Statistical potentials for improved structurally constrained evolutionary models

Molecular Biology and Evolution

Volumn 27, Issue 7, 2010, Pages 1546-1560

  Kleinman, Claudia L ^a   Rodrigue, Nicolas ^b   Lartillot, Nicolas ^a   Philippe, Hervé ^a  

^a Universite de Montreal   (Canada)

^b UNIVERSITY OF OTTAWA   (Canada)

Author keywords

Bayes factor; Maximum likelihood; Molecular evolution; Protein structure; Statistical potentials

Indexed keywords

SOLVENT; PROTEIN;

ARTICLE; MOLECULAR EVOLUTION; PROTEIN STRUCTURE; SCORING SYSTEM; ALGORITHM; AMINO ACID SEQUENCE; BAYES THEOREM; BIOLOGY; CHEMISTRY; COMPUTER SIMULATION; MOLECULAR GENETICS; PHYLOGENY; PROTEIN CONFORMATION; STATISTICAL MODEL;

ALGORITHMS; AMINO ACID SEQUENCE; BAYES THEOREM; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MODELS, STATISTICAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN CONFORMATION; PROTEINS;

EID: 77953771357     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq047     Document Type: Article

References (84)

1. Anisimova M, Kosiol C. 2009. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol Biol Evol. 26:255-271.
2. Artymiuk PJ, Blake CC, Grace DE, Oatley SJ, Phillips DC, Sternberg MJ. 1979. Crystallographic studies of the dynamic properties of lysozyme. Nature 280:563-568.
3. Bastolla U, Vendruscolo M, Knapp EW. 2000. A statistical mechanical method to optimize energy functions for protein folding. Proc Natl Acad Sci USA. 97:3977-3981.
4. Betancourt MR, Skolnick J. 2004. Local propensities and statistical potentials of backbone dihedral angles in proteins. J Mol Biol. 342:635-649.
5. Boas FE, Harbury PB. 2007. Potential energy functions for protein design. Curr Opin Struct Biol. 17:199-204.
6. Bolon DN, Grant RA, Baker TA, Sauer RT. 2005. Specificity versus stability in computational protein design. Proc Natl Acad Sci USA. 102:12724-12729.
7. Bonnard C, Kleinman CL, Rodrigue N, Lartillot N. 2009. Fast optimization of statistical potentials for structurally constrained phyloge-netic models. BMC Evol Biol. 9:227.
8. Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, Dewey C, Holmes I, Pachter L. 2009. Fast statistical alignment. PLoS Comput Biol. 5:e1000392.
9. Bucciantini M, Giannoni E, Chiti F, Baroni F, Formigli L, Zurdo J, Taddei N, Ramponi G, Dobson CM, Stefani M. 2002. Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases. Nature 416:507-511.
10. Buchete NV, Straub JE, Thirumalai D. 2004. Orientational potentials extracted from protein structures improve native fold recognition. Protein Sci. 13:862-874.
11. Bustamante CD, Townsend JP, Hartl DL. 2000. Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Mol Biol Evol. 17:301-308.
12. Chiu TL, Goldstein RA. 1998. Optimizing potentials for the inverse protein folding problem. Protein Eng. 11:749-752.
13. Choi SC, Hobolth A, Robinson DM, Kishino H, Thorne JL. 2007. Quantifying the impact of protein tertiary structure on molecular evolution. Mol Biol Evol. 24:1769-1782.
14. Choi SS, Vallender EJ, Lahn BT. 2006. Systematically assessing the influence of 3-dimensional structural context on the molecular evolution of mammalian proteomes. Mol Biol Evol. 23:2131-2133.
15. Conant GC, Stadler PF. 2009. Solvent exposure imparts similar selective pressures across a range of yeast proteins. Mol Biol Evol. 26:1155-1161.
16. Delport W, Scheffler K, Seoighe C. 2009. Models of coding sequence evolution. Brief Bioinform. 10:97-109.
17. Dimmic MW, Mindell DP, Goldstein RA. 2000. Modeling evolution at the protein level using an adjustable amino acid fitness model. Pac Symp Biocomput. 18-29.
18. Dobson CM. 2003. Protein folding and misfolding. Nature 426: 884-890.
19. Drummond DA, Raval A, Wilke CO. 2006. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 23: 327-337.
20. Drummond DA, Wilke CO. 2008. Mistranslation-induced protein mis-folding as a dominant constraint on coding-sequence evolution. Cell 134:341-352.
21. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
22. Flores TP, Orengo CA, Moss DS, Thornton JM. 1993. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci. 2:1811-1826.
