Equal Opportunity for Low-Degree Network Nodes: A PageRank-Based Method for Protein Target Identification in Metabolic Graphs

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Bánky, Dániel ^a,b   Iván, Gábor ^a,b   Grolmusz, Vince ^a,b  

^a EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^b URATIM LTD   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SYNTHESIS; ANALYTIC METHOD; ARTICLE; BACTERIAL GROWTH; CELL COMPARTMENTALIZATION; COMPUTER SIMULATION; DOWN REGULATION; IN VITRO STUDY; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; METABOLIC GRAPH; METABOLIC NETWORK; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PAGERANK BASED METHOD; PLASMODIUM FALCIPARUM; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING; PROTEOMICS; SCORING SYSTEM;

ALGORITHMS; DATABASES, PROTEIN; DRUG DELIVERY SYSTEMS; HUMANS; METABOLIC NETWORKS AND PATHWAYS; PROTEINS; SEARCH ENGINE; SOFTWARE;

EID: 84873815205     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0054204     Document Type: Article

References (53)

1. Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, et al. (2010) The intact molecular interaction database in 2010. Nucleic Acids Res 38: D525-D531.
2. Prasad TSK, Kandasamy K, Pandey A, (2009) Human protein reference database and human proteinpedia as discovery tools for systems biology. Methods Mol Biol 577: 67-79.
3. Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, et al. (2002) Mint: a molecular interaction database. FEBS Lett 513: 135-140.
4. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, et al. (2002) Dip, the database of interacting proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30: 303-305.
5. Bader GD, Betel D, Hogue CWV, (2003) Bind: the biomolecular interaction network database. Nucleic Acids Res 31: 248-250.
6. Bader S, Kuhner S, Gavin AC, (2008) Interaction networks for systems biology. FEBS Lett 582: 1220-1224.
7. Rivas JDL, de Luis A, (2004) Interactome data and databases: different types of protein interaction. Comp Funct Genomics 5: 173-178.
8. Cusick ME, Klitgord N, Vidal M, Hill DE, (2005) Interactome: gateway into systems biology. Hum Mol Genet 14 Spec No. 2: R171-R181.
9. Farkas IJ, Korcsmaros T, Kovacs IA, Mihalik A, Palotai R, et al. (2011) Network-based tools for the identification of novel drug targets. Sci Signal 4: pt3.
10. Overington JP, Al-Lazikani B, Hopkins AL, (2006) How many drug targets are there? Nat Rev Drug Discov 5: 993-996.
11. Ideker T, Bafna V, Lemberger T, (2007) Integrating scientific cultures. Mol Syst Biol 3: 105.
12. Lu X, Jain VV, Finn PW, Perkins DL, (2007) Hubs in biological interaction networks exhibit low changes in expression in experimental asthma. Mol Syst Biol 3: 98.
13. Pfeiffer T, Soyer OS, Bonhoeffer S, (2005) The evolution of connectivity in metabolic networks. PLoS Biol 3: e228.
14. Russell RB, Aloy P, (2008) Targeting and tinkering with interaction networks. Nat Chem Biol 4: 666-673.
15. Hwang WC, Zhang A, Ramanathan M, (2008) Identification of information flow-modulating drug targets: a novel bridging paradigm for drug discovery. Clin Pharmacol Ther 84: 563-572.
16. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, et al. (1999) Kegg: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27: 29-34.
17. Holme P, (2009) Signatures of currency vertices. Journal of the Physical Society of Japan 78: 034801.
18. Huss M, Holme P, (2007) Currency and commodity metabolites: their identification and relation to the modularity of metabolic networks. IET Syst Biol 1: 280-285.
19. Ivan G, Grolmusz V, (2011) When the web meets the cell: using personalized pagerank for analyzing protein interaction networks. Bioinformatics 27: 405-407.
20. Brin S, Page L, (1998) The anatomy of a large-scale hypertextual web search engine. COMPUTER NETWORKS AND ISDN SYSTEMS 30: 107-117.
21. Fortunato S, Boguna M, Flammini A, Menczer F (2008) Approximating pagerank from in-degree. In: Aiello W, Broder A, Janssen J, Milios E, editors, Algorithms and Models for the Web-Graph. Springer Berlin/ Heidelberg, volume 4936 of Lecture Notes in Computer Science, 59-71. Available at http://dx.doi.org/10.1007/978-3-540-78808-9-6. 10.1007/978-3-540-78808-9-6.
22. Grolmusz V (2012) A note on the pagerank of undirected graphs. arXiv Computing Research Repository (CoRR) abs/1205.1960.
23. Perra N, Fortunato S, (2008) Spectral centrality measures in complex networks. Phys Rev E 78: 036107.
24. Takayama K, Wang C, Besra GS, (2005) Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis. Clin Microbiol Rev 18: 81-101.
25. Rozwarski DA, Grant GA, Barton DH, Jacobs WR, Sacchettini JC, (1998) Modification of the NADH of the isoniazid target (InhA) from Mycobacterium tuberculosis. Science 279: 98-102.
26. Vilcheze C, Av-Gay Y, Attarian R, Liu Z, Hazbon MH, et al. (2008) Mycothiol biosynthesis is essential for ethionamide susceptibility in Mycobacterium tuberculosis. Mol Microbiol 69: 1316-1329.
