Empirical rules facilitate the search for binding sites on protein surfaces

Journal of Molecular Graphics and Modelling

Volumn 25, Issue 5, 2007, Pages 671-679

  te Heesen, Henrik ^a   Schlitter, Anna Melissa ^a   Schlitter, Jürgen ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

Binding sites; Docking; Drugs; Enzymes; Inhibition; Lead compounds; Lipinski's rule of five; Lysozyme; Proteins; Ras; Ras Raf interaction; RO5

Indexed keywords

BINDING ENERGY; DRUG PRODUCTS; ENZYME INHIBITION; LEAD COMPOUNDS; MOLECULAR DYNAMICS; SURFACE CHEMISTRY;

BINDING SITES; LYSOZYME; MOLECULAR GRAPHICAL EVALUATION; RAS-RAF INTERACTION;

PROTEINS;

BACTERIORHODOPSIN; LYSOZYME; PROTEIN; RAF PROTEIN; RAS PROTEIN;

ARTICLE; AUTOMATION; BINDING SITE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

BACTERIORHODOPSINS; BINDING SITES; COMPUTER GRAPHICS; COMPUTER SIMULATION; MODELS, MOLECULAR; MURAMIDASE; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; RAS PROTEINS;

EID: 33846696047     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2006.05.005     Document Type: Article

References (27)

1. Jones S., and Thornton J.M. Analysis of protein-protein interaction sites using surface patches. J. Mol. Biol. 272 (1997) 121-132
2. Jones S., and Thornton J.M. Prediction of protein-protein interaction sites using patch analysis. J. Mol. Biol. 272 (1997) 133-143
3. Halperin I., Ma B.Y., Wolfson H., and Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins-Structure Funct. Genet. 47 (2002) 409-443
4. Kuntz I.D., Blaney J.M., Oatley S.J., Langridge R., and Ferrin T.E. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161 (1982) 269-288
5. Laskowski R.A. Surfnet-a program for visualizing molecular-surfaces, cavities, and intermolecular interactions. J. Mol. Graph. 13 (1995) 323-330
6. Brady G.P., and Stouten P.F.W. Fast prediction and visualization of protein binding pockets with PASS. J. Comput-Aided Mol. Des. 14 (2000) 383-401
7. Binkowski T.A., Naghibzadeg S., and Liang J. CASTp: computed atlas of surface topography of proteins. Nucl. Acid Res. 31 (2003) 3352-3355
8. Lipinski C.A. Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov. Today: Technol. 1 (2004) 337-341
9. Lipinski C.A., Lombardo F., Dominy B.W., and Feeney P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 23 (1997) 3-25
10. Congreve M., Carr R., Murray C., and Jhoti H. A rule of three for fragment-based lead discovery?. Drug Discov. Today 8 (2003) 876-877
11. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The Protein Data Bank. Nucl. Acids Res. 28 (2000) 235-242
12. Vetter I.R., and Wittinghofer A. Signal transduction-the guanine nucleotide-binding switch in three dimensions. Science 294 (2001) 1299-1304
13. Wittinghofer A., and Waldmann H. Ras-a molecular switch involved in tumor formation. Angew. Chem. Int. Ed. 39 (2000) 4192-4214
14. Stryer L. Biochemistry (1995), Freeman, San Francisco
15. Belrhali H., Nollert P., Royant A., Menzel C., Rosenbusch J.P., Landau E.M., and Pebay-Peyroula E. Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 Å resolution. Structure 7 (1999) 909-917
16. Kandt C., Schlitter J., and Gerwert K. Dynamics of water molecules in the bacteriorhodopsin trimer in explicit lipid/water environment. Biophys. J. 86 (2004) 705-717
17. Kandt C., Gerwert K., and Schlitter J. Water dynamics simulation as a tool for probing proton transfer pathways in a heptahelical membrane protein. Proteins-Structure Funct. Bioinform. 58 (2005) 528-537
18. Agmon N. The Grotthus mechanism. Chem. Phys. Lett. 244 (1995) 456-462
19. Garczarek F., and Gerwert K. Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature 439 (2006) 109-112
20. Muller O., Gourzoulidou E., Carpintero M., Karaguni I.M., Langerak A., Herrmann C., Moroy T., Klein-Hitpass L., and Waldmann H. Identification of potent Ras signaling inhibitors by pathway-selective phenotype-based screening. Angew. Chem. Int. Ed. 43 (2004) 450-454
21. Spoerner M., Graf T., Konig B., and Kalbitzer H.R. A novel mechanism for the modulation of the Ras-effector interaction by small molecules. Biochem. Biophys. Res. Commun. 334 (2005) 709-713
22. Scheffzek K., Ahmadian M.R., Kabsch W., Wiesmuller L., Lautwein A., Schmitz F., and Wittinghofer A. The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science 277 (1997) 333-338
23. Boriack-Sjodin P.A., Margarit S.M., Bar-Sagi D., and Kuriyan J. The structural basis of the activation of Ras by Sos. Nature 394 (1998) 337-343
24. Klähn M., Schlitter J., and Gerwert K. Theoretical IR spectroscopy based on QM/MM calculations provides changes in charge distribution, bond lengths and bond angles of the GTP ligand induced by the Ras-protein. Biophys. J. 88 (2005) 3829-3844
25. Nassar M., Horn G., Herrmann C., Scherer A., McCormick F., and Wittinghofer A. The 2.2 Å crystal structure of the ras-binding domain of the serine threonine kinase c-raf1 in complex with rap1a and a gtp analogue. Nature 375 (1995) 554-560
26. Scheidig A.J., Burmester C., and Goody R.S. The pre-hydrolysis state of p21(ras) in complex with GTP: new insights into the role of water molecules in the GTP hydrolysis reaction of ras-like proteins. Structure 7 (1999) 1311-1324
27. Ahmadian M.R., Kiel C., Stege P., and Scheffzek K. Structural fingerprints of the Ras-GTPase activating proteins neurofibromin and p120GAP. J. Mol. Biol. 329 (2003) 699-710