1
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Bou Dagher L, Madern D, Malbos P, Brochier-Armanet C. Persistent homology reveals strong phylogenetic signal in 3D protein structures. PNAS NEXUS 2024; 3:pgae158. [PMID: 38689707 PMCID: PMC11058471 DOI: 10.1093/pnasnexus/pgae158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/01/2024] [Indexed: 05/02/2024]
Abstract
Changes that occur in proteins over time provide a phylogenetic signal that can be used to decipher their evolutionary history and the relationships between organisms. Sequence comparison is the most common way to access this phylogenetic signal, while those based on 3D structure comparisons are still in their infancy. In this study, we propose an effective approach based on Persistent Homology Theory (PH) to extract the phylogenetic information contained in protein structures. PH provides efficient and robust algorithms for extracting and comparing geometric features from noisy datasets at different spatial resolutions. PH has a growing number of applications in the life sciences, including the study of proteins (e.g. classification, folding). However, it has never been used to study the phylogenetic signal they may contain. Here, using 518 protein families, representing 22,940 protein sequences and structures, from 10 major taxonomic groups, we show that distances calculated with PH from protein structures correlate strongly with phylogenetic distances calculated from protein sequences, at both small and large evolutionary scales. We test several methods for calculating PH distances and propose some refinements to improve their relevance for addressing evolutionary questions. This work opens up new perspectives in evolutionary biology by proposing an efficient way to access the phylogenetic signal contained in protein structures, as well as future developments of topological analysis in the life sciences.
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Affiliation(s)
- Léa Bou Dagher
- Université Claude Bernard Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et BiologieÉvolutive, UMR5558, F-69622 Villeurbanne, France
- Université Claude Bernard Lyon 1, CNRS, Institut Camille Jordan, UMR5208, F-69622 Villeurbanne, France
- Université Libanaise, Laboratoire de Mathématiques, École Doctorale en Science et Technologie, PO BOX 5 Hadath, Liban
| | - Dominique Madern
- University Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Philippe Malbos
- Université Claude Bernard Lyon 1, CNRS, Institut Camille Jordan, UMR5208, F-69622 Villeurbanne, France
| | - Céline Brochier-Armanet
- Université Claude Bernard Lyon 1, CNRS, VetAgro Sup, Laboratoire de Biométrie et BiologieÉvolutive, UMR5558, F-69622 Villeurbanne, France
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2
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Nagar N, Tubiana J, Loewenthal G, Wolfson HJ, Ben Tal N, Pupko T. EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning. J Mol Biol 2023; 435:168155. [PMID: 37356902 DOI: 10.1016/j.jmb.2023.168155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/13/2023] [Accepted: 05/17/2023] [Indexed: 06/27/2023]
Abstract
Multiple sequence alignments (MSAs) are the workhorse of molecular evolution and structural biology research. From MSAs, the amino acids that are tolerated at each site during protein evolution can be inferred. However, little is known regarding the repertoire of tolerated amino acids in proteins when only a few or no sequence homologs are available, such as orphan and de novo designed proteins. Here we present EvoRator2, a deep-learning algorithm trained on over 15,000 protein structures that can predict which amino acids are tolerated at any given site, based exclusively on protein structural information mined from atomic coordinate files. We show that EvoRator2 obtained satisfying results for the prediction of position-weighted scoring matrices (PSSM). We further show that EvoRator2 obtained near state-of-the-art performance on proteins with high quality structures in predicting the effect of mutations in deep mutation scanning (DMS) experiments and that for certain DMS targets, EvoRator2 outperformed state-of-the-art methods. We also show that by combining EvoRator2's predictions with those obtained by a state-of-the-art deep-learning method that accounts for the information in the MSA, the prediction of the effect of mutation in DMS experiments was improved in terms of both accuracy and stability. EvoRator2 is designed to predict which amino-acid substitutions are tolerated in such proteins without many homologous sequences, including orphan or de novo designed proteins. We implemented our approach in the EvoRator web server (https://evorator.tau.ac.il).
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Affiliation(s)
- Natan Nagar
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jérôme Tubiana
- Blavatnik School of Computer Science, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gil Loewenthal
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Haim J Wolfson
- Blavatnik School of Computer Science, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nir Ben Tal
- School of Neurobiology, Biochemistry & Biophysics, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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3
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Sykes J, Holland BR, Charleston MA. A review of visualisations of protein fold networks and their relationship with sequence and function. Biol Rev Camb Philos Soc 2023; 98:243-262. [PMID: 36210328 PMCID: PMC10092621 DOI: 10.1111/brv.12905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/12/2023]
Abstract
Proteins form arguably the most significant link between genotype and phenotype. Understanding the relationship between protein sequence and structure, and applying this knowledge to predict function, is difficult. One way to investigate these relationships is by considering the space of protein folds and how one might move from fold to fold through similarity, or potential evolutionary relationships. The many individual characterisations of fold space presented in the literature can tell us a lot about how well the current Protein Data Bank represents protein fold space, how convergence and divergence may affect protein evolution, how proteins affect the whole of which they are part, and how proteins themselves function. A synthesis of these different approaches and viewpoints seems the most likely way to further our knowledge of protein structure evolution and thus, facilitate improved protein structure design and prediction.
