Detection of selective cationic amphipatic antibacterial peptides by Hidden Markov models

Acta Biochimica Polonica

Volumn 56, Issue 1, 2009, Pages 167-176

  Polanco, Carlos ^a   Samaniego, Jose L ^b  

^a INSTITUTO DE FISIOLOGÍA CELULAR   (Mexico)

^b UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

Author keywords

Antibacterial peptides; Hidden Markov models

Indexed keywords

EID: 67249124036     PISSN: 0001527X     EISSN: 1734154X     Source Type: Journal    
DOI: 10.18388/abp.2009_2529     Document Type: Article

References (76)

1. Aguero-Chapin G, Antunes A, Ubeira FM, Chou KC, Gonzalez-Diaz H. (2008a) Comparative Study of topological indices of macro/supramolecular RNA complex networks. J Chem Inf Model 48: 2265-2277.
2. Aguero-Chapin G, Gonzalez-Diaz H, de la Riva G, Rodriguez E, Sanchez-Rodriguez A, Podda G et al. (2008b) MMM-QSAR recognition of ribonucleases without alignment: comparison with an HMM model and isolation from Schizosaccharomyces pombe, prediction, and experimental assay of a new sequence. J Chem Inf Model 48: 434-448.
3. Andrés E, Dimarcq JL. (2007) Cationic antimicrobial peptides: from innate immunity study to drug development. Update. Med Mal Infect 37: 194-199.
4. Bailey TL, Gribskov M. (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14: 48-54.
5. Bailey TL, Gribskov M. (2000) Concerning the accuracy of MAST E-values. Bioinformatics 16: 488-489.
6. Boulanger N, Brun R, Ehret-Sabatier L, Kunz C, Bulet. (2002) Immunopeptides in the defense reactions of Glossina morsitans to bacterial and Trypanosoma brucei brucei infections. Insect Biochem Mol Biol 32: 369-375.
7. Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, Shallom SJ, van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoaibi A, Cummings LM, Florens L, Yates JR, Raine JD, Sinden RE, Harris MA, Cunningham DA, Preiser PR, Bergman LW, Vaidya AB, van Lin LH, Janse CJ, Waters AP, Smith HO, White OR, Salzberg SL, Venter JC, Fraser CM, Hoffman SL, Gardner MJ, Carucci DJ. (2002) Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419: 512-519.
8. Clark DP, Durell S, Maloy WL, Zasloff M. (1994) Ranalexin. A novel antimicrobial peptide from bullfrog (Rana catesbeiana) skin, structurally related to the bacterial antibiotic, polymyxin. J Biol Chem 269: 10849-10855.
9. Conde R, Zamudio FZ, Rodríguez MH, Possani LD. (2000) Scorpine, an anti-malaria and anti-bacterial agent purified from scorpion venom. FEBS Lett 471: 165-168.
10. Cruz-Monteagudo M, González-Díaz H, Aguero-Chapin G, Santana L, Borges F, Domínguez RE et al. (2007) Computational chemistry development of a unified free energy Markov Model for the distribution of 1300 chemicals to 38 different environmental or biological systems. J Comput Chem 28: 1909-1922.
11. Cruz-Monteagudo M, Munteanu CR, Borges F, Cordeiro MNDS, Uriartei E, Chou K-C et al. (2008a) Stochastic molecular descriptors for polymers. 4. Study of complex mixtures with topological indices of mass spectra spiral and star networks: The blood proteome case polymer. Polymer 49: 5575-5587.
12. Cruz-Monteagudo M, Munteanu CR, Borges F, Cordeiro MN, Uriarte E, Gonzalez-Diaz H. (2008b) Quantitative Proteome-Property Relationships (QPPRs). Part 1: finding biomarkers of organic drugs with mean Markov connectivity indices of spiral networks of blood mass spectra. Bioorg Med Chem 16: 9684-9693.
13. Cruz-Monteagudo M, González-Díaz H, Borges F, Dominguez ER, Cordeiro MN. (2008c) 3D-MEDNEs: An alternative in silico. Technique for chemical research in toxicology. 2. Quantitative Proteome-Toxicity Relationships (QPTR) based on mass spectrum spiral entropy. Chem Res Toxicol 21: 619-632.
14. Del Río G, Castro-Obregon S, Rao R, Ellerby MH, Bredesen DE. (2001) APAP, a sequence-pattern recognition approach identifies substance P as a potential apoptotic peptide. FEBS Lett 494: 213-219.
15. Eisenberg D, Weiss RM, Terwilliger TC. (1982) The helical hydrophobic moment: a measure of the amphiphilicity of a helix. Nature 23: 371-374.
