Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites

Physical Biology

Volumn 12, Issue 2, 2015, Pages

  Echave, Julian ^a   Jackson, Eleisha L ^b   Wilke, Claus O ^b  

^a UNIVERSIDAD NACIONAL DE SAN MARTÍN   (Argentina)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

biophysical model; protein evolution; rate variation among sites; stability; stress; thermodynamics

Indexed keywords

AMINO ACID SEQUENCE; BIOLOGICAL MODEL; MOLECULAR EVOLUTION; MUTATION; THERMODYNAMICS;

AMINO ACID SEQUENCE; EVOLUTION, MOLECULAR; MODELS, GENETIC; MUTATION; THERMODYNAMICS;

EID: 84928811331     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/12/2/025002     Document Type: Article

References (51)

1. Arenas M, dos Santos H G, Posada D and Bastolla U 2013 Protein evolution along phylogenetic histories under structurally constrained substitution models Bioinformatics 29 3020-8
2. Ashenberg O, Gong L I and Bloom J D 2013 Mutational effects on stability are largely conserved during protein evolution Proc. Natl Acad. Sci. USA 110 21071-6
3. Bershtein S, Segal M, Bekerman R, Tokuriki N and Tawfik D S 2006 Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein Nature 444 929-32
4. Bloom J D and Glassman M J 2009 Inferring stabilizing mutations from protein phylogenies: Application to influenza hemagglutinin PLoS Comput. Biol. 5 e1000349
5. Bloom J D, Labthavikul S T, Otey C R and Arnold F H 2006 Protein stability promotes evolvability Proc. Natl Acad. Sci. USA 103 5869-74
6. Bloom J D, Raval A and Wilke C O 2007 Thermodynamics of neutral protein evolution Genetics 175 255-66
7. Bloom J D, Silberg J J, Wilke C O, Drummond D A, Adami C and Arnold F H 2005 Thermodynamic prediction of protein neutrality Proc. Natl Acad. Sci. USA 102 606-11
8. Bustamante C D, Townsend J P and Hartl D L 2000 Solvent accessibility and purifying selection within proteins of escherichia coli and salmonella enterica Mol. Biol. Evol. 17 301-8
9. Chen P and Shakhnovich E I 2009 Lethal mutagenesis in viruses and bacteria Genetics 183 639-50
10. Dean A M, Neuhauser C, Grenier E and Golding G B 2002 The pattern of amino acid replacements in alpha/beta-barrels Mol. Biol. Evol. 19 1846-64
11. Drummond D A and Wilke C O 2008 Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution Cell 134 341-335
12. Franzosa E A and Xia Y 2009 Structural determinants of protein evolution are context-sensitive at the residue level Mol. Biol. Evol. 26 2387-95
13. Goldstein R A 2011 The evolution and evolutionary consequences of marginal thermostability in proteins Proteins 79 1396-407
14. Gong L I, Suchard M A and Bloom J D 2013 Stability-mediated epistasis constrains the evolution of an influenza protein eLife 2 e00631
15. Grahnen J A, Nandakumar P, Kubelka J and Liberles D A 2011 Biophysical and structural considerations for protein sequence evolution BMC Evol. Biol. 11 361
16. Guerois R, Nielsen J E and Serrano L 2002 Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations J. Mol. Biol. 320 369-87
17. Huang T T, Marcos M L, Hwang J K and Echave J 2014 A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility BMC Evol. Biol. 14 78
18. Katoh K, Kuma K I, Toh H and Miyata T 2005 MAFFT version 5: improvement in accuracy of multiple sequence alignment Nucl. Acids Res. 33 511-8
19. Katoh K and Standley D M 2013 MAFFT multiple sequence alignment software version 7: improvements in performance and usability Mol. Biol. Evol. 30 772-80
20. Kellogg E H, Leaver-Fay A and Baker D 2011 Role of conformational sampling in computing mutation-induced changes in protein structure and stability Proteins: Struct., Funct. Bioinformatics 79 830-8
21. Lemos B, Bettencourt B R, Meiklejohn C D and Hartl D L 2005 Evolution of proteins and gene expression levels are coupled in drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions Mol. Biol. Evol. 22 1345-54
22. Liao B Y, Weng M P and Zhang J 2010 Impact of extracellularity on the evolutionary rate of mammalian proteins Genome Biol. Evol. 2 39-43
23. Liao H, Yeh W, Chiang D, Jernigan R L and Lustig B 2005 Protein sequence entropy is closely related to packing density and hydrophobicity Protein Eng. Des. Sel. 18 59-64
