A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility

BMC Evolutionary Biology

Volumn 14, Issue 1, 2014, Pages

  Huang, Tsun Tsao ^a   Del Valle Marcos, María Laura ^b   Hwang, Jenn Kang ^a   Echave, Julian ^b  

^a NATIONAL CHIAO TUNG UNIVERSITY   (Taiwan)

^b UNIVERSIDAD NACIONAL DE SAN MARTÍN   (Argentina)

Author keywords

Elastic network model; Flexibility; Local packing density; Mean local mutational stress; Mean square fluctuation; Protein evolution; Site specific substitution rate; Stress

Indexed keywords

COMPARATIVE STUDY; DATA SET; EMPIRICAL ANALYSIS; ENZYME ACTIVITY; NATURAL SELECTION; PROTEIN;

PROTEIN;

ARTICLE; BIOLOGICAL MODEL; EVOLUTION; GENETICS; MECHANICAL STRESS; MOLECULAR EVOLUTION; PLIABILITY;

BIOLOGICAL EVOLUTION; EVOLUTION, MOLECULAR; MODELS, GENETIC; PLIABILITY; PROTEINS; STRESS, MECHANICAL;

EID: 84899480289     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-14-78     Document Type: Article

References (33)

1. An integrated view of protein evolution. Pal C, Papp B, Lercher MJ, Nat Rev Genet 2006 7 5 337 348 10.1038/nrg1838 16619049
2. Protein evolution constraints and model-based techniques to study them. Thorne JL, Curr Opin Struct Biol 2007 17 3 337 341 10.1016/j.sbi.2007.05.006 17572082
3. Structural and functional constraints in the evolution of protein families. Worth CL, Gong S, Blundell TL, Nat Rev Mol Cell Biol 2009 10 10 709 720 19756040
4. Signatures of protein biophysics in coding sequence evolution. Wilke CO, Drummond DA, Curr Opin Struct Biol 2010 20 3 385 389 10.1016/j.sbi.2010.03.004 20395125
5. Biophysical and structural considerations for protein sequence evolution. Grahnen JA, Nandakumar P, Kubelka J, Liberles DA, BMC Evol Biol 2011 11 1 361 10.1186/1471-2148-11-361 22171550
6. The interface of protein structure, protein biophysics, and molecular evolution. Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, 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, Sjolander K, Sunyaev S, Teufel AI, Thorne JL, et al. Protein Sci 2012 21 6 769 785 10.1002/pro.2071 22528593
7. Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Bustamante CD, Townsend JP, Hartl DL, Mol Biol Evol 2000 17 2 301 308 10.1093/oxfordjournals.molbev.a026310 10677853
8. The pattern of amino acid replacements in alpha/beta-barrels. Dean AM, Neuhauser C, Grenier E, Golding GB, Mol Biol Evol 2002 19 11 1846 1864 10.1093/oxfordjournals.molbev.a004009 12411594
9. Structural determinants of protein evolution are context-sensitive at the residue level. Franzosa EA, Xia Y, Mol Biol Evol 2009 26 10 2387 2395 10.1093/molbev/msp146 19597162
10. The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Ramsey DC, Scherrer MP, Zhou T, Wilke CO, Genetics 2011 188 2 479 488 10.1534/genetics.111.128025 21467571
11. Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure. Yeh S-W, Liu J-W, Yu S-H, Shih C-H, Hwang J-K, Echave J, Mol Biol Evol 2014 31 1 135 139 10.1093/molbev/mst178 24109601
12. Flexibility and packing in proteins. Halle B, Proc Natl Acad Sci U S A 2002 99 3 1274 1279 10.1073/pnas.032522499 11818549
13. Sequence evolution correlates with structural dynamics. Liu Y, Bahar I, Mol Biol Evol 2012 29 9 2253 2263 10.1093/molbev/mss097 22427707
14. Protein sequence entropy is closely related to packing density and hydrophobicity. Liao H, Yeh W, Chiang D, Jernigan RL, Lustig B, Protein Eng Des Sel 2005 18 2 59 64 10.1093/protein/gzi009 15788422
15. Evolutionary information hidden in a single protein structure. Shih C-H, Chang C-M, Lin Y-S, Lo W-C, Hwang J-K, Proteins 2012 80 6 1647 1657 10.1002/prot.24058 22454236
16. Structural dynamics flexibility informs function and evolution at a proteome scale. Nevin Gerek Z, Kumar S, Banu Ozkan S, Evol Appl 2013 6 3 423 433 10.1111/eva.12052 23745135
17. Global dynamics of proteins: bridging between structure and function. Bahar I, Lezon TR, Yang LW, Eyal E, Annu Rev Biophys 2010 39 23 42 10.1146/annurev.biophys.093008.131258 20192781
18. Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments. Micheletti C, Phys Life Rev 2013 10 1 1 26 10.1016/j.plrev.2012.10.009 23199577
19. Elastic network models: theoretical and empirical foundations. Sanejouand YH, Methods Mol Biol 2013 924 601 616 10.1007/978-1-62703-017-5-23 23034765
20. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I, Biophys J 2001 80 1 505 515 10.1016/S0006-3495(01)76033-X 11159421
21. Evolutionary divergence of protein structure: the linearly forced elastic network model. Echave J, Chem Phys Lett 2008 457 4-6 413 416
22. A perturbative view of protein structural variation. Echave J, Fernandez FM, Proteins 2010 78 1 173 180 10.1002/prot.22553 19731380
23. Why are the low-energy protein normal modes evolutionarily conserved? Echave J, Pure Appl Chem 2012 84 9 1931 1937
24. Evaluation of protein elastic network models based on an analysis of collective motions. Fuglebakk E, Reuter N, Hinsen K, J Chem Theory Comput 2013 9 12 5618 5628 10.1021/ct400399x
25. Protein elastic network models and the ranges of cooperativity. Yang L, Song G, Jernigan RL, Proc Natl Acad Sci U S A 2009 106 30 12347 12352 10.1073/pnas.0902159106 19617554
26. Deriving protein dynamical properties from weighted protein contact number. Lin C-P, Huang S-W, Lai Y-L, Yen S-C, Shih C-H, Lu C-H, Huang C-C, Hwang J-K, Proteins 2008 72 3 929 935 10.1002/prot.21983 18300253
27. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N, Bioinformatics 2002 18 Suppl 1 71 S77 10.1093/bioinformatics/18.suppl-1.S71 12169533
28. Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mayrose I, Graur D, Ben-Tal N, Pupko T, Mol Biol Evol 2004 21 9 1781 1791 10.1093/molbev/msh194 15201400
29. AIC model selection using Akaike weights. Wagenmakers EJ, Farrell S, Psychon Bull Rev 2004 11 1 192 196 10.3758/BF03206482 15117008
30. An evaluation of R2 as an inadequate measure for nonlinear models in pharmacological and biochemical research: a Monte Carlo approach. Spiess AN, Neumeyer N, BMC Pharmacol 2010 10 6 20529254
31. Evolutionary conservation of protein vibrational dynamics. Maguid S, Fernandez-Alberti S, Echave J, Gene 2008 422 1-2 7 13 18577430
32. Packing regularities in biological structures relate to their dynamics. Jernigan RL, Kloczkowski A, Methods Mol Biol 2007 350 251 276 16957327
33. Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative. Fernandes AD, Atchley WR, Bioinformatics 2008 24 19 2177 2183 10.1093/bioinformatics/btn395 18662926