Three-dimensional structure of the two peptides that constitute the two-peptide bacteriocin plantaricin EF

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1784, Issue 11, 2008, Pages 1711-1719

  Fimland, Nina ^a   Rogne, Per ^a   Fimland, Gunnar ^a   Nissen Meyer, Jon ^a   Kristiansen, Per Eugen ^a  

^a UNIVERSITY OF OSLO   (Norway)

Author keywords

Antimicrobial peptide; Lactic acid bacteria; NMR spectroscopy; Peptide structure; Plantaricin EF

Indexed keywords

BACTERIOCIN; PEPTIDE; PLANTARICIN E; PLANTARICIN F; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CIRCULAR DICHROISM; CONTROLLED STUDY; MICELLE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN MOTIF; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; BACTERIOCINS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDE FRAGMENTS; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 54049132071     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2008.05.003     Document Type: Article

References (79)

1. Boman H.G. Peptide antibiotics and their role in innate immunity. Annu. Rev. Immunol. 13 (1995) 61-92
2. Zasloff M. Antimicrobial peptides of multicellular organisms. Nature 415 (2002) 389-395
3. Nissen-Meyer J., and Nes I.F. Ribosomally synthesized antimicrobial peptides: their function, structure, biogenesis, and mechanism of action. Arch. Microbiol. 167 (1997) 67-77
4. Hancock R.E.W. Peptide antibiotics. Lancet 349 (1997) 418-422
5. Fimland G., and Nissen-Meyer J. Genetically modified bacteriocins. In: Riley M.A., and Gillor O. (Eds). Bacteriocins: Current Research and Applications (2007), Horizon Scientific Press, Norwich, United Kingdom 43-66
6. Cleveland J., Montville T.J., Nes I.F., and Chikindas M.L. Bacteriocins: safe, natural antimicrobials for food preservation. Int. J. Food Microbiol. 71 (2001) 1-20
7. Corr S.C., Li Y., Riedel C.U., O'Toole P.W., Hill C., and Gahan C.G.M. Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius UCC118. Proc. Natl. Acad. Sci. USA 104 (2007) 7617-7621
8. Nes I.F., Holo H., Fimland G., Hauge H.H., and Nissen-Meyer J. Unmodified peptide-bacteriocins (class II) produced by lactic acid bacteria. In: Dutton C.J., Haxell M.A., McArthur H.A.I., and Wax R.G. (Eds). Peptide Antibiotics, Discovery, Modes of Action and Application (2002), Marcel Decker, Inc., New York 81-115
9. Drider D., Fimland G., Hechard Y., McMullen L.M., and Prevost H. The continuing story of class IIa bacteriocins. Microbiol. Mol. Biol. Rev. 70 (2006) 564-582
10. Fimland G., Johnsen L., Dalhus B., and Nissen-Meyer J. Pediocin-like antimicrobial peptides (class IIa bacteriocins) and their immunity proteins: biosynthesis, structure, and mode of action. J. Pept. Sci. 11 (2005) 688-696
11. Oppegård C., Rogne P., Emanuelsen L., Kristiansen P.E., Fimland G., and Nissen-Meyer J. Two-peptide class II bacteriocins: structure production and mode of action. J. Mol. Microbiol. Biotechnol. 13 (2007) 210-219
12. Nissen-Meyer J., Holo H., Håvarstein L.S., Sletten K., and Nes I.F. A novel lactococcal bacteriocin whose activity depends on the complementary action of two peptides. J. Bacteriol. 174 (1992) 5686-5692
13. Anderssen E.L., Diep D.B., Nes I.F., Eijsink V.G., and Nissen-Meyer J. Antagonistic activity of Lactobacillus plantarum C11: two new two-peptide bacteriocins, plantaricins EF and JK, and the induction factor plantaricin A. Appl. Environ. Microbiol. 64 (1998) 2269-2272