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Affiliation(s)
- Janan Sykes
- School of Natural Sciences, University of Tasmania, Private Bag 37, Hobart, Tasmania, 7001, Australia
| | - Barbara R Holland
- School of Natural Sciences, University of Tasmania, Private Bag 37, Hobart, Tasmania, 7001, Australia
| | - Michael A Charleston
- School of Natural Sciences, University of Tasmania, Private Bag 37, Hobart, Tasmania, 7001, Australia
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4
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Susko E. Complex statistical modelling for phylogenetic inference. CAN J STAT 2022. [DOI: 10.1002/cjs.11741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Edward Susko
- Department of Mathematics and Statistics Dalhousie University Halifax Nova Scotia Canada B3H 3J5
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5
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Nagar N, Ben Tal N, Pupko T. EvoRator: Prediction of residue-level evolutionary rates from protein structures using machine learning. J Mol Biol 2022; 434:167538. [DOI: 10.1016/j.jmb.2022.167538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
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6
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Youssef N, Susko E, Roger AJ, Bielawski JP. Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work. Protein Sci 2021; 30:2009-2028. [PMID: 34322924 PMCID: PMC8442975 DOI: 10.1002/pro.4161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 11/08/2022]
Abstract
Amino acid preferences vary across sites and time. While variation across sites is widely accepted, the extent and frequency of temporal shifts are contentious. Our understanding of the drivers of amino acid preference change is incomplete: To what extent are temporal shifts driven by adaptive versus nonadaptive evolutionary processes? We review phenomena that cause preferences to vary (e.g., evolutionary Stokes shift, contingency, and entrenchment) and clarify how they differ. To determine the extent and prevalence of shifted preferences, we review experimental and theoretical studies. Analyses of natural sequence alignments often detect decreases in homoplasy (convergence and reversions) rates, and variation in replacement rates with time-signals that are consistent with temporally changing preferences. While approaches inferring shifts in preferences from patterns in natural alignments are valuable, they are indirect since multiple mechanisms (both adaptive and nonadaptive) could lead to the observed signal. Alternatively, site-directed mutagenesis experiments allow for a more direct assessment of shifted preferences. They corroborate evidence from multiple sequence alignments, revealing that the preference for an amino acid at a site varies depending on the background sequence. However, shifts in preferences are usually minor in magnitude and sites with significantly shifted preferences are low in frequency. The small yet consistent perturbations in preferences could, nevertheless, jeopardize the accuracy of inference procedures, which assume constant preferences. We conclude by discussing if and how such shifts in preferences might influence widely used time-homogenous inference procedures and potential ways to mitigate such effects.
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Affiliation(s)
- Noor Youssef
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Edward Susko
- Department of Mathematics and StatisticsDalhousie UniversityHalifaxNova ScotiaCanada
| | - Andrew J. Roger
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Joseph P. Bielawski
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- Department of Mathematics and StatisticsDalhousie UniversityHalifaxNova ScotiaCanada
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7
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Selberg AGA, Gaucher EA, Liberles DA. Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond. J Mol Evol 2021; 89:157-164. [PMID: 33486547 PMCID: PMC7828096 DOI: 10.1007/s00239-021-09993-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
As both a computational and an experimental endeavor, ancestral sequence reconstruction remains a timely and important technique. Modern approaches to conduct ancestral sequence reconstruction for proteins are built upon a conceptual framework from journal founder Emile Zuckerkandl. On top of this, work on maximum likelihood phylogenetics published in Journal of Molecular Evolution in 1996 was one of the first approaches for generating maximum likelihood ancestral sequences of proteins. From its computational history, future model development needs as well as potential applications in areas as diverse as computational systems biology, molecular community ecology, infectious disease therapeutics and other biomedical applications, and biotechnology are discussed. From its past in this journal, there is a bright future for ancestral sequence reconstruction in the field of evolutionary biology.
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Affiliation(s)
- Avery G A Selberg
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Eric A Gaucher
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
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8
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Laurin-Lemay S, Rodrigue N, Lartillot N, Philippe H. Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation-Selection Models. Mol Biol Evol 2019; 35:2819-2834. [PMID: 30203003 DOI: 10.1093/molbev/msy173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A key question in molecular evolutionary biology concerns the relative roles of mutation and selection in shaping genomic data. Moreover, features of mutation and selection are heterogeneous along the genome and over time. Mechanistic codon substitution models based on the mutation-selection framework are promising approaches to separating these effects. In practice, however, several complications arise, since accounting for such heterogeneities often implies handling models of high dimensionality (e.g., amino acid preferences), or leads to across-site dependence (e.g., CpG hypermutability), making the likelihood function intractable. Approximate Bayesian Computation (ABC) could address this latter issue. Here, we propose a new approach, named Conditional ABC (CABC), which combines the sampling efficiency of MCMC and the flexibility of ABC. To illustrate the potential of the CABC approach, we apply it to the study of mammalian CpG hypermutability based on a new mutation-level parameter implying dependence across adjacent sites, combined with site-specific purifying selection on amino-acids captured by a Dirichlet process. Our proof-of-concept of the CABC methodology opens new modeling perspectives. Our application of the method reveals a high level of heterogeneity of CpG hypermutability across loci and mild heterogeneity across taxonomic groups; and finally, we show that CpG hypermutability is an important evolutionary factor in rendering relative synonymous codon usage. All source code is available as a GitHub repository (https://github.com/Simonll/LikelihoodFreePhylogenetics.git).
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Affiliation(s)
- Simon Laurin-Lemay
- Robert-Cedergren Center for Bioinformatics and Genomics, Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Nicolas Rodrigue
- Department of Biology, Institute of Biochemistry, and School of Mathematics and Statistics, Carleton University, Ottawa, ON, Canada
| | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Lyon 1, Lyon, France
| | - Hervé Philippe
- Robert-Cedergren Center for Bioinformatics and Genomics, Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.,Centre de Théorisation et de Modélisation de la Biodiversité, Station d'Écologie Théorique et Expérimentale, UMR CNRS 5321, Moulis, France
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9
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Qiu X, Duvvuri VR, Bahl J. Computational Approaches and Challenges to Developing Universal Influenza Vaccines. Vaccines (Basel) 2019; 7:E45. [PMID: 31141933 PMCID: PMC6631137 DOI: 10.3390/vaccines7020045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/15/2019] [Accepted: 05/23/2019] [Indexed: 12/25/2022] Open
Abstract
The traditional design of effective vaccines for rapidly-evolving pathogens, such as influenza A virus, has failed to provide broad spectrum and long-lasting protection. With low cost whole genome sequencing technology and powerful computing capabilities, novel computational approaches have demonstrated the potential to facilitate the design of a universal influenza vaccine. However, few studies have integrated computational optimization in the design and discovery of new vaccines. Understanding the potential of computational vaccine design is necessary before these approaches can be implemented on a broad scale. This review summarizes some promising computational approaches under current development, including computationally optimized broadly reactive antigens with consensus sequences, phylogenetic model-based ancestral sequence reconstruction, and immunomics to compute conserved cross-reactive T-cell epitopes. Interactions between virus-host-environment determine the evolvability of the influenza population. We propose that with the development of novel technologies that allow the integration of data sources such as protein structural modeling, host antibody repertoire analysis and advanced phylodynamic modeling, computational approaches will be crucial for the development of a long-lasting universal influenza vaccine. Taken together, computational approaches are powerful and promising tools for the development of a universal influenza vaccine with durable and broad protection.
