publication . Article . Other literature type . 2017

Measuring evolutionary rates of proteins in a structural context.

Dariya K. Sydykova; Benjamin R. Jack; Stephanie J. Spielman; Claus O. Wilke;
Open Access
  • Published: 16 Oct 2017 Journal: F1000Research, volume 6, page 1,845 (eissn: 2046-1402, Copyright policy)
  • Publisher: F1000 Research Ltd
Abstract
<ns4:p>We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations, one based on relative amino-acid rates and the other based on site-specific codon rates measured as <ns4:italic>dN/dS</ns4:italic>. In addition to describing the specific analysis protocols we recommend, we also provide a code repository containing scripts to facilitate these kinds of analyses.</ns4:p>
Subjects
free text keywords: Method Article, Articles, Bioinformatics, Protein Chemistry & Proteomics, Protein evolution, protein structure, evolutionary rate, relative solvent accessibility, weighted contact number, multiple sequence alignment, Solvent accessibility, Contact number, Computational biology, Neuroscience, Structural context, Protein secondary structure, Biology
Funded by
NIH| The biophysical basis of translational selection
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM088344-03
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NSF| BEACON: An NSF Center for the Study of Evolution in Action
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0939454
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
55 references, page 1 of 4

1 Kimura M Ohta T: On some principles governing molecular evolution.Proc Natl Acad Sci U S A.1974;71(7):2848–2852. 4527913 [OpenAIRE] [PubMed]

2 Perutz MF Kendrew JC Watson HC: Structure and function of haemoglobin: II. Some relations between polypeptide chain configuration and amino acid sequence.J Mol Biol.1965;13(3):669–678. 10.1016/S0022-2836(65)80134-6 [DOI]

3 Echave J Spielman SJ Wilke CO: Causes of evolutionary rate variation among protein sites.Nat Rev Genet.2016;17(2):109–121. 10.1038/nrg.2015.18 26781812 [OpenAIRE] [PubMed] [DOI]

4 Dean AM Neuhauser C Grenier E: The pattern of amino acid replacements in alpha/beta-barrels.Mol Biol Evol.2002;19(11):1846–1864. 10.1093/oxfordjournals.molbev.a004009 12411594 [OpenAIRE] [PubMed] [DOI]

5 Kimura M Ohta T: Mutation and evolution at the molecular level.Genetics.1973;73(Suppl 73):19–35. 4711555 [PubMed]

6 Huang YW Chang CM Lee CW: The conservation profile of a protein bears the imprint of the molecule that is evolutionarily coupled to the protein.Proteins.2015;83(8):1407–1413. 10.1002/prot.24809 25846748 [OpenAIRE] [PubMed] [DOI]

7 Mintseris J Weng Z: Structure, function, and evolution of transient and obligate protein-protein interactions.Proc Natl Acad Sci U S A.2005;102(31):10930–10935. 10.1073/pnas.0502667102 16043700 [OpenAIRE] [PubMed] [DOI]

8 Kim PM Lu LJ Xia Y: Relating three-dimensional structures to protein networks provides evolutionary insights.Science.2006;314(5807):1938–1941. 10.1126/science.1136174 17185604 [OpenAIRE] [PubMed] [DOI]

9 Franzosa EA Xia Y: Structural determinants of protein evolution are context-sensitive at the residue level.Mol Biol Evol.2009;26(10):2387–2395. 10.1093/molbev/msp146 19597162 [OpenAIRE] [PubMed] [DOI]

10 Jack BR Meyer AG Echave J: Functional sites induce long-range evolutionary constraints in enzymes.PLoS Biol.2016;14(5):e1002452. 10.1371/journal.pbio.1002452 27138088 [OpenAIRE] [PubMed] [DOI]

11 Mirny LA Shakhnovich EI: Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function.J Mol Biol.1999;291(1):177–196. 10.1006/jmbi.1999.2911 10438614 [OpenAIRE] [PubMed] [DOI]

12 Zhou T Drummo nd DA Wilke CO: Contact density affects protein evolutionary rate from bacteria to animals.J Mol Evol.2008;66(4):395–404. 10.1007/s00239-008-9094-4 18379715 [OpenAIRE] [PubMed] [DOI]

13 Ramsey DC Scherrer MP Zhou T: The relationship between relative solvent accessibility and evolutionary rate in protein evolution.Genetics.2011;188(2):479–488. 10.1534/genetics.111.128025 21467571 [OpenAIRE] [PubMed] [DOI]

14 Scherrer MP Meyer AG Wilke CO: Modeling coding-sequence evolution within the context of residue solvent accessibility.BMC Evol Biol.2012;12:179. 10.1186/1471-2148-12-179 22967129 [OpenAIRE] [PubMed] [DOI]

15 Shahmoradi A Sydykova DK Spielman SJ: Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design.J Mol Evol.2014;79(3–4):130–142. 10.1007/s00239-014-9644-x 25217382 [OpenAIRE] [PubMed] [DOI]

