On the Evolution of Protein-based Machines (Toward Complexity of Structure and Diversity of Function)


This volume presents a consilient mechanism, “a common groundwork of explanation,” for energy conversions whereby protein-based machines interconvert the set of six energies interconverted by living organisms. This chapter examines the simple stepwise process whereby protein compositional changes can access each of the six energy sources and can improve the efficiency of each of a resulting 18 pairwise energy conversions.


Genetic Code Model Protein Molecular Machine Vitalist Debate Hydrophobic Association 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    P. Appleman, Ed., Darwin, Third Edition, W. W. Norton, New York, 2001, p. 1.Google Scholar
  2. 2.
    M.J. Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution. Simon and Schuster, New York, 1996, p. 5.Google Scholar
  3. 3.
    W.-H. Li, Z. Gu, H. Wang, and A. Nekutenko, “Evolutionary Analysis of the Human Genome.” Nature, 409, 847–849, 2001.PubMedCrossRefGoogle Scholar
  4. 4.
    Editorial Comments. Science, 291, 1218, 2001.Google Scholar
  5. 5.
    A. Toffler, Forward, to I. Prigogine and I. Stengers, Order Out of Chaos: Man’s New Dialogue with Nature. Bantam Books, New York, 1984, p. xx.Google Scholar
  6. 6.
    A. Szent-Györgyi, “Studies on Muscle.” Acta Physiol. Scand. 9(Suppl. XXV), 1–116, 1945.Google Scholar
  7. 7.
    D. W. Urry, “Molecular Machines: How Motion and Other Functions of Living Organisms Can Result from Reversible Chemical Changes.” Angew. Chem. [German], 105, 859–883, 1993; Angew. Chem. Int. Ed. Engl., 32, 819–841, 1993.CrossRefGoogle Scholar
  8. 8.
    D.W. Urry, “Elastic Biomolecular Machines: Synthetic Chains of Amino Acids, Patterned After Those in Connective Tissue, can Transform Heat and Chemical Energy into Motion.” Sci. Am., January, 1995, 64–69.Google Scholar
  9. 9.
    D.W. Urry, “Physical Chemistry of Biological Free Energy Transduction as Demonstrated by Elastic Protein-based Polymers.” J. Phys. Chem. B, 101, 11007–11028, 1997.CrossRefGoogle Scholar
  10. 10.
    D.W. Urry, R.D. Harris, and K.U. Prasad, “Chemical Potential Driven Contraction and Relaxation by Ionic Strength Modulation of an Inverse Temperature Transition.” J. Am. Chem. Soc., 110, 3303–3305, 1988.CrossRefGoogle Scholar
  11. 11.
    D.W. Urry, B. Haynes, H. Zhang, R.D. Harris, and K.U. Prasad, “Mechanochemical Coupling in Synthetic Polypeptides by Modulation of an Inverse Temperature Transition.” Proc. Natl. Acad. Sci. U.S.A., 85, 3407–3411, 1988.PubMedCrossRefGoogle Scholar
  12. 12.
    S.C. Schuster and S. Khan, “The Bacterial Flagellar Motor.” Annu. Rev. Biophys. Biomol. Struct., 23, 509–539, 1994.PubMedCrossRefGoogle Scholar
  13. 13.
    P.D. Boyer, “The Binding Change Mechanism for ATP Synthase—Some probabilities and possibilities.” Biochim. Biophys. Acta, 1140, 215–250, 1993.PubMedCrossRefGoogle Scholar
  14. 14.
    J.P. Abrahams, A.G.W. Leslie, R. Lutter, and J.E. Walker, “Structure at 2.8 Å Resolution of F1-ATPase from Bovine Heart Mitochondria.” Nature, 370, 621–628, 1994.PubMedCrossRefGoogle Scholar
  15. 15.
    K. Kinosita, Jr., R. Yasuda, H. Noji, and K. Adachi, “A Rotary Molecular Motor that can Work at Near 100% Efficiency.” Philos. Trans. R. Soc. Lond. B Biol. Sci., 355, 473–489, 2000.PubMedCrossRefGoogle Scholar
  16. 16.
    D.W. Urry, L.C. Hayes, T.M. Parker, and R.D. Harris, “Baromechanical Transduction in a Model Protein by the ΔTt Mechanism.” Chem. Phys. Lett., 201, 336–340, 1993.CrossRefGoogle Scholar
  17. 17.
    D.W. Urry, L.C. Hayes, and D. C. Gowda, “Electromechanical Transduction: Reductiondriven Hydrophobic Folding Demonstrated in a Model Protein to Perform Mechanical Work.” Biochem. Biophys. Res. Commun., 204, 230–237, 1994.PubMedCrossRefGoogle Scholar
  18. 18.
    D.W. Urry, L.C. Hayes, D.C. Gowda, S.-Q. Peng, and N. Jing, “Electro-chemical Transduction in Elastic Protein-based Polymers.” Biochem. Biophys. Res. Commun., 210, 1031–1039, 1995.PubMedCrossRefGoogle Scholar
  19. 19.
    D. Voet and J. Voet, Biochemistry, Second Edition, John Wiley & Sons, New York, 1995, p. 966, Table 30-2.Google Scholar
  20. 20.
    D.W. Urry, C.-H. Luan, S.Q. Peng, T.M. Parker, and D.C. Gowda, “Hierarchical and Modulable Hydrophobic Folding and Self-assembly in Elastic Protein-based Polymers: Implications for Signal Transduction.” Mater. Res. Soc. Symp. Proc., 255, 411–422, 1992.Google Scholar
  21. 21.
    C.-H. Luan, T. Parker, K.U. Prasad, and D.W. Urry, “DSC Studies of NaCl Effect on the Inverse Temperature Transition of Some Elastinbased Polytetra-, Polypenta-, and Polynonapeptides.” Biopolymers, 31, 465–475, 1991.PubMedCrossRefGoogle Scholar
  22. 22.
    D.W. Urry, L. Hayes, C.-X. Luan, D.C. Gowda, D. McPherson, J. Xu, and T. Parker, “ΔTt-Mechanism in the Design of Self-Assembling Structures.” In Self-assembling Peptide Systems in Biology, Medicine and Engineering, A. Aggeli, N. Boden, S. Zhang, Eds., Kluwer Academic Publishers, Dordrecht, The Netherlands, 2001, p. 323–340.Google Scholar
  23. 24.
    I. Prigogine and I. Stengers, Order Out of Chaos: Man’s New Dialogue with Nature. Bantam Books, New York, 1984, p. 13.Google Scholar
  24. 25.
    Preface to I. Prigogine and I. Stengers, Order Out of Chaos: Man’s New Dialogue with Nature. Bantam Books, New York, 1984, p. xxix.Google Scholar
  25. 26.
    Preface to G.N. Lewis and M. Randall, Thermodynamics and the Free Energy of Chemical Substances. McGraw-Hill, New York, 1923.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2006

Personalised recommendations