14. Diep D.B., Håvarstein L.S., and Nes I.F. Characterization of the locus responsible for the bacteriocin production in Lactobacillus plantarum C11. J. Bacteriol. 178 (1996) 4472-4483
15. Flynn S., van Sinderen D., Thornton G.M., Holo H., Nes I.F., and Collins J.K. Characterization of the genetic locus responsible for the production of ABP-118, a novel bacteriocin produced by the probiotic bacterium Lactobacillus salivarius subsp salivarius UCC118. Microbiology 148 (2002) 973-984
16. Allison G.E., Fremaux C., and Klaenhammer T.R. Expansion of bacteriocin activity and host-range upon complementation of two peptides encoded within the lactacin F operon. J. Bacteriol. 176 (1994) 2235-2241
17. Stephens S.K., Floriano B., Cathcart D.P., Bayley S.A., Witt V.F., Jimenez-Diaz R., Warner P.J., and Ruiz-Barba J.L. Molecular analysis of the locus responsible for production of plantaricin S, a two-peptide bacteriocin produced by Lactobacillus plantarum LPCO10. Appl. Environ. Microbiol. 64 (1998) 1871-1877
18. Maldonado A., Ruiz-Barba J.L., and Jimenez-Diaz R. Purification and genetic characterization of plantaricin NC8, a novel coculture-inducible two-peptide bacteriocin from Lactobacillus plantarum NC8. Appl. Environ. Microbiol. 69 (2003) 383-389
19. McCormick J.K., Poon A., Sailer M., Gao Y., Roy K.L., McMullen L.M., Vederas J.C., Stiles M.E., and Van Belkum M.J. Genetic characterization and heterologous expression of brochocin-C, an antibotulinal, two-peptide bacteriocin produced by Brochothrix campestris ATCC 43754. Appl. Environ. Microbiol. 64 (1998) 4757-4766
20. van Belkum M.J., Hayema B.J., Jeeninga R.E., Kok J., and Venema G. Organization and nucleotide sequences of two lactococcal bacteriocin operons. Appl. Environ. Microbiol. 57 (1991) 492-498
21. Franz C.M.A.P., Grube A., Herrmann A., Abriouel H., Stärke J., Lombardi A., Tauscher B., and Holzapfel W.H. Biochemical and genetic characterization of the two-peptide bacteriocin enterocin 1071 produced by Enterococcus faecalis FAIR-E 309. Appl. Environ. Microbiol. 68 (2002) 2550-2554
22. Balla E., Dicks L.M.T., Du Toit M., van der Merwe M.J., and Holzapfel W.H. Characterization and cloning of the genes encoding enterocin 1071A and enterocin 1071B, two antimicrobial peptides produced by Enterococcus faecalis BFE 1071. Appl. Environ. Microbiol. 66 (2000) 1298-1304
23. Zendo T., Koga S., Shigeri Y., Nakayama J., and Sonomoto K. Lactococcin Q, a novel two-peptide bacteriocin produced by Lactococcus lactis QU 4. Appl. Environ. Microbiol. 72 (2006) 3383-3389
24. Qi F., Chen P., and Caufield P.W. The group I strain of Streptococcus mutans, UA140, produces both the lantibiotic mutacin I and a nonlantibiotic bacteriocin, mutacin IV. Appl. Environ. Microbiol. 67 (2001) 15-21
25. Cuozzo S.A., Sesma F., Palacios J.M., de Ruiz Holgado A.P., and Raya R.R. Identification and nucleotide sequence of genes involved in the synthesis of lactocin 705, a two-peptide bacteriocin from Lactobacillus casei CRL 705. FEMS Microbiol. Lett. 185 (2000) 157-161
26. Marciset O., Jeronimus Stratingh M.C., Mollet B., and Poolman B. Thermophilin 13, a nontypical antilisterial poration complex bacteriocin, that functions without a receptor. J. Biol. Chem. 272 (1997) 14277-14284
