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

For citation:

Shuvalova E. V., Kubasov A. A., Romanovsky Y. M., Chikishev A. Y. Dynamics of proton transfer in ∝-chymotrypsin enzyme active site. Izvestiya VUZ. Applied Nonlinear Dynamics, 2000, vol. 8, iss. 5, pp. 23-35. DOI: 10.18500/0869-6632-2000-8-5-23-35

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Language: 
Russian
Heading: 
Applied Problems of Nonlinear Oscillation and Wave Theory
Article type: 
Article
UDC: 
539.194; 539.219; 621.328
DOI: 
10.18500/0869-6632-2000-8-5-23-35

Dynamics of proton transfer in ∝-chymotrypsin enzyme active site

Autors: 
Shuvalova Ekaterina Viktorovna, Lomonosov Moscow State University
Kubasov Alexei Aleksandrovich, Lomonosov Moscow State University
Romanovsky Yuri Mihajlovich, Lomonosov Moscow State University
Chikishev Andrei Yurevich, Lomonosov Moscow State University
Abstract: 

The ∝-chymotrypsin enzyme that splits peptide chains in е process of digestion is considered. The proton transfer in one of hydrogen bonds of catalytic group of enzyme
active site is process, which leads to peptide bond splitting. Such process in potential field of enzyme active site is studied. It is demonstrated а! energy surface profile of active
site is changed after substrate fixing to facilitate a proton transfer. The enzyme active site field fluctuating by the influence of random thermal oscillation of environment atoms, the proton transfer in nonstationary profile is accounted. Fluctuations of potential field are described by both of white and coloured noise. The influence amplitude and frequency of coloured noise, also asymmetry between depth of е double—well potential are шvestigated. It is showed that in addition to tunnelling in а nonstationary potential the non-coherent, dynamical irreversible process of the proton transfer exists. That is called because affect of the noise to the potential form.

