Thermodynamic and structural analysis of interactions between peptide ligands and SEB

Journal of Molecular Recognition

Volumn 23, Issue 4, 2010, Pages 369-378

  Dudaka, Fahriye Ceyda ^a   Soykuta, Esra Acar ^a   Oǧuzb, Murat Erman ^a   Yaşar, Fatih ^a   Boyaci, Ismail Hakki ^a  

^a HACETTEPE UNIVERSITY   (Turkey)

Author keywords

Circular dichroism (CD); Isothermal titration calorimetry (ITC); Molecular dynamics (MD); Peptide ligands; Phage display; Staphylococcal enterotoxin B (SEB)

Indexed keywords

ENTEROTOXIN; ENTEROTOXIN B, STAPHYLOCOCCAL; PEPTIDE; PEPTIDE LIBRARY;

ARTICLE; CALORIMETRY; CIRCULAR DICHROISM; METABOLISM; MOLECULAR DYNAMICS; PROTEIN BINDING; THERMODYNAMICS;

CALORIMETRY; CIRCULAR DICHROISM; ENTEROTOXINS; MOLECULAR DYNAMICS SIMULATION; PEPTIDE LIBRARY; PEPTIDES; PROTEIN BINDING; THERMODYNAMICS;

STAPHYLOCOCCUS AUREUS;

EID: 77954736691     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.1003     Document Type: Article

References (45)