55 references, page 1 of 4
Abstract
<ns4:p>We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations, one based on relative amino-acid rates and the other based on site-specific codon rates measured as <ns4:italic>dN/dS</ns4:italic>. In addition to describing the specific analysis protocols we recommend, we also provide a code repository containing scripts to facilitate these kinds of analyses.</ns4:p>
Subjects
free text keywords: Method Article, Articles, Bioinformatics, Protein Chemistry & Proteomics, Protein evolution, protein structure, evolutionary rate, relative solvent accessibility, weighted contact number, multiple sequence alignment, Solvent accessibility, Contact number, Computational biology, Neuroscience, Structural context, Protein secondary structure, Biology
Funded by
NIH| The biophysical basis of translational selection
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM088344-03
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NSF| BEACON: An NSF Center for the Study of Evolution in Action
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0939454
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
55 references, page 1 of 4

1 Kimura M Ohta T: On some principles governing molecular evolution.Proc Natl Acad Sci U S A.1974;71(7):2848–2852. 4527913 [OpenAIRE] [PubMed]

2 Perutz MF Kendrew JC Watson HC: Structure and function of haemoglobin: II. Some relations between polypeptide chain configuration and amino acid sequence.J Mol Biol.1965;13(3):669–678. 10.1016/S0022-2836(65)80134-6 [DOI]

3 Echave J Spielman SJ Wilke CO: Causes of evolutionary rate variation among protein sites.Nat Rev Genet.2016;17(2):109–121. 10.1038/nrg.2015.18 26781812 [OpenAIRE] [PubMed] [DOI]

4 Dean AM Neuhauser C Grenier E: The pattern of amino acid replacements in alpha/beta-barrels.Mol Biol Evol.2002;19(11):1846–1864. 10.1093/oxfordjournals.molbev.a004009 12411594 [OpenAIRE] [PubMed] [DOI]

5 Kimura M Ohta T: Mutation and evolution at the molecular level.Genetics.1973;73(Suppl 73):19–35. 4711555 [PubMed]

6 Huang YW Chang CM Lee CW: The conservation profile of a protein bears the imprint of the molecule that is evolutionarily coupled to the protein.Proteins.2015;83(8):1407–1413. 10.1002/prot.24809 25846748 [OpenAIRE] [PubMed] [DOI]

7 Mintseris J Weng Z: Structure, function, and evolution of transient and obligate protein-protein interactions.Proc Natl Acad Sci U S A.2005;102(31):10930–10935. 10.1073/pnas.0502667102 16043700 [OpenAIRE] [PubMed] [DOI]

8 Kim PM Lu LJ Xia Y: Relating three-dimensional structures to protein networks provides evolutionary insights.Science.2006;314(5807):1938–1941. 10.1126/science.1136174 17185604 [OpenAIRE] [PubMed] [DOI]

9 Franzosa EA Xia Y: Structural determinants of protein evolution are context-sensitive at the residue level.Mol Biol Evol.2009;26(10):2387–2395. 10.1093/molbev/msp146 19597162 [OpenAIRE] [PubMed] [DOI]

10 Jack BR Meyer AG Echave J: Functional sites induce long-range evolutionary constraints in enzymes.PLoS Biol.2016;14(5):e1002452. 10.1371/journal.pbio.1002452 27138088 [OpenAIRE] [PubMed] [DOI]

11 Mirny LA Shakhnovich EI: Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function.J Mol Biol.1999;291(1):177–196. 10.1006/jmbi.1999.2911 10438614 [OpenAIRE] [PubMed] [DOI]

12 Zhou T Drummo nd DA Wilke CO: Contact density affects protein evolutionary rate from bacteria to animals.J Mol Evol.2008;66(4):395–404. 10.1007/s00239-008-9094-4 18379715 [OpenAIRE] [PubMed] [DOI]

13 Ramsey DC Scherrer MP Zhou T: The relationship between relative solvent accessibility and evolutionary rate in protein evolution.Genetics.2011;188(2):479–488. 10.1534/genetics.111.128025 21467571 [OpenAIRE] [PubMed] [DOI]

14 Scherrer MP Meyer AG Wilke CO: Modeling coding-sequence evolution within the context of residue solvent accessibility.BMC Evol Biol.2012;12:179. 10.1186/1471-2148-12-179 22967129 [OpenAIRE] [PubMed] [DOI]

15 Shahmoradi A Sydykova DK Spielman SJ: Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design.J Mol Evol.2014;79(3–4):130–142. 10.1007/s00239-014-9644-x 25217382 [OpenAIRE] [PubMed] [DOI]

55 references, page 1 of 4
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publication . Article . Other literature type . 2017

Measuring evolutionary rates of proteins in a structural context.

Dariya K. Sydykova; Benjamin R. Jack; Stephanie J. Spielman; Claus O. Wilke;