Protein meta-functional signatures from combining sequence, structure, evolution, and amino acid property information

PLoS Computational Biology

Volumn 4, Issue 9, 2008, Pages

  Wang, Kai ^a,b   Horst, Jeremy A ^a   Cheng, Gong ^a   Nickle, David C ^a   Samudrala, Ram ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING SITES;

ACTIVE SITE; AMINO ACID PROPERTIES; AMINO ACID RESIDUES; AMINO-ACIDS; BINDING-SITES; FUNCTIONAL SIGNATURES; PROTEIN FUNCTIONS; PROTEIN SEQUENCES; SEQUENCE STRUCTURE; STRUCTURE EVOLUTION;

PROTEINS;

AMINO ACID; BACTERIAL PROTEIN; CELLULOSE 1,4 BETA CELLOBIOSIDASE; GLUTAMIC ACID; GUANOSINE DIPHOSPHATE; GUANOSINE TRIPHOSPHATE; HYDROXYAPATITE; ORNITHINE DECARBOXYLASE; OSTEOCALCIN; PROTEIN; TUBULIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIUM; BINDING SITE; CATALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; CRYSTAL STRUCTURE; ENZYME ACTIVITY; ENZYME STRUCTURE; ESCHERICHIA COLI; LOGISTIC REGRESSION ANALYSIS; NONHUMAN; OSSIFICATION; PREDICTION; PROSTHECOBACTER DEJONGEII; PROTEIN FUNCTION; PROTEIN STRUCTURE; SCORING SYSTEM; STATISTICAL MODEL; THREE DIMENSIONAL IMAGING; BIOLOGICAL MODEL; BIOLOGY; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; GENETICS; INTERNET; METHODOLOGY; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN TERTIARY STRUCTURE; REGRESSION ANALYSIS; SEQUENCE ALIGNMENT; SITE DIRECTED MUTAGENESIS; STATISTICS; THERMODYNAMICS;

AMINO ACID SEQUENCE; AMINO ACIDS; BACTERIAL PROTEINS; BINDING SITES; CELLULOSE 1,4-BETA-CELLOBIOSIDASE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CONSERVED SEQUENCE; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; INTERNET; MODELS, CHEMICAL; MODELS, GENETIC; MODELS, MOLECULAR; MOLECULAR STRUCTURE; MUTAGENESIS, SITE-DIRECTED; ORNITHINE DECARBOXYLASE; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN STRUCTURE, TERTIARY; PROTEINS; REGRESSION ANALYSIS; SEQUENCE ALIGNMENT; THERMODYNAMICS;

EID: 52949098360     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000181     Document Type: Article

References (64)

