ISSN 0869-6632 (Print)
ISSN 2542-1905 (Online)


For citation:

Netrebko A. V., Netrebko N. V., Romanovsky Y. M., Hurgin J. I., Ebeling W. Stochastic cluster dynamics of enzyme - substrate complex. Izvestiya VUZ. Applied Nonlinear Dynamics, 1996, vol. 4, iss. 3, pp. 53-66.

This is an open access article distributed under the terms of Creative Commons Attribution 4.0 International License (CC-BY 4.0).
Full text PDF(Ru):
(downloads: 0)
Language: 
Russian
Article type: 
Article
UDC: 
539.194

Stochastic cluster dynamics of enzyme - substrate complex

Autors: 
Netrebko Aleksej Vasilevich, Lomonosov Moscow State University
Netrebko Nina Vladimirovna, Lomonosov Moscow State University
Romanovsky Yuri Mihajlovich, Lomonosov Moscow State University
Hurgin Jurij Isaakovich, Lomonosov Moscow State University
Ebeling Werner, Humboldt University of Berlin
Abstract: 

Since the known paper о L.Pontryagin, А. Andronov and А. Vitt (1933) а lot of problems were considered in nonlinear dynamics, associated with the study of the transition of a multistable system from one stable state to another under the influence of noise. In the recent years new problems emerged in the studies of complex vibrational systems. These problems deal with the transitions of test particles in the 2D potential relieves with the fluctuating or periodically changing parameters. As a complex relief is a variant of Sinai billiards, the motions of test pasticles therein become stochastic even without any external action. The examples of the cluster dynamics of macromolecules are considered. The dependencies are established of the time of transition of a test particles from the area of one minimum to the zone of attraction of another one on the frequency of the periodic changes of the parameters of the potential relief. The study of these processes will allow us to get closer to the comprehension of principles of molecular machines.

Key words: 
Acknowledgments: 
The authors express their gratitude to A.Yu. Chikishev and L. Shimansky for their help and useful discussions. The program for determining Lyapunov exponents was kindly provided by employees of Saratov State University A. Neumann and M. Safonova. The work was carried out with the support of the Russian Foundation for Basic Research (RFBR), project 95-0205877 a.
Reference: 
  1. Netrebko AV, Netrebko NV, Romanovskii YuM, Khurgin YuI, Shidlovskaya EG. Complex modulation modes and stochasticization of oscillations in cluster dynamic models of macromolecules. Izvestiya VUZ. Applied Nonlinear Dynamics. 1994;2(3):26-43.
  2. Ebeling W, Romanovsky Yu, Khurgin Yu, Netrebko А, Netrebko N, Shidlovskaya E. Complex regimes in the simple models of molecular dynamics of enzymes. Рrос. SPIE. Laser Application in Life Sciences. 1994;2370:434-447. DOI: 10.1117/12.197474.
  3. Romanovskii YuM, Tikhomirova RL, Khurgin YuI. Electromechanical model of the enzyme-substrate complex. Biophysics. 1979;24(3):442-447.
  4. Tatuzov RL, Tikhomirova NK. Mathematical modeling of oscillatory enzymatic reaction in a non-flowing system. In: Mathematical problems of ecology. Gorky: Gorky University Publishing; 1980.
  5. Gilson MK, Straatsma TP, McCammon JA, Ripoll DR, Faerman CH, Axelsen PH, Silman I, Sussman JL. Open "back door" in a molecular dynamics simulation of acetylcholinesterase. Science. 1994;263(5151):1276-1278. DOI: 10.1126/science.8122110.
  6. Shaitan KV, Rubin АB, Chernavskii DS. Kinetics of conformational transitions in proteins. Biophysics. 1985;30(1):31-35.
  7. Shaitan KV. Dynamics of electron-conformational transitions and new approaches to the physical mechanisms of functioning of macromolecules. Biophysics. 1994;39:949-967.
  8. Romanovskii YuM, Khurgin YuI, Chikishev АYu. Analysis of the proton transfer process in the dynamic model of the active center of the enzyme protein chymotrypsin. J. Phys. Chem. 1985;59(8):2021-2025.
  9. Ebeling W, Romanovsky YuM. Energie Transfer and Chaotic Oscillations in Enzyme Catalysis. Z. Phys. Chem. 1985;266(5):836-843. DOI: 10.1515/zpch-1985-266103.
  10. Romanovsky YuM, Chikishev AYu, Khurgin Yul. Subglobular Motion and Proton Transfer Model in the A-Chymotrypsin Molecule. J. Mol. Catal. B Enzym. 1988;47:235-240.
  11. Khurgin YuI, Burshtein КYa. Proton transfer mechanism in the reactions of alpha-chymotrypsin acylation. Sov. Phys. Doklady. 1974;217(4):965-968.
  12. Chikishev АYu, Sokolina VA, Khurgin YuI, Pirogov VG, Romanovskii YuM, Fedorov MV. Laser spectroscopy of the enzyme protein alpha-chymotripsin and chemical models of its active center. In: Akhmanov SA, Piskaras AS, editors. Study of Structure, Physical Properties and Energy of Biologically Active Molecules. Vilnius: Mosklas; 1986. P. 11.
  13. Manevich LI, Savin AV, Smirnov VV, Volkov SN. Solitons in nondegenerate bistable systems. Phys. Usp. 1994;37(9):859-879. DOI: 10.1070/pu1994v037n09abeh000043.
  14. Schimansky-Geier L, Zulicke СА. Harmonic noise: Effect on bistable system. Z. Phys. В. Condenced Matter. 1980;79:451-460. DOI: 10.1007/BF01437657.
  15. Havsteen В. A new principle of enzyme catalysis: coupled vibrations facilitate conformational changes. J. Theor. Biol. 1989;140(1):101-127. DOI: 10.1016/s0022-5193(89)80032-3.
  16. Havsteen ВH. A stochastic attractor participates in chymotrypsin catalysis. A new facet of enzyme catalysis. J. Theor. Biol. 1991;151(4):551-571. DOI: 10.1016/s0022-5193(05)80370-4.
  17. Ebeling W, Podlipchuk VYu, Valuev AA. Molecular dynamics simulation of the activation оf soft molecules in condensed media. Physica А. 1995;217(1-2):22-37. DOI: 10.1016/0378-4371(95)00049-D.
  18. Sokolov ND. Dynamics of hydrogen bonding. In: Sokolov ND, editor. Hydrogen Bond. М.: Nauka; 1981. P. 638.
  19. Sakun VP. Theory of the shape of the longitudinal oscillation strip А-Н in IR spectra of complexes АН...В in the liquid phase. In: Sokolov ND, editor. Hydrogen Bond. М.: Nauka; 1981. P. 89.
  20. Agafonov VE, Zhivlyuk YuN, Chernikov FR. Deterministic chaos in the dynamics of hydrogen bond. Biophysics. 1995;40(3):497-505.
  21. Golubev NS, Denisov GS, Shraiber VM. Potential energy surfaces and proton transition in systems with hydrogen bonds. In: Sokolov ND, editor. Hydrogen Bond. М.: Nauka; 1981. P. 212.
  22. Elyutin PV. The quantum chaos problem. Sov. Phys. Usp. 1988;31(7):597-622. DOI: 10.1070/PU1988v031n07ABEH003572.
Received: 
08.11.1995
Accepted: 
28.12.1995
Published: 
15.12.1996