27. Moll G., Ubbink-Kok T., Hauge H.H., Nissen-Meyer J., Nes I.F., Konings W.N., and Driessen A.J.M. Lactococcin G is a potassium ion-conducting, two-component bacteriocin. J. Bacteriol. 178 (1996) 600-605
28. Moll G., Hauge H.H., Nissen-Meyer J., Nes I.F., Konings W.N., and Driessen A.J.M. Mechanistic properties of the two-component bacteriocin lactococcin G. J. Bacteriol. 180 (1998) 96-99
29. Moll G.N., van den Akker E., Hauge H.H., Nissen-Meyer J., Nes I.F., Konings W.N., and Driessen A.J.M. Complementary and overlapping selectivity of the two-peptide bacteriocins plantaricin EF and JK. J. Bacteriol. 181 (1999) 4848-4852
30. Abee T., Klaenhammer T.R., and Letellier L. Kinetic-studies of the action of lactacin F, a bacteriocin produced by Lactobacillus johnsonii that forms poration complexes in the cytoplasmic membrane. Appl. Environ. Microbiol. 60 (1994) 1006-1013
31. Cuozzo S.A., Castellano P., Sesma F.J.M., Vignolo G.M., and Raya R.R. Differential roles of the two-component peptides of lactocin 705 in antimicrobial activity. Curr. Microbiol. 46 (2003) 180-183
32. Gallagher N.L.F., Sailer M., Niemczura W.P., Nakashima T.T., Stiles M.E., and Vederas J.C. Three-dimensional structure of leucocin A in trifluoroethanol and dodecylphosphocholine micelles: spatial location of residues critical for biological activity in type IIa bacteriocins from lactic acid bacteria. Biochemistry 36 (1997) 15062-15072
33. Wang Y.J., Henz M.E., Gallagher N.L.F., Chai S.Y., Gibbs A.C., Yan L.Z., Stiles M.E., Wishart D.S., and Vederas J.C. Solution structure of carnobacteriocin B2 and implications for structure-activity relationships among type IIa bacteriocins from lactic acid bacteria. Biochemistry 38 (1999) 15438-15447
34. Uteng M., Hauge H.H., Markwick P.R.L., Fimland G., Mantzilas D., Nissen-Meyer J., and Muhle-Goll C. Three-dimensional structure in lipid micelles of the pediocin-like antimicrobial peptide sakacin P and a sakacin P variant that is structurally stabilized by an inserted C-terminal disulfide bridges. Biochemistry 42 (2003) 11417-11426
35. Haugen H.S., Fimland G., Nissen-Meyer J., and Kristiansen P.E. Three-dimensional structure in lipid micelles of the pediocin-like antimicrobial peptide curvacin A. Biochemistry 44 (2005) 16149-16157
36. Rogne P., Fimland G., Nissen-Meyer J., and Kristiansen P.E. Three-dimensional structure of the two peptides that constitute he two-peptide bacteriocin lactococcin G. Biochim. Biophys. Acta 1784 (2008) 543-554
37. Hauge H.H., Mantzilas D., Eijsink V.G.H., and Nissen-Meyer J. Membrane-mimicking entities induce structuring of the two-peptide bacteriocins plantaricin E/F and plantaricin J/K. J. Bacteriol. 181 (1999) 740-747
38. Huth J.R., Bewley C.A., Jackson B.M., Hinnebusch A.G., Clore G.M., and Gronenborn A.M. Design of an expression system for detecting folded protein domains and mapping macromolecular interactions by NMR. Prot. Sci. 6 (1997) 2359-2364
39. Koenig B.W., Rogowski M., and Louis J.M. A rapid method to attain isotope labeled small soluble peptides for NMR studies. J. Biomol. NMR 26 (2003) 193-202
40. Marley J., Lu M., and Bracken C. A method for efficient isotopic labeling of recombinant proteins. J. Biomol. NMR 20 (2001) 71-75
41. Sreerama N., and Woody R.W. Protein secondary structure from circular dichroism spectroscopy: combining variable selection principle and cluster analysis with neural network, ridge regression and self-consistent methods. J. Mol. Biol. 242 (1994) 497-507