1. Watson JD, Laskowski RA, Thornton JM (2005) Predicting protein function from sequence and structural data. Curr Opin Struct Biol 15: 275-284.
2. Whisstock JC, Lesk AM (2003) Prediction of protein function from protein sequence and structure. Q Rev Biophys 36: 307-340.
3. Friedberg I (2006) Automated protein function prediction - the genomic challenge. Brief Bioinform 7: 225-242.
4. Webb EC (1992) Enzyme Nomenclature 1992. San Diego (California): Academic Press.
5. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. Nat Genet 25: 25-29.
6. Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, et al. (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res 32: D226-D229.
7. Valdar WS (2002) Scoring residue conservation. Proteins 48: 227-241.
8. Sander C, Schneider R (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9: 56-68.
9. Shenkin PS, Erman B, Mastrandrea LD (1991) Information-theoretical entropy as a measure of sequence variability. Proteins 11: 297-313.
10. Williamson RM (1995) Information theory analysis of the relationship between primary sequence structure and ligand recognition among a class of facilitated transporters. J Theor Biol 174: 179-188.
11. Mirny LA, Shakhnovich EI (1999) Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J Mol Biol 291: 177-196.
12. Plaxco KW, Larson S, Ruczinski I, Riddle DS, Thayer EC, et al. (2000) Evolutionary conservation in protein folding kinetics. J Mol Biol 298: 303-312.
13. Gerstein M, Altman RB (1995) Average core structures and variability measures for protein families: application to the immunoglobulins. J Mol Biol 251: 161-175.
14. Pei J, Dokholyan NV, Shakhnovich EI, Grishin NV (2003) Using protein design for homology detection and active site searches. Proc Natl Acad Sci U S A 100: 11361-11366.
15. Valdar WS, Thornton JM (2001) Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 42: 108-124.
16. Greaves R, Warwicker J (2005) Active site identification through geometry-based and sequence profile-based calculations: burial of catalytic clefts. J Mol Biol 349: 547-557.
17. Pei J, Grishin NV (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 17: 700-712.
18. Capra JA, Singh M (2007) Predicting functionally important residues from sequence conservation. Bioinformatics 23: 1875-1882.
19. Wang K, Samudrala R (2006) Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinformatics 7: 385.
20. Lichtarge O, Bourne HR, Cohen FE (1996) An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257: 342-358.
21. Yao H, Kristensen DM, Mihalek I, Sowa ME, Shaw C, et al. (2003) An accurate, sensitive, and scalable method to identify functional sites in protein structures. J Mol Biol 326: 255-261.
22. Mihalek I, Res I, Lichtarge O (2006) Evolutionary trace report_maker: a new type of service for comparative analysis of proteins. Bioinformatics 22: 1656-1657.
23. Mihalek I, Res I, Lichtarge O (2004) A family of evolution-entropy hybrid methods for ranking protein residues by importance. J Mol Biol 336: 1265-1282.
24. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, et al. (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33: W299-W302.
25. Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, et al. (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163-164.
26. Soyer OS, Goldstein RA (2004) Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters. J Mol Biol 339: 227-242.
27. La D, Sutch B, Livesay DR (2005) Predicting protein functional sites with phylogenetic motifs. Proteins 58: 309-320.
28. del Sol Mesa A, Pazos F, Valencia A (2003) Automatic methods for predicting functionally important residues. J Mol Biol 326: 1289-1302.
29. Dessailly BH, Lensink MF, Wodak SJ (2007) Relating destabilizing regions to known functional sites in proteins. BMC Bioinformatics 8: 141.
30. Samudrala R, Moult J (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 275: 895-916.
31. Wang K, Fain B, Levitt M, Samudrala R (2004) Improved protein structure selection using decoy-dependent discriminatory functions. BMC Struct Biol 4: 8.
32. Liu T, Samudrala R (2006) The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection. Protein Eng Des Sel 19: 431-437.
33. Hung LH, Ngan SC, Liu T, Samudrala R (2005) PROTINFO: new algorithms for enhanced protein structure predictions. Nucleic Acids Res 33: W77-W80.
34. Chelliah V, Chen L, Blundell TL, Lovell SC (2004) Distinguishing structural and functional restraints in evolution in order to identify interaction sites. J Mol Biol 342: 1487-1504.
35. Wang K, Samudrala R (2005) FSSA: a novel method for identifying functional signatures from structural alignments. Bioinformatics 21: 2969-2977.
36. Cheng G, Qian B, Samudrala R, Baker D (2005) Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Res 33: 5861-5867.
37. Petrova NV, Wu CH (2006) Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties. BMC Bioinformatics 7: 312.
38. Fischer JD, Mayer CE, Soding J (2008) Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics 24: 613-620.
39. Youn E, Peters B, Radivojac P, Mooney SD (2007) Evaluation of features for catalytic residue prediction in novel folds. Protein Sci 16: 216-226.
40. Pugalenthi G, Kumar KK, Suganthan PN, Gangal R (2008) Identification of catalytic residues from protein structure using support vector machine with sequence and structural features. Biochem Biophys Res Commun 367: 630-634.
41. Tang YR, Sheng ZY, Chen YZ, Zhang Z (2008) An improved prediction of catalytic residues in enzyme structures. Protein Eng Des Sel 21: 295-302.
42. Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, et al. (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 34: D187-D191.
43. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
44. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
45. PHYLIP. http://evolution.genetics.washington.edu/phylip.html.
46. Samudrala R, Levitt M (2002) A comprehensive analysis of 40 blind protein structure predictions. BMC Struct Biol 2: 3.
47. Canutescu AA, Shelenkov AA, Dunbrack RL Jr (2003) A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 12: 2001-2014.
48. Levitt M, Hirshberg M, Sharon R, Daggett V (1995) Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comput Phys Commun 91: 215-231.
49. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277.
50. Porter CT, Bartlett GJ, Thornton JM (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 32: D129-D133.
51. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612.
52. Jenkins C, Samudrala R, Anderson I, Hedlund BP, Petroni G, et al. (2002) Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter. Proc Natl Acad Sci U S A 99: 17049-17054.
53. Schlieper D, Oliva MA, Andreu JM, Lowe J (2005) Structure of bacterial tubulin BtubA/B: evidence for horizontal gene transfer. Proc Natl Acad Sci U S A 102: 9170-9175.
54. Sontag CA, Staley JT, Erickson HP (2005) In vitro assembly and GTP hydrolysis by bacterial tubulins BtubA and BtubB. J Cell Biol 169: 233-238.
55. Hoang QQ, Sicheri F, Howard AJ, Yang DS (2003) Bone recognition mechanism of porcine osteocalcin from crystal structure. Nature 425: 977-980.
56. Poser JW, Price PA (1979) A method for decarboxylation of γ-carboxyglutamic acid in proteins. Properties of the decarboxylated γ-carboxyglutamic acid protein from calf bone. J Biol Chem 254: 431-436.
57. Hauschka PV, Lian JB, Cole DE, Gundberg CM (1989) Osteocalcin and matrix Gla protein: vitamin K-dependent proteins in bone. Physiol Rev 69: 990-1047.
58. Ducy P, Desbois C, Boyce B, Pinero G, Story B, et al. (1996) Increased bone formation in osteocalcin-deficient mice. Nature 382: 448-452.
59. Lee NK, Sowa H, Hinoi E, Ferron M, Ahn JD, et al. (2007) Endocrine regulation of energy metabolism by the skeleton. Cell 130: 456-469.
60. Ginalski K, Elofsson A, Fischer D, Rychlewski L (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19: 1015-1018.
61. Ward RM, Erdin S, Tran TA, Kristensen DM, Lisewski AM, et al. (2008) Deorphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PLoS ONE 3: e2136. doi:10.1371/journal.pone.0002136.
62. Hulo N, Bairoch A, Bulliard V, Cerutti L, De Castro E, et al. (2006) The PROSITE database. Nucleic Acids Res 34: D227-D230.
63. Ng PC, Henikoff S (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31: 3812-3814.
64. Wang K, Samudrala R (2006) Automated functional classification of experimental and predicted protein structures. BMC Bioinformatics 7: 278.