Molecular dynamics study on the ligand recognition by tandem SH3 domains of p47phox, regulating NADPH oxidase activity

Computational Biology and Chemistry

Volumn 30, Issue 4, 2006, Pages 303-312

  Watanabe, Yoko ^a   Tsuboi, Hideyuki ^a   Koyama, Michihisa ^a   Kubo, Momoji ^a,b   Del Carpio, Carlos A ^a   Broclawik, Ewa ^a   Ichiishi, Eiichiro ^a   Kohno, Masahiro ^a   Miyamoto, Akira ^a  

^a TOHOKU UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Ligand recognition; Molecular dynamics; NADPH oxidase; PPII helix; SH3 domain

Indexed keywords

LIGAND RECOGNITION; NADPH OXIDASE; PPII HELIX; SH3 DOMAIN;

ACTIVATION ANALYSIS; ENZYME KINETICS; IMMUNOLOGY; MICROBIOLOGY; MOLECULAR DYNAMICS; OXIDES;

ENZYMES;

CYBA PROTEIN, HUMAN; LIGAND; NEUTROPHIL CYTOSOLIC FACTOR 1; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE OXIDASE;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENZYME ACTIVATION; HUMAN; METABOLISM; PROTEIN BINDING; SRC HOMOLOGY DOMAIN; TIME; X RAY CRYSTALLOGRAPHY;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; ENZYME ACTIVATION; HUMANS; LIGANDS; MODELS, MOLECULAR; NADPH OXIDASE; PROTEIN BINDING; SRC HOMOLOGY DOMAINS; TIME FACTORS;

EID: 33746377929     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2006.04.004     Document Type: Article

References (29)

1. phox. J. Biol. Chem. 274 (1999) 33644-33653
2. phox directs phox homology domain from SH3 domain toward phosphoinositides. Leading to phagocyte NADPH oxidase activation. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 4474-4479
3. Benard V., Bokoch G.M., and Diebold B.A. Potential drug targets: small GTPases that regulate leukocyte function. Trends Pharmacol. Sci. 20 (1999) 365-370 10.1016/S0165-6147(99)01367-X
4. Born M. Volumen und hydratationswarme der ionen. Z. Phys. 1 (1920) 45-48
5. Casimir C., Chetty M., Bohler M.C., Garcia R., Fischer A., Griscelli C., Johnson B., and Segal A.W. Identification of the defective NADPH-oxidase component in chronic granulomatous disease: a study of 57 European families. Eur. J. Clin. Invest. 22 (1992) 403-406
6. DeLeo F.R., and Quinn M.T. Assembly of the phagocyte NADPH oxidase: molecular interaction of oxidase proteins. J. Leukocyte Biol. 60 (1996) 677-691
7. Ghosh A., Rapp C.S., and Friesner R.A. Generalized Born model based on a surface integral formulation. J. Phys. Chem. B 102 (1998) 10983-10990 10.1021/jp982533o
8. Groemping Y., Lapouge K., Smerdon S.J., and Rittinger K. Molecular basis of phosphorylation-induced activation of the NADPH oxidase. Cell 113 (2003) 343-355 10.1016/S0092-8674(03)00314-3
9. Guex N., and Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18 (1997) 2714-2723 10.1002/elps.1150181505
10. phox. J. Biol. Chem. 274 (1999) 19731-19737
11. 558. Biochemistry 34 (1995) 16753-16757
12. Jorgensen W.L., Maxwell D.S., and Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformation energetics and properties of organic liquids. J. Am. Chem. Soc. 118 (1996) 11225-11236 10.1021/ja9621760
13. Kuriyan J., and Cowburn J. Modular peptide recognition domains in eukaryotic signaling. Annu. Rev. Biophys. Biomol. Struct. 26 (1997) 259-288 10.1146/annurev.biophys.26.1.259
14. Leto T.L., Adams A.G., and de Mendez I. Assembly of the phagocyte NADPH oxidase: binding of Src homology 3 domains to proline-rich targets. Proc. Natl. Acad. Sci. U.S.A. 91 (1994) 10650-10654
15. Mayer B.J. SH3 domains: complexity in moderation. J. Cell Sci. 114 (2001) 1253-1263
16. Miller R.A., and Britigan B.E. The formation and biologic significance of phagocyte-derived oxidants. J. Invest. Med. 43 (1995) 39-49
17. Morris A.L., MacArthur M.W., Hutchinson E.G., and Thornton J.M. Assessing the accuracy of protein structural coordinates. Proteins: Struct. Funct. Genet. 12 (1992) 345-364
18. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., and Ferrin T.E. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25 (2004) 1605-1612 10.1002/jcc.20084
19. Roos D., de Boer M., Kuribayashi F., Meischl C., Weening R.S., Segal A.W., Ahlin A., Nemet K., Hossle J.P., Bernatowska-Matuszkiewicz E., and Middleton-Price H. Mutations in the X-linked and autosomal recessive forms of chronic granulomatous disease. Blood 87 (1996) 1663-1681
20. Shenkin P.S., and McDonald D.Q. Cluster analysis of molecular conformations. J. Comput. Chem. 15 (1994) 899-916
21. Still W.C., Tempczyk A., Hawley R.C., and Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112 (1990) 6127-6129
22. Sumimoto H., Kage Y., Nunoi H., Sasaki H., Nose T., Fukumaki Y., Ohno M., Minakami S., and Takeshige K. Role of Src homology 3 domains in assembly and activation of the phagocyte NADPH oxidase. Proc. Natl. Acad. Sci. U.S.A. 91 (1994) 5345-5349
23. Sumimoto H., Hata K., Mizuki K., Ito T., Kage Y., Sakaki Y., Fukumaki Y., Nakamura M., and Takeshige K. Assembly and activation of the phagocyte NADPH oxidase. J. Biol. Chem. 271 (1996) 22152-22158
24. Thrasher A.J., Keep N.H., Wientjes F., and Segal A.W. Chronic granulomatous disease. Biochim. Biophys. Acta 1227 (1994) 1-24 10.1016/0925-4439(94)90100-7
25. Verlet L. Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159 (1967) 98-103 10.1103/PhysRev.159.98
26. Wallace A.C., Laskowski R.A., and Thornton J.M. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8 (1995) 127-134
27. phox. Acta Crystallogr. D 59 (2003) 1479-1480
28. phox, the regulatory subunit of the phagocyte NADPH oxidase. Genes Cells 9 (2004) 443-456
29. Zhang L., Gallicchio E., Friesner R., and Levy R.M. Solvent models for protein-ligand binding: comparison of implicit solvent Poisson and surface generalized Born models with explicit solvent simulations. J. Comput. Chem. 22 (2001) 591-607 10.1002/jcc.1031