24. Liberles D A et al 2012 The interface of protein structure, protein biophysics, and molecular evolution Protein Sci. 21 769-85
25. Lin C P, Huang S W, Lai Y L, Yen S C, Shih C H, Lu C H, Huang C C and Hwang J K 2008 Deriving protein dynamical properties from weighted protein contact number Proteins 72 929-35
26. Mayrose I, Graur D, Ben-Tal N and Pupko T 2004 Comparison of site-specific rate-inference methods: Bayesian methods are superior Mol. Biol. Evol. 21 1781-91
27. Pal C, Papp B and Lercher M J 2006 An integrated view of protein evolution Nat. Rev. Genetics 7 337-48
28. Pang K, Cheng C, Xuan Z, Sheng H and Ma X 2010 Understanding protein evolutionary rate by integrating gene co-expression with protein interactions BMC Syst. Biol. 4 179
29. Potapov V, Cohen M and Schreiber G 2009 Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details Protein Eng. Des. Sel. 22 553-60
30. R Core Team 2014 R: A Language and Environment for Statistical Computing R Foundation for Statistical Computing Vienna, Austria (www.R-project.org)
31. Ramsey D C, Scherrer M P, Zhou T and Wilke C O 2011 The relationship between relative solvent accessibility and evolutionary rate in protein evolution Genetics 188 479-88
32. Raval A 2007 Molecular clock on a neutral network Phys. Rev. Lett. 99 138104
33. Schymkowitz J W, Rousseau F, Martins I C, Ferkinghoff-Borg J, Stricher F and Serrano L 2005 Prediction of water and metal binding sites and their affinities by using the Fold-X force field Proc. Natl Acad. Sci. USA 102 10147-52
34. Serohijos A W R, Rimas Z and Shakhnovich E I 2012 Protein biophysics explains why highly abundant proteins evolve slowly Cell Rep. 2 1-8
35. Serrano L, Day A G and Fersht A R 1993 Step-wise mutation of barnase to binase: A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability J. Mol. Biol. 233 305-12
36. Shahmoradi A, Sydykova D K, Spielman S J, Jackson E L, Dawson E T, Meyer A G and Wilke C O 2014 Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design J. Mol. Evol. 79 130-42
37. Stamatakis A 2014 RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies Bioinformatics 30 1312-3
38. Taverna D M and Goldstein R A 2002 Why are proteins marginally stable? Proteins 46 105-9
39. Thiltgen G and Goldstein R A 2012 Assessing predictors of changes in protein stability upon mutation using self-consistency PLoS One 7 e46084
40. Thorne J L 2007 Protein evolution constraints and model-based techniques to study them Curr. Opin. Struct. Biol. 17 337-41
41. Tokuriki N, Stricher F, Serrano L and Tawfik D S 2008 How protein stability and new functions trade off PLoS Comput. Biol. 4 e1000002
42. Tokuriki N and Tawfik D S 2009 Stability effects of mutations and protein evolvability Curr. Opin. Struct. Biol. 19 596-604
43. Wells J A 1990 Additivity of mutational effects in proteins Biochemistry 29 8509-17
44. Wilke C O and Drummond D A 2010 Signatures of protein biophysics in coding sequence evolution Curr. Opin. Struct. Biol. 20 385-9
45. Worth C L, Gong S and Blundell T L 2009 Structural and functional constraints in the evolution of protein families Nat. Rev. Mol. Cell. Biol. 10 709-20
46. Wylie C S and Shakhnovich E I 2011 A biophysical protein folding model accounts for most mutational fitness effects in viruses Proc. Natl Acad. Sci. USA 108 9916-21
47. Xia Y, Franzosa E A and Gerstein M B 2009 Integrated assessment of genomic correlates of protein evolutionary rate PLoS Comput. Biol. 5 e1000413
48. Yang L, Song G and Jernigan R L 2009 Protein elastic network models and the ranges of cooperativity Proc. Natl Acad. Sci. USA 106 12347-52
49. Yeh S W, Huang T T, Liu J W, Yu S H, Shih C H, Hwang J K and Echave J 2014b Local packing density is the main structural determinant of the rate of protein sequence evolution at site level Biomed. Res. Int. 2014 572409
50. Yeh S W, Liu J W, Yu S H, Shih C H, Hwang J K and Echave J 2014a Site-specific structural constraints on protein sequence evolutionary divergence: Local packing density versus solvent exposure Mol. Biol. Evol. 31 135-9
51. Zhang X J, Baase W A, Shoichet B K, Wilson K P and Matthews B W 1995 Enhancement of protein stability by the combination of point mutations in T4 lysozyme is additive Protein Eng. 8 1017-22