Prediction of neuropeptide cleavage sites in insects

Bioinformatics

Volumn 24, Issue 6, 2008, Pages 815-825

  Southey, Bruce R ^a   Sweedler, Jonathan V ^a   Rodriguez Zas, Sandra L ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INSECT PROTEIN; NEUROPEPTIDE; PROTEIN PRECURSOR;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CLASSIFICATION; DROSOPHILA MELANOGASTER; HONEYBEE; INTERMETHOD COMPARISON; LOGISTIC REGRESSION ANALYSIS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN DEGRADATION; SEQUENCE ANALYSIS;

APIS MELLIFERA; DROSOPHILA MELANOGASTER; HEXAPODA;

EID: 40749124939     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn044     Document Type: Article

References (45)

1. Agresti,A. (1996) An Introduction to Categorical Data Analysis. John Wiley and Sons, Inc., New York.
2. Amare,A. and Sweedler,J.V. (2007) Neuropeptide precursors in Tribolium castaneum. Peptides, 28, 1282-1291.
3. Amare,A. et al. (2006) Bridging neuropeptidomics and genomics with bioinformatics: Prediction of mammalian neuropeptide prohormone processing. J. Proteome Res., 5, 1162-1167.
4. Baggerman,G. et al. (2005) Peptidomic analysis of the larval Drosophila melanogaster central nervous system by two-dimensional capillary liquid chromatography quadrupole time-of-flight mass spectrometry. J. Mass Spectrom., 40, 250-260.
5. Baggerman,G. et al. (2002) Peptidomics of the larval Drosophila melanogaster central nervous system. J. Biol. Chem., 277, 40368-40374.
6. Bairoch,A. et al. (2005) The universal protein resource (UniProt). Nucl. Acids Res., 33, D154-D159.
7. Baldi,P. et al. (2000) Assessing the accuracy of prediction algorithms for classification: An overview. Bioinformatics, 16 412-424.
8. Bendtsen,J.D. et al. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol., 340, 783-795.
9. Cameron,A. et al. (2001) The enzymology of PC1 and PC2. In Dalby,R.E. and Sigman,D.S. (eds) The Enzymes Volume XXII. Academic Press, San Diego, pp. 291-332.
10. Chen,Y.Q. et al. (1997) On neural-network implementations of k-nearest neighbor pattern classifiers. IEEE Trans. circuits and Syst. - I: Fundam. Theory Appl., 44, 622-629.
11. Choi,M.Y. et al. (1998) Isolation and identification of the cDNA encoding the pheromone biosynthesis activating neuropeptide and additional neuropeptides in the oriental tobacco budworm, Helicoverpa assulta (Lepidoptera: Noctuidae). Insect Biochem. Mol. Biol., 28, 759-766.
12. Devi,L. (1991) Consensus sequence for processing of peptide precursors at monobasic sites. FEBS Lett., 280, 189-194.
13. Duckert,P. et al. (2004) Prediction of proprotein convertase cleavage sites. Protein Eng. Des. Sel., 17, 107-112.
14. Duportets,L. et al. (1998) The pheromone biosynthesis activating neuropeptide (PBAN) of the black cutworm moth, Agrotis ipsilon: immunohistochemistry, molecular characterization and bioassay of its peptide sequence. Insect Biochem. Mol. Biol., 28, 591-599.
15. Garczynski,S.F. et al. (2006) Structural studies of Drosophila short neuropeptide F: Occurrence and receptor binding activity. Peptides, 27, 575-582.
16. Hastie,T. et al. (2001) The Elements of Statistical Learning: Data Mining, Inference, and Prediction with 200 Full-color Illustrations Springer, New York.
17. Henrich,S. et al. (2003) The crystal structure of the proprotein processing proteinase furin explains its stringent specificity. Nat. Struct. Biol., 10, 520-526.
18. Holyoak,T. et al. (2003) 2.4A resolution crystal structure of the prototypical hormone-processing protease Kex2 in comparison with an Ala-Lys-Arg boronic acid inhibitor. Biochemistry, 42, 6709-6718.
19. Honeybee Genome Sequencing Consortium (2006) Insights into social insects from the genome of the honeybee Apis mellifera. Nature, 443, 931-949.
20. Hook,V.Y. (2006) Unique neuronal functions of cathepsin L and cathepsin B in secretory vesicles: Biosynthesis of peptides in neurotransmission and neurodegenerative disease. Biol.Chem., 387, 1429-1439.
