Voir la notice de l'article provenant de la source Math-Net.Ru
@article{SEMR_2019_16_a124, author = {Yu. N. Zhuravlev and M. A. Guzev and A. I. Gudimenko}, title = {Protein synthesis as an object of physical and mathematical research and modeling}, journal = {Sibirskie \`elektronnye matemati\v{c}eskie izvesti\^a}, pages = {340--368}, publisher = {mathdoc}, volume = {16}, year = {2019}, language = {ru}, url = {http://geodesic.mathdoc.fr/item/SEMR_2019_16_a124/} }
TY - JOUR AU - Yu. N. Zhuravlev AU - M. A. Guzev AU - A. I. Gudimenko TI - Protein synthesis as an object of physical and mathematical research and modeling JO - Sibirskie èlektronnye matematičeskie izvestiâ PY - 2019 SP - 340 EP - 368 VL - 16 PB - mathdoc UR - http://geodesic.mathdoc.fr/item/SEMR_2019_16_a124/ LA - ru ID - SEMR_2019_16_a124 ER -
%0 Journal Article %A Yu. N. Zhuravlev %A M. A. Guzev %A A. I. Gudimenko %T Protein synthesis as an object of physical and mathematical research and modeling %J Sibirskie èlektronnye matematičeskie izvestiâ %D 2019 %P 340-368 %V 16 %I mathdoc %U http://geodesic.mathdoc.fr/item/SEMR_2019_16_a124/ %G ru %F SEMR_2019_16_a124
Yu. N. Zhuravlev; M. A. Guzev; A. I. Gudimenko. Protein synthesis as an object of physical and mathematical research and modeling. Sibirskie èlektronnye matematičeskie izvestiâ, Tome 16 (2019), pp. 340-368. http://geodesic.mathdoc.fr/item/SEMR_2019_16_a124/
[1] N.V. Timofeeff-Ressovsky, N. N. Vorontsov, A.V. Yablokov, A Short Survey of the Theory of Evolution, Nauka, M., 1969 (in Russian)
[2] G.G. Simpson, Tempo and Mode in Evolution, Columbia Univ. Press, New York, 1944
[3] R.C. Lewontin, The Genetic Basis of Evolutionary Change, Columbia University Press, New York, 1974
[4] N.N. Vorontsov, Development of Evolution Ideas in Biology, Progress-Traditsiya, M., 1999 (in Russian)
[5] E. Schrödinger, What is Life? The Physical Aspect of the Living Cell, Sambridge University Press, 1944
[6] B.B. Kadomtsev, “Dynamics and Information”, Phys. Usp., 37 (1994), 425–499 (In Russian) | DOI | MR
[7] Yu.N. Zhuravlev, M.A. Guzev, “Quantum aspects in the study of life”, Vestnik of FEB RAS, 5 (2014), 5–17 (in Russian)
[8] Yu.N. Zhuravlev, M.A. Guzev, A.I. Gudimenko, “Modular organization of biosocial systems”, Vestnik of FEB RAS, 2 (2016), 5–23 (in Russian)
[9] D. Abbott, P.C.W. Davies, A.K. Pati (eds.), Quantum Aspects of Life, Imperial College Press, London, 2008 | MR
[10] S. Wright, Evolution and the Genetics of Populations, v. 2, Theory of Gene Frequencies, University of Chicago Press, Chicago, 1984
[11] M. Gromov, Great Circle of Mysteries: Mathematics, the World, the Mind, Birkhauser, Basel, 2018 | MR | Zbl
[12] A.S. Spirin, Molecular Biology: Ribosome Structure and Biosynthesis of Protein, Vysshaya Shkola Publishers, M., 1986 (in Russian)
[13] A.R. Rees, M.J.E. Sternberg, From Cells to Atoms: An Illustrated Introduction to Molecular Biology, Blackwell Science Inc, 1984
[14] W.H. Elliott, D.C. Elliott, Biochemistry and Molecular Biology, Oxford University Press, 2009
[15] W.S. Klug, M.R. Cummings, Concepts of genetics, 9th ed., San Francisco Pearson Education, 2009
[16] D.J. Taylor, N.P.O. Green, G.W. Stout, R. Soper, Biological Science, 2 volumes, Cambridge University Press, Cambridge, 2004
[17] I.F. Zhimulev, General and Molecular Genetics, Siberian University Publishers, Novosibirsk, 2007 (in Russian)
[18] V.V. Kuznetsov, G.A. Dmitrieva, Plant Physiology, 2 volumes, Urait Publishing House, M., 2016 (in Russian)
[19] P. Sergiev, The Nobel Prize 2009 in Chemistry. Molecular plant from preprotein world, Science and Life, 12, 2009 (in Russian)
[20] R. Pascal, A. Pross, J.D. Sutherland, “Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics”, Open Biol., 3:11 (2013) | DOI
[21] A. Pross, What is Life?: How Chemistry Becomes Biology, Oxford University Press, 2014
[22] de Duve, “Transfer RNAs: the second genetic code”, Nature, 333 (1988), 117–118 | DOI
[23] P. Schimmel, R. Giege, D. Moras, S. Yokoyama, “An operational RNA code for amino acids and possible relationship to genetic code”, Proc. Natl. Acad. Sci. USA, 90:19 (1993), 8763–8768 | DOI