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Affiliation(s)
- Xueting Qiu
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Venkata R Duvvuri
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA 30606, USA.
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore.
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10
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Ensembles from Ordered and Disordered Proteins Reveal Similar Structural Constraints during Evolution. J Mol Biol 2019; 431:1298-1307. [DOI: 10.1016/j.jmb.2019.01.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 01/08/2023]
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11
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Herman JL. Enhancing Statistical Multiple Sequence Alignment and Tree Inference Using Structural Information. Methods Mol Biol 2019; 1851:183-214. [PMID: 30298398 DOI: 10.1007/978-1-4939-8736-8_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
For highly divergent sequences, there is often insufficient information to reliably construct alignments and phylogenetic trees. Since protein structure may be strongly conserved despite large divergences in sequence, structural information can be used to help identify homology in such cases.While there exist well-studied models of sequence evolution, structurally informed alignment methods have typically made use of geometric measures of deviation that do not take into account the underlying mutational processes. In order to integrate structural information into sequence-based evolutionary models, we recently developed a stochastic model of structural evolution on a phylogenetic tree and implemented this as the StructAlign plugin for the StatAlign statistical alignment package.In this chapter, we will outline the types of analyses that can be carried out using StructAlign, illustrating how the inclusion of structural information can be used to inform joint estimation of alignments and trees. StructAlign can also be used to infer branch-specific rates of structural evolution, and analysis of an example globin dataset highlights strong variation in the inferred rate across the tree. While structure is more highly conserved within clades, the rate of structural divergence as a function of sequence variation is larger between functionally divergent proteins. Allowing for the rate of structural divergence to vary over the tree results in an improved fit to the empirically observed pairwise RMSD values.
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Affiliation(s)
- Joseph L Herman
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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12
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Chi PB, Kim D, Lai JK, Bykova N, Weber CC, Kubelka J, Liberles DA. A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution. Proteins 2017; 86:218-228. [PMID: 29178386 DOI: 10.1002/prot.25429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/14/2017] [Accepted: 11/22/2017] [Indexed: 02/06/2023]
Abstract
Improvements in the description of amino acid substitution are required to develop better pseudo-energy-based protein structure-aware models for use in phylogenetic studies. These models are used to characterize the probabilities of amino acid substitution and enable better simulation of protein sequences over a phylogeny. A better characterization of amino acid substitution probabilities in turn enables numerous downstream applications, like detecting positive selection, ancestral sequence reconstruction, and evolutionarily-motivated protein engineering. Many existing Markov models for amino acid substitution in molecular evolution disregard molecular structure and describe the amino acid substitution process over longer evolutionary periods poorly. Here, we present a new model upgraded with a site-specific parameterization of pseudo-energy terms in a coarse-grained force field, which describes local heterogeneity in physical constraints on amino acid substitution better than a previous pseudo-energy-based model with minimum cost in runtime. The importance of each weight term parameterization in characterizing underlying features of the site, including contact number, solvent accessibility, and secondary structural elements was evaluated, returning both expected and biologically reasonable relationships between model parameters. This results in the acceptance of proposed amino acid substitutions that more closely resemble those observed site-specific frequencies in gene family alignments. The modular site-specific pseudo-energy function is made available for download through the following website: https://liberles.cst.temple.edu/Software/CASS/index.html.
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Affiliation(s)
- Peter B Chi
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122.,Department of Mathematics and Computer Science, Ursinus College, Collegeville, Pennsylvania, 19426
| | - Dohyup Kim
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, 82071
| | - Jason K Lai
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, 82071
| | - Nadia Bykova
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, 82071.,Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119234, Russia
| | - Claudia C Weber
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122
| | - Jan Kubelka
- Department of Chemistry, University of Wyoming, Laramie, Wyoming, 82071
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122.,Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, 82071
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13
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Parto S, Lartillot N. Detecting consistent patterns of directional adaptation using differential selection codon models. BMC Evol Biol 2017. [PMID: 28645318 PMCID: PMC5481935 DOI: 10.1186/s12862-017-0979-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors. However, some organisms may be subject to systematic changes in selective pressure, resulting in reproducible molecular adaptations across independent lineages subject to similar conditions. RESULTS Here, we introduce a codon-based differential selection model, which aims to detect and quantify the fine-grained consistent patterns of adaptation at the protein-coding level, as a function of external conditions experienced by the organism under investigation. The model parameterizes the global mutational pressure, as well as the site- and condition-specific amino acid selective preferences. This phylogenetic model is implemented in a Bayesian MCMC framework. After validation with simulations, we applied our method to a dataset of HIV sequences from patients with known HLA genetic background. Our differential selection model detects and characterizes differentially selected coding positions specifically associated with two different HLA alleles. CONCLUSION Our differential selection model is able to identify consistent molecular adaptations as a function of repeated changes in the environment of the organism. These models can be applied to many other problems, ranging from viral adaptation to evolution of life-history strategies in plants or animals.