16. Ellerby MH, Arap W, Kain R, Andrusiak R, Del Río G, Krajewski S, Lombardo CR, Rao R, Ruoslahti E, Bredesen DE, Pasqualini R. (1999) Anti-cancer activity of targeted pro-apoptotic peptides. Nat Med 5: 1032-1038.
17. ExPASy. Proteomics Server. http://www.expasy.ch/sprot
18. Ferino G, Gonzalez-Diaz H, Delogu G, Podda G, Uriarte E. (2008) Using spectral moments of spiral networks based on PSA/mass spectra outcomes to derive quantitative proteome-disease relationships (QPDRs) and predicting prostate cancer. Biochem Biophys Res Commun 372: 320-325.
19. Ferino G, Delogu G, Podda G, Uriarte E, González-Díaz H. (2009) Quantitative proteome-disease relationships (QPDRs) in clinical chemistry: prediction of prostate cancer with spectral moments of PSA/MS star networks. In Clinical Chemistry Research; Mitchem BHaS, ChL, ed. NY: Nova Science Publisher.
20. Frith CM, Hansen U, Spouge JL, Weng Z. (2004) Finding functional sequence elements by multiple local alignment. Nucleic Acids Res 32: 189-200.
21. González-Díaz H, Molina RR, Uriarte E. (2003a) Stochastic molecular descriptors for polymers. 1. Modelling the properties of icosahedral viruses with 3D-Markovian negentropie. Polymer 45: 3845-3853.
22. González-Díaz H, de Armas RR, Molina R. (2003b) Markovian negentropies in bioinformatics. 1. A picture of footprints ater the interaction of the HIV-1 Psi-RNA packaging region with drugs Bioinformatics 19: 2079 2087.
23. González-Díaz H, Pérez-Bello A, Uriarte E. (2005) Stochastic molecular descriptors for polymers. 3. Markov electrostatic moments as polymer 2D-folding descriptors: RNA-QSAR for mycobacterial promoters. Polymer 46: 6461-6473.
24. González-Díaz H, Saiz-Urra L, Molina R, Santana L, Uriarte E. (2007a) A model for the recognition of protein kinases based on the entropy of 3D van der Waals interactions. J Proteome Res 6: 904-908.
25. Gonzalez-Diaz H, Saiz-Urra L, Molina R, Gonzalez-Diaz Y, Sanchez-Gonzalez A. (2007c) Computational chemistry approach to protein kinase recognition using 3D stochastic van der Waals spectral moments. Comput Chem 28: 1042-108.
26. González-Díaz H, Pérez-Castillo Y, Podda G, Uriarte E. (2007d) Computational chemistry comparison of stable/nonstable protein mutants classification models based on 3D and topological indices. J Comput Chem 28: 1990-1995.
27. González-Díaz H, Aguero-Chapin G, Varona J, Molina R, Delogu G, Santana. L et al. (2007e) 2D-RNA-coupling numbers: a new computational chemistry approach to link secondary structure topology with biological function. J Comput Chem 28: 1049-1056.
28. González-Díaz H, Vilar S, Santana L, Uriarte E. (2007f) Medicinal chemistry and bioinformatics - current trends in drugs discovery with networks topological indices. Curr Top Med Chem 7: 1025-1039.
29. Gonzalez-Diaz H, Prado-Prado F, Ubeira FM. (2008a) Predicting antimicrobial drugs and targets with the MARCH-INSIDE approach. Curr Top Med Chem 8: 1676-1690.
30. González-Díaz, Prado-Prado F. (2008b) Unified QSAR and network-based computational chemistry approach to antimicrobials. Part 1: multispecies activity models for antifungals. J Comput Chem 29: 656-657.
31. González-Díaz H, González-Díaz Y, Santana L, Ubeira FM, Uriarte E. (2008c) Proteomics, networks and connectivity indices Proteomics 8: 750-778.
32. Gudmundsson GH, Lidholm DA, Asling B, Gan R, Boman HG. (1991) The cecropin locus. Cloning and expression of a gene cluster encoding three antibacterial peptides in Hyalophora cecropia. J Biol Chem 266: 11510-11517.
33. Hemmi H, Ishibashi J, Hara S, Yamakawa M. (2002) Solution structure of moricin, an antibacterial peptide, isolated from the silkworm Bombyx mori. FEBS Lett 518: 33-38.
34. Hilpert K, Fjell CD, Cherkasov A. (2008) Short linear cationic antimicrobial peptides: screening, optimizing, and prediction. Methods Mol Biol 494: 127-159.
