Detection of protein catalytic residues at high precision using local network properties

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Slama, Patrick ^a   Filippis, Ioannis ^a   Lappe, Michael ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC RESIDUE; CLOSENESS CENTRALITIES; DIFFERENT STRUCTURE; PROTEIN SEQUENCES; SEQUENCE ALIGNMENTS; SITE DIRECTED MUTAGENESIS; STRUCTURE SIMILARITY; THREE-DIMENSIONAL STRUCTURE;

PROTEINS;

UBIQUITIN;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CATALYSIS; CHEMISTRY; CONFORMATION; ENZYME ACTIVE SITE; HUMAN; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN FOLDING; REPRODUCIBILITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; CATALYSIS; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; HUMANS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PROTEIN CONFORMATION; PROTEIN FOLDING; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; UBIQUITIN;

EID: 60849122829     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-517     Document Type: Article

References (42)

1. Liu F Kovalevsky AY Louis JM Boross PI Wang Y-F Harrison RW Weber IT Mechanism of Drug Resistance Revealed by the Crystal Structure of the Unliganded HIV-1 Protease with F53L Mutation Journal of Molecular Biology 2006, 358:1191-1199 10.1016/j.jmb.2006.02.076 16569415
2. Ofran Y Mysore V Rost B Prediction of DNA-binding residues from sequence Bioinformatics 2007, 23:i347-353 10.1093/bioinformatics/btm174 17646316
3. Rajagopal S Brinda KV Vishveshwara S Correlation of the Side-Chain Hubs with the Functional Residues in DNA Binding Protein Structures J Chem Inf Model 2006, 46:123-129 10.1021/ci050122g 16426048
4. Tsuchiya Y Kinoshita K Nakamura H Structure-based prediction of DNA-binding sites on proteins Using the empirical preference of electrostatic potential and the shape of molecular surfaces Proteins: Structure, Function, and Bioinformatics 2004, 55:885-894 10.1002/ prot.20111
5. Rosen M Lin SL Wolfson H Nussinov R Molecular shape comparisons in searches for active sites and functional similarity Protein Eng 1998, 11:263-277 10.1093/protein/11.4.263 9680188
6. Bartlett GJ Porter CT Borkakoti N Thornton JM Analysis of catalytic residues in enzyme active sites J Mol Biol 2002, 324:105-121 10.1016/ S0022-2836(02)01036-7 12421562
7. Gutteridge A Bartlett GJ Thornton JM Using a neural network and spatial clustering to predict the location of active sites in enzymes J Mol Biol 2003, 330:719-734 10.1016/S0022-2836(03)00515-1 12850142
8. Petrova NV Wu CH Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties BMC Bioinformatics 2006, 7:312 1534064 16790052 10.1186/1471-2105-7-312
9. Lichtarge O Bourne HR Cohen FE An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families Journal of Molecular Biology 1996, 257:342-358 10.1006/jmbi.1996.0167 8609628
10. Panchenko AR Kondrashov F Bryant S Prediction of functional sites by analysis of sequence and structure conservation Protein Sci 2004, 13:884-892 2280064 15010543 10.1110/ps.03465504
11. Yao H Kristensen DM Mihalek I Sowa ME Shaw C Kimmel M Kavraki L Lichtarge O An accurate, sensitive, and scalable method to identify functional sites in protein structures J Mol Biol 2003, 326:255-261 10.1016/S0022-2836(02)01336-0 12547207
12. Wangikar PP Tendulkar AV Ramya S Mali DN Sarawagi S Functional sites in protein families uncovered via an objective and automated graph theoretic approach J Mol Biol 2003, 326:955-978 10.1016/ S0022-2836(02)01384-0 12581652
13. del Sol Mesa A Pazos F Valencia A Automatic methods for predicting functionally important residues J Mol Biol 2003, 326:1289-1302 10.1016/ S0022-2836(02)01451-1 12589769
14. Amitai G Shemesh A Sitbon E Shklar M Netanely D Venger I Pietrokovski S Network analysis of protein structures identifies functional residues J Mol Biol 2004, 344:1135-1146 10.1016/j.jmb.2004.10.055 15544817
15. Thibert B Bredesen DE del Rio G Improved prediction of critical residues for protein function based on network and phylogenetic analyses BMC Bioinformatics 2005, 6:213 1208857 16124876 10.1186/1471-2105-6-213
16. del Sol A Fujihashi H Amoros D Nussinov R Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non-enzyme families Protein Sci 2006, 15:2120-2128 2242611 16882992 10.1110/ps.062249106
17. Nishikawa K Ooi T Isogai Y Saito N Tertiary Structure of Proteins. I. Representations and Computation of the Conformations Journal of the Physical Society of Japan 1972, 32:1331-1337 10.1143/JPSJ.32.1331
18. Phillips DC British Biochemistry, Past and Present London: Academic Press; 1970.