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Affiliation(s)
- Sahar Parto
- Département de Biochimie et Médecine Moléculaire, Centre Robert Cedergren, Bio-Informatique et Génomique, Université de Montréal, Montréal, Québec, Canada.
| | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, CNRS, UMR 5558, Lyon, France
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14
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Echave J, Wilke CO. Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence. Annu Rev Biophys 2017; 46:85-103. [PMID: 28301766 DOI: 10.1146/annurev-biophys-070816-033819] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
For decades, rates of protein evolution have been interpreted in terms of the vague concept of functional importance. Slowly evolving proteins or sites within proteins were assumed to be more functionally important and thus subject to stronger selection pressure. More recently, biophysical models of protein evolution, which combine evolutionary theory with protein biophysics, have completely revolutionized our view of the forces that shape sequence divergence. Slowly evolving proteins have been found to evolve slowly because of selection against toxic misfolding and misinteractions, linking their rate of evolution primarily to their abundance. Similarly, most slowly evolving sites in proteins are not directly involved in function, but mutating these sites has a large impact on protein structure and stability. In this article, we review the studies in the emerging field of biophysical protein evolution that have shaped our current understanding of sequence divergence patterns. We also propose future research directions to develop this nascent field.
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Affiliation(s)
- Julian Echave
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires, Argentina; .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Claus O Wilke
- Department of Integrative Biology, The University of Texas at Austin, Texas 78712;
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15
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Bastolla U, Dehouck Y, Echave J. What evolution tells us about protein physics, and protein physics tells us about evolution. Curr Opin Struct Biol 2017; 42:59-66. [DOI: 10.1016/j.sbi.2016.10.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/19/2016] [Accepted: 10/24/2016] [Indexed: 12/21/2022]
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16
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Bloom JD. Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models. Biol Direct 2017; 12:1. [PMID: 28095902 PMCID: PMC5240389 DOI: 10.1186/s13062-016-0172-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/14/2016] [Indexed: 12/23/2022] Open
Abstract
Background Sites of positive selection are identified by comparing observed evolutionary patterns to those expected under a null model for evolution in the absence of such selection. For protein-coding genes, the most common null model is that nonsynonymous and synonymous mutations fix at equal rates; this unrealistic model has limited power to detect many interesting forms of selection. Results I describe a new approach that uses a null model based on experimental measurements of a gene’s site-specific amino-acid preferences generated by deep mutational scanning in the lab. This null model makes it possible to identify both diversifying selection for repeated amino-acid change and differential selection for mutations to amino acids that are unexpected given the measurements made in the lab. I show that this approach identifies sites of adaptive substitutions in four genes (lactamase, Gal4, influenza nucleoprotein, and influenza hemagglutinin) far better than a comparable method that simply compares the rates of nonsynonymous and synonymous substitutions. Conclusions As rapid increases in biological data enable increasingly nuanced descriptions of the constraints on individual protein sites, approaches like the one here can improve our ability to identify many interesting forms of selection in natural sequences. Reviewers This article was reviewed by Sebastian Maurer-Stroh, Olivier Tenaillon, and Tal Pupko. All three reviewers are members of the Biology Direct editorial board. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0172-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jesse D Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, 98109, WA, USA.
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17
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Chi PB, Liberles DA. Selection on protein structure, interaction, and sequence. Protein Sci 2016; 25:1168-78. [PMID: 26808055 PMCID: PMC4918422 DOI: 10.1002/pro.2886] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 11/10/2022]
Abstract
Characterizing the probabilities of observing amino acid substitutions at specific sites in a protein over evolutionary time is a major goal in the field of molecular evolution. While purely statistical approaches at different levels of complexity exist, approaches rooted in underlying biological processes are necessary to characterize both the context-dependence of sequence changes (epistasis) and to extrapolate to sequences not observed in biological databases. To develop such approaches, an understanding of the different selective forces that act on amino acid substitution is necessary. Here, an overview of selection on and corresponding modeling of folding stability, folding specificity, binding affinity and specificity for ligands, the evolution of new binding sites on protein surfaces, protein dynamics, intrinsic disorder, and protein aggregation as well as the interplay with protein expression level (concentration) and biased mutational processes are presented.
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Affiliation(s)
- Peter B Chi
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122
- Department of Mathematics and Computer Science, Ursinus College, Collegeville, Pennsylvania, 19426
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122
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18
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Echave J, Spielman SJ, Wilke CO. Causes of evolutionary rate variation among protein sites. Nat Rev Genet 2016; 17:109-21. [PMID: 26781812 DOI: 10.1038/nrg.2015.18] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It has long been recognized that certain sites within a protein, such as sites in the protein core or catalytic residues in enzymes, are evolutionarily more conserved than other sites. However, our understanding of rate variation among sites remains surprisingly limited. Recent progress to address this includes the development of a wide array of reliable methods to estimate site-specific substitution rates from sequence alignments. In addition, several molecular traits have been identified that correlate with site-specific mutation rates, and novel mechanistic biophysical models have been proposed to explain the observed correlations. Nonetheless, current models explain, at best, approximately 60% of the observed variance, highlighting the limitations of current methods and models and the need for new research directions.
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Affiliation(s)
- Julian Echave
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires, Argentina
| | - Stephanie J Spielman
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Claus O Wilke
- Department of Integrative Biology, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
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19
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Parisi G, Zea DJ, Monzon AM, Marino-Buslje C. Conformational diversity and the emergence of sequence signatures during evolution. Curr Opin Struct Biol 2015; 32:58-65. [DOI: 10.1016/j.sbi.2015.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/02/2015] [Accepted: 02/09/2015] [Indexed: 02/03/2023]
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20
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Wang K, Yu S, Ji X, Lakner C, Griffing A, Thorne JL. Roles of solvent accessibility and gene expression in modeling protein sequence evolution. Evol Bioinform Online 2015; 11:85-96. [PMID: 25987828 PMCID: PMC4415675 DOI: 10.4137/ebo.s22911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 02/04/2015] [Accepted: 02/09/2015] [Indexed: 11/05/2022] Open
Abstract
Models of protein evolution tend to ignore functional constraints, although structural constraints are sometimes incorporated. Here we propose a probabilistic framework for codon substitution that evaluates joint effects of relative solvent accessibility (RSA), a structural constraint; and gene expression, a functional constraint. First, we explore the relationship between RSA and codon usage at the genomic scale as well as at the individual gene scale. Motivated by these results, we construct our framework by determining how probable is an amino acid, given RSA and gene expression, and then evaluating the relative probability of observing a codon compared to other synonymous codons. We come to the biologically plausible conclusion that both RSA and gene expression are related to amino acid frequencies, but, among synonymous codons, the relative probability of a particular codon is more closely related to gene expression than RSA. To illustrate the potential applications of our framework, we propose a new codon substitution model. Using this model, we obtain estimates of 2N s, the product of effective population size N, and relative fitness difference of allele s. For a training data set consisting of human proteins with known structures and expression data, 2N s is estimated separately for synonymous and nonsynonymous substitutions in each protein. We then contrast the patterns of synonymous and nonsynonymous 2N s estimates across proteins while also taking gene expression levels of the proteins into account. We conclude that our 2N s estimates are too concentrated around 0, and we discuss potential explanations for this lack of variability.
