Probing Protein Sequences as Sources for Encrypted Antimicrobial Peptides

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Brand, Guilherme D ^a,d   Magalhães, Mariana T Q ^a   Tinoco, Maria L P ^a   Aragão, Francisco J L ^a   Nicoli, Jacques ^b   Kelly, Sharon M ^c   Cooper, Alan ^d   Bloch, Carlos ^a  

^a EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA   (Brazil)

^b FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

^c UNIVERSITY OF GLASGOW   (United Kingdom)

^d UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DIMYRISTOYLPHOSPHATIDYLCHOLINE; DIMYRISTOYLPHOSPHATIDYLGLYCEROL; INTRAGENIC ANTIMICROBIAL PEPTIDE; MYOINOSITOL 1 PHOSPHATE SYNTHASE; MYOINOSITOL 3 PHOSPHATE SYNTHASE; POLYPEPTIDE ANTIBIOTIC AGENT; SOYBEAN PROTEIN; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID SEQUENCE; ANTIMICROBIAL ACTIVITY; ARTICLE; ARTIFICIAL MEMBRANE; BIOTECHNOLOGY; CIRCULAR DICHROISM; COMPUTER PROGRAM; CONTROLLED STUDY; DIFFERENTIAL SCANNING CALORIMETRY; ESCHERICHIA COLI; FUNGAL SPORE GERMINATION; FUNGUS; MEMBRANE BINDING; MINIMUM INHIBITORY CONCENTRATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTIDE ANALYSIS; PHAKOPSORA PACHYRHIZI; PHASE TRANSITION; PHOSPHOLIPID MEMBRANE; PHOSPHOLIPID VESICLE; PHYSICAL CHEMISTRY; PLANT GENOME; PLANT LEAF; PRINCIPAL COMPONENT ANALYSIS; PROTEIN DATABASE; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PSEUDOMONAS AERUGINOSA; SOYBEAN; STAPHYLOCOCCUS AUREUS; SYNTHESIS; XANTHOMONAS AXONOPODIS;

AMINO ACID SEQUENCE; ANTI-BACTERIAL AGENTS; ANTIFUNGAL AGENTS; BASIDIOMYCOTA; CALORIMETRY, DIFFERENTIAL SCANNING; ESCHERICHIA COLI; MICROBIAL SENSITIVITY TESTS; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; PLANT DISEASES; PLANT PROTEINS; PRINCIPAL COMPONENT ANALYSIS; PROTEIN STRUCTURE, SECONDARY; PSEUDOMONAS AERUGINOSA; SEQUENCE ANALYSIS, PROTEIN; SOYBEANS; SPORES, FUNGAL; STAPHYLOCOCCUS AUREUS;

GLYCINE MAX; PHAKOPSORA PACHYRHIZI;

EID: 84867025847     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0045848     Document Type: Article

References (54)

