In silico identification of novel hevein-like peptide precursors

Peptides

Volumn 38, Issue 1, 2012, Pages 127-136

  Porto, William F ^a   Souza, Valéria A ^a   Nolasco, Diego O ^a,b   Franco, Octávio L ^a  

^a UNIVERSIDADE CATÓLICA DE BRASÍLIA   (Brazil)

^b Curso de Educação Física da UCB   (Brazil)

Author keywords

Data mining; Fungal hevein like peptide; Hevein domain; Molecular dynamics simulation; Molecular modeling; Regular expression

Indexed keywords

GLUCOSAMINE; HEVEIN; HEVEIN LIKE PEPTIDE PRECURSOR; N,N,N TRIACETYLGLUCOSAMINE; UNCLASSIFIED DRUG;

ARTICLE; BETA SHEET; COMPLEX FORMATION; COMPUTER MODEL; DATA BASE; DISULFIDE BOND; FUNGUS; FUNGUS IDENTIFICATION; GRAPE; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PHAEOSPHAERIA NODORUM; PLANT DEFENSE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE; RICE; SELAGINELLA; SELAGINELLA MOELLENDORFFII; SEQUENCE ANALYSIS; SIMULATION;

ACETYLGLUCOSAMINE; AMINO ACID SEQUENCE; ANTIMICROBIAL CATIONIC PEPTIDES; ASCOMYCOTA; COMPUTER SIMULATION; DATABASES, PROTEIN; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PLANT LECTINS; PLANT PROTEINS; PROTEIN CONFORMATION; PROTEIN PRECURSORS; SELAGINELLACEAE; VITIS;

FUNGI; ORYZA SATIVA; PHAEOSPHAERIA NODORUM; SELAGINELLA MOELLENDORFFII; VITIS VINIFERA;

EID: 84866280179     PISSN: 01969781     EISSN: 18735169     Source Type: Journal    
DOI: 10.1016/j.peptides.2012.07.025     Document Type: Article

References (65)