21. Hummon,A.B. et al. (2006a) Discovering new invertebrate neuropeptides using mass spectrometry. Mass Spectrom. Rev., 25 77-98.
22. Hummon,A.B. et al. (2006b) From the genome to the proteome: uncovering peptides in the Apis brain. Science, 314, 647-649.
23. Hummon,A.B. et al. (2003) From precursor to final peptides: A statistical sequence-based approach to predicting prohormone processing. J. Proteome Res., 2, 650-656.
24. Jacquin-Joly,E. et al. (1998) cDNA cloning and sequence determination of the pheromone biosynthesis activating neuropeptide of Mamestra brassicae: A new member of the PBAN family. Insect Biochem. Mol. Biol., 28, 251-258.
25. Kandel,E.R. et al. (2000) Principles of neural science. McGraw-Hill, Health Professions Division, New York.
26. Liu,F. et al. (2006) In silico identification of new secretory peptide genes in Drosophila melanogaster. Mol. Cell. Proteomics, 5, 510-522.
27. Ma,P.W. et al. (1994) Structural organization of the Helicoverpa zea gene encoding the precursor protein for pheromone biosynthesis-activating neuropeptide and other neuropeptides. Proc. Natl Acad. Sci. USA, 91, 6506-6510.
28. Matthews,B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
29. Mirabeau,O. et al. (2007) Identification of novel peptide hormones in the human proteome by hidden Markov model screening. Genome Res. 17, 320-327.
30. Nanni,L. and Lumini,A. (2007) Ensemblator: An ensemble of classifiers for reliable classification of biological data. Pattern Recognit. Lett., 28, 622-630.
31. Nassel,D.R. (2002) Neuropeptides in the nervous system of Drosophila and other insects: Multiple roles as neuromodulators and neurohormones. Prog. Neurobiol., 68, 1-84.
32. Ohlsson,M. (2004) WeAidU - a decision support system for myocardial perfusion images using multi-layer perceptron neural networks. Artif. Intell. Med., 30, 49-60.
33. Predel,R. et al. (2004a) Unique accumulation of neuropeptides in an insect: FMRFamide-related peptides in the cockroach, Periplaneta americana. Eur. J. Neurosci., 20, 1499-1513.
34. Predel,R. et al. (2004b) Peptidomics of CNS-associated neurohemal systems of adult Drosophila melanogaster: A mass spectrometric survey of peptides from individual flies. J. Comp. Neurol., 474 379-392.
35. Rholam,M. et al. (1995) Role of amino acid sequences flanking dibasic cleavage sites in precursor proteolytic processing. The importance of the first residue C-terminal of the cleavage site. Eur. J. Biochem., 227, 707-714.
36. Rockwell,N.C. et al. (2002) Precursor processing by kex2/furib proteases. Chem. Rev., 102, 4525-4548.
37. Sato,Y. et al. (1993) Precursor polyprotein for multiple neuropeptides secreted from the suboesophageal ganglion of the silkworm Bombyx mori: Characterization of the cDNA encoding the diapause hormone precursor and identification of additional peptides. Proc. Natl Acad. Sci. USA., 90, 3251-3255.
38. Schechter,I. and Berger,A, (1967) On the size of the active site in proteases. I. Papain. Biochem. Biophys. Res. Commun., 27, 157-162.
39. Schumacher,M. et al. (1996) Neural networks and logistic regression: Part I. Comp. Stat. Data Anal., 21, 661-682.
40. Seidah,N.G. and Prat,A. (2002) Precursor convertases in the secretory pathway, cytosol and extracellular milieu. Essays Biochem., 38 79-94.
41. Southey,B.R. et al. (2006a) NeuroPred: A tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides. Nucl. Acids Res., 34, W267-W272.
42. Southey,B.R. et al. (2006b) Prediction of neuropeptide prohormone cleavages with application to RFamides. Peptides, 27, 1087-1098.
43. Vach,W. et al. (1996) Neural networks and logistic regression: Part II. Comp. Stat. Data Anal., 21, 683-701.
44. Veenstra,J.A. (2000) Mono- and dibasic proteolytic cleavage sites in insect neuroendocrine peptide precursors. Arch. Insect Biochem. Physiol., 43, 49-63.
45. Wegener,C. et al. (2006) Direct mass spectrometric peptide profiling and fragmentation of larval peptide hormone release sites in Drosophila melanogaster reveals tagma-specific peptide expression and differential processing. J. Neurochem., 96, 1362-1374.