Key words: 
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Acknowledgments: 
The authors are grateful to B.A. Grishanin for invaluable help in developing theoretical methods for solving the problem and critical comments made in the course of the work, as well as to P.V. Elyutin for many constructive advices. The work was supported by the Center for Fundamental Research of Nature (Higher School, Russia), State Program “Scientific Schools of Russia” (grant № 95-15-97782), RFBR (grant №. 98-03-331191a).
Reference: 
  1. Netrebko AV, Netrebko NV, Romanovskii YuM, Hurgin YuI, Ebeling V. Stochastic cluster dynamics of the enzyme-substrate complex. Izvestiya VUZ. Applied Nonlinear Dynamics. 1996;4(3):53-66. (in Russian).
  2. Netrebko AV, Netrebko NV, Romanovskii YuM, Hurgin YuI, Shidlovskaya EG. Complex modulation modes and oscillation stochastization in cluster dynamic models of macromolecules. Izvestiya VUZ. Applied Nonlinear Dynamics. 1994;2(3):26-43. (in Russian).
  3. Romanovsky YuM, Netrebko AV. Some problems of claster dynamics: models of molecular scissors. Izvestiya VUZ. Applied Nonlinear Dynamics. 1998;6(4):31.
  4. Romanovsky YuM. Some problems оf cluster dynamics of biological macromolecules. In: Shimansky— Geier L, Peschel T, editor. Stochastic Dynamics. Lecture Notes in Physics. Vol. 484. Berlin: Springer; 1997. Р. 140-152. DOI: 10.1007/BFb0105606.
  5. Grishanin BA, Romanovskii YM, Chikishev A, Shuvalova EV. Quantum mechanical model of proton transfer in a fluctuating potential field of the active site of α-chymotrypsin. In: Freund JA, Poschel T, editors. Stochastic Processes in Physics, Chemistry, and Biology. Lecture Notes in Physics. Vol 557. Berlin:Springer; 2000. P. 338-349. DOI: 10.1007/3-540-45396-2_31.
  6. Chikishev AYu, Netrebko NV, Romanovsky YuM, Ebeling W, Schimansky— Geier L, Netrebko AV. Stochastic cluster dynamics оf macromolecules. Int. J. Bifurc. Chaos. 1998;8(5):921-926. DOI: 10.1142/S0218127498000723.
  7. Shydlovskaya E, Shymansky—Geier L, Romanovsky YuM. Nonlinear vibrations in a 2-dimensional protein cluster model with linear bonds. Zeitschrift für Physikalische Chemie. 2000;214(1):65-82. DOI: 10.1524/zpch.2000.214.1.065.
  8. Shaitan KV. Dynamics of electron-conformational transitions and new approaches to the physical mechanisms of functioning of macromolecules. Biophysics. 1994;39:949-967. (in Russian).
  9. Fersht A. Enzyme structure and mechanism. San Francisco : W.H. Freeman; 1977. 371 p.
  10. Quinn DM. Acetylcholinesterase: Ensyme, structure, reaction dynamics and: virtual transition states. Chem. Rev. 1987;87:955-979. DOI: 10.1021/Cr00081A005.
  11. Davydov A. Solitons in molecular systems. Dordrecht: Springer; 1985. 319 p. DOI: 10.1007/978-94-017-3025-9.
  12. Nylund E, Lindenberg K, Tsironis G. Proton dynamics in hydrogen—bonded system. J. Stat. Phys. 1993;70:163-181. DOI: 10.1007/BF01053961.
  13. Manevitch LI, Mihlin YuV, Pilipchuk VN. Normal oscillation method for essentially nonlinear systems. М.: Nauka; 1989. 216 p.
  14. Stewart JJP. Optimization оf parameters for semi—empirical methods I. J. Comput. Chem. 1989;10:209-220. DOI: 10.1002/jcc.540100208.
  15. Romanovskii YuM, Chikishev АYu, Khurgin Yul. Subglobular motion аnd proton transfer model in the a—chymotrypsin molecule. J. Mol. Catalysis, 1988;47(2-3);235-240. DOI: 10.1016/0304-5102(88)85047-8.
  16. Rubin AB. Biophysics. Vol. 1. M.: Vysshaya shkola; 1987. 319 p.
  17. Kasparov NV, Popov ME, Andreeva NS. The role of water molecules located near the active center of asparatin proteinases. Molecular Biology. 1997;31:1030. (in Russian).
  18. Romanovskii YuM, Tikhomirova NK, Khurgin Yul. Electromechanical model of the enzyme-substrate complex. Biophysics. 1979;24:442.
  19. Schimansky-Geier L, Zulicke Ch. Harmonic noise: Effect оn bistable system. Z. Physik B - Condensed Matter. 1980;79:451-460. DOI: 10.1007/BF01437657.
  20. Kosloff В. Time-dependent quantum—mechanical methods for molecular dynamics. J. Phys. Chem. 1998;92(8):2087-2100. DOI: 10.1021/j100319a003.
  21. Grishanin BA, Shuvalova EV, Chikishev АYu. Dynamics of proton transport in the active center of the protein-enzyme o-chymotrypsin. In: Romanovskii YuM,  Ebeling W, editors. Molecular dynamics of enzymes. М.: Moscow University Press; 2000. P. 139-151. (in Russian).
  22. Landau LD, Livshits EM. Quantum mechanics. M.: Nauka; 1989. 768 p.
  23. Feynman RP, Leighton R, Sands M. The Feynman’s Lectures on Physics. Vol. 3. Quantum mechanics. New York: Basic Books. 380 p.
  24. Grishanin BA, Romanovskii YM, Chikishev A, Shuvalova EV. Quantum mechanical model of proton transfer in a fluctuating potential field of the active site of α-chymotrypsin. In: Freund JA, Poschel T, editors. Stochastic Processes in Physics, Chemistry, and Biology. Lecture Notes in Physics. Vol. 557. Berlin: Springer; 2000. P. 338–349. DOI: 10.1007/3-540-45396-2_31.
  25. Lax M. Fluctuation and coherence phenomena in classical and quantum physics. In: Brandeis University Summer Institute in Theoretical Physics. New York: Gordon and Breach; 1966. P. 269–478.
  26. Kramers НА. Brownian motion in а field of force and the diffusion model оf chemical reactions. Physica. 1940;7(4):284-304. DOI: 10.1016/S0031-8914(40)90098-2.
  27. Kagan Yu. The Role of Barrier Fluctuations in the Tunneling Problem. Berichte der Bunsengesellschaft für physikalische Chemie. 1991;95(3):411-422. DOI: 10.1002/bbpc.19910950333.
  28. Blumfeld LA, Goldansky VI, Podgoretskaya MI, Chernavsky DS. Spatial and temporal delocalization of electrons in molecular systems. Journal of Structural Chemistry. 1967;8(5):854.
  29. Elyutin PV, Rogovenko AN. Stimulated transitions between the self-trapped states of the nonlinear Schrödinger equation. Phys. Rev. E. 2001;63(2):026610. DOI: 10.1103/PhysRevE.63.026610.
Received: 
21.06.2000
Accepted: 
27.10.2000
Published: 
07.02.2001
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