1. Berendsen HJC, Postma JPM, van Gunsteren WF, Dinola A, Haak JR. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81: 3684-3690.
2. Berendsen HJC, Postma JPM, van Gusteren WF, Hermans J. 1981. Interaction Models for Water in Relation to Protein Hydration. D. Reidel: Dordrecht; 331-342.
3. Bussi G, Donadio D, Parrinello M. 2007. Canonical sampling through velocity rescaling. J. Chem. Phys. 126: 014101.
4. Darden T, York D, Pedersen L. 1993. Particle mesh Ewald: an N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 98: 10089-10092.
5. Drabik P, Liwo A, Czaplewski C, Ciarkowski J. 2001. The investigation of the effects of counterions in protein dynamics simulations. Protein Eng. Des. Sel. 14: 747-752.
6. Enever C, Tomlinson IM, Lund J, Levens M, Holliger P. 2005. Engineering high affinity superantigens by phage display. J. Mol. Biol. 347: 107-120.
7. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. 1995. A smooth particle mesh Ewald method. J. Chem. Phys. 103: 8577-8593.
8. Goldman ER, Pazirandeh MP, Mauro JM, King KD, Frey JC, Anderson GP. 2000. Phage-displayed peptides as biosensor reagents. J. Mol. Recognit. 13: 382-387.
9. Goud H, Yanai Y, Sugawar A, Sunazuka T, Omura S, Hirono S. 2008. Computational analysis of the binding affinities of the naturalproduct cyclopentapeptides argifin and argadin to chininase B from Serratia marcescens. Bioorg. Med. Chem. 16: 3565-3579.
10. Greenfield N, Fasman GD. 1969. Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 8: 4108-4116.
11. Harteveld JLN, Nieuwenhuizen MS, Wils ERJ. 1997. Detection of staphylococcal enterotoxin B employing a piezoelectric crystal immunosensor. J. Microbiol. Meth. 7: 661-667.
12. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18: 1463-1472.
13. Homola J, Dostalek J, Chen S, Rasooly A, Jiang S, Yee SS. 2002. Spectral surface plasmon resonance biosensor for detection of staphylococcal enterotoxin B in milk. Int. J. Food Microbiol. 7: 61-69.
14. Humphrey W, Dalke A, Schulten K. 1996. VMD: Visual molecular dynamics. J. Mol. Graph. 14: 33-38.
15. Jelesarov I, Bosshard HR. 1999. Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetic of biomolecular recognition. J. Mol. Recognit. 12: 3-18.
16. Jorgensen WL, Severance DL. 1990. Aromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzene. J. Am. Chem. Soc. 112: 4768-4774.
17. Kabsch W, Sander C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers 22: 2577-2637.
18. King KD, Anderson GP, Bullock KE, Regina MJ, Saaski EW, Ligler FS. 1999. Detecting staphylococcal enterotoxin B using an automated fiber optic biosensor. Biosens. Bioelectron. 14: 163-170.
19. Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE. 2009. Long-timescale molecular dynamics simulations of protein structure and function. Curr. Opin. Struc. Biol. 19: 120-127.
20. Ladner RC, Sato AK, Gorzelany J, Souza M. 2004. Phage display-derived peptides as therapeutic alternatives to antibodies. Drug Discov. Today 9: 525-529.
21. Ler SG, Lee FK, Gopalakrishnakone P. 2006. Trends in detection of warfare agents: detection methods for ricin, staphylococcal enterotoxin B and T-2 toxin. J. Chromatogr. A 1133: 1-12.
22. Lin HC, Tsai WC. 2003. Piezoelectric crystal immunosensor for the detection of staphylococcal enterotoxin B. Biosens. Bioelectron. 18: 1479-1483.
23. Majava V, Petoukhov MV, Hayashi N, Pirila P, Svergun DI, Kursula P. 2008. Interaction between the C-terminal region of human myelin basic protein and calmodulin: analysis of complex formation and solution structure. BMC Struct. Biol. 8: 10.
24. Mourez M, Kane RS, Mogridge J, Metallo S, Deschateletes P, Sellman BR, Whitesides GM, Collier RJ. 2001. Designing a polyvalent inhibitor of anthrax toxin. Nat. Biotechnol. 19: 958-961.
25. Naimushin AN, Soelberg SD, Nguyen DK, Dunlap L, Bartholomew D, Elkind J, Melendez J, Furlong CE. 2002. Detection of Staphylococcus aureus enterotoxin B at femtomolar levels with a miniature integrated two-channel surface plasmon resonance (SPR) sensor. Biosens. Bioelectron. 17: 573-584.
26. Parrinello M, Rahman A. 1981. Polymorphic transitions in single-crystals: a new molecular dynamics method. J. Appl. Phys. 52: 7182-7190.
27. Petrenko VA, Vodyanoy VJ. 2003. Phage display for detection of biological threat agents. J. Microbiol. Meth. 53: 253-262.
28. Petrenko VA, Sorokulova IB. 2004. Detection of biological threats: a challenge for directed molecular evolution. J. Microbiol. Meth. 58: 147-168.
29. Ren PY, Ponder JW. 2002. Consistent treatment of interand intramolecular polarization in molecular mechanics calculations. J. Comput. Chem. 23: 1497-1506.
30. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning-A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press: New York.
31. Samoylov AM, Samoylova TI, Pathirana ST, Globa LP, Vodyanoy VJ. 2002. Peptide biosensor for recognition of cross-species cell surface markers. J. Mol. Recognit. 15: 197-203.
32. Sarikaya M, Tamerler C, Jen AKY, Schulten K, Baneyx F. 2003. Molecular biomimetics: nanotechnology through biology. Nat. Mater. 2: 577-585.
33. Schaeffer RD, Fersht A, Daggett V. 2008. Combining experiment and simulation in protein folding: closing the gap for small model systems. Curr. Opin. Struct. Biol. 18: 4-9.
34. Seibert M, Patrickson A, Hess B, van der Spoel D. 2005. Reproducible polypeptide folding and structure prediction using molecular dynamic simulations. J. Mol. Biol. 354: 173-183.
35. Sidhu SS, Fairbrother WJ, Deshayes K. 2003. Exploring protein-protein interactions with phage display. Chem. Bio. Chem. 4: 14-15.
36. Slavik R, Homola J, Brynda E. 2002. A miniature fiber optic surface plasmon resonance sensor for fast detection of staphylococcal enterotoxin B. Biosens. Bioelectron. 17: 591-595.
37. Smith GP. 1985. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228: 1315-1317.
38. Smith GP, Petrenko VA. 1997. Phage display. Chem. Rev. 97: 391-410.
39. Soykut EA, Dudak FC, Boyaci I.H. 2008. Selection of staphylococcal enterotoxin B (SEB)-binding peptide using phage display technology. Biochem. Bioph. Res. Co. 370: 104-108.
40. Sreerama N, Woody RW. 2000. Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set. Anal. Biochem. 287: 252-260.
41. Turnbough CL Jr. 2003. Discovery of phage display peptide ligands for species-specific detection of Bacillus spores. J. Microbiol. Meth. 53: 263-271.
42. Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC. 2005. GROMACS: Fast, flexible, and free. J. Comput. Chem. 26: 1701-1718.
43. Wang G, De J, Schoeniger JS, Roe DC, Carbonell RG. 2004. A hexamer peptide ligand that binds selectively to staphylococcal enterotoxin B: isolation from a solid phase combinatorial library. J. Peptide Res. 64: 51-64.
44. Zdanovsky AG, Karassina NV, Simpson D, Zdanovskaia MV. 2001. Peptide phage display library as source for inhibitors of clostridial neurotoxins. J. Protein Chem. 20: 73-80.
45. Zhao SW, Shen PP, Zhou Y, Wei Y, Xin XB, Hua ZC. 2005. Selecting peptide ligands of microcystin-LR from phage displayed random libraries. Environ. Int. 31: 535-541.