23. Franzosa EA, Xia Y. 2009. Structural determinants of protein evolution are context-sensitive at the residue level. Mol Biol Evol. 26: 2387-2395.
24. Frauenfelder H, Petsko GA, Tsernoglou D. 1979. Temperature-dependent X-ray diffraction as a probe of protein structural dynamics. Nature 280:558-563.
25. Gilis D, Rooman M. 1997. Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence. J Mol Biol. 272:276-290.
26. Gilis D, Rooman M. 2001. Identification and ab initio simulations of early folding units in proteins. Proteins 42:164-176.
27. Glaser F, Rosenberg Y, Kessel A, Pupko T, Ben-Tal N. 2005. The consurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins 58:610-617.
28. Goldman N, Thorne JL, Jones DT. 1996. Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J Mol Biol. 263:196-208.
29. Goldman N, Thorne JL, Jones DT. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149:445-458.
30. Gong S, Worth CL, Bickerton GR, Lee S, Tanramluk D, Blundell TL. 2009. Structural and functional restraints in the evolution of protein families and superfamilies. Biochem Soc Trans. 37: 727-733.
31. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.
32. Hoeflich KP, Ikura M. 2002. Calmodulin in action: diversity in target recognition and activation mechanisms. Cell 108:739-742.
33. Hubbard SJ, Thornton JM. 1993. Naccess. London: Department of Biochemistry and Molecular Biology, University College.
34. Huelsenbeck JP, Jain S, Frost SW, Pond SL. 2006. A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proc Natl Acad Sci USA. 103:6263-6268.
35. Jensen JL, Pedersen AK. 2000. Probabilistic models of DNA sequence evolution with context dependent rates of substitution. Adv Appl Prob. 32:499-517.
36. Jones DT. 1997. Successful ab initio prediction of the tertiary structure of NK-lysin using multiple sequences and recognized supersecondary structural motifs. Proteins Suppl 1:185-191.
37. Jones DT, Taylor WR, Thornton JM. 1992a. A new approach to protein fold recognition. Nature 358:86-89.
38. Jones DT, Taylor WR, Thornton JM. 1992b. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275-282.
39. Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern-recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
40. Kleinman CL, Rodrigue N, Bonnard C, Philippe H, Lartillot N. 2006. A maximum likelihood framework for protein design. BMC Bioinfor-matics 7:326.
41. Kocher, JPA., Rooman MJ, Wodak SJ. 1994. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol. 235:1598-1613.
42. Koshi JM, Goldstein RA. 1995. Context-dependent optimal substitution matrices. Protein Eng. 8:641-645.
43. Kuhlman B, Baker D. 2000. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA. 97:10383-10388.
44. Laskowski RA. 2009. PDBsum new things. Nucleic Acids Res. 37: D355-D359.
45. Laskowski RA, Macarthur MW, Moss DS, Thornton JM. 1993. PROCHECK\a program to check the stereochemical quality of protein structures. J Appl Crystallogr. 26:283-291.
46. Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM. 1996. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR. 8:477-486.
47. Lazaridis T, Karplus M. 2000. Effective energy functions for protein structure prediction. Curr Opin Struct Biol. 10:139-145.
48. Lio P, Goldman N, Thorne JL, Jones DT. 1998. PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics 14:726-733.
49. Maguid S, Fernandez-Alberti S, Parisi G, Echave J. 2006. Evolutionary conservation of protein backbone flexibility. J Mol Evol. 63: 448-457.
50. Melo F, Sanchez R, Sali A. 2002. Statistical potentials for fold assessment. Protein Sci. 11:430-448.
51. Miyazawa S, Jernigan RL. 1996. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol. 256:623-644.
52. Muse SV, Gaut BS. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol. 11:715-724.
53. Overington J, Johnson MS, Sali A, Blundell TL. 1990. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc Biol Sci. 241:132-145.
54. Pal C, Papp B, Lercher MJ. 2006. An integrated view of protein evolution. Nat Rev Genet. 7:337-348.