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Affiliation(s)
- Kuangyu Wang
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Shuhui Yu
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA. ; College of Life Science, Chongqing University, Chongqing, China
| | - Xiang Ji
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Clemens Lakner
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Alexander Griffing
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey L Thorne
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
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21
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Sikosek T, Chan HS. Biophysics of protein evolution and evolutionary protein biophysics. J R Soc Interface 2015; 11:20140419. [PMID: 25165599 DOI: 10.1098/rsif.2014.0419] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence-structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by 'hidden' conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution.
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Affiliation(s)
- Tobias Sikosek
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Physics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Department of Physics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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22
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Goldstein RA, Pollard ST, Shah SD, Pollock DD. Nonadaptive Amino Acid Convergence Rates Decrease over Time. Mol Biol Evol 2015; 32:1373-81. [PMID: 25737491 PMCID: PMC4572784 DOI: 10.1093/molbev/msv041] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Convergence is a central concept in evolutionary studies because it provides strong evidence for adaptation. It also provides information about the nature of the fitness landscape and the repeatability of evolution, and can mislead phylogenetic inference. To understand the role of adaptive convergence, we need to understand the patterns of nonadaptive convergence. Here, we consider the relationship between nonadaptive convergence and divergence in mitochondrial and model proteins. Surprisingly, nonadaptive convergence is much more common than expected in closely related organisms, falling off as organisms diverge. The extent of the convergent drop-off in mitochondrial proteins is well predicted by epistatic or coevolutionary effects in our "evolutionary Stokes shift" models and poorly predicted by conventional evolutionary models. Convergence probabilities decrease dramatically if the ancestral amino acids of branches being compared have diverged, but also drop slowly over evolutionary time even if the ancestral amino acids have not substituted. Convergence probabilities drop-off rapidly for quickly evolving sites, but much more slowly for slowly evolving sites. Furthermore, once sites have diverged their convergence probabilities are extremely low and indistinguishable from convergence levels at randomized sites. These results indicate that we cannot assume that excessive convergence early on is necessarily adaptive. This new understanding should help us to better discriminate adaptive from nonadaptive convergence and develop more relevant evolutionary models with improved validity for phylogenetic inference.
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Affiliation(s)
- Richard A Goldstein
- Division of Infection & Immunity, University College London, London, United Kingdom
| | - Stephen T Pollard
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora
| | - Seena D Shah
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora
| | - David D Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora
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23
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Katsonis P, Lichtarge O. A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness. Genome Res 2014; 24:2050-8. [PMID: 25217195 PMCID: PMC4248321 DOI: 10.1101/gr.176214.114] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The relationship between genotype mutations and phenotype variations determines health in the short term and evolution over the long term, and it hinges on the action of mutations on fitness. A fundamental difficulty in determining this action, however, is that it depends on the unique context of each mutation, which is complex and often cryptic. As a result, the effect of most genome variations on molecular function and overall fitness remains unknown and stands apart from population genetics theories linking fitness effect to polymorphism frequency. Here, we hypothesize that evolution is a continuous and differentiable physical process coupling genotype to phenotype. This leads to a formal equation for the action of coding mutations on fitness that can be interpreted as a product of the evolutionary importance of the mutated site with the difference in amino acid similarity. Approximations for these terms are readily computable from phylogenetic sequence analysis, and we show mutational, clinical, and population genetic evidence that this action equation predicts the effect of point mutations in vivo and in vitro in diverse proteins, correlates disease-causing gene mutations with morbidity, and determines the frequency of human coding polymorphisms, respectively. Thus, elementary calculus and phylogenetics can be integrated into a perturbation analysis of the evolutionary relationship between genotype and phenotype that quantitatively links point mutations to function and fitness and that opens a new analytic framework for equations of biology. In practice, this work explicitly bridges molecular evolution with population genetics with applications from protein redesign to the clinical assessment of human genetic variations.
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Affiliation(s)
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Department of Biochemistry & Molecular Biology, Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030, USA; Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas 77030, USA
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24
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Fu M, Huang Z, Mao Y, Tao S. Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog. Int J Mol Sci 2014; 15:15963-80. [PMID: 25210846 PMCID: PMC4200849 DOI: 10.3390/ijms150915963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/27/2014] [Accepted: 09/02/2014] [Indexed: 12/23/2022] Open
Abstract
Amino acids show apparent propensities toward their neighbors. In addition to preferences of amino acids for their neighborhood context, amino acid substitutions are also considered to be context-dependent. However, context-dependence patterns of amino acid substitutions still remain poorly understood. Using relative entropy, we investigated the neighbor preferences of 20 amino acids and the context-dependent effects of amino acid substitutions with protein sequences in human, mouse, and dog. For 20 amino acids, the highest relative entropy was mostly observed at the nearest adjacent site of either N- or C-terminus except C and G. C showed the highest relative entropy at the third flanking site and periodic pattern was detected at G flanking sites. Furthermore, neighbor preference patterns of amino acids varied greatly in different secondary structures. We then comprehensively investigated the context-dependent effects of amino acid substitutions. Our results showed that nearly half of 380 substitution types were evidently context dependent, and the context-dependent patterns relied on protein secondary structures. Among 20 amino acids, P elicited the greatest effect on amino acid substitutions. The underlying mechanisms of context-dependent effects of amino acid substitutions were possibly mutation bias at a DNA level and natural selection. Our findings may improve secondary structure prediction algorithms and protein design; moreover, this study provided useful information to develop empirical models of protein evolution that consider dependence between residues.