1. N. Aboitiz, M. Vila-Perelló, P. Groves, J.L. Asensio, D. Andreu, and F.J. Cañada NMR and modeling studies of protein-carbohydrate interactions: synthesis, three-dimensional structure, and recognition properties of a minimum hevein domain with binding affinity for chitooligosaccharides Chembiochem 5 9 2004 1245 1255
2. S.F. Altschul, T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, and W. Miller Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res 25 17 1997 3389 3402
3. Y.A. Andreev, T.V. Korostyleva, A.A. Slavokhotova, E.A. Rogozhin, L.L. Utkina, and A.A. Vassilevski Genes encoding hevein-like defense peptides in wheat: distribution, evolution, and role in stress response Biochimie 94 2012 1009 1016 10.1016/j.biochi.2011.12.023
4. B.L. Archer The proteins of Hevea brasiliensis Latex. 4. Isolation and characterization of crystalline hevein Biochem J 75 1960 236 240
5. N.A. Baker, D. Sept, S. Joseph, M.J. Holst, and J.A. McCammon Electrostatics of nanosystems: application to microtubules and the ribosome Proc Natl Acad Sci USA 98 18 2001 10037 10041
6. J.J. Beintema, and W.J. Peumans The primary structure of stinging nettle (Urtica dioica) agglutinin. A two-domain member of the hevein family FEBS Lett 299 2 1992 131 134
7. J.J. Beintema Structural features of plant chitinases and chitin-binding proteins FEBS Lett 350 1994 159 163 10.1016/0014-5793(94)00753-5
8. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans Interaction models for water in relation to protein hydration B. Pullman, Intermolecular Force 1981 Dordrecht Reidel 331 342
9. W.F. Broekaert, W. Marien, F.R.G. Terras, M.F.C. De Bolle, P. Proost, and J. Van Damme Antimicrobial peptides from Amaranthus caudatus seeds with sequence homology to the cysteine/glycine-rich domain of chitin-binding proteins Biochemistry 31 17 1992 4308 4314
10. M.I. Chávez, M. Vila-Perelló, F.J. Cañada, D. Andreu, and J. Jiménez-Barbero Effect of a serine-to-aspartate replacement on the recognition of chitin oligosaccharides by truncated hevein. A 3D view by using NMR Carbohydr Res 345 10 2010 1461 1468 10.1016/j.carres.2010.02.019
11. T. Darden, D. York, and L. Pedersen Particle mesh Ewald: An N log(N) method for Ewald sums in large systems J Chem Phys 98 1993 10089 10092
12. P.L. De Holf, L.M. Brill, and A.M. Hirsch Plant lectins: the ties that bind in root symbiosis and plant defense Mol Genet Genomics 282 2009 1 15 10.1007/s00438-009-0460-8
13. R.A. Dean, N.J. Talbot, D.J. Ebbole, M.L. Farman, T.K. Mitchell, and M.J. Orbach The genome sequence of the rice blast fungus Magnaporthe grisea Nature 434 7036 2005 980 986
14. N. Eswar, M.A. Marti-Renomet, B. Webb, M.S. Madhusudhan, D. Eramian, and M. Shen Comparative protein structure modeling with MODELLER Curr Protoc Bioinform Suppl. 15 2007 5.6.1 5.6.30
15. F.C. Fernandes, W.F. Porto, and O.L. Franco A wide antimicrobial peptides search method using fuzzy modeling. Advances in bioinformatics and computational biology LNCS 5676 2009 147 150 10.1007/978-3-642-03223-3-14
16. O.L. Franco Peptide promiscuity: an evolutionary concept for plant defense FEBS Lett 585 7 2011 995 1000
17. N. Guex, and M.C. Peitsch SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling Electrophoresis 18 15 1997 2714 2723
18. H. Hasegawa, and L. Holm Advances and pitfalls of protein structural alignment Curr Opin Struct Biol 19 2009 341 348
19. M. Hayashida, T. Fujii, M. Hamasu, M. Ishiguro, and Y. Hata Similarity between protein-protein and protein-carbohydrate interactions, revealed by two crystal structures of lectins from the roots of pokeweed J Mol Biol 334 3 2003 551 565
20. J.J. Hernández-Gay, A. Ardá, S. Eller, S. Mezzato, B.R. Leeflang, and C. Unverzagt Insights into the dynamics and molecular recognition features of glycopeptides by protein receptors: the 3D solution structure of hevein bound to the trisaccharide core of N-glycoproteins Chem Eur J 16 2010 10715 10726 10.1002/chem.201000939
21. B. Hess, H. Bekker, H.J.C. Berendsen, and J.G.E.M. Fraaije LINCS. A linear constant solver for molecular simulations J Comp Chem 18 12 1997 1463 1472
22. B. Hess, C. Kutzner, D. van der Spoel, and E. LIndahl GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J Chem Theory Comput 4 2008 435 447
23. L. Holm, and P. Rosenström Dali server: conservation mapping in 3D Nucleic Acids Res 38 2010 W545 W549
