Modeling coding-sequence evolution within the context of residue solvent accessibility

BMC Evolutionary Biology

Volumn 12, Issue 1, 2012, Pages

  Scherrer, Michael P ^a   Meyer, Austin G ^a   Wilke, Claus O ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; DATA SET; DIVERGENCE; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; MOLECULAR ANALYSIS; NUMERICAL MODEL; PROTEIN;

SOLVENT;

ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETICS; MOLECULAR EVOLUTION; OPEN READING FRAME; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MODELS, GENETIC; OPEN READING FRAMES; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SOLVENTS;

EID: 84866021249     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-12-179     Document Type: Article

References (61)

1. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Overington J, Donnelly D, Johnson MS, Šali A, Blundell TL, Prot Sci 1992 1 216 226 (Pubitemid 23007288)
2. Context-dependent optimal substitution matrices. Koshi JM, Goldstein RA, Protein Eng 1995 8 641 645 8577693
3. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. Mirny LA, Shakhnovich EI, J Mol Biol 1999 291 177 196 10.1006/jmbi.1999.2911 10438614 (Pubitemid 29391413)
4. Understanding hierarchical protein evolution from first principles. Dokholyan NV, Shakhnovich EI, J Mol Biol 2001 312 289 307 10.1006/jmbi.2001.4949 11545603 (Pubitemid 32835693)
5. Combining protein evolution and secondary structure. Thorne JL, Goldman N, Jones DT, Mol Biol Evol 1996 13 666 673 10.1093/oxfordjournals.molbev.a025627 8676741 (Pubitemid 26131888)
6. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Goldman N, Thorne JL, Jones DT, Genetics 1998 149 445 458 9584116
7. Structural determinants of the rate of protein evolution in yeast. Bloom JD, Drummond DA, Arnold FH, Wilke CO, Mol Biol and Evol 2006 23 1751 1761 10.1093/molbev/msl040 (Pubitemid 44309769)
8. Contact density affects protein evolutionary rate from bacteria to animals. Zhou T, Drummond DA, Wilke CO, Mol Biol and Evol 2008 66 395 404 (Pubitemid 351643081)
9. Structural determinants of protein evolution are context-sensitive at the residue level. Franzosa EA, Xia Y, Mol Biol and Evol 2009 26 10 2387 2395 10.1093/molbev/msp146
10. Protein evolution with dependence among codons due to tertiary structure. Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL, Mol Biol Evol 2003 20 1692 1704 10.1093/molbev/msg184 12885968 (Pubitemid 41070832)
11. Site interdependence attributed to tertiary structure in amino acid sequence evolution. Rodrigue N, Lartillot N, Bryant D, Philippe H, Gene 2005 347 207 217 10.1016/j.gene.2004.12.011 15733531 (Pubitemid 40403760)
12. Assessing site-interdependent phylogenetic models of sequence evolution. Rodrigue N, Philippe H, Lartillot N, Mol Biol Evol 2006 23 1762 1775 10.1093/molbev/msl041 16787998 (Pubitemid 44309770)
13. Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons. Rodrigue N, Kleinman CL, Philippe H, Lartillot N, Mol Biol Evol 2009 26 1663 1676 10.1093/molbev/msp078 19383983
14. Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Bustamante CD, Townsend JP, Hartl DL, Mol Biol and Evol 2000 17 2 301 308 10.1093/oxfordjournals.molbev.a026310 (Pubitemid 30075599)
15. The pattern of amino acid replacements in β-barrels. Dean AM, Neuhauser C, Grenier E, Golding GB, Mol Biol Evol 2002 19 1846 1864 10.1093/oxfordjournals.molbev.a004009 12411594 (Pubitemid 35388108)
16. Protein structural influences in rhodopsin evolution. Marsh L, Griffiths CS, Mol Biol Evol 2005 22 894 904 10.1093/molbev/msi081 15647521 (Pubitemid 40471403)
17. Solvent exposure imparts similar selective pressures across a range of yeast proteins. Conant GC, Stadler PF, Mol Biol Evol 2009 26 1155 1161 10.1093/molbev/msp031 19233963
