Conformational and dynamics simulation study of antimicrobial peptide hedistin-heterogeneity of its helix-turn-helix motif

Biochimica et Biophysica Acta - Biomembranes

Volumn 1788, Issue 12, 2009, Pages 2497-2508

  Xu, Guohua ^a   Wu, Min ^a   Wang, Lin ^a   Zhang, Xu ^b   Cao, Shufen ^a   Liu, Maili ^b   Cui, Yanfang ^a  

^a CENTRAL CHINA NORMAL UNIVERSITY   (China)

^b Wuhan National Laboratory for Optoelectronics   (China)

Author keywords

Antimicrobial peptide; Hedistin; Helix turn helix motif; Heterogeneity; Molecular dynamics simulation; Nuclear magnetic resonance

Indexed keywords

ALANINE; DODECYLPHOSPHORYLCHOLINE; HEDISTIN; LEUCINE; LYSINE; POLYPEPTIDE ANTIBIOTIC AGENT; THREONINE; UNCLASSIFIED DRUG; VALINE;

ALPHA HELIX; ANTIBACTERIAL ACTIVITY; AQUEOUS SOLUTION; ARTICLE; BACTERIAL MEMBRANE; CONTROLLED STUDY; DRUG CONFORMATION; DRUG STRUCTURE; LIPID BILAYER; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN LIPID INTERACTION; SIMULATION; STAPHYLOCOCCUS AUREUS;

ANIMALS; ANTI-INFECTIVE AGENTS; HELIX-LOOP-HELIX MOTIFS; LIPID BILAYERS; METHICILLIN RESISTANCE; PEPTIDES; PHOSPHATIDYLCHOLINES; POLYCHAETA; STAPHYLOCOCCUS AUREUS; VIBRIO ALGINOLYTICUS;

BACTERIA (MICROORGANISMS); METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; NEANTHES DIVERSICOLOR; VIBRIO ALGINOLYTICUS;

EID: 71749108758     PISSN: 00052736     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbamem.2009.10.001     Document Type: Article

References (69)

