Molecular dynamics simulations on the free and complexed N-terminal SH2 domain of SHP-2

In Silico Biology

Volumn 2, Issue 3, 2002, Pages 305-311

  Wieligmann, Karion ^a   Pineda De Castro, Luis Felipe ^a   Zacharias, Martin ^a  

^a Inst fuk Molek Biotechnol (IMB)   (Germany)

Author keywords

Allosteric conformational change; Conformational flexibility; Ligand receptor binding; Molecular dynamics; SH2 domains; SHP 2 phosphatase; Signal transduction

Indexed keywords

DNA; LIGAND; PEPTIDE; PHOSPHATASE; PHOSPHOTYROSINE; PROTEIN; RECEPTOR PROTEIN; PROTEIN TYROSINE PHOSPHATASE; SIGNAL PEPTIDE; SRC HOMOLOGY 2 (SH2) DOMAIN CONTAINING PHOSPHATASES; SRC HOMOLOGY-2 (SH2) DOMAIN-CONTAINING PHOSPHATASES;

ALLOSTERISM; AMINO TERMINAL SEQUENCE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; COMPARATIVE STUDY; CONFERENCE PAPER; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DISSOCIATION CONSTANT; DNA FLANKING REGION; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME INACTIVATION; LIGAND BINDING; MOLECULAR DYNAMICS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; SIMULATION; SRC HOMOLOGY DOMAIN; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN CONFORMATION;

ALLOSTERIC REGULATION; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN-TYROSINE-PHOSPHATASE; SIGNAL TRANSDUCTION; SRC HOMOLOGY DOMAINS;

EID: 0036459375     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (11)

1. Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheathman III, T.E., Ross, W.S., Simmerling, C., Darden, T., Merz, K.M., Stanton, R.V., Cheng, A., Vincent, J.J., Crowley, M., Ferguson, D.M., Radmer, R., Seibel, G.L., Singh, U.C., Weiner, P. and Kollman, P.A., (1997). AMBER 5.0 (San Francisco, CA, UCSF).
2. Cornell, W.D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz Jr., K.M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W. and Kollman, P.A., (1995). A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117, 5179-5197.
3. Darden, T., York, D. and Pedersen, L., (1993). Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089-10092.
4. Eck, M.J., Plusky, S., Trüb, T., Harrison, S.C. and Shoelson, S.E., (1996). Spatial constraints on the recognition of phosphoproteins by tandem SH2 domains of the phosphatase SH-PTP2. Nature 379, 277-280.
5. Hof, P., Pluskey, S., Dhe-Paganon, S., Eck, M.J. and Shoelson, S.E., (1998). Crystal structure of the tyrosine phosphatase SHP-2. Cell 92, 441-450.
6. Huyer, G. and Ramachandran, C., (1998). The specifity of the N-terminal SH2 domain of SHP-2 is modified by a single point mutation. Biochemistry 37, 2741-2747.
7. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W. and Klein M.L., (1983). Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
8. Kuriyan, J. and Cowburn, D., (1993). Structures of SH2 and SH3 domains. Curr. Opin. Struct. Biol. 3, 828-837.
9. Lee, C.H., Kominos, D., Jacques, S., Margolis, B., Schlessinger, J., Shoelson, S.E. and Kuriyan, J., (1994). Crystal structures of peptide complexes of the amino-terminal SH2 domain of the Syp tyrosine phosphatase. Structure 2, 423-438.
10. Shoelson, S.E., (1997). SH2 and PTB domain interactions in tyrosine kinase signal transduction. Curr. Opin. Chem. Biol. 1, 227-234.
11. Waksman, G., Shoelson, S.E., Pant, N., Cowburn, D. and Kuriyanm, J. (1993). Binding of a high affinity phosphotyrosyl peptide to the Src SH2 domain: Crystal structures of the complexed and peptide-free forms. Cell 72, 779-790.