18. Loss of protein structure stability as a major causative factor in monogenic disease. Yue P, Li Z, Moult J, J Mol Biol 2005 353 459 473 10.1016/j.jmb.2005.08.020 16169011 (Pubitemid 41356624)
19. Protein stability promotes evolvability. Bloom JD, Labthavikul ST, Otey CR, Arnold FH, Proc Natl Acad Sci USA 2006 103 5869 5874 10.1073/pnas.0510098103 16581913
20. The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Ramsey DC, Scherrer MP, Zhou T, Wilke CO, Genetics 2011 188 479 488 10.1534/genetics.111.128025 21467571
21. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Goldman N, Yang Z, Mol Biol and Evol 1994 11 5 725 736
22. HyPhy: hypothesis testing using phylogenetics. Kosakovsky Pond SL, Frost SDW, Muse SV, Bioinformatics 2005 21 5 676 679 10.1093/bioinformatics/bti079 15509596 (Pubitemid 40424796)
23. A new look at the statistical model identification. Akaike H, IEEE Trans Autom Control 1974 19 6 716 723 10.1109/TAC.1974.1100705
24. Multimodel inference: understanding AIC and BIC in model selection. Burnham KP, Anderson DR, Sociological Methods & Res 2004 33 261 304 10.1177/0049124104268644 23235646 (Pubitemid 39519124)
25. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Muse SV, Gaut BS, Mol Biol Evol 1994 11 715 724 7968485 (Pubitemid 24274880)
26. Likelihood models for detecting positive selected amino acid sites and applications to the HIV-1 envelope gene. Nielsen R, Yang Z, Genetics 1998 148 929 936 9539414 (Pubitemid 28169008)
27. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Yang ZH, Nielsen R, Goldman N, Pedersen AMK, Genetics 2000 155 431 449 10790415 (Pubitemid 30257141)
28. Site-to-site variation of synonymous substitution rates. Kosakovsky Pond S, Muse SV, Mol Biol Evol 2005 22 2375 2385 10.1093/molbev/msi232 16107593 (Pubitemid 41661376)
29. Yang Z, Computational Molecular Evolution New York: Oxford University Press 2006
30. The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias. Bierne N, Eyre-Walker A, Genetics 2003 165 1587 1597 14668405 (Pubitemid 38020272)
31. Why highly expressed genes evolve slowly. Drummond DA, Bloom JD, Adami C, Wilke CO, PNAS USA 2005 102 14338 14343 10.1073/pnas.0504070102 16176987 (Pubitemid 41429699)
32. A single determinant dominates the rate of protein evolution. Drummond DA, Raval A, Wilke CO, Mol Biol Evol 2006 23 327 337 16237209 (Pubitemid 43100047)
33. Evolutionary fingerprinting of genes. Kosakovsky Pond SL, Scheffler K, Gravenor MB, Poon AFY, Frost SDW, Mol Biol Evol 2010 27 520 536 10.1093/molbev/msp260 19864470
34. Integrating sequence variation and protein structure to identify sites under selection. Meyer AG, Wilke CO, Mol Biol Evol 10.1093/molbev/mss217
35. Benchmarking multi-rate codon models. Delport W, Scheffler K, Gravenor MB, Muse SV, Kosakovsky Pond S, PLoS One 2010 5 11587 10.1371/journal.pone. 0011587 20657773
36. A model of evolutionary change in proteins. Dayhoff MO, Eck EV, Park CM, Atlas of protein sequence and structure, Volume 5 Washington D.C.: National Biomedical Research Foundation, Dayhoff MO, 1972 89 99
37. The rapid generation of mutation data matrices from protein sequences. Jones D, Taylor W, Thornton J, Comput Appl Biosci 1992 8 275 282 1633570
38. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Whelan S, Goldman N, Mol Biol Evol 2001 18 691 699 10.1093/oxfordjournals.molbev.a003851 11319253 (Pubitemid 32372940)
39. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Lartillot N, Philippe H, Mol Biol Evol 2004 21 1095 1109 10.1093/molbev/msh112 15014145 (Pubitemid 38658218)
40. CodonTest: modeling amino acid substitution preferences in coding sequences. Delport W, Scheffler K, Botha G, Gravenor MB, Muse SV, Kosakovsky Pond SL, PLoS Comp Biol 2010 6 1000885 10.1371/journal.pcbi.1000885