1. Hancock R.E.W., and Lehrer R. Cationic peptides: a new source of antibiotics. Trends Biotechnol. 16 (1998) 82-88
2. Marri L., Dallai R., and Marchini D. The novel antibacterial peptide ceratotoxin A alters permeability of the inner and outer membrane of Escherichia coli K-12. Curr. Microbiol. 33 (1996) 40-43
3. Hancock R.E.W. Cationic antimicrobial peptides: towards clinical applications. Expert Opin. Invest. Drugs 9 (2000) 1723-1729
4. Fridkin S.K., Yokoe D.S., Whitney C.G., Onderdonk A., and Hooper D.C. Epidemiology of a dominant clonal strain of vancomycin-resistant Enterococcus faecium at separate hospitals in Boston, Massachusetts. J. Clin. Microbiol. 36 (1998) 965-970
5. Donskey C.J., Schreiber J.R., Jacobs M.R., Shekar R., Salata R.A., Gordon S., Whalen C.C., Smith F., and Rice L.B. A polyclonal outbreak of predominantly VanB vancomycin-resistant enterococci in northeast Ohio. Northeast Ohio Vancomycin-Resistant Enterococcus Surveillance Program. Clin. Infect. Dis. 29 (1999) 573-579
6. Maple P.A., Hamilton-Miller J.M., and Brumfitt W. World-wide antibiotic resistance in methicillin-resistant Staphylococcus aureus. Lancet 11 (1989) 537-540
7. Martin M.A. Methicillin-resistant Staphylococcus aureus: the persistent resistant nosocomial pathogen. Curr. Clin. Top. Infect. Dis. 14 (1994) 170-191
8. Medzhitov R., and Janeway C.J. Innate immune recognition: mechanisms and pathways. Immunol. Rev. 173 (2000) 89-97
9. Mitta G., Vandenbulcke F., and Roch P. Original involvement of antimicrobial peptides in mussel innate immunity. FEBS Lett. 486 (2000) 185-190
10. Iwanaga S. The molecular basis of innate immunity in the horseshoe crab. Curr. Opin. Immunol. 14 (2002) 87-95
11. Bachere E., Gueguen Y., Gonzalez M., de Lorgeril J., Garnier J., and Romestand B. Insights into the anti-microbial defense of marine invertebrates: the penaeid shrimps and the oyster Crassostrea gigas. Immunol. Rev. 198 (2004) 149-168
12. Lee I.H., Zhao C., Cho Y., Harwig S.S., Cooper E.L., and Lehrer R.I. Clavanins, alpha-helical antimicrobial peptides from tunicate hemocytes. FEBS Lett. 400 (1997) 158-162
13. Lee I.H., Lee Y.S., Kim C.H., Kim C.R., Hong T., Menzel L., Boo L.M., Pohl J., Sherman M.A., Waring A., and Lehrer R.I. Dicynthaurin: an antimicrobial peptide from hemocytes of the solitary tunicate, Halocynthia aurantium. Biochim. Biophys. Acta 1527 (2001) 141-148
14. Tasiemski A., Schikorski D., Le Marrec-Croq F., Pontoire-Van Camp C., Boidin-Wichlacz C., and Sautière P.E. Hedistin, a novel antimicrobial peptide containing bromotryptophan constitutively expressed in the NK cells-like of the marine annelid, Nereis diversicolor. Dev. Comp. Immunol. 31 (2007) 749-762
15. Solé M., Kopecka-Pilarczyk J., and Blasco J. Pollution biomarkers in two estuarine invertebrates, Nereis diversicolor and Scrobicularia plana, from a Marsh ecosystem in SW Spain. Environ. Int. 35 (2009) 523-531
16. Tieleman D.P., and Marrink S.J. Lipids out of equilibrium: energetics of desorption and pore mediated flip-flop. J. Am. Chem. Soc. 128 (2006) 12462-12467
17. Pastor R.W., Venable R.M., and Feller S.E. Lipid bilayers, NMR relaxation, and computer simulations. Acc. Chem. Res. 35 (2002) 438-446
18. Ulmschneider M.B., Tieleman D.P., and Sansom M.S. The role of extra-membranous inter-helical loops in helix-helix interactions. Protein Eng. Des. Sel. 18 (2005) 563-570
19. Klauda J.B., Kucerka N., Brooks B.R., Pastor R.W., and Nagle J.F. Simulation-based methods for interpreting x-ray data from lipid bilayers. Biophys. J. 90 (2006) 2796-2807
20. Wade D., Boman A., Wahlin B., Drain C.M., Andreu D., Boman H.G., and Merrifield R.B. All-D amino acid-containing channel-forming antibiotic peptides. Proc. Natl. Acad. Sci. U. S. A. 87 (1990) 4761-4765
21. Bessalle R., Kapitkovsky A., Gorea A., Shalit I., and Fridkin M. All-d-magainin: chirality, antimicrobial activity and proteolytic resistance. FEBS Lett. 274 (1990) 151-155
