Structure and Age Jointly Influence Rates of Protein Evolution
Publication Date
May 31, 2012
Journal
PLOS Computational Biology
Authors
Macarena Toll Riera, David Bostick, M. Mar Albà & Joshua B. Plotkin
Volume
8
Issue
5
Pages
e1002542
DOI
http://doi.org/10.1371/journal.pcbi.1002542
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1002542
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22693443
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3364943
Europe PMC
http://europepmc.org/abstract/MED/22693443
Web of Science
000305964600041
Scopus
84863663815
Mendeley
http://www.mendeley.com/research/structure-age-jointly-influence-rates-protein-evolution
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/326141", "https://ndownloader.figshare.com/files/326181", "https://ndownloader.figshare.com/files/326223", "https://ndownloader.figshare.com/files/326275", "https://ndownloader.figshare.com/files/326317", "https://ndownloader.figshare.com/files/326363"], "description"=>"<div><p>What factors determine a protein's rate of evolution are actively debated. Especially unclear is the relative role of intrinsic factors of present-day proteins versus historical factors such as protein age. Here we study the interplay of structural properties and evolutionary age, as determinants of protein evolutionary rate. We use a large set of one-to-one orthologs between human and mouse proteins, with mapped PDB structures. We report that previously observed structural correlations also hold within each age group – including relationships between solvent accessibility, designabililty, and evolutionary rates. However, age also plays a crucial role: age modulates the relationship between solvent accessibility and rate. Additionally, younger proteins, despite being less designable, tend to evolve faster than older proteins. We show that previously reported relationships between age and rate cannot be explained by structural biases among age groups. Finally, we introduce a knowledge-based potential function to study the stability of proteins through large-scale computation. We find that older proteins are more stable for their native structure, and more robust to mutations, than younger ones. Our results underscore that several determinants, both intrinsic and historical, can interact to determine rates of protein evolution.</p> </div>", "links"=>[], "tags"=>["jointly", "rates"], "article_id"=>124366, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Macarena Toll-Riera", "David Bostick", "M. Mar Albà", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002542.s001", "https://dx.doi.org/10.1371/journal.pcbi.1002542.s002", "https://dx.doi.org/10.1371/journal.pcbi.1002542.s003", "https://dx.doi.org/10.1371/journal.pcbi.1002542.s004", "https://dx.doi.org/10.1371/journal.pcbi.1002542.s005", "https://dx.doi.org/10.1371/journal.pcbi.1002542.s006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Structure_and_Age_Jointly_Influence_Rates_of_Protein_Evolution/124366", "title"=>"Structure and Age Jointly Influence Rates of Protein Evolution", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-05-31 01:12:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/628527"], "description"=>"<p>Eukarya: Pearson correlation: 0.957, p-value = 4.477e<sup>−11</sup>; Metazoans: Pearson correlation: 0.950, p-value = 1.445e<sup>−10</sup>; Vertebrates: Pearson correlation: 0.941, p-value = 7.005e<sup>−10</sup>. Errors bars indicate the standard error for the <i>d</i><sub>N</sub> calculation.</p>", "links"=>[], "tags"=>["solvent", "accessibility", "metazoans", "vertebrates"], "article_id"=>299018, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Macarena Toll-Riera", "David Bostick", "M. Mar Albà", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002542.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Linear_relationship_between_solvent_accessibility_and_d_N_in_Eukarya_Metazoans_and_Vertebrates_age_groups_/299018", "title"=>"Linear relationship between solvent accessibility and <i>d</i><sub>N</sub> in Eukarya, Metazoans and Vertebrates age groups.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 02:30:18"}
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  • {"files"=>["https://ndownloader.figshare.com/files/628636"], "description"=>"<p>Wilcoxon tests were performed to assess the significance of the difference: Eukarya vs Metazoans: p-value<1.684e<sup>−14</sup> , Eukarya vs Vertebrate: p-value<2.2e<sup>−16</sup> , Metazoans vs Vertebrates: p-value = 1.119e<sup>−8</sup>). Low rank suggests that the native structure is relatively robust to mutations.</p>", "links"=>[], "tags"=>["wildtype", "1000", "mutated", "sequences", "metazoans"], "article_id"=>299128, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Macarena Toll-Riera", "David Bostick", "M. Mar Albà", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002542.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rank_of_the_stability_score_of_wildtype_protein_sequence_among_1000_mutated_sequences_in_3_age_groups_Eukarya_Metazoans_and_Vertebrates_/299128", "title"=>"Rank of the stability score of wildtype protein sequence among 1000 mutated sequences in 3 age groups: Eukarya, Metazoans and Vertebrates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 02:32:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/628697"], "description"=>"<p>An inverse correlation between the age of the protein and evolutionary rate occurs within each structural category. Wilcoxon tests were performed (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002542#pcbi-1002542-t001\" target=\"_blank\">Table 1</a>).</p>", "links"=>[], "tags"=>["rates", "accessibility"], "article_id"=>299191, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Macarena Toll-Riera", "David Bostick", "M. Mar Albà", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002542.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolutionary_rates_by_age_and_secondary_structure_solvent_accessibility_categories_/299191", "title"=>"Evolutionary rates by age and secondary structure/solvent accessibility categories.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-31 02:33:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/628767"], "description"=>"<p>Comparisons between the 3 age classes in each secondary structure and solvent accessibility types.</p>", "links"=>[], "tags"=>["classes", "solvent", "accessibility"], "article_id"=>299259, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Macarena Toll-Riera", "David Bostick", "M. Mar Albà", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002542.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparisons_between_the_3_age_classes_in_each_secondary_structure_and_solvent_accessibility_types_/299259", "title"=>"Comparisons between the 3 age classes in each secondary structure and solvent accessibility types.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-31 02:34:19"}

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Relative Metric

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