42. Johnson W.C. Analyzing protein circular dichroism spectra for accurate secondary structures. Proteins, Struct., Funct., Genet. 35 (1999) 307-312
43. Sreerama N., and Woody R.W. A self-consistent method for the analysis of protein secondary structure from circular dichroism. Anal. Biochem. 209 (1993) 32-44
44. Sreerama N., and Woody R.W. Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal. Biochem. 287 (2000) 252-260
45. Scholtz J.M., Hong Q., York E.J., Stewart J.M., and Baldwin R.L. Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water. Biopolymers 31 (1991) 1463-1470
46. Sklenar V., and Bax A. Two-dimensional heteronuclear chemical-shift correlation in proteins at natural abundance N-15 and C-13 levels. J. Magn. Reson. 71 (1987) 379-383
47. Davis A.L., Keeler J., Laue E.D., and Moskau D. Experiments for recording pure-absorption heteronuclear correlation spectra using pulsed field gradients. J. Magn. Reson. 98 (1992) 207-216
48. Palmer A.G., Cavanagh J., Wright P.E., and Rance M. Sensitivity improvement in proton-detected two-dimensional heteronuclear correlation NMR-spectroscopy. J. Magn. Reson. 93 (1991) 151-170
49. Kay L.E., Keifer P., and Saarinen T. Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. J. Amer. Chem. Soc. 114 (1992) 10663-10665
50. Schleucher J., Schwendinger M., Sattler M., Schmidt P., Schedletzky O., Glaser S.J., Sorensen O.W., and Griesinger C. A general enhancement scheme in heteronuclear multidimensional NMR employing pulsed-field gradients. J. Biomol. NMR 4 (1994) 301-306
51. Jeener J., Meier B.H., Bachmann P., and Ernst R.R. Investigation of exchange processes by two-dimensional NMR-spectroscopy. J. Chem. Phys. 71 (1979) 4546-4553
52. Wuthrich K. NMR of Proteins and Nucleic Acids (1986), Wiley Interscience, New York
53. Braunschweiler L., and Ernst R.R. Coherence transfer by isotropic mixing: application to proton correlation spectroscopy. J. Mag. Res. 53 (1983) 521
54. Vuister G.W., and Bax A. Quantitative J correlation - a new approach for measuring homonuclear 3-bond J(H(N)H(alpha) coupling-constants in N-15-enriched proteins. Measurement of two-bond Jcoh alpha coupling-constants in proteins uniformly enriched with C-13. J. Am. Chem. Soc. 115 (1993) 7772-7777
55. Cavanagh J., and Rance M. Suppression of cross-relaxation effects in TOCSY spectra via a modified dipsi-2 mixing sequence. J. Magn. Reson. 96 (1992) 670-678
56. Rucker S.P., and Shaka A.J. Broad-band homonuclear cross polarization in 2d NMR using dipsi-2. Mol. Phys. 68 (1989) 509-517
57. Hwang T.L., and Shaka A.J. Water suppression that works - excitation sculpting using arbitrary wave-forms and pulsed-field gradients. J. Magn. Reson. Series A 112 (1995) 275-279
58. Wishart D.S., Bigam C.G., Yao J., Abildgaard F., Dyson H.J., Oldfield E., Markley J.L., and Sykes B.D. H-1, C-13 and N-15 chemical-shift referencing in biomolecular NMR. J. Biomol. NMR 6 (1995) 135-140
59. T.D. Goddard, D.G. Kneller, SPARKY 3, University of California, San Francisco.
60. Cornilescu G., Delaglio F., and Bax A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13 (1999) 289-302
61. Guntert P., Mumenthaler C., and Wuthrich K. Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol. 273 (1997) 283-298
