Quantum-dynamical picture of a multistep enzymatic process: Reaction catalyzed by phospholipase A2

Biophysical Journal

Volumn 79, Issue 3, 2000, Pages 1253-1262

  Bala P ^a,b   Grochowski, P ^a   Nowinski K ^a   Lesyng, B ^a,c   McCammon, J A ^d  

^a UNIVERSITY OF WARSAW   (Poland)

^b NICOLAUS COPERNICUS UNIVERSITY   (Poland)

^c UNIVERSITY OF WARSAW   (Poland)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONYL DERIVATIVE; PHOSPHOLIPASE A;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; ENZYME ACTIVE SITE; ENZYME MECHANISM; MOLECULAR DYNAMICS; MOLECULAR MODEL; PROTON TRANSPORT; QUANTUM MECHANICS; REACTION ANALYSIS;

EID: 0033857499     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(00)76379-X     Document Type: Article

References (16)

1. Alagona, G., C. Ohio, and P. A. Kollman. 1996. Chemical reaction mechanisms in vacuo, in solution and in enzyme fields: isomerization catalyzed by triose phosphate isomerase (TIM). Theochemistry. 371:287-298.
2. Alhambra, C., J. L. Gao, J. C. Corchado, D. Villa, and D. G. Truhlar. 1999. Quantum mechanical dynamical effects in an enzyme-catalyzed proton transfer reaction. J. Am. Chem. Soc. 121:2253-2258.
3. Bahnson, B. J., and J. P. Klinman. 1995. Hydrogen tunneling in enzyme catalysis. Methods Enzymol. 249:373-397.
4. Bala, P., T. W. Clark, P. Grochowski, B. Lesyng, and J. A. McCammon. 1997. Parallel version of the combined quantum classical molecular dynamics code for complex molecular and biomolecular systems. In Recent Advances in Parallel Virtual Machine and Message Passing Interface. M. Bubak and J. Dongarra, editors. Lecture Notes in Computer Science, Vol. 1332. Springer-Verlag, Berlin and Heidelberg. 409-416.
5. Bala, P., T. Clark, P. Grochowski, B. Lesyng, K. Nowinski, and J. A. McCammon. 1998a. Advanced simulations and visualization of enzymatic reactions using a combined quantum-classical molecular dynamics code. In Recent Advances in Applied Parallel Computing. B. Kågström, J. Dongarra, E. Elmroth, and J. Wasniewski, editors. Lecture Notes in Computer Science, Vol. 1541. Springer-Verlag, Berlin. 20-27.
6. Bala, P., P. Grochowski, B. Lesyng, and J. A. McCammon. 1995. Quantum-classical molecular dynamics and its computer implementation. Comput. Chem. 19:155-160.
7. 2. In Quantum Mechanical Simulations Methods for Studying Biological Systems. M. Field, editor. Springer-Verlag, Berlin, Heidelberg, and Les Editions de Physique, Les Ulis.115-196.
8. Bala, P., P. Grochowski, B. Lesyng, and J. A. McCammon. 1996b. Quantum-classical molecular dynamics simulations of proton transfer processes in molecular complexes and in enzymes. J. Phys. Chem. 100:2535-2545.
9. 2. Her. Bunsenges. Phys. Chem. 102:580-586.
10. Bala, P., B. Lesyng, and J. A. McCammon. 1994a. Applications of quantum-classical and quantum-stochastic molecular dynamics simulations for proton transfer processes. Chem. Phys. 180:271-285.
11. Bala, P., B. Lesyng, and J. A. McCammon. 1994b. Extended Hellmann-Feynman theorem for non-stationary states and its application in quantum-classical molecular dynamics simulations. Chem. Phys. Lett. 219:259-266.
12. Bala, P., B. Lesyng, T. N. Truong, and J. A. McCammon. 1992. Ab initio studies and quantum-classical molecular dynamics for proton transfer in model systems and in enzymes. In The Role of Computational Models and Theories in Biotechnology. J. Bertran, editor. NATO ASI Series. Kluwer, Dordrecht, the Netherlands. 299-326.
13. Bamford, C. H. 1978. Proton Transfer. Elsevier Scientific Publishers, Amsterdam and New York.
14. Basran, J., M. J. Sutcliffe, and N. S. Scrutton. 1999. Enzymatic H-transfer requires vibration-driven extreme tunneling. Biochemistry. 38:3218-3222.
15. Bell, R. P. 1980. The Tunnel Effect in Chemistry. Chapman and Hall, New York.
16. Bennion, C., S. Connolly, and N. P. Gensmantel. 1992. Design and synthesis of some substrate analogue inhibitors of phospholipase A2. and investigations by NMR and molecular modeling into the binding interactions in the enzyme-inhibitor complex. J. Med. Chem. 35:2939-2946.