Computational characterization of moonlighting proteins

Biochemical Society Transactions

Volumn 42, Issue 6, 2014, Pages 1780-1785

  Khan, Ishita K ^a   Kihara, Daisuke ^a,b  

^a Purdue University   (United States)

^b PURDUE UNIVERSITY   (United States)

Author keywords

Bioinformatics; Computational analysis; Moonlighting protein; Multitasking protein; Protein function

Indexed keywords

INTRINSICALLY DISORDERED PROTEIN; MOONLIGHTING PROTEIN; PROTEIN; UNCLASSIFIED DRUG; BIOPOLYMER;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; AUTOPHAGY; BINDING SITE; BIOINFORMATICS; CARBOXY TERMINAL SEQUENCE; CELL VACUOLE; GENE ONTOLOGY; LIGAND BINDING; MYCOBACTERIUM TUBERCULOSIS; PEROXISOME; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEOMICS; SIGNAL TRANSDUCTION; BIOLOGY; CHEMISTRY; GENETICS; METABOLISM; PHYSIOLOGY; PROTEIN DATABASE;

BIOPOLYMERS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; PROTEINS;

EID: 84911913899     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20140214     Document Type: Article

References (44)

1. Jeffery, C. (1999) Moonlighting proteins. Trends Biochem. Sci. 24, 8-11 CrossRef PubMed
2. Piatigorsky, J. (1998) Multifunctional lens crystallins and corneal enzymes. More than meets the eye. Ann. N.Y. Acad. Sci. 842, 7-15 CrossRef PubMed
3. Jeffery, C. (2009) Moonlighting proteins: an update. Mol. Biosyst. 5, 345-350 CrossRef PubMed
4. Jeffery, C.J. (2004) Moonlighting proteins: complications and implications for proteomics research. Drug Discov. Today: Targets 3, 71-78 CrossRef
5. Huberts, D.H. and van der Klei, I.J. (2010) Moonlighting proteins: an intriguing mode of multitasking. Biochim. Biophys. Acta 1803, 520-525 CrossRef PubMed
6. Jeffery, C.J. (2005) Mass spectrometry and the search for moonlighting proteins. Mass Spectrom. Rev. 24, 772-782 CrossRef PubMed
7. Jeffery, C.J. (2011) Proteins with neomorphic moonlighting functions in disease. IUBMB Life 63, 489-494 CrossRef PubMed
8. Sriram, G., Martinez, J.A., McCabe, E.R., Liao, J.C. and Dipple, K.M. (2005) Single-gene disorders: what role could moonlighting enzymes play? Am. J. Hum. Genet. 76, 911-924 CrossRef PubMed
9. Ovádi, J. (2011) Moonlighting proteins in neurological disorders. IUBMB Life 63, 453-457 CrossRef PubMed
10. Khan, I., Chitale, M., Rayon, C. and Kihara, D. (2012) Evaluation of function predictions by PFP, ESG, and PSI-BLAST for moonlighting proteins. BMC Proc. 6 (Suppl. 7), S5 CrossRef PubMed
11. Gómez, A., Domedel, N., Cedano, J., Piñol, J. and Querol, E. (2003) Do current sequence analysis algorithms disclose multifunctional (moonlighting) proteins? Bioinformatics 19, 895-896 CrossRef PubMed
12. Gómez, A., Hernández, S., Amela, I., Piñol, J., Cedano, J. and Querol, E. (2011) Do protein-protein interaction databases identify moonlighting proteins? Mol. Biosyst. 7, 2379-2382 CrossRef PubMed
13. Hernández, S., Amela, I., Cedano, J., Piñol, J., Perez-Pons, J., Mozo-Villarias, A. and Querol, E. (2011) Do moonlighting proteins belong to the intrinsically disordered protein class? J. Proteomics Bioinform. 5, 262-264
14. Hernández, S., Ferragut, G., Amela, I., Perez-Pons, J., Piñol, J., Mozo-Villarias, A., Cedano, J. and Querol, E. (2014) MultitaskProtDB: a database of multitasking proteins. Nucleic Acids Res. 42, D517-D520 CrossRef PubMed
15. Ashburner, M., Ball, C., Blake, J., Botstein, D., Butler, H., Cherry, J., Davis, A., Dolinski, K., Dwight, S., Eppig, J. et al. (2000) Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25-34 CrossRef PubMed
16. UniProt Consortium (2014) Activities at the universal protein resource (UniProt). Nucleic Acids Res. 42, D191-D198 CrossRef PubMed
17. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410 CrossRef PubMed
18. Pearson, W.R. (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol. 183, 63-98 CrossRef PubMed
19. Bru, C., Courcelle, E., Carrère, S., Beausse, Y., Dalmar, S. and Kahn, D. (2005) The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res. 33, 212-215 CrossRef
