Interaction of a Salmonella enteritidis O-antigen octasaccharide with the phage P22 tailspike protein by NMR spectroscopy and docking studies

Glycoconjugate Journal

Volumn 25, Issue 2, 2008, Pages 137-143

  Landström, Jens ^a   Nordmark, Eva Lisa ^a   Eklund, Robert ^a   Weintraub, Andrej ^b   Seckler, Robert ^c   Widmalm, Göran ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

^b KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^c UNIVERSITY OF POTSDAM   (Germany)

Author keywords

Carbohydrates; Conformation; Docking; Hydrolase; Molecular dynamics; STD

Indexed keywords

BACTERIAL PROTEIN; CARBOHYDRATE DERIVATIVE; O ANTIGEN; OCTASACCHARIDE; PROTON; TAILSPIKE PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIOPHAGE P22; CONFORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; GENETIC ANALYSIS; MOLECULAR DOCKING; MOLECULAR DYNAMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN BINDING; SALMONELLA ENTERITIDIS; SIMULATION;

BACTERIOPHAGE P22; CARBOHYDRATE CONFORMATION; CARBOHYDRATE SEQUENCE; COMPUTER SIMULATION; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; O ANTIGENS; OLIGOSACCHARIDES; SALMONELLA ENTERITIDIS; VIRAL TAIL PROTEINS;

SALMONELLA ENTERITIDIS;

EID: 39049153352     PISSN: 02820080     EISSN: 15734986     Source Type: Journal    
DOI: 10.1007/s10719-007-9065-9     Document Type: Article

References (27)

1. Steinbacher S., Miller S., Baxa U., Budisa N., Weintraub A., Seckler R., Huber R.: Phage P22 tailspike protein: Crystal structure of the head-binding domain at 2.3 Å, fully refined structure of the endorhamnosidase at 1.56 Å resolution, and the molecular basis of the O-antigen recognition and cleavage. J. Mol. Biol. 267, 865-880 (1997)
2. Bundle D.R., Baumann H., Brisson J.-R., Gagné S.M., Zdanov A., Cygler M.: Solution structure of a trisaccharide-antibody complex: Comparison of NMR measurements with a crystal structure. Biochemistry 33, 5183-5192 (1994)
3. 1 predicted by semi-empirical, hard-sphere (HSEA) calculations. Carbohydr. Res. 130, 23-34 (1984)
4. Lemieux R.U., Koto S.: The conformational properties of glycosidic linkages. Tetrahedron 30, 1933-1944 (1974)
5. 13C-nuclear magnetic resonance spectroscopy. Carbohydr. Res. 130, 35-53 (1984)
6. Tang L., Marion W.R., Cingolani G., Prevelige Jr P.E., Johnson J.E.: Three-dimensional structure of the bacteriophage P22 tail machine. EMBO J. 24, 2087-2095 (2005)
7. Eriksson U., Svenson S.B., Lönngren J., Lindberg A.A.: Salmonella phage glycanases: Substrate specificity of the phage P22 endo-rhamnosidase. J. Gen. Virol. 43, 503-511 (1979)
8. Baxa U., Steinbacher S., Miller S., Weintraub A., Huber R., Seckler R.: Interactions of phage P22 tails with their cellular receptor, Salmonella O-antigen polysaccharide. Biophys. J. 71, 2040-2048 (1996)
9. Hwang T.-L., Kadkhodaei M., Mohebbi A., Shaka A.J.: Coherent and incoherent magnetization transfer in the rotating frame. Magn. Reson. Chem. 30, S24-S34 (1992).
10. Steinbacher S., Baxa U., Miller S., Weintraub A., Seckler R., Huber R.: Crystal structure of phage P22 tailspike protein complexed with Salmonella sp. O-antigen receptors. Proc. Natl. Acad. Sci. U S A 93, 10584-10588 (1996)
11. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., Olson A.J.: Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19, 1639-1662 (1998).
12. Eklund R.: Computational analysis of carbohydrates: Dynamical properties and interactions. Doctoral thesis, Stockholm University, Sweden (2005).
13. Kalé L., Skeel R., Bhandarkar M., Brunner R., Gursoy A., Krawetz N., Phillips J., Shinozaki A., Varadarajan K., Schulten K.: NAMD2: Greater scalability for parallel molecular dynamics. J. Comput. Phys. 151, 283-312 (1999).
14. Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kalé L., Schulten K.: Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781-1802 (2005)
15. MacKerell Jr A.D., Bashford D., Bellott M., Dunbrack Jr R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kushnir L., Kuczera K., Lau F.T.K., Mattos C., Michnick S., Ngo T., Nguyen T.D., Prodhom B., Reiher III W.E., Roux B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiórkiewicz-Kuczera J., Yin D., Karplus M.: All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102, 3586-3616 (1998)
16. Eklund R., Widmalm G.: Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates. Carbohydr. Res. 338, 393-398 (2003)
17. Pedretti A., Villa L., Vistoli G.: VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs. J. Mol. Graph Model. 21, 47-49 (2002).
18. Snyder D.S., Gibson D., Heiss C., Kay W., Azadi P.: Structure of a capsular polysaccharide isolated from Salmonella enteritidis. Carbohydr. Res. 341, 2388-2397 (2006).
19. Bevilacqua V.L., Thomson D.S., Prestegard J.H.: Conformation of a methyl β-lactoside bound to the ricin B-chain: Interpretation of transferred nuclear Overhauser effects facilitated by spin simulation and selective deuteration. Biochemistry 29, 5529-5537 (1990)
20. Baxa U., Cooper A., Weintraub A., Pfeil W., Seckler R.: Enthalpic barrier to the hydrophobic binding of oligosaccharides to phage P22 tailspike protein. Biochemistry 40, 5144-5150 (2001)
21. Clore G.M., Gronenborn A.M.: Theory and applications of the transferred nuclear Overhauser effect to the study of the conformations of small ligands bound to proteins. J. Magn. Reson. 48, 402-417 (1982)
22. Jackson P.L., Moseley H.N.B., Krishna N.R.: Relative effects of protein-mediated spin-diffusion pathways on transferred NOESY, and implications on the accuracy of the bound ligand conformation. J. Magn. Reson. Ser. B. 107, 289-292 (1995).
23. Poveda A., Jiménez-Barbero J.: NMR studies of carbohydrate-protein interactions in solution. Chem. Soc. Rev. 27, 133-143 (1998)
24. Meyer B., Peters T.: NMR spectroscopic techniques for screening and identifying ligand binding to protein receptors. Angew. Chem. Int. Ed. 42, 864-890 (2003)
25. Forsén S., Hoffman R.A.: Study of moderately rapid chemical exchange by means of nuclear magnetic double resonance. J. Chem. Phys. 39, 2892-2901 (1963)
26. Balaram P., Bothner-By A.A., Dadok J.: Negative nuclear Overhauser effects as probes of macromolecular structure. J. Am. Chem. Soc. 94, 4015-4017 (1972).
27. Yan J., Kline A.D., Mo H., Shapiro M.J., Zartler E.R.: The effect of relaxation on the epitope mapping by saturation transfer difference NMR. J. Magn. Reson. 163, 270-276 (2003)