19. Rossman MG Liljas A Letter: Recognition of structural domains in globular proteins J Mol Biol 1974, 85:177-181 10.1016/ 0022-2836(74)90136-3 4365123
20. Holm L Sander C Protein structure comparison by alignment of distance matrices J Mol Biol 1993, 233:123-138 10.1006/jmbi.1993.1489 8377180
21. Greene LH Higman VA Uncovering network systems within protein structures J Mol Biol 2003, 334:781-791 10.1016/j.jmb.2003.08.061 14636602
22. Carey FA Sundberg RJ Advanced organic chemistry 4 2004.
23. Porter CT Bartlett GJ Thornton JM The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data Nucleic Acids Res 2004, 32:D129-133 308762 14681376 10.1093/nar/ gkh028
24. Beauchamp MA An improved index of centrality Behavioral Science 1965, 10:161-163 10.1002/bs.3830100205 14284290
25. Hubbard SJ Naccess, Biomolecular Structure and Molecular Unit, University College London, UK; 1996.
26. Lewis DD Gale WA A Sequential Algorithm for Training Text Classifiers Proceedings of the Seventeenth Annual International ACM SIGIR Conference on Research and Development in Information Retrieval 1994, 3-12
27. Herzberg O Moult J Bacterial resistance to beta-lactam antibiotics: crystal structure of beta-lactamase from Staphylococcus aureus PC1 at 2.5 A resolution Science 1987, 236:694-701 10.1126/science.3107125 3107125
28. Lietz EJ Truher H Kahn D Hokenson MJ Fink AL Lysine-73 is involved in the acylation and deacylation of beta-lactamase Biochemistry 2000, 39:4971-4981 10.1021/bi992681k 10819961
29. Minasov G Wang X Shoichet BK An ultrahigh resolution structure of TEM-1 beta-lactamase suggests a role for Glu166 as the general base in acylation J Am Chem Soc 2002, 124:5333-5340 10.1021/ja0259640 11996574
30. Sauvage E Fonze E Quinting B Galleni M Frere J-M Charlier P Crystal Structure of the Mycobacterium fortuitum Class A {beta}-Lactamase: Structural Basis for Broad Substrate Specificity Antimicrob Agents Chemother 2006, 50:2516-2521 1489783 16801434 10.1128/AAC.01226-05
31. Pan YH Bahnson BJ Structural basis for bile salt inhibition of pancreatic phospholipase A2 J Mol Biol 2007, 369:439-450 1933606 17434532 10.1016/j.jmb.2007.03.034
32. Dijkstra BW Renetseder R Kalk KH Hol WG Drenth J Structure of porcine pancreatic phospholipase A2 at 2.6 A resolution and comparison with bovine phospholipase A2 J Mol Biol 1983, 168:163-179 10.1016/ S0022-2836(83)80328-3 6876174
33. Daniels DS Woo TT Luu KX Noll DM Clarke ND Pegg AE Tainer JA DNA binding and nucleotide flipping by the human DNA repair protein AGT Nat Struct Mol Biol 2004, 11:714-720 10.1038/nsmb791 15221026
34. Daniels DS Mol CD Arvai AS Kanugula S Pegg AE Tainer JA Active and alkylated human AGT structures: A novel zinc site, inhibitor and extrahelical base binding Embo J 2000, 19:1719-1730 310240 10747039 10.1093/emboj/19.7.1719
35. Xu-Welliver M Kanugula S Loktionova NA Crone TM Pegg AE Conserved residue lysine165 is essential for the ability of O6-alkylguanine-DNA alkyltransferase to react with O6-benzylguanine Biochem J 2000, 347:527-534 1220986 10749683 10.1042/0264-6021:3470527
36. Hamilton KS Ellison MJ Barber KR Williams RS Huzil JT McKenna S Ptak C Glover M Shaw GS Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail Structure 2001, 9:897-904 10.1016/S0969-2126(01)00657-8 11591345
37. Erlandsen H Kim JY Patch MG Han A Volner A Abu-Omar MM Stevens RC Structural comparison of bacterial and human iron-dependent phenylalanine hydroxylases: Similar fold, different stability and reaction rates J Mol Biol 2002, 320:645-661 10.1016/ S0022-2836(02)00496-5 12096915
38. Lu KP Zhou XZ The prolyl isomerase PIN1: A pivotal new twist in phosphorylation signalling and disease Nat Rev Mol Cell Biol 2007, 8:904-916 10.1038/nrm2261 17878917
39. Ranganathan R Lu KP Hunter T Noel JP Structural and Functional Analysis of the Mitotic Rotamase Pin1 Suggests Substrate Recognition Is Phosphorylation Dependent Cell 1997, 89:875-886 10.1016/ S0092-8674(00)80273-1 9200606
40. Zhang Y Daum S Wildemann D Zhou XZ Verdecia MA Bowman ME Lucke C Hunter T Lu KP Fischer G Noel JP Structural basis for high-affinity peptide inhibition of human Pin1 ACS Chem Biol 2007, 2:320-328 10.1021/cb7000044 17518432
41. Sherawat M Kaur P Perbandt M Betzel C Slusarchyk WA Bisacchi GS Chang C Jacobson BL Einspahr HM Singh TP Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 A resolution Acta Crystallogr D Biol Crystallogr 2007, 63(Pt 4):500-507 10.1107/ S090744490700697X 17372355
42. Sacquin-Mora S Laforet E Lavery R Locating the active sites of enzymes using mechanical properties Proteins: Structure, Function, and Bioinformatics 2007, 67:350-359 10.1002/prot.21353