Skip to main content
SpringerLink
Log in
Book cover

Molecular Theory of the Living Cell pp 203–230Cite as

Molecular Mechanisms: From Enzymes to Evolution

  • Chapter
  • First Online:

  • 1380 Accesses

Abstract

Binding is prerequisite for practically all molecular processes occurring inside the cell, including messenger (or molecular) recognition, enzymic catalysis, transport processes, and control of gene expression. Furthermore, binding must be followed by de-binding if molecular machines are to work more than one cycle. Otherwise, molecular machines will get stuck in a substrate- or a product-bound state and not be able to move on to the next state to perform molecular work in continuous cycles. Molecular machines stuck in either a substrate- or a product-bound state is akin to the gear shift of a car stuck in either the drive or the neutral position.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Alberts, B.: The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291–294 (1998)

    Article  Google Scholar 

  • Anderson, B., Harrison, M., Sheinberg, D.L.: A multielectrode study of the inferotemporal cortex in the monkey: effects of grouping on spike rates and synchrony. Neuroreport 17(4), 407–411 (2006)

    Article  Google Scholar 

  • Andrews, F.C.: Equilibrium Statistical Mechanics. Wiley, New York (1963)

    MATH  Google Scholar 

  • 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)

    Article  Google Scholar 

  • Astumian, D.: Making molecules into motors. Sci. Am. 285(1), 57–64 (2001)

    Article  Google Scholar 

  • Averbeck, B.B., Lee, D.: Coding and transmission of information by neural Ensembles. Trends Neurosci. 27(4), 225–30 (2004)

    Article  Google Scholar 

  • Bagshaw, C.R., Cherny, D.: Blinking fluorophores: what do they tell us about protein dynamics? Biochem. Soc. Trans. 34, 979–982 (2006)

    Article  Google Scholar 

  • Bedregal, B.R.C., Figueira, S.: Classical computability and fuzzy turing machines. Lect. Notes Comput. Sc. 3887, 154–165 (2006)

    Article  MathSciNet  Google Scholar 

  • Berg, J.M., Tymoczko, J.L., Stryer, L.: Biochemistry, 5th edn, pp. 440–442. W. H. Freeman and Company, New York (2002)

    Google Scholar 

  • Boyer, P.D.: Catalytic site occupancy during ATP synthase catalysis. FEBS Lett. 512(1–3), 29–32 (2002)

    Article  ADS  Google Scholar 

  • Domb, C.: The Critical Point: A Historical Introduction to the Modern Theory of Critical Phenomena. Taylor & Francis, London (1996)

    Google Scholar 

  • Elsasser, W.M.: Reflections on a Theory of Organisms: Holism in Biology. The Johns Hopkins University Press, Baltimore (1998)

    Google Scholar 

  • Fenimore, P.W., Frauenfeld, H., McMahon, B.H., Young, R.D.: Proteins are paradigms of stochastic complexity. Physica A 351, 1–13 (2005)

    Article  ADS  Google Scholar 

  • Fisher, M.E.: Renormalization group theory: its basis and formulation in statistical physics. Rev. Mod. Phys. 70(2), 653–681 (1998)

    Article  ADS  MATH  Google Scholar 

  • Halle, J.-P., Meisterernst, M.: Gene expression: increasing evidence for a transcriptosome. Trends Genet. 12(5), 161–163 (1996)

    Article  Google Scholar 

  • Jencks, W.: Binding energy, specificity, and enzymic catalysis: the circe effect. Adv. Enzymol. 43, 219–410 (1975)

    Google Scholar 

  • Ji, S.: Energy and negentropy in enzymic catalysis. Ann. N. Y. Acad. Sci. 227, 419–437 (1974a)

    Article  ADS  Google Scholar 

  • Ji, S.: A general theory of ATP synthesis and utilization. Ann. N. Y. Acad. Sci. 227, 211–226 (1974b)

    Article  ADS  Google Scholar 

  • 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)

    Google Scholar 

  • 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)

    Google Scholar 

  • Ji, S.: Isomorphism between cell and human languages: molecular biological, bioinformatics and linguistic implications. Biosystems 44, 17–39 (1997a)

    Article  Google Scholar 

  • Ji, S.: Free energy and information contents of Conformons in proteins and DNA. Biosystems 54, 107–130 (2000)

    Article  Google Scholar 

  • 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)

    Chapter  Google Scholar 

  • Ji, S.: Info-statistical mechanics of cell metabolism. In Abstract, 56th Statistical Mechanics Conference, Rutgers University, Piscataway, 17–19 Dec 2006, p. 6.. Available at http://www.math.rutgers.edu/events/smm/smm96_shorttlks.abs.html (2006a)

  • Junge, W., Müller, D.J.: Seeintg a molecular motor at work. Science 333, 704–705 (2011)

    Article  ADS  Google Scholar 

  • Kondepudi, D., Prigogine, I.: Modern Thermodynamics: From Heat Engine to Dissipative Structures. Wiley, Chichester (1998)

    Google Scholar 

  • Konig, P., Engel, A.K., Singer, W.: Integrator or coincidence detector? The role of the cortical neuron revisited. Trends Neurosci. 19, 130–137 (1996)

    Article  Google Scholar 

  • Koshland Jr., D.E.: Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. U. S. A. 44, 98–104 (1958)

