Determination of a unique solution to parallel proton transfer reactions using the genetic algorithm

Biophysical Journal

Volumn 87, Issue 1, 2004, Pages 47-57

  Moscovitch, D ^a   Noivirt, O ^a   Mezer, A ^a   Nachliel, E ^a   Mark, T ^a   Gutman, M ^a   Fibich, G ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BICARBONATE; BUFFER; CARBOXYLIC ACID; FLUORESCEIN; PYRAN DERIVATIVE; PYRANINE; UNCLASSIFIED DRUG; XANTHENE;

ACCURACY; ARTICLE; BINDING SITE; CALCULATION; DYNAMICS; GENETIC ALGORITHM; KINETICS; MATHEMATICAL MODEL; PH; PKA; PROTON TRANSPORT;

EID: 3042858789     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.039925     Document Type: Article

References (23)

1. Checover, S., Y. Marantz, E. Nachliel, M. Gutman, M. Pfeiffer, J. Tittor, D. Oesterhelt, and N. A. Dencher. 2001. Dynamics of the proton transfer reaction on the cytoplasmic surface of bacteriorhodopsin. Biochemistry. 40:4281-4292.
2. Checover, S., E. Nachliel, N. A. Dencher, and M. Gutman. 1997. Mechanism of proton entry into the cytoplasmic section of the proton-conducting channel of bacteriorhodopsin. Biochemistry. 36:13919-13928.
3. Eigen, M. 1964. Proton transfer, acid-base catalysis, and enzyme hydrolysis. Angew Chem. Int. Ed. Engl. 3:1-19.
4. Filipic, B., I. Zun, and M. Perpar. 2000. Skill-based interpretation of noisy probe signals enhanced with a genetic algorithm. Int. J. Hum. Comput. Stud. 53:517-535.
5. Gutman, M. 1984. The pH jump: probing of macromolecules and solutions by a laser-induced, ultrashort proton pulse-theory and applications in biochemistry. Methods Biochem. Anal. 30:1-103.
6. Gutman, M., and D. Huppert. 1979. Rapid pH and deltamuH+ jump by short laser pulse. J. Biochem. Biophys. Methods. 1:9-19.
7. Gutman, M., and E. Nachliel. 1990. The dynamic aspects of proton transfer processes. Biochim. Biophys. Acta. 1015:391-414.
8. Gutman, M., and E. Nachliel. 1997. Time-resolved dynamics of proton transfer in proteinous systems. Annu. Rev. Phys. Chem. 48:329-356.
9. Gutman, M., E. Nachliel, and E. Gershon. 1985. Effect of buffer on kinetics of proton equilibration with a protonable group. Biochemistry. 24:2937-2941.
10. Holland, J. H. 1970. Robust algorithms for adaptation set in a general formal framework. Proceedings of the 1970 IEEE Symposium on Adaptive Processes Decision and Control: XVII. ACM PRESS, New York.
11. Hongqing, C., Y. Jingxian, K. Lishan, C. Yuping, and C. Yongyan. 1999. The kinetic evolutionary modeling of complex systems of chemical reactions. Comput. Chem. 23:143-151.
12. Houck, C. J. J., and M. A. Kay. 1995. Genetic Algorithm for Function Optimization: A Matlab Implementation NCSU-IE TR 95-09.
13. Leardi, R. 2001. Genetic algorithm in chemometrics and chemistry: a review. ET J. 15:559-569.
14. Marantz, Y., E. Nachliel, and M. Gutman. 2001. Proton-collecting properties of bovine heart cytochrome C oxidase: kinetic and electrostatic analysis. Biochemistry. 40:15086-15097.
15. Gutman, M., E. Nachliel, A. Mezer, and O. Noivirt. 2003. Gauging of local micro-environment at protein water interface by time-resolved single-proton transfer reactions. Annals of the European Academy of Sciences. 1:75-107.
16. Nachliel, E., M. Gutman, S. Kiryati, and N. A. Dencher. 1996. Protonation dynamics of the extracellular and cytoplasmic surface of bacteriorhodopsin in the purple membrane. Proc. Natl. Acad. Sci. USA. 93:10747-10752.
17. Nachliel, E., M. Gutman, J. Tittor, and D. Oesterhelt. 2002. Proton transfer dynamics on the surface of the late M state of bacteriorhodopsin. Biophys. J. 83:416-426.
18. Nachliel, E., and M. Gutman. 2001. Probing the substrate binding domain of lactose permease by a proton pulse. Biochim. Biophys. Acta. 1514:33-50.
19. Robinson, R. A., and R. H. Stock. 1959. Electrolyte Solutions. Butterworths Publications Ltd., London, UK.
20. Shimoni, E., E. Nachliel, and M. Gutman. 1993. Gaugement of the inner space of the apomyoglobin's heme binding site by a single free diffusing proton. II. Interaction with a bulk proton. Biophys. J. 64:480-483.
21. Terry, D. B., and M. Messina. 1998. Heuristic search algorithms for the determination of rate constants and reaction mechanisms from limited concentration data. J. Chem. Inf. Comput. Sci. 38:1232-1238.
22. Viappiani, C., G. Bonetti, M. Carelli, F. Ferrati, and A. Stemieni. 1998. Study of proton transfer processes in solutions using the laser induced pH jump: a new experimental setup and an improved data analysis based on genetic algorithms. Rev. Sci. Instrum. 69:270-276.
23. Yam, R., E. Nachliel, and M. Gutman. 1988. Time-resolved proton-protein interaction. Methodology and kinetic analysis. J. Am. Chem. Soc. 110:2636-2640.