1. Dores RM, Lecaude S, Bauer D, Danielson PB, (2002) Analyzing the evolution of the opioid/orphanin gene family. Mass Spectrom Rev 21: 220-243.
2. Lewis RV, Stern AS, (1983) Biosynthesis of the enkephalins and enkephalin-containing polypeptides. Annu Rev Pharmacol Toxicol 23: 353-372.
3. Meisel H, Bockelmann W, (1999) Bioactive peptides encrypted in milk proteins: proteolytic activation and thropho-functional properties. Antonie Van Leeuwenhoek 76: 207-215.
4. Phelan M, Aherme A, FitzGerald RJ, O'Brien NM, (2009) Casein-derived bioactive peptides: Biological effects, industrial uses, safety aspects and regulatory status. International Dairy Journal 19: 643-654.
5. Ivanov VT, Karelin AA, Philippova MM, Nazimov IV, Pletnev VZ, (1997) Hemoglobin as a source of endogenous bioactive peptides: the concept of tissue-specific peptide pool. Biopolymers 43: 171-188.
6. Fukudome S, Yoshikawa M, (1992) Opioid peptides derived from wheat gluten: their isolation and characterization. FEBS Lett 296: 107-111.
7. Fukudome S, Yoshikawa M, (1993) Gluten exorphin C. A novel opioid peptide derived from wheat gluten. FEBS Lett 316: 17-19.
8. Zhao Q, Garreau I, Sannier F, Piot JM, (1997) Opioid peptides derived from hemoglobin: hemorphins. Biopolymers 43: 75-98.
9. Regoli D, Barabe J, (1980) Pharmacology of bradykinin and related kinins. Pharmacol Rev 32: 1-46.
10. Vanhoye D, Bruston F, Nicolas P, Amiche M, (2003) Antimicrobial peptides from hylid and ranin frogs originated from a 150-million-year-old ancestral precursor with a conserved signal peptide but a hypermutable antimicrobial domain. Eur J Biochem 270: 2068-2081.
11. Tossi A, Sandri L, Giangaspero A, (2000) Amphipathic, alpha-helical antimicrobial peptides. Biopolymers 55: 4-30.
12. Yeaman MR, Yount NY, (2003) Mechanisms of antimicrobial peptide action and resistance. Pharmacol Rev 55: 27-55.
13. Zasloff M, (2002) Antimicrobial peptides of multicellular organisms. Nature 415: 389-395.
14. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183.
15. Wang G, Li X, Wang Z, (2009) APD2: the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Res 37: D933-937.
16. Conchillo-Sole O, de Groot NS, Aviles FX, Vendrell J, Daura X, et al. (2007) AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides. BMC Bioinformatics 8: 65.
17. Dathe M, Wieprecht T, (1999) Structural features of helical antimicrobial peptides: their potential to modulate activity on model membranes and biological cells. Biochim Biophys Acta 1462: 71-87.
18. Dathe M, Wieprecht T, Nikolenko H, Handel L, Maloy WL, et al. (1997) Hydrophobicity, hydrophobic moment and angle subtended by charged residues modulate antibacterial and haemolytic activity of amphipathic helical peptides. FEBS Lett 403: 208-212.
19. Zhu WL, Shin SY, (2009) Antimicrobial and cytolytic activities and plausible mode of bactericidal action of the cell penetrating peptide penetratin and its lys-linked two-stranded peptide. Chem Biol Drug Des 73: 209-215.
20. Seto GW, Marwaha S, Kobewka DM, Lewis RN, Separovic F, et al. (2007) Interactions of the Australian tree frog antimicrobial peptides aurein 1.2, citropin 1.1 and maculatin 1.1 with lipid model membranes: differential scanning calorimetric and Fourier transform infrared spectroscopic studies. Biochim Biophys Acta 1768: 2787-2800.
21. Jain MK, Wu NM, (1977) Effect of small molecules on the dipalmitoyl lecithin liposomal bilayer: III. Phase transition in lipid bilayer. Journal of Membrane Biology 34: 157-201.
22. Epand RM, Sturtevant JM, (1981) A calorimetric study of peptide-phospholipid interactions: the glucagon-dimyristoylphosphatidylcholine complex. Biochemistry 20: 4603-4606.
23. Lewis RN, Zhang YP, McElhaney RN, (2005) Calorimetric and spectroscopic studies of the phase behavior and organization of lipid bilayer model membranes composed of binary mixtures of dimyristoylphosphatidylcholine and dimyristoylphosphatidylglycerol. Biochim Biophys Acta 1668: 203-214.
24. Jolliffe IT (2002) Principal component analysis. New York: Springer. xxix, 487 p.
25. Fraley C, Raftery A (2006) mclust Version 3 for R: Normal Mixture Modeling and Model-based Clustering. Technical Report 504 University of Washington, Department of Statistics.
26. Ladokhin AS, Fernandez-Vidal M, White SH, (2010) CD spectroscopy of peptides and proteins bound to large unilamellar vesicles. J Membr Biol 236: 247-253.
27. Kelly SM, Jess TJ, Price NC, (2005) How to study proteins by circular dichroism. Biochimica et Biophysica Acta- Proteins and Proteomics 1751: 119-139.
28. Chen YH, Yang JT, Chau KH, (1974) Determination of the helix and beta form of proteins in aqueous solution by circular dichroism. Biochemistry 13: 3350-3359.