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Affiliation(s)
- Mingchuan Fu
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling 712100, China.
| | - Zhuoran Huang
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling 712100, China.
| | - Yuanhui Mao
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling 712100, China.
| | - Shiheng Tao
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling 712100, China.
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25
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Herman JL, Challis CJ, Novák Á, Hein J, Schmidler SC. Simultaneous Bayesian estimation of alignment and phylogeny under a joint model of protein sequence and structure. Mol Biol Evol 2014; 31:2251-66. [PMID: 24899668 PMCID: PMC4137710 DOI: 10.1093/molbev/msu184] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
For sequences that are highly divergent, there is often insufficient information to infer accurate alignments, and phylogenetic uncertainty may be high. One way to address this issue is to make use of protein structural information, since structures generally diverge more slowly than sequences. In this work, we extend a recently developed stochastic model of pairwise structural evolution to multiple structures on a tree, analytically integrating over ancestral structures to permit efficient likelihood computations under the resulting joint sequence-structure model. We observe that the inclusion of structural information significantly reduces alignment and topology uncertainty, and reduces the number of topology and alignment errors in cases where the true trees and alignments are known. In some cases, the inclusion of structure results in changes to the consensus topology, indicating that structure may contain additional information beyond that which can be obtained from sequences. We use the model to investigate the order of divergence of cytoglobins, myoglobins, and hemoglobins and observe a stabilization of phylogenetic inference: although a sequence-based inference assigns significant posterior probability to several different topologies, the structural model strongly favors one of these over the others and is more robust to the choice of data set.
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Affiliation(s)
- Joseph L Herman
- Department of Statistics, University of Oxford, Oxford, United KingdomDivision of Mathematical Biology, National Institute of Medical Research, London, United Kingdom
| | | | - Ádám Novák
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Jotun Hein
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Scott C Schmidler
- Department of Statistical Science, Duke UniversityDepartment of Computer Science, Duke University
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26
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Bloom JD. An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs. Mol Biol Evol 2014; 31:2753-69. [PMID: 25063439 PMCID: PMC4166927 DOI: 10.1093/molbev/msu220] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Phylogenetic analyses of molecular data require a quantitative model for how
sequences evolve. Traditionally, the details of the site-specific selection that
governs sequence evolution are not known a priori, making it challenging to
create evolutionary models that adequately capture the heterogeneity of
selection at different sites. However, recent advances in high-throughput
experiments have made it possible to quantify the effects of all single
mutations on gene function. I have previously shown that such high-throughput
experiments can be combined with knowledge of underlying mutation rates to
create a parameter-free evolutionary model that describes the phylogeny of
influenza nucleoprotein far better than commonly used existing models. Here, I
extend this work by showing that published experimental data on TEM-1
beta-lactamase (Firnberg E, Labonte JW, Gray JJ, Ostermeier M. 2014. A
comprehensive, high-resolution map of a gene’s fitness landscape.
Mol Biol Evol. 31:1581–1592) can be combined with a
few mutation rate parameters to create an evolutionary model that describes
beta-lactamase phylogenies much better than most common existing models. This
experimentally informed evolutionary model is superior even for homologs that
are substantially diverged (about 35% divergence at the protein level)
from the TEM-1 parent that was the subject of the experimental study. These
results suggest that experimental measurements can inform phylogenetic
evolutionary models that are applicable to homologs that span a substantial
range of sequence divergence.
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Affiliation(s)
- Jesse D Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA
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27
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Solis AD. Deriving high-resolution protein backbone structure propensities from all crystal data using the information maximization device. PLoS One 2014; 9:e94334. [PMID: 24896099 PMCID: PMC4045576 DOI: 10.1371/journal.pone.0094334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 03/12/2014] [Indexed: 11/28/2022] Open
Abstract
The most informative probability distribution functions (PDFs) describing the Ramachandran phi-psi dihedral angle pair, a fundamental descriptor of backbone conformation of protein molecules, are derived from high-resolution X-ray crystal structures using an information-theoretic approach. The Information Maximization Device (IMD) is established, based on fundamental information-theoretic concepts, and then applied specifically to derive highly resolved phi-psi maps for all 20 single amino acid and all 8000 triplet sequences at an optimal resolution determined by the volume of current data. The paper shows that utilizing the latent information contained in all viable high-resolution crystal structures found in the Protein Data Bank (PDB), totaling more than 77,000 chains, permits the derivation of a large number of optimized sequence-dependent PDFs. This work demonstrates the effectiveness of the IMD and the superiority of the resulting PDFs by extensive fold recognition experiments and rigorous comparisons with previously published triplet PDFs. Because it automatically optimizes PDFs, IMD results in improved performance of knowledge-based potentials, which rely on such PDFs. Furthermore, it provides an easy computational recipe for empirically deriving other kinds of sequence-dependent structural PDFs with greater detail and precision. The high-resolution phi-psi maps derived in this work are available for download.
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Affiliation(s)
- Armando D. Solis
- Biological Sciences Department, New York City College of Technology, The City University of New York, Brooklyn, New York, United States of America
- * E-mail:
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28
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Abstract
All modern approaches to molecular phylogenetics require a quantitative model for how genes evolve. Unfortunately, existing evolutionary models do not realistically represent the site-heterogeneous selection that governs actual sequence change. Attempts to remedy this problem have involved augmenting these models with a burgeoning number of free parameters. Here, I demonstrate an alternative: Experimental determination of a parameter-free evolutionary model via mutagenesis, functional selection, and deep sequencing. Using this strategy, I create an evolutionary model for influenza nucleoprotein that describes the gene phylogeny far better than existing models with dozens or even hundreds of free parameters. Emerging high-throughput experimental strategies such as the one employed here provide fundamentally new information that has the potential to transform the sensitivity of phylogenetic and genetic analyses.