24. R.H. Huang, Y. Xiang, G.Z. Tu, Y. Zhang, and D.C. Wang Solution structure of Eucommia antifungal peptide: a novel structural model distinct with a five-disulfide motif Biochemistry 43 20 2002 6005 6012
25. J. Inbar, and I. Chet A newly isolated lectin from the plant pathogenic fungus Sclerotium roltsii: purification, characterization and role in mycoparasitism Microbiology 140 1994 651 657 10.1099/00221287-140-3-651
26. M. Jayanthi, P. Kangueane, N.A.U. Prakash, D.V.A. Jigisha, and K. Sekar Influence of disulfide bonds on the conformation of the antifungal protein from Eucommia ulmoides Oliver Open Struct Biol J 3 2009 94 103
27. I. Jonassen, J.F. Collins, and D.G. Higgins Finding flexible patterns in unaligned protein sequences Protein Sci 4 8 1995 1587 1595
28. L. Käll, A. Krogh, and E.L. Sonnhammer Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server Nucleic Acids Res 35 2007 W429 W432 [Web Server issue]
29. T. Kamakura, S. Yamaguchi, K. Saitoh, T. Teraoka, and I. Yamaguchi A novel gene, CBP1, encoding a putative extracellular chitin-binding protein, may play an important role in the hydrophobic surface sensing of Magnaporthe grisea during appressorium differentiation Mol Plant Microbe Interact 15 5 2002 437 444
30. Y. Kezuka, M. Kojima, R. Mizuno, K. Suzuki, T. Watanabe, and T. Nonaka Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering Proteins 78 10 2010 2295 2305
31. M.R. Khaliluev, A.G. Mamonov, A.N. Smirnov, P.N. Kharchenko, and S.V. Dolgov Expression of genes encoding chitin binding proteins (PR 4) and hevein like antimicrobial peptides in transgenic tomato plants enhanced resistance to Phytophthora infestance Russ Agric Sci 37 4 2011 297 302 10.3103/ S1068367411040082
32. S. Kolbe, S. Fischer, A. Becirevic, P. Hinz, and H. Schrempf The Streptornyces reticuli α-chitin-binding protein CHBZ and its gene Microbiology 144 1998 1291 1297 10.1099/00221287-144-5-1291
33. J.C. Koo, H.J. Chun, H.C. Park, M.C. Kim, Y.D. Koo, and S.C. Koo Over-expression of a seed specific hevein-like antimicrobial peptide from Pharbitis nil enhances resistance to a fungal pathogen in transgenic tobacco plants Plant Mol Biol 50 3 2002 441 452
34. J.C. Koo, S.Y. Lee, H.J. Chun, Y.H. Cheong, J.S. Choi, and S. Kawabata Two hevein homologs isolated from the seed of Pharbitis nil L. exhibit potent antifungal activity Biochim Biophys Acta 1382 1998 80 90
35. R.A. Laskowski, J.A. Rullmannn, M.W. MacArthur, R. Kaptein, and J.M. Thornton AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR J Biomol NMR 8 4 2007 477 486
36. S. Lata, B.K. Sharma, and G.P. Raghava Analysis and prediction of antibacterial peptides BMC Bioinform 8 2007 263 10.1186/1471-2105-8-263
37. A. Lipkin, V. Anisimova, A. Nikonorova, A. Babakov, E. Krause, and M. Bienert An antimicrobial peptide Ar-AMP from amaranth (Amaranthus retroflexus L.) seeds Phytochemistry 66 2005 2426 2431 10.1016/j.phytochem.2005.07.015
38. C. Loose, K. Jensen, I. Rigoutsos, and G. Stephanopoulos A linguistic model for the rational design of antimicrobial peptides Nature 443 7113 2006 867 869
39. Y. Luo, X. Xu, J. Liu, J. Li, Y. Sun, and Z. Liu A novel mannose-binding tuber lectin from Typhonium divaricatum (L.) Decne (family Araceae) with antiviral activity against HSV-II and anti-proliferative effect on human cancer cell lines J Biochem Mol Biol 40 3 2007 358 367
40. J.C. Martins, D. Maes, R. Loris, H.A. Pepermans, L. Wyns, and R. Willem H NMR study of the solution structure of Ac-AMP2, a sugar binding antimicrobial protein isolated from Amaranthus caudatus J Mol Biol 258 2 1996 322 333
41. S. Miyamoto, and P.A. Kollman SETTLE. An analytical version of the SHAKE and RATTLE algorithm for rigid water models J Comp Chem 13 8 1992 952 962
42. J.P. Mulvenna, J.S. Mylne, R. Bharathi, R.A. Burton, N.J. Shirley, and G.B. Fincher Discovery of cyclotide-like protein sequences in graminaceous crop plants: ancestral precursors of circular proteins? Plant Cell 18 9 2006 2134 2144
43. T.I. Odintsova, A.A. Vassilevski, A.A. Slavokhotova, A.K. Musolyamov, E.I. Finkina, and N.V. Khadeeva A novel antifungal hevein-type peptide from Triticum kiharae seeds with a unique 10-cysteine motif FEBS J 276 15 2009 4266 4275
