Computational protein design: Validation and possible relevance as a tool for homology searching and fold recognition

PLoS ONE

Volumn 5, Issue 5, 2010, Pages

  Schmidt am Busch, Marcel ^a   Sedano, Audrey ^a   Simonson, Thomas ^a  

^a LABORATOIRE DE BIOCHIMIE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

APROTININ; CASPASE; CHEMOKINE; INTERLEUKIN 8; PDZ PROTEIN; AMINO ACID; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CALCULATION; COMPUTER PROGRAM; HIDDEN MARKOV MODEL; MATHEMATICAL ANALYSIS; MOLECULAR MECHANICS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; SCORING SYSTEM; SEQUENCE HOMOLOGY; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; ENTROPY; GENETICS; METHODOLOGY; MUTATION; PDZ DOMAIN; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; REPRODUCIBILITY; SEQUENCE ANALYSIS; STRUCTURAL HOMOLOGY;

AMINO ACIDS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; ENTROPY; MODELS, MOLECULAR; MUTATION; PDZ DOMAINS; POSITION-SPECIFIC SCORING MATRICES; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, PROTEIN; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 77956280650     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010410     Document Type: Article

References (86)

1. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
2. Todd AE, Marsden RL, Thornton JM, Orengo CA (2005) Progress of structural genomics initiatives: An analysis of solved target structures. J Mol Biol 348: 1235-1260.
3. George RA, Spriggs RV, Bartlett GJ, Gutteridge A, MacArthur MW, et al. (2005) Effective function annotation through catalytic residue conservation. Proc Natl Acad Sci USA 102: 12229-12304.
4. Sillitoe I, Dibley M, Bray J, Addou S, Orengo C (2005) Assessing strategies for improved superfamily recognition. Prot Sci 14: 1800-1810.
5. Lee D, Redfern O, Orengo C (2007) Predicting protein function from sequence and structure. Nature Rev Molec Cell Biol 8: 995-1005.
6. Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC (2006) The genomes on line database (GOLD) v.2: a monitor of genome projects worldwide. Nucl Acids Res 34: D332-D334.
7. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler L (2006) GenBank. Nucl Acids Res 34: D16-D20.
8. Dessailly B, Nair R, Jaroszewski L, Fajardo JE, Kouranov A, et al. (2009) PSI-2: Structural genomics to cover protein domain family space. Structure 17: 869-881.
9. Chandonia JM, Brenner SE (2006) The impact of structural genomics: Expectations and outcomes. Science 311: 347-351.
10. Levitt M (2009) Nature of the protein universe. Proc Natl Acad Sci USA 106: 1079-11084.
11. Andreeva A, Howorth D, Brenner SE, Hubbard JJ, Chothia C, et al. (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucl Acids Res 32: D226-229.
12. Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJP, et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucl Acids Res 36: 419-425.
13. Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, et al. (2005) The CATH domain structure database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucl Acids Res 33: D247-251.
14. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucl Acids Res 28: 235-242.
15. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, et al. (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29: 291-325.
16. Venclovas C (2001) Comparative modeling of CASP4 target proteins: Combining results of sequence search with three-dimensional structure assessment. Proteins 45 (Suppl5): 47-54.
17. Schwede T, Kopp J, Guex N, Peitsch MC (2003) Swiss-Model: an automated protein homology-modeling server. Nucl Acids Res 31: 3381-3385.
18. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25: 3389-3402.
19. Schaffer AA, Aravind L, Madden TL, Shavirin JL, Spouge S, et al. (2001) Improving the accuracy of PSI-BLAST protein database searches with compositionbased statistics and other refinements. Nucl Acids Res 29: 2994-3005.
20. Karplus K, Barrett C, Cline M, Diekhans M, Grate L, et al. (1999) Predicting protein structure using only sequence information. Proteins 3: 121-125.
21. Marchler-Bauer A, Anderson JB, Cherukuri PF, DeWweese-Scott C, Geer LY, et al. (2005) CDD: a conserved domain database for protein classification. Nucl Acids Res 33: D192-D196.
22. Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, et al. (1999) Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucl Acids Res 27: 260-262.
23. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, et al. (2004) The Pfam protein families database. Nucl Acids Res 10: D138-D141.
24. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, et al. (2008) The Pfam protein families database. Nucl Acids Res 36: D281-D288.
25. Gough J, Karplus K, Hughey R, Chothia C (2001) Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 313: 903-919.
26. Madera M, Gough J (2002) A comparison of profile hidden Markov model procedures for remote homology detection. Nucl Acids Res 32: 4321-4328.
27. Madera M, Vogel C, Kummerfeld SK, Chothia C, Gough J (2004) The SUPERFAMILY database in 2004: additions and improvements. Nucl Acids Res 32: D235-D239.
28. Krogh A, Brown M, Mian IS, Sjolander K, Haussler D (1994) Hidden Markov models in computational biology: applications to protein modelling. J Mol Biol 235: 1501-1531.
29. Finn RD, Mistry J, Schuster-Böckler B, Griffiths-Jones S, Hollich V, et al. (2006) Pfam: clans, web tools and services. Nucl Acids Res 34: D247-251.
30. Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R (1998) Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucl Acids Res 26: 320-322.
31. Wang Y, Sadreyev RI, Grishin NV (2009) PROCAIN: protein profile comparison with assisting information. Nucl Acids Res 37: 3522-3530.
32. Liu X, Fang K, Wang W (2004) The number of protein folds and the distribution over families in nature. Proteins 54: 491-499.
33. Guerler A, Knapp EW (2008) Novel protein folds and their nonsequential structural analogs. Prot Sci 17: 1374-1382.
34. Koehl P, Levitt M (1999) De novo protein design. II. Plasticity in sequence space. J Mol Biol 293: 1183-1193.
35. Larson S, Garg A, Desjarlais J, Pande V (2003) Increased detection of structural templates using alignments of designed sequences. Proteins 51: 390-396.
36. Larson S, Pande V (2003) Sequence optimization for native stability determines the evolution and folding kinetics of a small protein. J Mol Biol 332: 275-286.
37. Larson S, England JE, Desjarlais J, Pande V (2002) Thoroughly sampling sequence space: Large-scale protein design of structural ensembles. Prot Sci 11: 2804-2813.
38. Dantas G, Kuhlman B, Callender D, Wong M, Baker D (2003) A large test of computational protein design: Folding and stability of nine completely redesigned globular proteins. J Mol Biol 332: 449-460.
39. Saunders C, Baker D (2005) Recapitulation of protein family divergence using flexible backbone protein design. J Mol Biol 346: 631-644.
40. Zhou H, Zhou Y (2005) Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 58: 321-328.
41. Ding F, Dokholyan NV (2006) Emergence of protein fold families through rational design. PLOS Comp Biol 2: e85.
42. Schmidt am Busch M, Mignon D, Simonson T (2009) Computational protein design as a tool for fold recognition. Proteins 77: 139-158.
43. Ponder J, Richards FM (1988) Tertiary templates for proteins: Use of packing criteria in the enumeration of allowed sequences for different structural classes. J Mol Biol 193: 775-791.
44. Hellinga H, Richards F (1994) Optimal sequence selection in proteins of known structure by simulated evolution. Proc Natl Acad Sci USA 91: 5803-5807.
45. Dahiyat BI, Mayo SL (1996) Protein design automation. Prot Sci 5: 895-903.
46. Harbury PB, Plecs JJ, Tidor B, Alber T, Kim PS (1998) High-resolution protein design with backbone freedom. Science 1998: 1462-1467.
47. Dokholyan NV, Shakhnovich EI (2001) Understanding hierachical protein evolution from first principles. J Mol Biol 312: 289-307.
48. Desjarlais J, Handel T (1999) Sidechain and backbone flexibility in protein core design. J Mol Biol 289: 305-318.
49. Kuhlman B, Baker D (2000) Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 97: 10383-10388.
50. Wernisch L, Héry S, Wodak S (2000) Automatic protein design with all atom force fields by exact and heuristic optimization. J Mol Biol 301: 713-736.
51. Jaramillo A, Wernisch L, Héry S, Wodak S (2002) Folding free energy function selects native-like protein sequences in the core but not on the surface. Proc Natl Acad Sci USA 99: 13554-13559.
52. Kuhlman B, Dantas G, Ireton G, Varani G, Stoddard B, et al. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302: 1364-1368.
53. Dwyer M, Looger L, Hellinga H (2004) Computational design of a biologically active enzyme. Science 304: 1967-1971.
54. Havranek J, Harbury P (2003) Automated design of specifity in molecular recognition. Nat Struct Biol 10: 45-52.
55. Ventura S, Serrano L (2004) Designing proteins inside out. Proteins 56: 1-10.
56. Wollacott AM, Zanghellini A, Murphy P, Baker D (2007) Prediction of structures of multidomain proteins from structures of the individual domains. Prot Sci 16: 165-175.