55. Parisi G, Echave J. 2001. Structural constraints and emergence of sequence patterns in protein evolution. Mol Biol Evol. 18:750-756.
56. Pedersen AM, Jensen JL. 2001. A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames. Mol Biol Evol. 18:763-776.
57. Ramachandran GN, Ramakrishnan C, Sasisekharan V. 1963. Stereochemistry of polypeptide chain configurations. J Mol Biol. 7:95-99.
58. Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL. 2003. Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol. 20:1692-1704.
59. Rodrigue N, Kleinman CL, Philippe H, Lartillot N. 2009. Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons. Mol Biol Evol. 26:1663-1676.
60. Rodrigue N, Lartillot N, Bryant D, Philippe H. 2005. Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene 347:207-217.
61. Rodrigue N, Philippe H, Lartillot N. 2006. Assessing site-interdependent phylogenetic models of sequence evolution. Mol Biol Evol. 23:1762-1775.
62. Russell RB, Saqi MA, Sayle RA, Bates PA, Sternberg MJ. 1997. Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J Mol Biol. 269:423-439.
63. Schlessinger A, Rost B. 2005. Protein flexibility and rigidity predicted from sequence. Proteins 61:115-126.
64. Seno F, Micheletti C, Maritan A, Banavar JR. 1998. Variational approach to proteindesignandextractionof interactionpotentials. Phys Rev Lett. 81:2172-2175.
65. Sippl MJ. 1993. Boltzmann?s principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J Comput Aided Mol Des. 7: 473-501.
66. Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E. 2005. Protein structure and evolutionary history determine sequence space topology. Genome Res. 15:385-392.
67. Shakhnovich EI, Gutin AM. 1993. Engineering of stable and fast-folding sequences of model proteins. Proc Natl Acad Sci USA. 90: 7195-7199.
68. Socolich M, Lockless SW, Russ WP, Lee H, Gardner KH, Ranganathan R. 2005. Evolutionary information for specifying a protein fold. Nature 437:512-518.
69. Sternberg MJ, Grace DE, Phillips DC. 1979. Dynamic information from protein crystallography. An analysis of temperature factors from refinement of the hen egg-white lysozyme structure. J Mol Biol. 130:231-252.
70. Suel GM, Lockless SW, Wall MA, Ranganathan R. 2002. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol. 10:59-69.
71. Sun S, Brem R, Chan HS, Dill KA. 1995. Designing amino acid sequences to fold with good hydrophobic cores. Protein Eng. 8:1205-1213.
72. Taverna DM, Goldstein RA. 2002a. Why are proteins marginally stable? Proteins 46:105-109.
73. Taverna DM, Goldstein RA. 2002b. Why are proteins so robust to site mutations? J Mol Biol. 315:479-484.
74. Thorne JL, Choi SC, Yu J, Higgs PG, Kishino H. 2007. Population genetics without intraspecific data. Mol Biol Evol. 24:1667-1677.
75. Thorne JL, Goldman N, Jones DT. 1996. Combining protein evolution and secondary structure. Mol Biol Evol. 13:666-673.
76. Wako H, Blundell TL. 1994a. Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. i. Solvent accessibility classes. J Mol Biol. 238:682-692.
77. Wako H, Blundell TL. 1994b. Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. ii. Secondary structures. J Mol Biol. 238:693-708. (Pubitemid 24168629)
78. Wang G, Dunbrack RL Jr. 2003. PISCES: a protein sequence culling server. Bioinformatics 19:1589-1591.
79. Williams SG, Lovell SC. 2009. The effect of sequence evolution on protein structural divergence. Mol Biol Evol. 26:1055-1065.
80. Xia Y, Huang ES, Levitt M, Samudrala R. 2000. Ab initio construction of protein tertiary structures using a hierarchical approach. J Mol Biol. 300:171-185.
81. Yang Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 10:1396-1401. (Pubitemid 23352619)
82. Yang Z, Nielsen R, Goldman N, Pedersen AM. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
83. Yuan Z, Bailey TL, Teasdale RD. 2005. Prediction of protein B-factor profiles. Proteins 58:905-912.
84. Zaman MH, Shen MY, Berry RS, Freed KF, Sosnick TR. 2003. Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the flory isolated-pair hypothesis for peptides. J Mol Biol. 331:693-711.