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Affiliation(s)
- Jesse D Bloom
- Division of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA
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29
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Palopoli N, Lanzarotti E, Parisi G. BeEP Server: Using evolutionary information for quality assessment of protein structure models. Nucleic Acids Res 2013; 41:W398-405. [PMID: 23729471 PMCID: PMC3692104 DOI: 10.1093/nar/gkt453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The BeEP Server (http://www.embnet.qb.fcen.uba.ar/embnet/beep.php) is an online resource aimed to help in the endgame of protein structure prediction. It is able to rank submitted structural models of a protein through an explicit use of evolutionary information, a criterion differing from structural or energetic considerations commonly used in other assessment programs. The idea behind BeEP (Best Evolutionary Pattern) is to benefit from the substitution pattern derived from structural constraints present in a set of homologous proteins adopting a given protein conformation. The BeEP method uses a model of protein evolution that takes into account the structure of a protein to build site-specific substitution matrices. The suitability of these substitution matrices is assessed through maximum likelihood calculations from which position-specific and global scores can be derived. These scores estimate how well the structural constraints derived from each structural model are represented in a sequence alignment of homologous proteins. Our assessment on a subset of proteins from the Critical Assessment of techniques for protein Structure Prediction (CASP) experiment has shown that BeEP is capable of discriminating the models and selecting one or more native-like structures. Moreover, BeEP is not explicitly parameterized to find structural similarities between models and given targets, potentially helping to explore the conformational ensemble of the native state.
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Affiliation(s)
- Nicolas Palopoli
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes, B1876BXD, Bernal, Buenos Aires, Argentina, Centre for Biological Sciences, University of Southampton, SO17 1BJ, Southampton, UK and Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Esteban Lanzarotti
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes, B1876BXD, Bernal, Buenos Aires, Argentina, Centre for Biological Sciences, University of Southampton, SO17 1BJ, Southampton, UK and Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes, B1876BXD, Bernal, Buenos Aires, Argentina, Centre for Biological Sciences, University of Southampton, SO17 1BJ, Southampton, UK and Departamento de Quimica Biologica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
- *To whom correspondence should be addressed. Tel: +54 011 43657100 (ext. 4135); Fax: +54 011 437657101;
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30
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Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning APJ, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci 2012; 21:769-85. [PMID: 22528593 PMCID: PMC3403413 DOI: 10.1002/pro.2071] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 12/20/2022]
Abstract
Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction.
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Affiliation(s)
- David A Liberles
- Department of Molecular Biology, University of WyomingLaramie, Wyoming 82071
| | - Sarah A Teichmann
- MRC Laboratory of Molecular BiologyHills Road, Cambridge CB2 0QH, United Kingdom
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of PittsburghPittsburgh, Pennsylvania 15213
| | - Ugo Bastolla
- Bioinformatics Unit. Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autonoma de Madrid28049 Cantoblanco Madrid, Spain
| | - Jesse Bloom
- Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattle, Washington 98109
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, University of MuensterGermany
| | - Lucy J Colwell
- MRC Laboratory of Molecular BiologyHills Road, Cambridge CB2 0QH, United Kingdom
| | - A P Jason de Koning
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of ColoradoAurora, Colorado
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel HillNorth Carolina 27599
| | - Julian Echave
- Escuela de Ciencia y Tecnología, Universidad Nacional de San MartínMartín de Irigoyen 3100, 1650 San Martín, Buenos Aires, Argentina
| | - Arne Elofsson
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm Bioinformatics Center, Science for Life Laboratory, Swedish E-science Research Center, Stockholm University106 91 Stockholm, Sweden
| | - Dietlind L Gerloff
- Biomolecular Engineering Department, University of CaliforniaSanta Cruz, California 95064
| | - Richard A Goldstein
- Division of Mathematical Biology, National Institute for Medical Research (MRC)Mill Hill, London NW7 1AA, United Kingdom
| | - Johan A Grahnen
- Department of Molecular Biology, University of WyomingLaramie, Wyoming 82071
| | - Mark T Holder
- Department of Ecology and Evolutionary Biology, University of KansasLawrence, Kansas 66045
| | - Clemens Lakner
- Bioinformatics Research Center, North Carolina State UniversityRaleigh, North Carolina 27695
| | - Nicholas Lartillot
- Département de Biochimie, Faculté de Médecine, Université de MontréalMontréal, QC H3T1J4, Canada
| | - Simon C Lovell
- Faculty of Life Sciences, University of ManchesterManchester M13 9PT, United Kingdom
| | - Gavin Naylor
- Department of Biology, College of CharlestonCharleston, South Carolina 29424
| | - Tina Perica
- MRC Laboratory of Molecular BiologyHills Road, Cambridge CB2 0QH, United Kingdom
| | - David D Pollock
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of ColoradoAurora, Colorado
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel Aviv, Israel
| | - Lynne Regan
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven 06511
| | - Andrew Roger
- Department of Biochemistry and Molecular Biology, Dalhousie UniversityHalifax, NS, Canada
| | - Nimrod Rubinstein
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv UniversityTel Aviv, Israel
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridge, Massachusetts 02138
| | - Kimmen Sjölander
- Department of Bioengineering, University of CaliforniaBerkeley, Berkeley, California 94720
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School77 Avenue Louis Pasteur, Boston, Massachusetts 02115
| | - Ashley I Teufel
- Department of Molecular Biology, University of WyomingLaramie, Wyoming 82071
| | - Jeffrey L Thorne
- Bioinformatics Research Center, North Carolina State UniversityRaleigh, North Carolina 27695
| | - Joseph W Thornton
- Howard Hughes Medical Institute and Institute for Ecology and Evolution, University of OregonEugene, Oregon 97403
- Department of Human Genetics, University of ChicagoChicago, Illinois 60637
- Department of Ecology and Evolution, University of ChicagoChicago, Illinois 60637
| | - Daniel M Weinreich
- Department of Ecology and Evolutionary Biology, and Center for Computational Molecular Biology, Brown UniversityProvidence, Rhode Island 02912
| | - Simon Whelan
- Faculty of Life Sciences, University of ManchesterManchester M13 9PT, United Kingdom
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31