[24] G. Yusupova, M. Yusupov, “Crystal structure of eukaryotic ribosome and its complexes with inhibitors”, Philos Trans R Soc Lond B Biol Sci., 372:1716 (2017), 20160184 | DOI
[25] S. Uemura, C.E. Aitken, J. Korlach, B.A. Flusberg, S.W. Turner, J.D. Puglisi, “Real-time tRNA transit on single translating ribosomes at codon resolution”, Nature, 464 (2010), 1012–1017 | DOI
[26] J.B. Munro, R.B. Altman, C.-S. Tung, K.Y. Sanbonmatsu, S.C. Blanchard, “A fast dynamic mode of the EF-G-bound ribosome”, The EMBO Journal, 29:4 (2010), 770–781 | DOI
[27] S. Kirmizialtin, S. Hennelly, A. Schug, J. Onuchic, K. Sanbonmatsu, “Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT”, Methods Enzymol., 553 (2015), 215–234 | DOI
[28] N. Desai, A. Brown, A. Amunts, V. Ramakrishnan, “The structure of the yeast mitochondrial ribosome”, Science, 355:6324 (2017), 528–531 | DOI
[29] G. Stetz, G.M. Verkhivker, “Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication”, PLoS Comput Biol., 13:1 (2017), e1005299 | DOI
[30] V.A. Avetisov, Life could not have emerged by chance. It was created by something with the help of nanotechnology, (in Russian) https://radiovesti.ru/brand/61009/episode/1372400
[31] R. Dawkins, The Greatest Show on Earth: The Evidence for Evolution, Simon and Schuster, 2009
[32] L. Randau, “RNA processing in the minimal organism Nanoarchaeum equitans”, Genome Biology, 13 (2012), R63 | DOI
[33] Yu.N. Zhuravlev, “Definition by means of indefiniteness (comment)”, J. Biomol. Struct. Dyn., 29 (2012), 643–644 | DOI
[34] G.P. Georgiev, Genes of Higher Organisms and Their Expression, Nauka, M., 1989 (in Russian)
[35] K. Takahashi, S. Yamanaka, “Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors”, Cell, 126 (2006), 663–676 | DOI
[36] M. Stadtfeld, K. Hochedlinger, “Induced pluripotency: history, mechanisms, and applications”, Genes $\$ Dev., 24 (2010), 2239–2263 | DOI
[37] L.E. Orgel, F.H. Crick, “Selfish DNA: the ultimate parasite”, Nature, 284:5757 (1980), 604–607 | DOI
[38] M. Ares, Jr, L. Grate, M.H. Pauling, “A handful of intron-containing genes produces the lion's share of yeast mRNA”, RNA, 5 (1999), 1138–1139 | DOI
[39] K.S. Makarova, D.H. Haft, R. Barrangou, et al., “Evolution and classification of the CRISPR-Cas systems”, Nature reviews. Microbiology, 9:6 (2011), 467–477 | DOI
[40] A. Panchin, “How a human being is corrected with the help of bacterial genes: in detail about the complex issue”, Popular Mechanics (Russian version), 5 (2016), 38–41 (in Russian)
[41] J.R. Stagno, Y. Liu, Y.R. Bhandari, et al., “Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography”, Nature, 541:7636 (2017), 242–246 | DOI
[42] M. Guo, P. Schimmel, “Essential nontranslational functions of tRNA synthetases”, Nature Chemical Biology, 9 (2013), 145–153 | DOI
[43] R. Rosen, Life itself: A Comprehensive Inquiry into the Nature? Origin and Fabrication of Life, Columbia Universuty Press, 1991
[44] R. Goldblatt, TOPOI: The categorial analysis of logic, North-Holland Publ Co, Amsterdam–NY–Oxford, 1979 | MR | Zbl
[45] Yu.N. Zhuravlev, M.A. Guzev, E.E. Skurichin, “Towards the Manifold Representations of Biological Object”, J. Biomol. Structure and Dynamics, 31:1 (2013), 70–71 | DOI
[46] Yu.N. Zhuravlev, M.A. Guzev, E.E. Skurichin, “Modeling ontogeny in biology”, Int. J. of Advances in Computer Science Its Applications, 5 (2015), 314–320
[47] A.I Gudimenko, Yu.N. Zhuravlev, M.A. Guzev, “On applicability of category theory to the description of the fundamental events of ontogenesis”, Dal'nevostochnyi Matematicheskii Zhurnal, 16 (2016), 147–159 (in Russian) | MR | Zbl
[48] N. Rashevsky, “Topology and life: In search of general mathematical principles in biology and sociology”, Bull. Math. Biophys., 16 (1954), 317–348 | DOI | MR
[49] R. Rosen, “A relational theory of the living systems”, Bull. Math. Biophys., 20 (1958), 245–260 | DOI | MR
