Computational prediction of heme-binding residues by exploiting residue interaction network

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Liu, Rong ^a   Hu, Jianjun ^a  

^a University of South Carolina   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEME; HEMOPROTEIN; AMINO ACID; APOPROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; COMPUTER PREDICTION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; LIGAND BINDING; PROTEIN BINDING; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; SUPPORT VECTOR MACHINE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; METABOLISM; METHODOLOGY; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; RECEIVER OPERATING CHARACTERISTIC; REPRODUCIBILITY;

AMINO ACIDS; APOPROTEINS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HEME; MODELS, BIOLOGICAL; PROTEIN BINDING; PROTEIN INTERACTION MAPS; REPRODUCIBILITY OF RESULTS; ROC CURVE; SOFTWARE;

EID: 80053447047     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025560     Document Type: Article

References (35)

1. Bikiel DE, Boechi L, Capece L, Crespo A, De Biase PM, et al. (2006) Modeling heme proteins using atomistic simulations. Phys Chem Chem Phys 8: 5611-5628.
2. Gray HB, Winkler JR, (1996) Electron transfer in proteins. Annu Rev Biochem 65: 537-561.
3. Guengerich FP, Macdonald TL, (1984) Chemical Mechanisms of Catalysis by Cytochromes-P-450- a Unified View. Accounts Chem Res 17: 9-16.
4. Mense SM, Zhang L, (2006) Heme: a versatile signaling molecule controlling the activities of diverse regulators ranging from transcription factors to MAP kinases. Cell Res 16: 681-692.
5. Paoli M, Marles-Wright J, Smith A, (2002) Structure-function relationships in heme-proteins. DNA Cell Biol 21: 271-280.
6. Reedy CJ, Gibney BR, (2004) Heme protein assemblies. Chem Rev 104: 617-649.
7. Smith A, Alam J, Escriba PV, Morgan WT, (1993) Regulation of Heme Oxygenase and Metallothionein Gene-Expression by the Heme Analogs, Cobalt-Protoporphyrin, and Tin-Protoporphyrin. J Biol Chem 268: 7365-7371.
8. Terwilliger NB, (1998) Functional adaptations of oxygen-transport proteins. J Exp Biol 201: 1085-1098.
9. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
10. Schneider S, Marles-Wright J, Sharp KH, Paoli M, (2007) Diversity and conservation of interactions for binding heme in b-type heme proteins. Nat Prod Rep 24: 621-630.
11. Fufezan C, Zhang J, Gunner MR, (2008) Ligand preference and orientation in b- and c-type heme-binding proteins. Proteins 73: 690-704.
12. Smith LJ, Kahraman A, Thornton JM, (2010) Heme proteins-diversity in structural characteristics, function, and folding. Proteins 78: 2349-2368.
13. Li T, Bonkovsky HL, Guo JT, (2011) Structural analysis of heme proteins: implications for design and prediction. BMC Struct Biol 11: 13.
14. Liu R, Hu J, (2011) HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information. BMC Bioinformatics 12: 207.
15. Greene LH, Higman VA, (2003) Uncovering network systems within protein structures. J Mol Biol 334: 781-791.
16. Bagler G, Sinha S, (2005) Network properties of protein structures. Physica A 346: 27-33.
17. Vendruscolo M, Dokholyan NV, Paci E, Karplus M, (2002) Small-world view of the amino acids that play a key role in protein folding. Phys Rev E 65: 061910.
18. Vendruscolo M, Paci E, Dobson CM, Karplus M, (2001) Three key residues form a critical contact network in a protein folding transition state. Nature 409: 641-645.
19. Brinda KV, Vishveshwara S, (2005) A network representation of protein structures: Implications for protein stability. Biophys J 89: 4159-4170.
20. Amitai G, Shemesh A, Sitbon E, Shklar M, Netanely D, et al. (2004) Network analysis of protein structures identifies functional residues. J Mol Biol 344: 1135-1146.
21. del Sol A, Fujihashi H, O'Meara P, (2005) Topology of small-world networks of protein-protein complex structures. Bioinformatics 21: 1311-1315.
22. del Sol A, O'Meara P, (2005) Small-world network approach to identify key residues in protein-protein interaction. Proteins 58: 672-682.
23. Li Y, Wen Z, Xiao J, Yin H, Yu L, et al. (2011) Predicting disease-associated substitution of a single amino acid by analyzing residue interactions. BMC Bioinformatics 12: 14.
24. Chea E, Livesay DR, (2007) How accurate and statistically robust are catalytic site predictions based on closeness centrality? BMC Bioinformatics 8: 153.
25. Sobolev V, Sorokine A, Prilusky J, Abola EE, Edelman M, (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics 15: 327-332.
26. Dijkstra KE, (1959) A note on two problems in connexion with graphs. Num Math 1: 269-271.
27. 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.
28. Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
29. Rost B, Sander C, (1994) Conservation and prediction of solvent accessibility in protein families. Proteins 20: 216-226.
30. Mihel J, Sikic M, Tomic S, Jeren B, Vlahovicek K, (2008) PSAIA- protein structure and interaction analyzer. BMC Struct Biol 8: 21.
31. LIBSVM: a library for support vector machines. http://www.csie.ntu.edu.tw/~cjlin/libsvm. Accessed 2011 Sep 15.
32. Porollo A, Meller J, (2007) Prediction-based fingerprints of protein-protein interactions. Proteins 66: 630-645.
33. Illingworth CJ, Scott PD, Parkes KE, Snell CR, Campbell MP, et al. (2010) Connectivity and binding-site recognition: applications relevant to drug design. J Comput Chem 31: 2677-2688.
34. del Sol A, Fujihashi H, Amoros D, Nussinov R, (2006) Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families. Protein Sci 15: 2120-2128.
35. Capra JA, Laskowski RA, Thornton JM, Singh M, Funkhouser TA, (2009) Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput Biol 5: e1000585.