57. Swift J, Wehbi WA, Kelly BD, Stowell XF, Saven JG, et al. (2006) Design of functional ferritin-like proteins with hydrophobic cavities. J Am Chem Soc 128: 6611-6619.
58. Kang SG, Saven JG (2007) Computational protein design: structure, function and combinatorial diversity. Curr Opin Chem Biol 11: 329-334.
59. Koehl P, Levitt M (1999) De novo protein design. I. In search of stability and specificity. J Mol Biol 293: 1161-1181.
60. Koehl P, Levitt M (1999) Structure-based conformational preferences of amino acids. Proc Natl Acad Sci USA 96: 12524-12529.
61. Hubner IA, Deeds EJ, Shakhnovich EI (2006) Understanding ensemble protein folding at atomic detail. Proc Natl Acad Sci USA 103: 17747-17752.
62. Pokala N, Handel T (2004) Energy functions for protein design I: Efficient and accurate continuum electrostatics and solvation. Prot Sci 13: 925-936.
63. Pokala N, Handel TM (2005) Energy functions for protein design: Adjustement with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity. J Mol Biol 347: 203-227.
64. Chowdry AB, Reynolds KA, Hanes MS, Voorhies M, Pokala N, et al. (2007) An object-oriented library for computational protein design. J Comp Chem 28: 2378-2388.
65. Raha K, Wollacott AM, Italia MJ, Desjarlais JR (2000) Prediction of amino acid sequence from structure. Prot Sci 9: 1106-1119.
66. Lopes A, Aleksandrov A, Bathelt C, Archontis G, Simonson T (2007) Computational sidechain placement and protein mutagenesis with implicit solvent models. Proteins 67: 853-867.
67. Schmidt am Busch M, Lopes A, Mignon D, Simonson T (2008) Computational protein design: software implementation, parameter optimization, and performance of a simple model. J Comp Chem 29: 1092-1102.
68. Schmidt am Busch M, Lopes A, Amara N, Bathelt C, Simonson T (2008) Testing the coulomb/accessible surface area solvent model for protein stability, ligand binding, and protein design. BMC Bioinformatics 9: 148-163.
69. Panchenko AR, Bryant SH (2002) A comparison of position-specific score matrices based on sequence and structure alignments. Prot Sci 11: 361-370.
70. Socolich M, Lockless SW, Russ WP, Lee H, Gardner KH, et al. (2005) Evolutionary information for specifying a protein fold. Nature 437: 512-518.
71. Wlodawer A, Deisenhofer J, Huber R (1987) Comparison of two highly refined structures of bovine pancreatic trypsin inhibitor. J Mol Biol 193: 145-156.
72. Tuffery P, Etchebest C, Hazout S, Lavery R (1991) A new approach to the rapid determination of protein side chain conformations. J Biomol Struct Dyn 8: 1267.
73. Brooks B, Bruccoleri R, Olafson B, States D, Swaminathan S, et al. (1983) Charmm: a program for macromolecular energy, minimization, and molecular dynamics calculations. J Comp Chem 4: 187-217.
74. Lee B, Richards F (1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55: 379-400.
75. Street A, Mayo S (1998) Pairwise calculation of protein solvent-accessible surface areas. Folding and Design 3: 253-258.
76. Brünger AT (1992) X-plor version 3.1, A System for X-ray crystallography and NMR Yale University Press, New Haven.
77. Anderson DP (2004) BOINC: A system for public-resource computing and storage. In: 5th IEEE/ACM International Workshop on Grid Computing IEEE Computer Society Press, USA.
78. Durbin R, Eddy SR, Krogh A, Mitchison G (2002) Biological sequence analysis Cambridge University Press.
79. Murphy LR, Wallqvist A, Levy RM (2000) Simplified amino acid alphabets for protein fold recognition and implications for folding. Prot Eng 13: 149-152.
80. Launay G, Mendez R, Wodak SJ, Simonson T (2007) Recognizing proteinprotein interfaces with empirical potentials and reduced amino acid alphabets. BMC Bioinf 8: 270-291.
81. Halperin I, Wolfson H, Nussinov R (2006) Correlated mutations: Advances and limitations. A study on fusion proteins and on the cohesion-dockerin families. Proteins 63: 832-845.
82. Marin A, Pothier J, Zimmermann K, Gibrat JF (2002) FROST: a filter-based fold recognition method. Proteins 49: 493-509.
83. Lin D, Gish GD, Songyang Z, Pawson T (1999) The carboxyl terminus of B class ephrins constitutes a PDZ domain binding motif. J Biol Chem 274: 3726-3733.
84. Tonikian R, Zhang YN, Sazinsky SL, Currell B, Yeh JH, et al. (2008) A specifity map for the PDZ domain family. Plos Biology 6: 2043-2059.
85. Shoichet BK, Baase WA, Kuroki R, Matthews BW (1995) A relationship between protein stability and protein function. Proc Natl Acad Sci USA 92: 452-456.
86. Elcock AH (2001) Prediction of functionally important residues based solely on the computed energetics of protein structure. J Mol Biol 312: 885-896.