protein site, as a proxy of the evolutionary feasibility of the corresponding change (mutation). They are often derived from curated sets of MSAs assumed to contain real representations of the amino acids allowed at a given protein site.

Benchmark

In bioinformatics, this term describes the assessment of the performance of a method using a set of examples of known outcome (the 'gold standard'), particularly by testing its predictive power relative to current best practice tools.

Clades

Groups of entities (such as genes or organisms) in a phylogenetic tree that have all arisen from a common ancestor.

Homology modelling

Protein structure prediction technique that, on the basis of the proven relationship between sequence similarity and structural similarity, models the three-dimensional structure of a protein based on the (experimentally determined) structure of a homologue (known as a 'template' in this context). Also known as 'comparative modelling'.

De novo protein modelling

Any approach for predicting protein structure that does not make use of information on other existing protein structures (such as those of homologues). Also known as 'ab initio modelling'.

Mutual information

In information theory, this is entropy-based formulation for quantifying the interdependence between the values of two random categorical variables.

Continuous-time Markov process

Process in which a system explores along time different states of a finite 'state space' in such a way that the Markov property is satisfied. This property means that the probability distribution of the system at a time point given the whole history of the process up to a previous time depends only on the state of the system at that previous time.

Monte Carlo algorithm

An algorithm based on simulated repeated random sampling to obtain approximate solutions to complex mathematical and statistical problems.

Heuristic approaches

Methods that makes use of approximations or assumptions so as to reduce the search space but that consequently do not ensure the exact solution to be found.

Bayesian network

Probabilistic model in which a set of random variables (nodes) and their conditional dependencies (directed edges) are arranged in a network representation.

Residue entropy

Quantification of the evolutionary variability of the position of a multiple sequence alignment corresponding to a given protein residue based on the 'entropy' parameter of information theory.

Orthologues

Homologous genes or proteins split in a speciation event, ending up in different organisms.

Horizontal gene transfer

(HGT). Transmission of genetic material between organisms different from that which occurs between the parents and the offspring ('vertical transfer'). Also known as 'lateral gene transfer'.

Principal component analysis

(PCA). Multivariate data analysis technique that consists of calculating a lower dimensionality space in which the axes explain most of the variability of the original data. The rationale is that such lower dimensionality space is easy to handle and to visualize, whereas most of the information of the original data (for example, in terms of relative distances) is retained and some contributions of noise are removed.

Multiple correspondence analysis

(MCA). Multivariate data analysis technique similar to principal component analysis but more suitable for categorical data.

Spectral decomposition

Decomposition of a squared matrix (A) as the product of its eigenvectors (V) times the diagonal matrix of its eigenvalues (D) times the inverse of its eigenvectors: A = V·D·V−1. Also known as 'eigendecomposition'.

Paralogues

Homologous genes or proteins split in a gene duplication event, resulting in two copies of the parental gene in the same organism that latter diverge in sequence and function.

Protein domains

Pieces of a protein defined according to given criteria: for example, structural domains or functional domains.

Genetic saturation

Apparent reduction with time of the observed divergence between two genes owing to factors such as reversed or convergent mutations.

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de Juan, D., Pazos, F. & Valencia, A. Emerging methods in protein co-evolution. Nat Rev Genet 14, 249–261 (2013). https://doi.org/10.1038/nrg3414

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