22. Merrifield E.L., Mitchell S.A., Ubach J., Boman H.G., Andreu D., and Merrifield R.B. D-enantiomers of 15-residue cecropin A-melittin hybrids. Int. J. Pept. Protein Res. 46 (1995) 214-220
23. Ludtke S.J., He K., Heller W.T., Harroun T.A., Yang L., and Huang H.W. Membrane pores induced by magainin. Biochemistry 35 (1996) 13723-13728
24. Matsuzaki K., Murase O., Fujii N., and Miyajima K. An antimicrobial peptide, magainin 2, induced rapid flip-flop of phospholipids coupled with pore formation and peptide translocation. Biochemistry 35 (1996) 11361-11368
25. Gazit E., Boman A., Boman H.G., and Shai Y. Interaction of the mammalian antibacterial peptide cecropin P1 with phospholipid vesicles. Biochemistry 34 (1995) 11479-11488
26. Pouny Y., Rapaport D., Mor A., Nicolas P., and Shai Y. Interaction of antimicrobial dermaseptin and its fluorescently labeled analogs with phospholipid membranes. Biochemistry 31 (1992) 12416-12423
27. Choi G., Guo J., and Makriyannis A. The conformation of the cytoplasmic helix 8 of the CB1 cannabinoid receptor using NMR and circular dichroism. Biochim. Biophys. Acta 1668 (2005) 1-9
28. Perez C., Paul M., and Bazerque P. An antibiotic assay by the agar well diffusion method. Acta Biol. Med. Exp. 15 (1990) 113-115
29. Braunschweiler L., and Ernst R.R. Coherence transfer by isotropic mixing; application to proton correlation spectroscopy. J. Magn. Reson. 53 (1983) 521-528
30. 1HNMR spectra of proteins via double quantum filtering. Biochem. Biophys. Res. Commun. 117 (1983) 479-485
31. Kumar A., Ernst R.R., Wüthrich K., and two-dimensional nuclear Overhauser enhancement A. (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem. Biophys. Res. Commun. 95 (1980) 1-6
32. Marion D., Ikura M., Tschudin R., and Bax A. Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins. J. Magn. Reson. 85 (1989) 393-399
33. Piotto M., Saudek V., and Sklenar V. Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J. Biomol. NMR 2 (1992) 661-665
34. Smallcomb S.H., Patt S.L., and Keifer P.A. WET solvent suppression and its applications to LC NMR and high-resolution NMR spectroscopy. J. Magn. Reson. Ser. A 117 (1995) 295-303
35. Bax A., and Davis D.G. MLEV-17 based two-dimensional homonuclear magnetization transfer spectroscopy. J. Magn. Reson. 65 (1985) 355-360
36. Delaglio F., Grzesiek S., Vuister G.W., Zhu G., Pfeifer J., and Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6 (1995) 277-293
37. T. D. Goddard, D. G. Kneller, SPARKY 3, University of California, San Francisco.
38. Clore G.M., and Gronenborn A.M. Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy. Crit. Rev. Biochem. Mol. Biol. 24 (1989) 479-564
39. Wüthrich K., Billeter M., and Braun W. Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance. J. Mol. Biol. 169 (1983) 949-961
40. Clore G.M., Gronenborn A.M., Nilges M., and Ryan C.A. Three-dimensional structure of potato carboxypeptidase inhibitor in solution. A study using nuclear magnetic resonance, distance geometry, and restrained molecular dynamics. Biochemistry 26 (1987) 8012-8023
41. Brünger A.T., Adams P.D., Clore G.M., Delano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., Read R.J., Rice L.M., Simonson T., and Warren G.L. Crystallography and NMR system: a new software suit for macromolecular structure determination. Acta Crystallogr., Sect. D: Biol. Crystallogr. 54 (1998) 905-921
42. Koradi R., Billeter M., and Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structure. J. Mol. Graph. 14 (1996) 51-55
43. W.L. DeLano, The PyMOL Molecular Graphics System, DeLano Scientific, San Carlos, CA, USA ( http://www.pymol.org ), 2002.
44. Laskowski R., MacArthur M., Moss D., and Thornton J. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26 (1993) 283-291
