Abstract
Cells are examples of self-organizing chemical reaction–diffusion systems that have evolved to perform (or been selected because of their ability to perform) myriads of goal-directed (purposive or teleonomic) motions in space and time. The goal-directed molecular motions inside the living cell are carried out by biopolymers acting as molecular machines (Alberts et al. 1998), and each molecular machine is postulated to be driven by conformons. Conformons, sequence-specific mechanical strains of biopolymers, can be generated from the binding energy of ligands as in the Circe effect of Jencks (1975) or from the free energy of chemical reactions as in stress-induced duplex destabilizations (SIDDSs) in supercoiled DNA described by Benham (1992, 1996a, b; Benham and Bi 2004). The living cell can be represented as a system of molecular machines (e.g., myosin, kinesin, dynein, dynamin, RNA polymerase, DNA polymerase, topoisomerases, and ion pumps) that are organized in space and time in various combinations in order to carry out cell functions demanded by a given environmental condition.
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References
Alberts, B.: The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291–294 (1998)
Alvarez, A., Romero, F.R., Archilla, J.F.R., Cuevas, J.A., Larsen, P.V: Breather trapping and breather transmission in a DNA model with an interface, ArXiv:nlin/0503062v3 [nlin.PS] 27 Mar (2006)
Astumian, D.: The role of thermal activation in motion and force generation by molecular motors. Philos. Trans. R. Soc. Lond. B 355, 511–22 (2000)
Astumian, D.: Making molecules into motors. Sci. Am. 285(1), 57–64 (2001)
Baker, T.A., Bell, S.P.: Polymerases and the replisome: machines within machines. Cell 92, 295–305 (1998)
Bauer, W.R., Crick, F.H.C., White, J.H.: Supercoiled DNA. Sci. Am. 243(1), 118–133 (1980)
Benham, C.J.: Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory sites. Proc. Natl. Acad. Sci. U. S. A. 90, 2999–3003 (1992)
Benham, C.J.: Duplex destabilization in supercoiled DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol. 255, 425–434 (1996a)
Benham, C.J.: Computation of DNA structural variability – a new predictor of DNA regulatory regions. Comput. Appl. Biosci. 12(5), 375–381 (1996b)
Benham, C.J., Bi, C.: The analysis of stress-induced duplex destabilization in long genomic DNA sequences. J. Comput. Biol. 11(4), 519–543 (2004)
Boyer, P.D.: Catalytic site occupancy during ATP synthase catalysis. FEBS Lett. 512(1–3), 29–32 (2002)
Cheetham, G.M.T., Steitz, T.A.: Structure of a transcribing T7 RNA polymerase initiation complex. Science 286, 2305–9 (1999)
Crompton, M.: The mitochondrial permeability transition pore and its role in cell death. Biochem. J. 341, 233–249 (1999)
Cuevas, J., Starikov, E.B., Archilla, J.F.R., Hennig, D.: Moving breathers in bend DNA with realistic parameters. Mod. Phys. Lett. B. 18(25), 1319–1326 (2004)
Domb, C.: The Critical Point: A Historical Introduction to the Modern Theory of Critical Phenomena. Taylor & Francis, London (1996)
Frauenfelder, H.: Function and dynamics of myoglobin. N. Y. Acad. Sci. 504, 151–167 (1987)
Green, D.E., Ji, S.: The electromechanochemical model of mitochondrial strucutre and funciton. In: Schulz, J., Cameron, B.F. (eds.) Molecular Basis of Electron Transport, pp. 1–44. Academic Press, New York (1972a)
Green, D.E., Ji, S.: Electromechanochemical model of mitochondrial structure and function. Proc. Natl. Acad. Sci. U. S. A. 69, 726–729 (1972b)
Han, M.Y.: Quarks and Gluons: A Century of Particle Charges. World Scientific, Singapore (1999)
Hine, J.: Physical Organic Chemistry, 2nd edn, pp. 69–70. McGraw-Hill Book Company, New York (1962)
Hisakado, M.: Breather trapping mechanism in piecewise homogeneous DNA. Phys. Lett. A 227(1–2), 87–93 (1997)
Jablonka, E.: Genes as followers in evolution – a post-synthesis synthesis? Biol. Philos. 21, 143–154 (2006)
Jencks, W.: Binding energy, specificity, and enzymic catalysis: the circe effect. Adv. Enzymol. 43, 219–410 (1975)
Ji, S.: Energy and negentropy in enzymic catalysis. Ann. N. Y. Acad. Sci. 227, 419–437 (1974a)
Ji, S.: A general theory of ATP synthesis and utilization. Ann. N. Y. Acad. Sci. 227, 211–226 (1974b)
Ji, S.: A model of oxidative phosphorylation that accommodates the chemical intermediate, chemiosmotic, localized proton and conformational hypotheses. J. Theor. Biol. 59, 319–330 (1976)
Ji, S.: A possible molecular mechanism of free energy transfer in oxidative phosphorylation. J. Theor. Biol. 68, 607–612 (1977)
Ji, S.: The principles of ligand-protein interactions and their application to the mechanism of oxidative phosphorylation. In: Yagi, K. (ed.) Structure and Function of Biomembranes, pp. 25–37. Japan Scientific Societies Press, Tokyo (1979)