62. Herrmann T., Guntert P., and Wuthrich K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J. Mol. Biol. 319 (2002) 209-227
63. Koradi R., Billeter M., and Wuthrich K. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14 (1996) 51
64. Wishart D.S., Sykes B.D., and Richards F.M. Simple techniques for the quantification of protein secondary structure by H-1-NMR spectroscopy. FEBS Lett. 293 (1991) 72-80
65. Wishart D.S., Sykes B.D., and Richards F.M. Relationship between nuclear-magnetic-resonance chemical-shift and protein secondary structure. J. Mol. Biol. 222 (1991) 311-333
66. Cavanagh J., Faribrother W.J., Palmer A.G.I., Rance M., and Skeleton N.J. Protein NMR Spectroscopy, Principles and Practice. Second edition (2007), Academic Press, London
67. Chou J.J., Kaufman J.D., Stahl S.J., Wingfield P.T., and Bax A. Micelle-Induced Curvature in a Water-Insoluble HIV-1 Env Peptide Revealed by NMR Dipolar Coupling Measurement in Stretched Polyacrylamide. Gel. J. Am. Chem. Soc. 124 (2002) 2450-2451
68. Garneau S., Ference C.A., van Belkum M.J., Stiles M.E., and Vederas J.C. Purification and characterization of brochocin A and brochocin B(10-43), a functional fragment generated by heterologous expression in Carnobacterium piscicola. Appl. Environ. Microbiol. 69 (2003) 1352-1358
69. Hauge H.H., Nissen-Meyer J., Nes I.F., and Eijsink V.G.H. Amphiphilic alpha-helices are important structural motifs in the alpha and beta peptides that constitute the bacteriocin lactococcin G: enhancement of helix formation upon alpha-beta interaction. Eur. J. Biochem. 251 (1998) 565-572
70. Cordes F.S., Bright J.N., and Sansom M.S.P. Proline-induced distortions of transmembrane helices. J. Mol. Biol. 323 (2002) 951-960
71. Bright J.N., and Sansom M.S.P. The flexing/twirling helix: exploring the flexibility about molecular hinges formed by proline and glycine motifs in transmembrane helices. J. Phys. Chem. B 107 (2003) 627-636
72. Chang D.K., Cheng S.F., Trivedi V.D., and Lin K.L. Proline affects oligomerization of a coiled coil by inducing a kink in a long helix. J. Struct. Biol. 128 (1999) 270-279
73. Yun R.H., Anderson A., and Hermans J. Proline in alpha-helix - stability and conformation studied by dynamics simulation. Proteins, Struct. Funct., Genet. 10 (1991) 219-228
74. Macarthur M.W., and Thornton J.M. Influence of proline residues on protein conformation. J. Mol. Biol. 218 (1991) 397-412
75. Senes A., Engel D.E., and DeGrado W.F. Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. Curr. Opin. Struct. Biol. 14 (2004) 465-479
76. Schneider D., and Engelman D.M. Motifs of two small residues can assist but are not sufficient to mediate transmembrane helix interactions. J. Mol. Biol. 343 (2004) 799-804
77. Sal-Man N., Gerber D., and Shai Y. The composition rather than position of polar residues (QxxS) drives aspartate receptor transmembrane domain dimerization in Vivo. Biochemistry 43 (2004) 2309-2313
78. Oppegard C., Fimland G., Thorbaek L., and Nissen-Meyer J. Analysis of the two-peptide bacteriocins lactococcin G and enterocin 1071 by site-directed mutagenesis. Appl. Environ. Microbiol. 73 (2007) 2931-2938
79. Diep D.B., Skaugen M., Salehian Z., Holo H., and Nes I.F. Common mechanisms of target cell recognition and immunity for class II bacteriocins. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 2384-2389