27. Tonge PJ, Kisker C, Slayden RA, (2007) Development of modern InhA inhibitors to combat drug resistant strains of Mycobacterium tuberculosis. Curr Top Med Chem 7: 489-498.
28. Brown AK, Taylor RC, Bhatt A, Futterer K, Besra GS, (2009) Platensimycin activity against mycobacterial beta-ketoacyl-acp synthases. PLoS One 4: e6306.
29. Veyron-Churlet R, Molle V, Taylor RC, Brown AK, Besra GS, et al. (2009) The Mycobacterium tuberculosis beta-ketoacyl-acyl carrier protein synthase iii activity is inhibited by phosphorylation on a single threonine residue. J Biol Chem 284: 6414-6424.
30. Alhamadsheh MM, Musayev F, Komissarov AA, Sachdeva S, Wright HT, et al. (2007) Alkyl-CoA disulfides as inhibitors and mechanistic probes for FabH enzymes. Chem Biol 14: 513-524.
31. Choi KH, Kremer L, Besra GS, Rock CO, (2000) Identification and substrate specificity of beta-ketoacyl (acyl carrier protein) synthase iii (mtFabH) from Mycobacterium tuberculosis. J Biol Chem 275: 28201-28207.
32. Pedelacq JD, Rho BS, Kim CY, Waldo GS, Lekin TP, et al. (2006) Crystal structure of a putative pyridoxine 5′-phosphate oxidase (Rv2607) from Mycobacterium tuberculosis. Proteins 62: 563-569.
33. Singh V, Chandra D, Srivastava BS, Srivastava R, (2011) Downregulation of Rv0189c, encoding a dihydroxyacid dehydratase, affects growth of Mycobacterium tuberculosis in vitro and in mice. Microbiology 157: 38-46.
34. Bange FC, Brown AM, Jacobs WR, (1996) Leucine auxotrophy restricts growth of Mycobacterium bovis BCG in macrophages. Infect Immun 64: 1794-1799.
35. Agren D, Schnell R, Schneider G, (2009) The C-terminal of CysM from Mycobacterium tuberculosis protects the aminoacrylate intermediate and is involved in sulfur donor selectivity. FEBS Lett 583: 330-336.
36. Agren D, Schnell R, Oehlmann W, Singh M, Schneider G, (2008) Cysteine synthase (CysM) of Mycobacterium tuberculosis is an O-phosphoserine sulfhydrylase: evidence for an alternative cysteine biosynthesis pathway in mycobacteria. J Biol Chem 283: 31567-31574.
37. Grandoni JA, Marta PT, Schloss JV, (1998) Inhibitors of branched-chain amino acid biosynthesis as potential antituberculosis agents. J Antimicrob Chemother 42: 475-482.
38. Bach S, Knockaert M, Reinhardt J, Lozach O, Schmitt S, et al. (2005) Roscovitine targets, protein kinases and pyridoxal kinase. J Biol Chem 280: 31208-31219.
39. Manhani KK, Arcuri HA, da Silveira NJF, Uchoa HB, de Azevedo WF, et al. (2005) Molecular models of protein kinase 6 from Plasmodium falciparum. J Mol Model 12: 42-48.
40. Muller IB, Wu F, Bergmann B, Knockel J, Walter RD, et al. (2009) Poisoning pyridoxal 5-phosphate-dependent enzymes: a new strategy to target the malaria parasite Plasmodium falciparum. PLoS One 4: e4406.
41. Gonzalez-Bulnes P, Bobenchik AM, Augagneur Y, Cerdan R, Vial HJ, et al. (2011) PG12, a phospholipid analog with potent antimalarial activity, inhibits Plasmodium falciparum CTP:phosphocholine cytidylyltransferase activity. J Biol Chem 286: 28940-28947.
42. Choubey V, Maity P, Guha M, Kumar S, Srivastava K, et al. (2007) Inhibition of Plasmodium falciparum choline kinase by hexadecyltrimethylammonium bromide: a possible antimalarial mechanism. Antimicrob Agents Chemother 51: 696-706.
43. McMillan PJ, Stimmler LM, Foth BJ, McFadden GI, Muller S, (2005) The human malaria parasite Plasmodium falciparum possesses two distinct dihydrolipoamide dehydrogenases. Mol Microbiol 55: 27-38.
44. Olafsson P, Matile H, Certa U, (1992) Molecular analysis of Plasmodium falciparum hexokinase. Mol Biochem Parasitol 56: 89-101.
45. Muller IB, Hyde JE, Wrenger C, (2010) Vitamin B metabolism in Plasmodium falciparum as a source of drug targets. Trends Parasitol 26: 35-43.
46. Aparicio IM, Marin-Menendez A, Bell A, Engel PC, (2010) Susceptibility of Plasmodium falciparum to glutamate dehydrogenase inhibitors-a possible new antimalarial target. Mol Biochem Parasitol 172: 152-155.
47. Prigge ST, He X, Gerena L, Waters NC, Reynolds KA, (2003) The initiating steps of a type ii fatty acid synthase in Plasmodium falciparum are catalyzed by pfACP, pfMCAT, and pfKASIII. Biochemistry 42: 1160-1169.
48. Muller IB, Bergmann B, Groves MR, Couto I, Amaral L, et al. (2009) The vitamin B1 metabolism of Staphylococcus aureus is controlled at enzymatic and transcriptional levels. PLoS One 4: e7656.
49. McNamara PJ, Proctor RA, (2000) Staphylococcus aureus small colony variants, electron transport and persistent infections. Int J Antimicrob Agents 14: 117-122.
50. Haley KP, Skaar EP, (2012) A battle for iron: host sequestration and Staphylococcus aureus acquisition. Microbes Infect 14: 217-227.
51. Lei T, Yang J, Zheng L, Markowski T, Witthuhn BA, et al. (2012) The essentiality of staphylococcal gcp is independent of its repression of branched-chain amino acids biosynthesis. PLoS One 7: e46836.
52. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
53. Hagberg AA, Schult DA, Swart PJ (2008) Exploring network structure, dynamics, and function using NetworkX. In: Proceedings of the 7th Python in Science Conference (SciPy2008). Pasadena, CA USA, 11-15.