Ji, S.: The bhopalator – a molecular model of the living cell based on the concepts of conformons and dissipative structures. J. Theor. Biol. 116, 399–426 (1985a)
Ji, S.: The Bhopalator: a molecular model of the living cell. Asian J. Exp. Sci 1, 1–33 (1985b)
Ji, S.: Watson-crick and prigoginian forms of genetic information. J. Theor. Biol. 130, 239–245 (1988)
Ji, S.: Biocybernetics: a machine theory of biology. In: Ji, S. (ed.) Molecular Theories of Cell Life and Death, pp. 1–237. Rutgers University Press, New Brunswick (1991)
Ji, S.: The linguistics of DNA: words, sentences, grammar, phonetics, and semantics. Ann. N. Y. Acad. Sci. 870, 411–417 (1999b)
Ji, S.: Free energy and information contents of Conformons in proteins and DNA. Biosystems 54, 107–130 (2000)
Ji, S.: The Bhopalator: an information/energy dual model of the living cell (II). Fundam. Inform. 49(1–3), 147–165 (2002b)
Ji, S.: Molecular information theory: solving the mysteries of DNA. In: Ciobanu, G., Rozenberg, G. (eds.) Modeling in Molecular Biology, Natural Computing Series, pp. 141–150. Springer, Berlin (2004a)
Junge, W., Müller, D.J.: Seeintg a molecular motor at work. Science 333, 704–705 (2011)
Kapanidis, A.N., Margeat, E., Ho, S.O., Kortkhonjia, E., Weiss, S., Ebright, R.H.: Initial transcriptionby RNA polymerase proceeds through a DNA- scrunching mechanism. Science 314(5802), 1144–47 (2006)
Kirschner, M., Gerhart, J.: Evolvability. Proc. Natl. Acad. Sci. U. S. A. 95, 8420–8427 (1998)
Kirschner, M.W., Gerhart, J.C.: The Plausibility of Life: Resolving Darwin’s Dilemma. Yale University Press, New Haven (2005)
Lumry, R.: Conformational mechanisms for free energy transduction in protein systems: old ideas and new facts. Ann. N. Y. Acad. Sci. 227, 46–73 (1974)
Lumry, R.: The Protein Primer, available at http://www.chem.umn.edu/groups/lumry/Volume_2_Protein_Primer/ (2009)
Lumry, R., Gregory, R.B.: Free-energy management in protein reactions: concepts, complications, and compensation. In: Welch, G.R. (ed.) The Fluctuating Enzymes, pp. 1–190. Wiley, New York (1986)
MacLennan, D.H., Green, N.M.: Pumping ions. Nature 405, 633–634 (2000)
McClare, C.W.F.: Chemical machines, maxwell's demon and living organisms. J. theoret. Biol. 30, 1–34 (1971)
McGuffee, S.R., Elcock, A.H.: Diffusion, crowding and protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput. Biol. 6(3), e1000694 (2010). doi:10.1371/journal.pcbi.1000694
Minton, A.P.: The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J. Biol. Chem. 276, 10577–10580 (2001)
Mitchell, P.: Coupling of phosphorylation to electron and hydrogen transfer by a chemiosmotic type of mechanism. Nature 191, 144–148 (1961)
Mitchell, P.: Chemiosmotic Coupling and Energy Transduction. Glyn Research Ltd, Bodmin (1968)
Myung, J., Jencks, W.P.: There is only one phosphoenzyme intermediate with bound calcium on the reaction pathway of the sarcoplasmic reticulum calcium ATPase. Biochemistry 34, 3077–3083 (1995)
Pattee, H.: The physics of symbols and the evolution of semiotic controls. In: Coombs M.,Sulcoski M.(eds) Proceedings of the 1996 International Workshop on Control Mechanisms for Complex Systems, Issues of Measurement & Semiotic Analysis (1996)
Pattee, H.: The physics of symbols: bridging the epistemic cut. Biosystems 60, 5–12 (2001)
Pielak, G.J.: A model of intracellular organization. Proc. Nat. Acad. Sci. 102(17), 5901–5902 (2005)
Qian, H.: Open-system nonequilibrium steady state: statistical thermodynamics, fluctuations, and chemical oscillations. J. Phys. Chem. B 110, 15063–15074 (2006)
Qian, H.: Phosphorylation energy hypothesis: open chemical systems and their biological functions. Annu. Rev. Phys. Chem. 58, 113–42 (2007)
Revyakin, A., Liu, C., Ebright, R.H., Strick, T.R.: Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314(5802), 1139–43 (2006)
Stryer, L.: Biochemistry, 3rd edn. W. H. Freeman and Company, New York (1995)
Toyoshima, C., Nakasako, M., Nomura, H., Ogawa, H.: Crystal structure of calcium ion pump of sarcoplasmic reticulum at 2.6 Å resolutions. Nature 405, 647–55 (2000)
Uchihashi, T., Iino, R., Ando, T., Noji, H.: High-speed atomic force microscopy reveals rotary catalysis of Rotorless F1-ATPase. Science 333, 755–758 (2011)
Volkov, S.N.: Conformational breather in a DNA macromolecule. Phys. Letters A 224(1–2), 93–98 (1996)
von Neumann, J.: In: Burks, A.W. (ed.) Theory of Self-reproducing Automata, p. 77. University of Illinois Press, Urbana (1966)
Waddington, C.H.: The Strategy of the Genes. Allen and Unwin, London (1957)
West-Eberhard, M.J.: Evolution in the light of developmental and cell biology, and vice versa. Proc. Nat. Acad. Sci. USA 95, 8417–8419 (1998)
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Ji, S. (2012). The Conformon. In: Molecular Theory of the Living Cell. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-2152-8_8
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