35. HMMER, UBC Bioinformatics Centre. http://bioinformatics.ubc.ca/resources/tools/hmmer
36. Hoskins RA, Carlson JW, Kennedy C, Acevedo D, Evans-Holm M, Frise E, Wan KH, Park S, Mendez-Lago M, Rossi F, Villasante A, Dimitri P, Karpen GH, Celniker SE. (2007) Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science 316: 1625-1628.
37. Goraya J, Wang Y, Li Z, O'Flaherty M, Knoop FC, Platz JE, Conlon JM. (2000) Peptides with antimicrobial activity from four different families isolated from the skins of the North American frogs Rana luteiventris, Rana berlandieri and Rana pipiens. Eur J Biochem 267: 894-900.
38. Halverson T, Basir YJ, Knoop FC, Conlon JM. (2000) Purification and characterization of antimicrobial peptides from the skin of the North American green frog Rana clamitans. Peptides 21: 469-476.
39. Kanai A, Natori S. (1989) Cloning of gene cluster for sarcotoxin I, antibacterial proteins of Sarcophaga peregrine. FEBS Lett 258: 199-202.
40. Kreyszig E. (1970) Introductory Mathematical Statistics, Principles and Methods. John Wiley & Sons. Inc. New York.
41. Kolonin MG, Saha PK, Chan L, Pasqualini R, Arap W (2004) Reversal of obesity by targeted ablation of adipose tissue. Nat Med 10: 625-632.
42. Lacroix E, Viguera AR, Serrano L. (1997) Elucidating the folding problem of α-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. J Mol Biol 1: 173-191.
43. Linzmeier R, Michaelson D, Liu L, Ganz T. (1993) The structure of neutrophil defensin genes. FEBS Lett 321: 267-273.
44. Mahoney MM, Lee AY, Brezinski-Caliguri DJ, Huttner KM. (1995) Molecular analysis of the sheep cathelin family reveals a novel antimicrobial peptide. FEBS Lett 377: 519-522.
45. Mak P, Wójcik K, Thogersen IB, Dubin A. (1996) Isolation, antimicrobial activities, and primary structures of hamster neutrophil defensins. Infect Immun 64: 4444-4449.
46. Marenah L, Flatt PR, Orr DF, Shaw C, Abdel-Wahab YH. (2006) Skin secretions of Rana saharica frogs reveal antimicrobial peptides esculentins-1 and -1B and brevinins-1E and -2EC with novel insulin releasing activity. J Endocrinol 188: 1-9.
47. Matutte B, Storey KB, Knoop FC, Conlon JM. (2000) Induction of synthesis of an antimicrobial peptide in the skin of the freeze-tolerant frog, Rana sylvatica, in response to environmental stimuli. FEBS Lett 483: 135-138.
48. Moerman L, Bosteels S, Noppe W, Willems J, Clynen E, Schoofs L, Thevissen K, Tytgat J, Van Eldere J, Van Der Walt J, Verdonck F. (2002) Antibacterial and antifungal properties of α-helical, cationic peptides in the venom of scorpions from southern Africa. Eur J Biochem 269: 4799-4810.
49. Moore KS, Bevins CL, Brasseur MM, Tomassini N, Turner K, Eck H, Zasloff M. (1991) Antimicrobial peptides in the stomach of Xenopus laevis. J Biol Chem 266: 19851-19857.
50. Morikawa N, Hagiwara K, Nakajima T. (1992) Brevinin-1 and -2, unique antimicrobial peptides from the skin of the frog, Rana brevipoda porsa. Biochem Biophys Res Commun 189: 184-190.
51. NCBI, National Center for Biotechnology Information (NCBI) Protein BLAST. http://www.ncbi.nlm.nih.gov
52. Oh D, Shin SY, Kang JH, Hahm KS, Kim KL, Kim Y. (1999) NMR structural characterization of cecropin A(1-8) - magainin 2(1-12) and cecropin A (1-8) - melittin (1-12) hybrid peptides J Pept Res 53: 578-589.
53. Orivel J, Redeker V, Le-Caer JP, Krier F, Revol-Junelles AM, Longeon A, Chaffotte A, Dejean A, Rossier J. (2001) Ponericins, new antibacterial and insecticidal peptides from the venom of the ant Pachycondyla goeldii. J Biol Chem 276: 17823-17829.
54. Park JM, Jung JE, Lee BJ. (1995) Antimicrobial peptides from the skin of a Korean frog, Rana rugosa. Biochem Biophys Res Commun 205: 948-954.
55. Popsueva AE, Zinovjeva MV, Visser JW, Zijlmans JM, Fibbe WE, Belyavsky AV. (1996) A novel murine cathelinlike protein expressed in bone marrow. FEBS Lett 391: 5-8.