20. Finn, R.D., Mistry, J., Schuster-Böckler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Moxon, S., Marshall, M., Khanna, A., Durbin, R. et al. (2006) Pfam: clans, web tools and services. Nucleic Acids Res. 34, 247-251 CrossRef
21. Hunter, S., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Das, U., Daugherty, L., Duquenne, L. et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res. 37, 211-215 CrossRef
22. Hawkins, T., Luban, S. and Kihara, D. (2006) Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Sci. 15, 1550-1556 CrossRef PubMed
23. Hawkins, T., Chitale, M., Luban, S. and Kihara, D. (2009) PFP: automated prediction of gene ontology functional annotations with confidence scores using protein sequence data. Proteins 74, 566-582 CrossRef PubMed
24. Chitale, M., Hawkins, T., Park, C. and Kihara, D. (2009) ESG: extended similarity group method for automated protein function prediction. Bioinformatics 25, 1739-1745 CrossRef PubMed
25. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 CrossRef PubMed
26. Brun, C., Chevenet, F., Martin, D., Wojcik, J., Guénoche, A. and Jacq, B. (2003) Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol. 5, R6 CrossRef PubMed
27. Chua, H.N., Sung, W.K. and Wong, L. (2006) Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 22, 1623-1630 CrossRef PubMed
28. Letovsky, S. and Kasif, S. (2003) Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics 19, i197-i204 CrossRef PubMed
29. Nariai, N., Kolaczyk, E.D. and Kasif, S. (2007) Probabilistic protein function prediction from heterogeneous genome-wide data. PLoS ONE 2, e337 CrossRef PubMed
30. Sharan, R., Ulitsky, I. and Shamir, R. (2007) Network-based prediction of protein function. Mol. Syst. Biol. 3, 88-100 CrossRef PubMed
31. Deng, M., Tu, Z, Sun, F. and Chen, T. (2004) Mapping gene ontology to proteins based on protein-protein interaction data. Bioinformatics 20, 895-902 CrossRef PubMed
32. Prieto, C. and De Las Rivas, J. (2006) APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res. 34, W298-W302 CrossRef PubMed
33. Dunker, A.K., Brown, C.J., Lawson, J.D., Iakoucheva, L.M. and Obradović, Z. (2002) Intrinsic disorder and protein function. Biochemistry 41, 6573-6582 CrossRef PubMed
34. Tompa, P., Szász, C. and Buday, L. (2005) Structural disorder throws new light on moonlighting. Trends Biochem. Sci. 30, 484-489 CrossRef PubMed
35. Dyson, H.J. (2011) Expanding the proteome: disordered and alternatively folded proteins. Q. Rev. Biophys. 44, 467-518 CrossRef PubMed
36. Mani, M.K. (2014) Moonlighting protein database (MoonProt): a database for proteins that are known to moonlight. M.S. Dissertation. University of Illinois, Chicago, IL, U.S.A.
37. Yuan, W., Tuttle, D.L., Shi, Y.J., Ralph, G.S. and Dunn, Jr, W.A. (1997) Glucose-induced microautophagy in Pichia pastoris requires the α-subunit of phosphofructokinase. J. Cell Sci. 110, 1935-1945 PubMed
38. Sengupta, S., Ghosh, S. and Nagaraja, V. (2008) Moonlighting function of glutamate racemase from Mycobacterium tuberculosis: racemization and DNA gyrase inhibition are two independent activities of the enzyme. Microbiology 154, 2796-2803 CrossRef PubMed
39. Chen, H. and Kihara, D. (2011) Effect of using suboptimal alignments in template-based protein structure prediction. Proteins 79, 315-334 CrossRef PubMed
40. Kihara, D., Lu, H., Kolinski, A. and Skolnick, J. (2003) TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc. Natl. Acad. Sci. U.S.A. 98, 10125-10130 CrossRef
41. Kihara, D., Zhang, Y., Lu, H, Kolinski, A. and Skolnick, J. (2002) Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc. Natl. Acad. Sci. U.S.A. 99, 5993-5998 CrossRef PubMed
42. Li, B., Turuvekere, S., Agrawal, M., La, D., Ramani, K. and Kihara, D. (2008) Characterization of local geometry of protein surfaces with the visibility criterion. Proteins 71, 670-683 CrossRef PubMed
43. Chikhi, R., Sael, L. and Kihara, D. (2010) Real-time ligand binding pocket database search using local surface descriptors. Proteins 78, 2007-2028 CrossRef PubMed
44. Sael, L. and Kihara, D. (2012) Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison. Proteins 80, 1177-1195 CrossRef PubMed