[50] M.L. Cardenas, J.C. Letelier, C. Gutierrez, et al., “Closure to efficient causation, computability and artificial life”, J Theor Biol., 263:1 (2010), 79–92 | DOI | MR | Zbl
[51] A.H. Louie, “Robert Rosen's anticipatory systems”, Foresight, 12:3 (2010), 18–29 | DOI | MR
[52] https://en.wikiversity.org/wiki/Relational_biology
[53] U.A. Shreyder, A.A. Sharov, Systems and Models, Radio i svyaz', M., 1982 (in Russian) | MR
[54] https://en.wikipedia.org/wiki/Tuple
[55] O.O. Favorova, “Transfer RNAs structure and functioning at the first stage of protein biosynthesis”, Sorosovskiy obrazovatel'nyy zhurnal, 4:11 (1998), 71–77 (in Russian)
[56] S. Ledoux, O.C. Uhlenbeck, “Different aa-tRNAs are selected uniformly on the ribosome”, Molecular Cell, 31:1 (2008), 114–123 | DOI
[57] F. Crick, “The origin of the genetic code”, J. Mol. Biol., 38:3 (1968), 367–379 | DOI
[58] A.N. Kolmogorov, “Three approaches to the quantitative definition of information”, Problemy Peredachi Informatsii, 1:1 (1965), 3–11 (in Russian) | MR | Zbl
[59] Hawking S. W., A Brief History Of Time, Bantam, 1988
[60] E.P. Wigner, Symmetries and Reflections, Indiana University Press, Bloomington–London, 1967
[61] W. Gilbert, S.J. Souza, Introns and the RNA World, eds. R.F. Gesteland, T.R. Cech, J.F. Atkins, The RNA World, Cold Spring Harbor Laboratory Press, 1999, 221–232
[62] O. Caramello, Grothendieck toposes as unifying 'bridges' in Mathematics, Memoire pour l'obtention de l'habilitation a diriger des recherches, 2016 http://www.oliviacaramello.com/Unification/HDROliviaCaramello.pdf | MR
[63] T.M. Makarova, A.A. Bogdanov, “The ribosome as an allosterically regulated molecular machine”, Uspekhi Biologicheskoi Khimii, 57 (2017), 3–323 (in Russian)
[64] J. Achenbach, K.H. Nierhaus, “Translocation at work”, Nat. Struct. Mol. Biol., 20 (2013), 1019–1022 | DOI
[65] N. O. Kjeldgaard, K. Gausing, “Regulation of biosynthesis of ribosomes”, Ribosomes, eds. M. Nomura et al., Cold Spring Harbor, NY, 1974, 369–392
[66] D. Kennell, H. Riezman, “Transcription and translation initiation frequencies of the Escherichia coli lac operon”, J. Mol. Biol., 114 (1977), 1–21 | DOI
[67] K. Kinosita Jr., “Real time imaging of rotating molecular machines”, FASEB J., 13 (1999), S201–S208 | DOI
[68] A.D. Mehta, M. Rief, J.A. Spudich, et al., “Single-molecule biomechanics with optical methods”, Science, 283 (1999), 1689–1695 | DOI
[69] A. Ishijima, T. Yanagida, “Single molecule nanobioscience”, Trends Biochem. Sci., 26 (2001), 438–444 | DOI
[70] J.W. Steed, J.L. Atwood, Supramolecular Chemistry, Wiley, 2000
[71] V. Ramakrishnan, “The ribosome emerges from a black box”, Cell, 159:5 (2014), 979–984 | DOI
[72] M.D. Daily, J.J. Gray, “Allosteric communication occurs via networks of tertiary and quaternary motions in proteins”, PLoS Comput Biol., 5:2 (2009), e1000293 | DOI | MR
[73] S. Brakmann, “Single-molecule analysis: a ribosome in action”, Nature, 464 (2010), 987–988 | DOI
[74] P.F. Egea, H. Tsuruta, G.P. de Leon, et al., “Structures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane”, PLoS One, 3:11 (2008), e3619 | DOI
[75] D. Akopian, K. Shen, X. Zhang, S. Shan, “Signal recognition particle: an essential protein-targeting machine”, Annu Rev Biochem., 82 (2013), 693–721 | DOI
[76] A.I. Oparin, The origin of life, Izd. Moskovskii Rabochii, M., 1924 (in Russian)
[77] M. Montevil, M. Mossio, “Biological organisation as closure of constraints”, Journal of Theoretical Biology, 372 (2015), 179–191 | DOI | MR | Zbl
[78] D.E. Koshland, G. Nemethy, D. Filmer, “Comparison of experimental binding data and theoretical models in proteins containing subunits”, Biochemistry, 5 (1966), 365–385 | DOI
[79] V.J. Hilser, J.O. Wrabl, H.N. Motlagh, “Structural and energetic basis of allostery”, Annu Rev. Biophys., 41 (2012), 585–609 | DOI
[80] H.N. Motlagh, J.O. Wrabl, J. Li, V.J. Hilser, “The ensemble nature of allostery”, Nature, 508:7496 (2014), 331–339 | DOI
[81] H.G. Saavedra, J.O. Wrabl, J.A. Anderson, et al., “Dynamic allostery can drive cold adaptation in enzymes”, Nature, 558 (2018), 324–328 | DOI