56. Prado-Prado FJ, de la Vega OM, Uriarte E, Ubeira FM, Chou KC, Gonzalez-Diaz H. (2007a) Unified QSAR approach to antimicrobials. 4. Multi-target QSAR modelling and comparative multi-distance study of the giant components of antiviral drug-drug complex networks. Bioorg Med Chem 17: 569-575.
57. Prado-Prado FJ, Gonzalez-Diaz H, Santana L, Uriarte E. (2007b) Unified QSAR approach to antimicrobials. Part 2: predicting activity against more than 90 different species in order to halt antibacterial resistance. Bioorg Med Chem 15: 897-902.
58. Prado-Prado FJ, Gonzalez-Diaz H, de la Vega OM, Ubeira FM, Chou KC. (2008) Unified QSAR approach to antimicrobials. Part 3: first multi-tasking QSAR model for input-coded prediction, structural back-projection, and complex networks clustering of antiprotozoal compounds. Bioorg Med Chem 16: 5871-5880.
59. Ramos de Armas R, González-Díaz H, Molina R, Uriarte E. (2005) Stochastic-based descriptors studying biopolymers biological properties: extended MARCH-INSIDE methodology describing antibacterial activity of lactoferricin derivatives. Biopolymers 77: 247-256.
60. Rosetto M, Manetti AG, Marchini D, Dallai R, Telford JL, Baldari CT. (1993) Sequences of two cDNA clones from the medfly Ceratitis capitata encoding antibacterial peptides of the cecropin family. Gene 134: 241-243.
61. Resch B. (2004) Hidden Markov Models. A tutorial for the course computational intelligence. Signal processing and speech communication laboratory. http://www.igi.tugraz.at/lehre/CI/tutorials/HMM/HMM.pdf
62. Shin SY, Kang JH, Janq SY, Kim Y, Kim KL, Kahm KS. (2000) Effects of the hinge region of cecropin A(1-8)-magainin 2(1-12), a synthetic antimicrobial peptide, on liposomes, bacterial and tumor cells. Biochim Biophys Acta 1463: 209-218.
63. Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak, SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, Marra MA. (2002) Generation and initial analysis of more than 15000 fulll-ength human and mouse cDNA sequences. Proc Natl Acad Sci USA 99: 16899-16903.
64. Torres-Larios A, Gurrola GB, Zamudio FZ, Possani LD. (2000) Hadrurin, a new antimicrobial peptide from the venom of the scorpion Hadrurus aztecus. Eur J Biochem 267: 5023-5031.
65. Tossi A, Scocchi M, Zanetti M, Storici P, Gennaro R. (1995) PMAP-37, a novel antibacterial peptide from pig myeloid cells. cDNA cloning, chemical synthesis and activity. Eur J Biochem 228: 941-946.
66. Qu Z, Steiner H, Engströn A, Bennich H, Boman HG. (1982) Insect immunity: isolation and structure of cecropins B and D from pupae of the Chinese oak silk moth, Antheraea pernyi. Eur J Biochem 127: 219-224.
67. Santana L, Uriarte E, González-Díaz H, Zagotto G, Soto-Otero R, Mendez-Alvarez E. (2006) A QSAR model for in silico screening of MAO-A inhibitors. Prediction, synthesis, and biological assay of novel coumarins. Med Chem 49: 1149-1156.
68. Swiss, European Bioinformatics Institute 2006-2008. EBI is an Outstation of the European Molecular Biology Laboratory. http://www.ebi.ac.uk/swissprot/
69. Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R. (1998) Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res 26: 320-322.
70. Spivak M. (1965) Calculus on Manifolds. Benjamin. New York.
71. Tennessen JA, Blouin MS. (2007) Selection for antimicrobial peptide diversity in frogs leads to gene duplication and low allelic variation. J Mol Evol 65: 605-615.
72. Uniprot. Swiss-prot ftp://ftp.expasy.org/databases/swissprot/release_compressed/<>uniprot_sprot.fasta.gz
73. Uversky VN, Gillespie JR, Fink AL (2000) Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins 41: 415-427
74. Uversky VN (2002) What does it mean to be natively unfolded? Eur J Biochem 269: 2-12
75. Vizioli J, Bulet P, Hoffmann JA, Kafatos FC, Müller HM, Dimopoulos G. (2001) Gambicin: a novel immune responsive antimicrobial peptide from the malaria vector Anopheles gambiae. Proc Natl Acad Sci USA 98: 12630-12635.
76. Zimin AV, Smith DR, Sutton G, Yorke JA. (2008) Assembly reconciliation. Bioinformatics 1: 142-145.