Prediction of solvation sites at the interface of Src SH2 domain complexes using molecular dynamics simulations

Chemical Biology and Drug Design

Volumn 70, Issue 2, 2007, Pages 87-99

  Geroult, Sebastien ^a   Hooda, Manisha ^a   Virdee, Satpal ^a   Waksman, Gabriel ^a,b  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Accessible surface area; Computational chemistry; Heat capacity change; Molecular dynamics; Phosphotyrosine; Protein ligand interaction; SH2 domain; Solvation; Structure; Thermodynamics

Indexed keywords

LIGAND; PROTEIN SH2;

ARTICLE; BINDING SITE; COMPUTER PROGRAM; COMPUTER SIMULATION; CRYSTAL STRUCTURE; ENTROPY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN PHOSPHORYLATION; PROTEIN STRUCTURE; SOLVATION; THERMODYNAMICS;

BINDING SITES; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; SOFTWARE; SRC HOMOLOGY DOMAINS; THERMODYNAMICS; WATER;

EID: 34547774584     PISSN: 17470277     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2007.00545.x     Document Type: Article

References (34)

1. Pawson T., Scott J.D. (1997) Signaling through scaffold, anchoring, and adaptor proteins. Science 278 : 2075 2080.
2. Pawson T. (2003) Organization of cell-regulatory systems through modular-protein-interaction domains. Philos Transact A Math Phys Eng Sci 361 : 1251 1262.
3. Kuriyan J., Cowburn D. (1997) Modular peptide recognition domains in eukaryotic signaling. Annu Rev Biophys Biomol Struct 26 : 259 288.
4. Bradshaw J.M., Waksman G. (2002) Molecular recognition by SH2 domains. Adv Protein Chem 61 : 161 210.
5. Waksman G., Kumaran S., Lubman O. (2004) SH2 domains: role, structure and implications for molecular medicine. Expert Rev Mol Med 6 : 1 18.
6. Bradshaw J.M., Grucza R.A., Ladbury J.E., Waksman G. (1998) Probing the "two-pronged plug two-holed socket" model for the mechanism of binding of the Src SH2 domain to phosphotyrosyl peptides: a thermodynamic study. Biochemistry 37 : 9083 9090.
7. Bradshaw J.M., Waksman G. (1998) Calorimetric investigation of proton linkage by monitoring both the enthalpy and association constant of binding: application to the interaction of the Src SH2 domain with a high-affinity tyrosyl phosphopeptide. Biochemistry 37 : 15400 15407.
8. Bradshaw J.M., Waksman G. (1999) Calorimetric examination of high-affinity Src SH2 domain-tyrosyl phosphopeptide binding: dissection of the phosphopeptide sequence specificity and coupling energetics. Biochemistry 38 : 5147 5154.
9. Bradshaw J.M., Mitaxov V., Waksman G. (1999) Investigation of phosphotyrosine recognition by the SH2 domain of the Src kinase. J Mol Biol 293 : 971 985.
10. Davidson J.P., Lubman O., Rose T., Waksman G., Martin S.F. (2002) Calorimetric and structural studies of 1,2,3-trisubstituted cyclopropanes as conformationally constrained peptide inhibitors of Src SH2 domain binding. J Am Chem Soc 124 : 205 215.
11. Grucza R.A., Bradshaw J.M., Mitaxov V., Waksman G. (2000) Role of electrostatic interactions in SH2 domain recognition: salt-dependence of tyrosyl-phosphorylated peptide binding to the tandem SH2 domain of the Syk kinase and the single SH2 domain of the Src kinase. Biochemistry 39 : 10072 10081.
12. Bradshaw J.M., Mitaxov V., Waksman G. (2000) Mutational investigation of the specificity determining region of the Src SH2 domain. J Mol Biol 299 : 521 535.
13. Lubman O.Y., Waksman G. (2003) Structural and thermodynamic basis for the interaction of the Src SH2 domain with the activated form of the PDGF beta-receptor. J Mol Biol 328 : 655 668.
14. Lubman O.Y., Waksman G. (2002) Dissection of the energetic coupling across the Src SH2 domain-tyrosyl phosphopeptide interface. J Mol Biol 316 : 291 304.
15. Waksman G., Shoelson S.E., Pant N., Cowburn D., Kuriyan 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.
16. Geroult S., Virdee S., Waksman G. (2006) The role of water in computational and experimental derivation of binding thermodynamics in SH2 domains. Chem Biol Drug Des 67 : 38 45.
17. Luque I., Freire E. (1998) Structure-based prediction of binding affinities and molecular design of peptide ligands. Methods Enzymol 295 : 100 127.
18. Baker B.M., Murphy K.P. (1997) Dissecting the energetics of a protein-protein interaction: the binding of ovomucoid third domain to elastase. J Mol Biol 268 : 557 569.
19. Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kale L., Schulten K. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26 : 1781 1802.
20. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 4 : 187 217.
21. Humphrey W., Dalke A., Schulten K. (1996) VMD: visual molecular dynamics. J Mol Graph 14 : 33 38.
22. Baker B.M., Murphy K.P. (1998) Prediction of binding energetics from structure using empirical parameterization. Methods Enzymol 295 : 294 315.
23. Henriques D.A., Ladbury J.E., Jackson R.M. (2000) Comparison of binding energies of SrcSH2-phosphotyrosyl peptides with structure-based prediction using surface area based empirical parameterization. Protein Sci 9 : 1975 1985.
24. Lee B., Richards F.M. (1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55 : 379 400.
25. Murphy K.P., Freire E. (1992) Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv Protein Chem 43 : 313 361.
26. D'Aquino J.A., Gomez J., Hilser V.J., Lee K.H., Amzel L.M., Freire E. (1996) The magnitude of the backbone conformational entropy change in protein folding. Proteins 25 : 143 156.
27. Lee K.H., Xie D., Freire E., Amzel L.M. (1994) Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation. Proteins 20 : 68 84.
28. Henchman R.H., McCammon J.A. (2002) Extracting hydration sites around proteins from explicit water simulations. J Comput Chem 23 : 861 869.
29. Henchman R.H., Tai K., Shen T., McCammon J.A. (2002) Properties of water molecules in the active site gorge of acetylcholinesterase from computer simulation. Biophys J 82 : 2671 2682.
30. Ladbury J.E. (1996) Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design. Chem Biol 3 : 973 980.
31. Chung E., Henriques D., Renzoni D., Zvelebil M., Bradshaw J.M., Waksman G., Robinson C.V., Ladbury J.E. (1998) Mass spectrometric and thermodynamic studies reveal the role of water molecules in complexes formed between SH2 domains and tyrosyl phosphopeptides. Structure 6 : 1141 1151.
32. Dunitz J. (1994) The entropic cost of bound water in crystals and biomolecules. Science 264 : 670 674.
33. Clarke C., Woods R.J., Gluska J., Cooper A., Nutley M.A., Boons G.J. (2001) Involvement of water in carbohydrate-protein binding. J Am Chem Soc 123 : 12238 12247.
34. Ladbury J.E., Williams M.A. (2004) The extended interface: measuring non-local effects in biomolecular interactions. Curr Opin Struct Biol 14 : 562 569.