Association and dissociation kinetics of colicin E3 and immunity protein 3: Convergence of theory and experiment

Protein Science

Volumn 12, Issue 10, 2003, Pages 2379-2382

  Zhou, Huan Xiang ^a  

^a Florida State University   (United States)

Author keywords

Electrostatic rate enhancement; Flexible linker; Immunity protein; Protein protein association; Ribonuclease colicin

Indexed keywords

COLICIN; COLICIN E3; IMMUNITY PROTEIN 3; PROTEIN; PROTEIN IM3; RIBONUCLEASE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; DISSOCIATION; ELECTRICITY; ENZYME BINDING; IONIC STRENGTH; KINETICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; X RAY ANALYSIS;

ALGORITHMS; BACTERIAL PROTEINS; BINDING SITES; CATALYTIC DOMAIN; COLICINS; ELECTROSTATICS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; KINETICS; MODELS, MOLECULAR; PROTEIN BINDING; RIBONUCLEASES;

EID: 0141746353     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.03216203     Document Type: Article

References (23)

1. Baerga-Ortiz, A., Rezaie, A.R., and Komives, E.A. 2000. Electrostatic dependence of the thrombin-thrombomodulin interaction. J. Mol. Biol. 296: 651-658.
2. Carr, S., Walker, D., James, R., Kleanthous, C., and Hemmings, A.M. 2000. Inhibition of a ribosome-inactivating ribonuclease: The crystal structure of the cytotoxic domain of colicin E3 in complex with its immunity protein. Struct. Fold. Des. 8: 949-960.
3. Darling, R.J., Kuchibhotla, U., Glaesner, W., Micanovic, R., Witcher, D.R., and Beals, J.M. 2002. Glycosylation of erythropoietin affects receptor binding kinetics: Role of electrostatic interactions. Biochemistry 41: 14524-14531.
4. Elcock, A.H., Gabdoulline, R.R., Wade, R.C., and McCammon, J.A. 1999. Computer simulation of protein-protein association kinetics: Acetylcholinesterase-fasciculin. J. Mol. Biol. 291: 149-162.
5. Escobar, L., Root, M.J., and MacKinnon, R. 1993. Influence of protein surface charge on the bimolecular kinetics of a potassium channel peptide inhibitor. Biochemistry 32: 6982-6987.
6. Gabdoulline, R.R. and Wade, R.C. 1997. Simulation of the diffusional association of barnase and barstar. Biophys. J. 72: 1917-1929.
7. -. 2001. Protein-protein association: Investigation of factors influencing association rates by Brownian dynamics simulations. J. Mol. Biol. 306: 1139-1155.
8. Li, C., Zhao, D., Djebli, A., and Shoham, M. 1999. Crystal structure of colicin E3 immunity protein: An inhibitor of a ribosome inactivating RNase. Struct. Fold. Des. 7: 1365-1378.
9. Masaki, H., Akutsu, A., Uozumi, T., and Ohta, T. 1991. Identification of a unique specificity determinant of the colicia E3 immunity protein. Gene 107: 133-138.
10. Murrell-Lagnado, R.D. and Aldrich, R.W. 1993. Energetics of Shaker K channel's block by inactivation peptides. J. Gen. Physiol. 102: 977-1003.
11. Radic, Z., Kirchhoff, P.D., Quinn, D.M., McCammon, J.A., and Taylor, P. 1997. Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin. J. Biol. Chem. 272: 23266-23277.
12. Schreiber, G. and Fersht, A.R. 1993. Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering. Biochemistry 32: 5145-5150.
13. Shen, B.-J., Hage, T., and Sebald, W. 1996. Global and local determinants for the kinetics of interleukin-4/interleukin-4 receptor α chain interaction. A biosensor study employing recombinant interleukin-4-binding protein. Eur. J. Biochem. 240: 252-261.
14. Soelaiman, S., Jakes, K., Wu, N., Li, C., and Shoham, M. 2001. Crystal structure of colicin E3: Implications for cell entry and ribosome inactivation. Mol. Cell 8: 1053-1062.
15. Vijayakumar, M., Wong, K.-Y., Schreiber, G., Fersht, A.R., Szabo, A., and Zhou, H.-X. 1998. Electrostatic enhancement of diffusion-controlled protein-protein association: Comparison of theory and experiment on barnase and barstar. J. Mol. Biol. 278: 1015-1024.
16. Walker, D., Moore, G.R., James, R., and Kleanthous, C. 2003. Thermodynamic consequences of bipartite immunity protein binding to the ribosomal ribonuclease colicin E3. Biochemistry 42: 4161-4171.
17. Wallis, R., Moore, G.R., James, R., and Kleanthous, C. 1995. Protein-protein interactions in colicin E9 DNase-immunity protein complexes. 1. Diffusion-controlled association and femtomolar binding for the cognate complex. Biochemistry 34: 13743-13750.
18. Wendt, H., Leder, L., Harma, H., Jelesarov, I., Baici, A., and Bosshard, H.R. 1997. Very rapid, ionic strength-dependent association and folding of a heterodimeric leucine zipper. Biochemistry 36: 204-213.
19. Zhou, H.-X. 1993. Brownian dynamics study of the influences of electrostatic interaction and diffusion on protein-protein association kinetics. Biophys. J. 64: 1711-1726.
20. -. 1997. Enhancement of protein-protein association rate by interaction potential: Accuracy of prediction based on local Boltzmann factor. Biophys. J. 73: 2441-2445.
21. - 2001a. Disparate ionic-strength dependence of on and off rates in protein-protein association. Biopolymers 59: 427-433.
22. -. 2001b. The affinity-enhancing roles of flexible linkers in two-domain DNA-binding proteins. Biochemistry 40: 15069-15073.
23. -. 2003. Quantitative account of the enhanced affinity of two linked scFvs specific for different epitopes on the same antigen. J. Mol. Biol. 329: 1-8.