45. Lindahl E., Hess B., and van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model 7 (2001) 306-317
46. Tieleman D.P., Sansom M.S.P., and Berendsen H.J.C. An alamethicin channel in a lipid bilayer: molecular dynamics simulation. Biophys. J. 76 (1999) 1757-1769
47. Hess B., Bekker H., Berendsen H.J.C., and Fraaije J.G.E.M. LINCS: a linear constraint solver for molecular simulations. J. Comp. Chem. 18 (1997) 1463-1472
48. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., and Pedersen L.G. A smooth particle mesh Ewald method. J. Chem. Phys. 103 (1995) 8577-8593
49. Humphrey W., Dalke A., and Schulten K. VMD: visual molecular dynamics. J. Mol. Graphics 14 (1996) 33-38
50. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Dinola A., and Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81 (1984) 3684-3690
51. Kandasamy S.K., and Larson R.G. Binding and insertion of alpha-helical anti-microbial peptides in POPC bilayers studied by molecular dynamics simulations. Chem. Phys. lipids 132 (2004) 113-132
52. Wüthrich K. NMR of protein and nucleic acid (1986), Wiley, New York
53. Wishart D.S., Sykes B.D., and Richards F.M. The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry 31 (1992) 1647-1651
54. Kabsch W., and Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (1983) 2577-2637
55. Wienk H.L.J., Czisch M., and Kruijff B. The structural flexibility of the preferredoxin transit peptide. FEBS Lett. 453 (1999) 318-326
56. 1H NMR spectroscopy: implications for biological functions. Biochemistry 37 (1998) 8527-8538
57. Gilbert G.E., and Baleja J.D. Membrane-binding peptide from the C2 domain of factor VIII forms an amphipathic structure as determined by NMR spectroscopy. Biochemistry 34 (1995) 3022-3031
58. Crowley P.B., and Golovin A. Cation-pi interactions in protein-protein interfaces. Proteins 59 (2005) 231-239
59. Khandelia H., and Kaznessis Y.N. Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations. J. Phys. Chem. B. 111 (2007) 242-250
60. Wang G.S. Structures of human host defense cathelicidin LL-37 and its smallest antimicrobial peptide KR-12 in lipid micelles. J. Biol. Chem. 283 (2008) 32637-32643
61. Wong H., Bowie J.H., and Carver J.A. The solution structure and activity of caerin 1.1, an antimicrobial peptide from the Australian green tree frog, Litoria spzendida. Eur. J. Biochem. 247 (1997) 545-557
62. Chia B.C., Carver J.A., Mulhern T.D., and Bowie J.H. Maculatin 1.1, an anti-microbial peptide from the Australian tree frog, Litoria genimaculata solution structure and biological activity. Eur. J. Biochem. 267 (2000) 1894-1908
63. Holak T.A., Engström A., Kraulis P.J., Lindeberg G., Bennich H., Jones T.A., Gronenborn A.M., and Clore G.M. The solution conformation of the antibacterial peptide cecropin A: a nuclear magnetic resonance and dynamical simulated annealing study. Biochemistry 27 (1988) 7620-7629
64. Subasinghage A.P., Conlon J.M., and Hewage C.M. Conformational analysis of the broad-spectrum antibacterial peptide, ranatuerin-2CSa: identification of a full length helix-turn-helix motif. Biochim. Biophys. Acta 1784 (2008) 924-929
65. Kohn W.D., Mant C.T., and Hodges R.S. α-helical protein assembly motifs. J. Biol. Chem 272 (1997) 2583-2586
66. Pukala T.L., Brinkworth C.S., Carver J.A., and Bowie J.H. Investigating the importance of the flexible hinge in caerin 1.1: solution structures and activity of two synthetically modified caerin peptides. Biochemistry 43 (2004) 937-944
67. Suh J.Y., Lee K.H., Chi S.W., Hong S.Y., Choi B.W., Moon H.M., and Choi B.S. Unusually stable helical kink in the antimicrobial peptide-a derivative of gaegurin. FEBS Lett. 392 (1996) 309-312
68. Mátyus E., Kandt C., and Tieleman D.P. Computer simulation of antimicrobial peptides. Curr. Med. Chem. 14 (2007) 2789-2798
69. Elmore D.E. Molecular dynamics simulation of phosphatidylglycerol membrane. FEBS Lett. 580 (2006) 144-148