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Juritz E, Palopoli N, Fornasari MS, Fernandez-Alberti S, Parisi G. Protein Conformational Diversity Modulates Sequence Divergence. Mol Biol Evol 2012; 30:79-87. [DOI: 10.1093/molbev/mss080] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Estimating the distribution of selection coefficients from phylogenetic data using sitewise mutation-selection models. Genetics 2011; 190:1101-15. [PMID: 22209901 PMCID: PMC3296245 DOI: 10.1534/genetics.111.136432] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Estimation of the distribution of selection coefficients of mutations is a long-standing issue in molecular evolution. In addition to population-based methods, the distribution can be estimated from DNA sequence data by phylogenetic-based models. Previous models have generally found unimodal distributions where the probability mass is concentrated between mildly deleterious and nearly neutral mutations. Here we use a sitewise mutation–selection phylogenetic model to estimate the distribution of selection coefficients among novel and fixed mutations (substitutions) in a data set of 244 mammalian mitochondrial genomes and a set of 401 PB2 proteins from influenza. We find a bimodal distribution of selection coefficients for novel mutations in both the mitochondrial data set and for the influenza protein evolving in its natural reservoir, birds. Most of the mutations are strongly deleterious with the rest of the probability mass concentrated around mildly deleterious to neutral mutations. The distribution of the coefficients among substitutions is unimodal and symmetrical around nearly neutral substitutions for both data sets at adaptive equilibrium. About 0.5% of the nonsynonymous mutations and 14% of the nonsynonymous substitutions in the mitochondrial proteins are advantageous, with 0.5% and 24% observed for the influenza protein. Following a host shift of influenza from birds to humans, however, we find among novel mutations in PB2 a trimodal distribution with a small mode of advantageous mutations.
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Grahnen JA, Nandakumar P, Kubelka J, Liberles DA. Biophysical and structural considerations for protein sequence evolution. BMC Evol Biol 2011; 11:361. [PMID: 22171550 PMCID: PMC3292521 DOI: 10.1186/1471-2148-11-361] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 12/16/2011] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. RESULTS Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS < 1 and gamma-distributed rates across sites. CONCLUSIONS Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model.
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Affiliation(s)
- Johan A Grahnen
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Priyanka Nandakumar
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jan Kubelka
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, USA
| | - David A Liberles
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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The evolution of protein structures and structural ensembles under functional constraint. Genes (Basel) 2011; 2:748-62. [PMID: 24710290 PMCID: PMC3927589 DOI: 10.3390/genes2040748] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 10/15/2011] [Accepted: 10/19/2011] [Indexed: 02/06/2023] Open
Abstract
Protein sequence, structure, and function are inherently linked through evolution and population genetics. Our knowledge of protein structure comes from solved structures in the Protein Data Bank (PDB), our knowledge of sequence through sequences found in the NCBI sequence databases (http://www.ncbi.nlm.nih.gov/), and our knowledge of function through a limited set of in-vitro biochemical studies. How these intersect through evolution is described in the first part of the review. In the second part, our understanding of a series of questions is addressed. This includes how sequences evolve within structures, how evolutionary processes enable structural transitions, how the folding process can change through evolution and what the fitness impacts of this might be. Moving beyond static structures, the evolution of protein kinetics (including normal modes) is discussed, as is the evolution of conformational ensembles and structurally disordered proteins. This ties back to a question of the role of neostructuralization and how it relates to selection on sequences for functions. The relationship between metastability, the fitness landscape, sequence divergence, and organismal effective population size is explored. Lastly, a brief discussion of modeling the evolution of sequences of ordered and disordered proteins is entertained.
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Grahnen JA, Kubelka J, Liberles DA. Fast Side Chain Replacement in Proteins Using a Coarse-Grained Approach for Evaluating the Effects of Mutation During Evolution. J Mol Evol 2011; 73:23-33. [DOI: 10.1007/s00239-011-9454-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 07/14/2011] [Indexed: 11/28/2022]
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Sammet SG, Bastolla U, Porto M. Comparison of translation loads for standard and alternative genetic codes. BMC Evol Biol 2010; 10:178. [PMID: 20546599 PMCID: PMC2909233 DOI: 10.1186/1471-2148-10-178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 06/14/2010] [Indexed: 11/25/2022] Open
Abstract
Background The (almost) universality of the genetic code is one of the most intriguing properties of cellular life. Nevertheless, several variants of the standard genetic code have been observed, which differ in one or several of 64 codon assignments and occur mainly in mitochondrial genomes and in nuclear genomes of some bacterial and eukaryotic parasites. These variants are usually considered to be the result of non-adaptive evolution. It has been shown that the standard genetic code is preferential to randomly assembled codes for its ability to reduce the effects of errors in protein translation. Results Using a genotype-to-phenotype mapping based on a quantitative model of protein folding, we compare the standard genetic code to seven of its naturally occurring variants with respect to the fitness loss associated to mistranslation and mutation. These fitness losses are computed through computer simulations of protein evolution with mutations that are either neutral or lethal, and different mutation biases, which influence the balance between unfolding and misfolding stability. We show that the alternative codes may produce significantly different mutation and translation loads, particularly for genomes evolving with a rather large mutation bias. Most of the alternative genetic codes are found to be disadvantageous to the standard code, in agreement with the view that the change of genetic code is a mutationally driven event. Nevertheless, one of the studied alternative genetic codes is predicted to be preferable to the standard code for a broad range of mutation biases. Conclusions Our results show that, with one exception, the standard genetic code is generally better able to reduce the translation load than the naturally occurring variants studied here. Besides this exception, some of the other alternative genetic codes are predicted to be better adapted for extreme mutation biases. Hence, the fixation of alternative genetic codes might be a neutral or nearly-neutral event in the majority of the cases, but adaptation cannot be excluded for some of the studied cases.
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Affiliation(s)
- Stefanie Gabriele Sammet
- Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr, 8, 64289 Darmstadt, Germany
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