41. Modeling amino acid substitution patterns in orthologous and paralogous genes. Conant GC, Wagner GP, Stadler PF, Mol Phylogenet Evol 2007 42 298 307 10.1016/j.ympev.2006.07.006 16942891 (Pubitemid 44751513)
42. Models of natural mutations including site heterogeneity. Koshi JM, Goldstein RA, Proteins 1998 32 289 295 10.1002/(SICI)1097-0134(19980815)32: 3<289::AID-PROT4>3.0.CO;2-D 9715905 (Pubitemid 28360825)
43. Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences. Porto M, Roman HE, Vendruscolo M, Bastolla U, Mol Biol Evol 2004 22 630 638 10.1093/molbev/msi048 15537801 (Pubitemid 40299512)
44. Ribosome-mediated translational pause and protein domain organization. Thanaraj TA, Argos P, Protein Sci 1996 5 1594 1612 10.1002/pro.5560050814 8844849 (Pubitemid 26257223)
45. Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. Komar AA, Lesnik T, Reiss C, FEBS Lett 1999 462 387 391 10.1016/S0014-5793(99)01566-5 10622731
46. Silent mutations affect in vivo protein folding in Escherichia coli. Cortazzo P, Cervenansky C, Marin M, Reiss C, Ehrlich R, Deana A, Biochem Biophys Res Commun 2002 293 537 541 10.1016/S0006-291X(02)00226-7 12054634 (Pubitemid 34694241)
47. A "silent" polymorphism in the MDR1 gene changes substrate specificity. Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM, Science 2007 315 525 528 10.1126/science.1135308 17185560 (Pubitemid 46175758)
48. Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Zhang G, Hubalewska M, Ignatova Z, Nat Struct Mol Biol 2009 16 274 280 10.1038/nsmb.1554 19198590
49. Translationally optimal codons associate with structurally sensitive sites in proteins. Zhou T, Weems M, Wilke CO, Mol Biol Evol 2009 26 7 1571 1580 10.1093/molbev/msp070 19349643
50. Translationally optimal codons associate with aggregation-prone sites in proteins. Lee Y, Zhou T, Tartaglia GG, Vendruscolo M, Wilke CO, Proteomics 2010 10 4163 4171 10.1002/pmic.201000229 21046618
51. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Yang Z, Nielsen R, Mol Biol Evol 2008 25 568 579 10.1093/molbev/msm284 18178545 (Pubitemid 351301912)
52. The relation between the divergence of sequence and structure in proteins. Chothia C, Lesk AM, EMBO J 1986 5 823 826 3709526
53. SGD: Saccharomyces Genome Database. Cherry JM, Alder C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D, Nucleic Acids Res 1998 26 1 73 79 10.1093/nar/26.1.73 9399804 (Pubitemid 28295265)
54. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Edgar R, Nucleic Acids Res 2004 32 5 1792 1797 10.1093/nar/gkh340 15034147 (Pubitemid 38832724)
55. The protein data bank. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Wessig H, Shindyalov IN, Bourne PE, Nucleic Acids Res 2000 28 1 235 242 10.1093/nar/28.1.235 10592235 (Pubitemid 30047768)
56. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D, Nucleic Acids Res 1997 25 17 3389 3402 10.1093/nar/25.17.3389 9254694 (Pubitemid 27359211)
57. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W, Sander C, Biopolymers 1983 22 12 2577 2637 10.1002/bip.360221211 6667333
58. Creighton T, Proteins: Structures and Molecular Properties New York: Freeman 1992
59. Dissecting the regulatory circuitry of a eukaryotic genome. Holstege FCP, Jennings EG, Wyrick JJ, Lee TI, Hengartner CJ, Green MR, Golub TR, Lander ES, Young RA, Cell 1998 95 717 728 10.1016/S0092-8674(00)81641-4 9845373 (Pubitemid 28544132)
60. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Sharp PM, Li WH, Nucleic Acids Res 1987 15 1281 1295 10.1093/nar/15.3.1281 3547335
61. R: a language for data analysis and graphics. Ihaka R, Gentleman R, J Comput and Graphical Stat 1996 5 299 314