44. T.N. Petersen, S. Brunak, G. von Heijne, and H. Nielsen SignalP 4.0: discriminating signal peptides from transmembrane regions Nat Methods 8 10 2011 785 786 10.1038/nmeth.1701
45. W.J. Peumans, and J.M. Van Damme Lectins as piant defense proteins Plant Physiol 109 1995 347 352
46. W.F. Porto, F.C. Fernandes, and O.L. Franco An SVM model based on physicochemical properties to predict antimicrobial activity from protein sequences with cysteine knot motifs LNCS 6268 2010 59 62 10.1007/978-3-642- 15060-9-6
47. E. Quevillon, V. Silventoinen, S. Pillai, N. Harte, N. Mulder, and R. Apweiler InterProScan: protein domains identifier Nucleic Acids Res 33 2005 W116 W120 [Web Server issue]
48. C.A. Reyes-López, A. Hernández-Santoyo, M. Pedraza-Escalona, G. Mendoza, A. Hernández-Arana, and A. Rodríguez-Romero Insights into a conformational epitope of Hev b 6.02 (hevein) Biochem Biophys Res Commun 314 2004 123 130
49. D. Schwefel, C. Maierhofer, J.G. Beck, S. Seeberger, K. Diederichs, and H.M. Möller Structural basis of multivalent binding to wheat germ agglutinin J Am Chem Soc 132 25 2010 8704 8719
50. H. Shinshi, J.M. Neuhas, J. Ryals, and F. Meins Jr. Structure of a tobacco endochitinase gene: evidence that different chitinase genes can arise by transposition of sequences encoding a cysteine-rich domain Plant Mol Biol 14 3 1990 357 368
51. K.K. Shukurov, V.D. Voblikoba, A.K. Nikonorova, T.A. Egorov, E.V. Grishin, and A.V. Babakov Increase of resistance of Arabidopsis thaliana plants to phytopathogenic fungi expressing hevein like peptides from weed plant Stellaria media Russ Agric Sci 36 4 2010 265 267 10.3103/S1068367410040117
52. K.K. Shukurov, V.D. Voblikova, A.K. Nikonorova, R.A. Komakhin, V.V. Komakhina, and T.A. Egorov Transformation of tobacco and Arabidopsis plants with Stellaria media genes encoding novel hevein-like peptides increases their resistance to fungal pathogens Transgenic Res 2011 10.1007/s11248-011-9534-6
53. H.C. Siebert, S.Y. Lu, R. Wechselberger, K. Born, T. Eckert, and S. Liang A lectin from the Chinese bird-hunting spider binds sialic acids Carbohydr Res 344 12 2009 1515 1525 10.1016/j.carres.2009.06.002
54. K.A.T. Silverstein, W.A. Moskal, H.C. Wu, B.A. Underwood, M.A. Graham, and C.D. Town Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants Plant J 51 2 2007 262 280 10.1111/j.1365-313X.2007.03136.x
55. U.M. Soedjanaatmadja, J. Hofsteenge, C.M. Jeronimus-Stratingh, A.P. Bruins, and J.J. Beintema Demonstration by mass spectrometry that pseudo-hevein and hevein have ragged C-terminal sequences Biochim Biophys Acta 1209 1994 144 148
56. The UniProt Consortium Reorganizing the protein space at the Universal Protein Resource (UniProt) Nucleic Acids Res 40 2012 D71 D75
57. S. Thomas, S. Karnik, R.S. Barai, V.K. Jayaraman, and S. Idicula-Thomas CAMP: a useful resource for research on antimicrobial peptides Nucleic Acids Res 38 2010 D774 D778 [Database issue]
58. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 22 22 1994 4673 4680
59. H.P. van Esse, M.D. Bolton, I. Stergiopoulos, P.J.G.M. de Wit, and B.P.H.J. Thomma The chitin-binding Cladosporium fulvum effector protein Avr4 is a virulence factor Mol Plant Microbe Interact 20 9 2007 1092 1101 10.1094/MPMI-20-9-1092
60. W. Voelter, R. Wacker, M. Franz, T. Maier, and S. Stoeva Complete structural characterization of a chitin-binding lectin from mistletoe extracts J Prakt Chem 342 2000 812 818 10.1002/1521-3897(200010)342:8<812::AID- PRAC812>3.0.CO;2-J
61. M. Wiederstein, and M.J. Sippl ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins Nucleic Acids Res 35 2007 W407 W410 [Web Server issue]
62. H.T. Wright, G. Sandrasegaram, and C.S. Wright Evolution of a family of N-acetylglucosamine binding proteins containing the disulfide-rich domain of wheat germ agglutinin J Mol Evol 33 3 1991 283 294 10.1007/BF02100680
63. S. Wu, and Y. Zhang LOMETS: a local meta-threading-server for protein structure prediction Nucleic Acids Res 35 10 2007 3375 3382
64. Y. Xiang, R.H. Huang, X.Z. Liu, Y. Zhang, and D.C. Wang Crystal structure of a novel antifungal protein distinct with five disulfide bridges from Eucommia ulmoides Oliver at an atomic resolution J Struct Biol 148 2004 86 97
65. S. Zhu Discovery of six families of fungal defensin-like peptides provides insights into origin and evolution of the CSαβ defensins Mol Immunol 45 3 2008 828 838