    Article  ADS  Google Scholar 

  • Kosko, B.: Fuzzy Thinking: The New Science of Fuzzy Logic. Hyperion, New York (1993)

    Google Scholar 

  • Laidler, K.J.: Chemical Kinetics. McGraw-Hill Book Company, New York (1965). Chapter 3

    Google Scholar 

  • Livnah, O., Stura, E.A., Mideleton, S.A., Johnson, D.L., Jolliffe, L.K., Wilson, I.: Crystallographic evidence for preformed dimmers of erythropoietin receptor before ligand activation. Science 283, 987–990 (1999)

    Article  ADS  Google Scholar 

  • Lu, H.P., Xun, L., Xie, X.S.: Single-molecule enzymatic dynamics. Science 282, 1877–1882 (1998)

    Article  ADS  Google Scholar 

  • 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)

    Article  ADS  Google Scholar 

  • 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)

    Google Scholar 

  • McClare, C.W.F.: Chemical machines, maxwell's demon and living organisms. J. theoret. Biol. 30, 1–34 (1971)

    Article  Google Scholar 

  • McClare, C.W.F.: Resonance in bioenergetics. Ann. N. Y. Acad. Sci. 227, 74–97 (1974)

    Article  ADS  Google Scholar 

  • Mikula, S., Niebur, E.: The effects of input rate and synchrony on a coincidence detector - analytical solution. Neural Computat. 5(3), 539–547 (2003)

    Article  Google Scholar 

  • Min, W., English, B.P., Luo, G., Cherayil, B.J., Kou, S.C., Xie, X.S.: Fluctuating enzymes: lessons from single-molecule studies. Acc. Chem. Res. 38, 923–931 (2005)

    Article  Google Scholar 

  • Mok, K.C., Wingreen, N.S.D., Bassler, B.L.: Vibrio harveyi quorum sensing: a coincidence detector for two autoinducers controls gene expression. EMBO J. 22, 870–881 (2003)

    Article  Google Scholar 

  • Moore, W.J.: Physical Chemistry, 3rd edn. Prentice-Hall, Englewood Cliffs (1963)

    Google Scholar 

  • Nase, G., Singer, W., Monyer, H., Engel, A.K.: Features of neuronal synchrony in mouse visual cortex. J. Neurophysiol. 90, 1115–1123 (2003)

    Article  Google Scholar 

  • Peeva, K., Zahariev, Z.: Computing behavior of finite fuzzy machines – algorithm and its application to reduction and minimization. Inform. Sci. 178, 4152–4165 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  • Prigogine, I.: Dissipative structures and biological order. Adv. Biol. Med. Phys. 16, 99–113 (1977)

    MathSciNet  Google Scholar 

  • Prigogine, I.: From Being To Becoming: Time and complexity in Physical Sciences, pp. 19–26. W. H. Freeman and Company, San Francisco (1980)

    Google Scholar 

  • Ravindranathan, K.P.: Free energy landscape for the allosteric conformational change of the ribose binding protein. In: Abstracts, 17th Annual Molecular Biophysics Minisymposium Center for Molecular Biophysics and Biophysical Chemistry, Rutgers University, Piscataway, N.J, 6 May (2005)

    Google Scholar 

  • Ravindranathan, K.P., Galllichio, E., Levy, R.M.: Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein. J. Mol. Biol. 353, 196–210 (2005b)

    Article  Google Scholar 

  • Reynolds, W.L., Lumry, R.: Mechanisms of Electron Transfer. The Ronald Press Company, New York (1966). Chapter 1

    Google Scholar 

  • Stein, W.D., Eilam, Y., Lieb, W.R.: Active transport of cations across biological membranes. Ann. N. Y. Acad. Sci. 227, 328–336 (1974)

    Article  ADS  Google Scholar 

  • Swindale, N.V.: Neural synchrony, axonal path lengths, and general anesthesia: a hypothesis. Neuroscientist 9, 440–445 (2003)

    Article  Google Scholar 

  • 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)

    Article  ADS  Google Scholar 

  • Wang, Q., Zhang, Y., Yang, C., et al.: Acetylation of metabolic enzymes coordinates carbon source untilization and metabolic flux. Science 327, 1004–1007 (2010)

    Article  ADS  Google Scholar 

  • Woelbern, T., Eckhorn, R., Frien, A., Bauer, R.: Perceptual grouping correlates with short synchronization in monkey prestriate cortex. Neuroreport 13(15), 1881–6 (2002)

    Article  Google Scholar 

  • Zhaio, S., Xu, W., Jiang, W., et al.: Regulation of cellular metabolism by protein lysine acetylation. Science 327, 1000–1004 (2010)

    Article  ADS  Google Scholar 

  • Zwanzig, R.: Rate processes with dynamic disorder. Acc. Chem. Res. 23, 148–152 (1990)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dept. of Pharmacol. & Toxicol. Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, 08854, USA

    Sungchul Ji PhD

Authors
  1. Sungchul Ji PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sungchul Ji PhD .

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Ji, S. (2012). Molecular Mechanisms: From Enzymes to Evolution. In: Molecular Theory of the Living Cell. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-2152-8_7

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-2152-8_7

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4614-2151-1

  • Online ISBN: 978-1-4614-2152-8

  • eBook Packages: Physics and AstronomyPhysics and Astronomy (R0)

Publish with us

Policies and ethics

Search

Navigation