29. Greenfield N, Fasman GD, (1969) Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 8: 4108-4116.
30. Rech EL, Vianna GR, Aragao FJL, (2008) High-efficiency transformation by biolistics of soybean, common bean and cotton transgenic plants. Nat Protocols 3: 410-418.
31. Aragao FJL, Sarokin L, Vianna GR, Rech EL, (2000) Selection of transgenic meristematic cells utilizing a herbicidal molecule results in the recovery of fertile transgenic soybean [Glycine max (L.) Merril] plants at a high frequency. Theoretical and Applied Genetics 101: 1-6.
32. Murphy AM, Otto B, Brearley CA, Carr JP, Hanke DE, (2008) A role for inositol hexakisphosphate in the maintenance of basal resistance to plant pathogens. Plant J 56: 638-652.
33. Shewry PR, Lucas JA (1997) Plant Proteins that Confer Resistance to Pests and Pathogens. In: Callow JA, editor. Advances in Botanical Research: Academic Press. 135-192.
34. Lata S, Mishra NK, Raghava GP, (2010) AntiBP2: improved version of antibacterial peptide prediction. BMC Bioinformatics 11 (Suppl 1):: S19.
35. Torrent M, Di Tommaso P, Pulido D, Nogues MV, Notredame C, et al. (2012) AMPA: an automated web server for prediction of protein antimicrobial regions. Bioinformatics 28: 130-131.
36. Torrent M, Andreu D, Nogues VM, Boix E, (2011) Connecting peptide physicochemical and antimicrobial properties by a rational prediction model. PLoS ONE 6: e16968.
37. McElhaney RN, (1982) The use of differential scanning calorimetry and differential thermal analysis in studies of model and biological membranes. Chem Phys Lipids 30: 229-259.
38. Papahadjopoulos D, Moscarello M, Eylar EH, Isac T, (1975) Effects of proteins on thermotropic phase transitions of phospholipid membranes. Biochim Biophys Acta 401: 317-335.
39. Epand RM, Epand RF, (2009) Lipid domains in bacterial membranes and the action of antimicrobial agents. Biochim Biophys Acta 1788: 289-294.
40. Epand RM, Epand RF, Arnusch CJ, Papahadjopoulos-Sternberg B, Wang G, et al. (2010) Lipid clustering by three homologous arginine-rich antimicrobial peptides is insensitive to amino acid arrangement and induced secondary structure. Biochim Biophys Acta 1798: 1272-1280.
41. Epand RF, Maloy WL, Ramamoorthy A, Epand RM, (2010) Probing the "charge cluster mechanism" in amphipathic helical cationic antimicrobial peptides. Biochemistry 49: 4076-4084.
42. Epand RM, Rotem S, Mor A, Berno B, Epand RF, (2008) Bacterial membranes as predictors of antimicrobial potency. J Am Chem Soc 130: 14346-14352.
43. Jean-Francois F, Castano S, Desbat B, Odaert B, Roux M, et al. (2008) Aggregation of cateslytin beta-sheets on negatively charged lipids promotes rigid membrane domains. A new mode of action for antimicrobial peptides? Biochemistry 47: 6394-6402.
44. Ponti D, Mangoni ML, Mignogna G, Simmaco M, Barra D, (2003) An amphibian antimicrobial peptide variant expressed in Nicotiana tabacum confers resistance to phytopathogens. Biochem J 370: 121-127.
45. Rivero M, Furman N, Mencacci N, Picca P, Toum L, et al. (2012) Stacking of antimicrobial genes in potato transgenic plants confers increased resistance to bacterial and fungal pathogens. J Biotechnol 157: 334-343.
46. Jung YJ, Lee SY, Moon YS, Kang KK, (2012) Enhanced resistance to bacterial and fungal pathogens by overexpression of a human cathelicidin antimicrobial peptide (hCAP18/LL-37) in Chinese cabbage. Plant Biotechnol Rep 6: 39-46.
47. Waddell WJ, (1956) A simple ultraviolet spectrophotometric method for the determination of protein. J Lab Clin Med 48: 311-314.
48. Garnier J, Gibrat JF, Robson B, (1996) GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol 266: 540-553.
49. Zhao G, London E, (2006) An amino acid "transmembrane tendency" scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: relationship to biological hydrophobicity. Protein Sci 15: 1987-2001.
50. Kyte J, Doolittle RF, (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
51. Bjellqvist B, Hughes GJ, Pasquali C, Paquet N, Ravier F, et al. (1993) The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 14: 1023-1031.
52. Stewart JC, (1980) Colorimetric determination of phospholipids with ammonium ferrothiocyanate. Anal Biochem 104: 10-14.
53. Cunha WG, Tinoco MLP, Pancoti HL, Ribeiro RE, Aragão FJL, (2010) High resistance to Sclerotinia sclerotiorum in transgenic soybean plants transformed to express an oxalate decarboxylase gene. Plant Pathology 59: 654-660.
54. Fehr WR, Caviness CE, Burmood DT, Penningt JS, (1971) Stage of development descriptions for soybeans, Glycine max (L) merrill. Crop Science 11: 929-931.