Profiling charge complementarity and selectivity for binding at the protein surface

Biophysical Journal

Volumn 84, Issue 5, 2003, Pages 2883-2896

  Sulea, Traian ^a   Purisima, Enrico O ^a  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

SOLVENT;

ARTICLE; ELECTRIC POTENTIAL; MOLECULAR RECOGNITION; PROTEIN BINDING; PROTEIN TARGETING; SIMULATION; SURFACE PROPERTY;

EID: 0038298792     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)70016-2     Document Type: Article

References (27)

1. Bayly, C, I., P. Cieplak, W. D. Comell, and P. A. Kollman. 1993. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 97:10269-10280.
2. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
3. Chong, L. T., S. E. Dempster, Z. S. Hendsch, L.-P. Lee, and B. Tidor. 1998. Computation of electrostatic complements to proteins: a case of charge stabilizing binding. Protein Sci. 7:206-210.
4. Cornell, W. D., P. Cieplak, C. I. Bayly, and P. A. Kollman. 1993. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J. Am. Chem. Soc. 115:9620-9631.
5. Comell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
6. Dewar, M. J. S., E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart. 1985. AM1: A new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 107:3902-3909.
7. Doyle, D. A., A. Lee, J. Lewis, E. Kim, M. Sheng, and R. MacKinnon. 1996. Crystal structure of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell. 85:1067-1076.
8. Helland, R., J. Otlewski, O. Sundheim, M. Dadlez, and A. O. Smalas. 1999. The crystal structures of the complexes between bovine β-trypsin and ten P1 variants of BPTI. J. Mol. Biol. 287:923-942.
9. Kangas, E., and B. Tidor. 2001. Electrostatic complementarity at ligand binding sites: application to chorismate mutase. J. Phys. Chem. B. 105: 880-888.
10. Kangas, E., and B. Tidor. 1998. Optimizing electrostatic affinity in ligand-receptor binding: theory, computation, and ligand properties. J. Chem. Phys. 109:7522-7545.
11. Katz, B. A., J. Finer-Moore, R. Mortezaei, D. H. Rich, and R. M. Stroud. 1995. Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface. Biochemistry. 34:8264-8280.
12. Krowarsch, D., M. Dadlez, O. Buczek, I. Krokoszynska, A. O. Smalas, and J. Otlewski. 1999. Interscaffolding additivity: binding of P1 variants of bovine pancreatic trypsin inhibitor to four serine proteases. J. Mol. Biol. 289:175-186.
13. Lee, L.-P., and B. Tidor. 2001a. Optimization of binding electrostatics: charge complementarity in the barnase-barstar protein complex. Protein Sci. 10:362-377.
14. Lee, L.-P., and B. Tidor. 2001b. Barstar is electrostatically optimized for tight binding to barnase. Nat. Struct. Biol. 8:73-76.
15. Lim, I. A., D. D. Hall, and J. W. Hell. 2002. Selectivity and promiscuity of the first and second PDZ domains of PSD-95 and synapse-associated protein 102. J. Biol. Chem. 277:21697-21711.
16. Mares-Guia, M., D. L. Nelson, and E. Rogana. 1977. Electronic effects in the interaction of para-substituted benzamidines with trypsin: the involvement of the π-electronic density at the central atom of the substituent in binding. J. Am. Chem. Soc. 99: 2331-2336.
17. Nicholls, A., K. A. Sharp, and B. Honig. 1991. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 11:281-296.
18. Niethammer, M., J. G. Valtschanoff, T. M. Kapoor, D. W. Allison, T. M. Weinberg, A. M. Craig, and M. Sheng. 1998. CRIPT, a novel postsynaptic protein that binds to the third PDZ domain of PSD-95/SAP90. Neuron. 20:693-707.
19. Purisima, E. O. 1998. Fast summation boundary element method for calculating solvation free energies of macromolecules. J. Comput. Chem. 19:1494-1504.
20. Purisima, E. O., and S. H. Nilar. 1995. A simple yet accurate boundary element method for continuum dielectric calculations. J. Comput. Chem. 16:681-689.
21. Schmidt, M. W., K. K. Baldridge, J. A. Boatz, S. T. Elbert, M. S. Gordon, J. H. Jensen, S. Koseki, N. Matsunaga, K. A. Nguyen, S. Su, T. L. Windus, M. Dupuis, and J. A. Montgomery. 1993. General atomic and molecular electronic structure system. J. Comput. Chem. 14: 1347-1363.
22. Sitkoff, D., K. A. Sharp, and B. Honig. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1978-1988.
23. Songyang, Z., A. S. Fanning, C. Fu, J. Xu, S. M. Marfatia, A. H. Chishti, A. Crompton, A. C. Chan, J. M. Anderson, and L. C. Cantley. 1997. Recognition of unique carboxyl-terminal motifs by distinct PDZ domains. Science. 275:73-77.
24. Stewart, J. J. P. 1990. MOPAC: A semiempirical molecular orbital program. J. Comput. Aided Mol. Des. 4:1-105.
25. Sulea, T., and E. O. Purisima. 2001. Optimizing ligand charges for maximum binding affinity. A solvated interaction energy approach. J. Phys. Chem. B. 105:889-899.
26. Vaccaro, P., B. Brannetti, L. Montecchi-Palazzi, S. Philipp, M. H. Citterich, G. Cesareni, and L. Dente. 2001. Distinct binding specificity of the multiple PDZ domains of INADL, a human protein with homology to INAD from Drosophila melanogaster. J. Biol. Chem. 276: 42122-42130.
27. Vorobjev, Y. N., and J. Hermans. 1997. SIMS: Computation of a smooth invariant molecular surface. Biophys. J. 73:722-732.