Ultrametricity as a basis for organization of protein molecules: CO binding to myoglobin
- Authors: Avetisov V.A.1, Bikulov A.K.1, Zubarev A.P.2
-
Affiliations:
- N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences
- Samara State Transport University
- Issue: Vol 17, No 1 (2013)
- Pages: 315-325
- Section: Articles
- URL: https://journals.eco-vector.com/1991-8615/article/view/34719
- DOI: https://doi.org/10.14498/vsgtu1154
- ID: 34719
Cite item
Full Text
Abstract
In this paper, the basic notions of ultrametric ($p$-adic) description of protein conformational dynamics and CO rebinding to myoglobin are presented. It is shown that one and the same model of the reaction — ultrametric diffusion type describes essentially different features of the rebinding kinetics at high-temperatures ($300{\div}200$ K) and low-temperatures ($180{\div}60$ K). We suggest this result indicates a special structural order in a protein molecule. Besides all the other structural features, it is organized by such a way that its conformational mobility changes self-similar from room temperature up to the cryogenic temperatures.
Full Text
Вестн. Сам. гос. техн. ун-та. Сер. Физ.-мат. науки. 2013. 1 (30). С. 315-325 УДК 517.958:57 УЛЬТРАМЕТРИКА КАК ПРИНЦИП ОРГАНИЗАЦИИ БЕЛКОВЫХ МОЛЕКУЛ: КИНЕТИКА СВЯЗЫВАНИЯ СО МИОГЛОБИНОМ В. А. Аветисов1 , А. Х. Бикулов1 , А. П. Зубарев2 1 Институт химической физики им. Н. Н. Семенова РАН, Россия, 119991, Москва, ул. Косыгина, 4 2 Самарский государственный университет путей сообщения, Россия, 443066, Самара, 1-й Безымянный пер., 18. E-mails: vladik.avetisov@gmail.com, bikulov1903@rambler.ru, apzubarev@mail.ru Изложены основные идеи ультраметрического (p-адического) описания конфор- мационной динамики белковой молекулы и кинетики связывания СО миогло- бином. Показано, что существенно различные свойства кинетики связывания в высокотемпературной (300×
About the authors
Vladik Avanesovich Avetisov
N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences
Email: avetisov@chph.ras.ru
Doctor of physico-mathematical sciences, Professor
Al'bert Khakimovich Bikulov
N. N. Semenov Institute of Chemical Physics, Russian Academy of Sciences
Email: bikulov1903@rambler.ru, beecul@mail.ru
Candidate of physico-mathematical sciences
Alexander Petrovich Zubarev
Samara State Transport University
Email: apzubarev@mail.ru
Candidate of physico-mathematical sciences, Associate professor
References
- A. Ansary, J. Berendzen, S. F. Bowne, G. Frauenfelder, I. E. T. Iben, T. B. Sauke, E. Shyamsunder, R. D. Young, "Protein states and proteinquakes", Proc. Natl. Acad. Sci. USA, 82:15 (1985), 5000-5004
- P. J. Steinbach, A. Ansary, J. Berendzen, D. Braunstein, K. Chu, B. R. Cowen, D. Ehrenstein, G. Frauenfelder, J. B. Johnson, D. C. Lamb, S. Luck, J. R. Mourant, G. U. Nienhaus, P. Ormos, R. Philipp, A. Xie, R. D. Young, "Ligand binding to heme proteins: connection between dynamics and function", Biochemistry, 30:16 (1991), 3988-4001
- A. A. Zharikov, S. F. Fischer, "Scaling law for the non-exponential ligand rebinding of CO in myoglobin", Chem. Phys. Lett., 263:6 (1996), 749-758
- A. A. Zharikov, S. F. Fischer, "Nonexponential ligand rebinding of and $O_2$ in myoglobin controlled by fluctuations of the protein", Chem. Phys. Lett., 249:5-6 (1996), 459-469
- N. G. Van Kampen, Stochastic Processes in Physics and Chemistry, North Holland, Amsterdam, 1981
- G. Parisi, "Infinite number of order parameters for spin-glasses", Phys. Rev. Lett., 43:23 (1979), 1754-1756
- A. T. Ogielski, D. L. Stein, "Dynamics on ultrametric spaces", Phys. Rev. Lett., 55:15 (1985), 1634-1637
- V. A. Avetisov, A. Kh. Bikulov, S. V. Kozyrev, "Application of -adic analysis to models of spontaneous breaking of the replica symmetry", J. Phys. A, 32:50 (1999), 8785-8791
- G. Parisi, N. Sourlas, "-Adic numbers and replica symmetry breaking", Eur. Phys. J. B Condens. Matter Phys., 14:3 (2000), 535-542
- B. C. Владимиров, И. В. Волович, Е. И. Зеленов, -Aдический анализ и математическая физика, Физматлит, М., 1994, 352 с.
- В. М. Шелкович, А. Ю. Хренников, Современный -адический анализ и математическая физика. Теория и приложения, Физматлит, М., 2012, 452 с.
- M. V. Dolgopolov, A. P. Zubarev, "Some aspects of -adic analysis and its applications to -adic stochastic processes", p-Adic Numbers Ultrametric Anal. Appl., 3:1 (2011), 39–51
- V. A. Avetisov, A. Kh. Bikulov, S. V. Kozyrev, V. A. Osipov, "-Adic models of ultrametric diffusion constrained by hierarchical energy landscapes", J. Phys. A, 35:2 (2002), 177-189
- V. A. Avetisov, A. Kh. Bikulov, V. A. Osipov, "-Adic description of characteristic relaxation in complex systems", J. Phys. A, 36:15 (2003), 4239-4246
- V. Avetisov, A. Bikulov, "Protein ultrametricity and spectral diffusion in deeply frozen proteins", Biophys. Rev. Lett., 5:3 (2008), 387-396
- V. A. Avetisov, A. Kh. Bikulov, A. P. Zubarev, "First passage time distribution and the number of returns for ultrametric random walks", J. Phys. A, 42:8 (2009), 085005, 18 pp.