The Rise and Fall of the Hydrophobic Effect in Protein Folding and Protein-Protein Association, and Molecular Recognition

Arieh Ben-Naim
DOI: 10.4236/ojbiphy.2011.11001                

Abstract

In the beginning everything was explained in Biochemistry in terms of hydrogen-bonds (HB). Then, the devastating blow, known as the HB-inventory argument came; hydrogen bonding with water molecules compete with intramolecular hydrogen-bonds. As a result, the HBs paradigm fell from grace. The void created was immediately filled by Kauzmann’s idea of hydrophobic (HφO) effect which reigned supreme in biochemical literature for over 50 years (1960-2010). Cracks in the HB-inventory argument on one hand, and doubts about the adequacy of Kauzmann’s model for the HφO effect, have led to a comeback of the HBs, along with a host of new hydrophilic (HφI) effects. The HφO effects lost much of its power - which it never really had - in explaining protein folding and protein-protein association. Instead, the more powerful and richer repertoire of HφI effects took over the reins. The interactions also offered simple and straightforward answers to the problems of protein folding, and protein-protein association.

Keywords

Protein Folding, Protein Association, Molecular Recognition, Hydrophobic, Hydrophilic Interactions

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	L. Pauling, “The Nature of Chemical Bond,” 2nd ed., Cornell University Press, Ithaca, New York, 1948.
[2]	L. Pauling, “The Nature of Chemical Bond,” 3rd ed., Cornell University Press, Ithaca, New York, 1960.
[3]	M. L. Anson, and A. E. Mirsky, “The Equilibria Between Native and Denatured Hemoglobin in Salicylate Solutions and the Theoretical Consequences of The Equilibrium Between Native and Denatured Protein,” Journal General Physiology, Vol. 17, 1934, pp. 393-408.
[4]	A. E. Mirsky, and L. Pauling, “On the structure of native, denatured and coagulated proteins,” Proceedings of the National Academy Science, USA, Vol. 22, 1936, pp. 439-449.
[5]	L. Pauling, and R. B. Corey, “Atomic Coordinates and Structure Factors for Two Helical Configurations of Polypeptide Chains,” Proceedings of the National Academy of Science, USA, Vol. 37, 1951, pp. 235-248.
[6]	L. Pauling, and R. B. Corey, “The Pleated Sheet, A New Layer Configuration of Polypeptide Chains,” Proceedings of the National Academy Science, USA, Vol. 37, 1951, pp. 251-256.
[7]	L. Pauling, and R. B. Corey, “The Structure of Fibrous Proteins of the Collagen-Gelatin Group,” Proceedings of the National Academy Science, USA, Vol. 37, 1951, pp. 272-281.
[8]	L. Pauling, and R. B. Corey, “Configurations of peptide chains with favored orientations around single bonds: two new pleated sheets,” Proceedings of the National Academy. Science, USA, Vol. 37, 1951, pp. 729-740.
[9]	C. Tanford and J. Reynold, “Nature’s Robots, A History of Proteins,” Oxford University Press, Oxford, U.K., 2003.
[10]	J. A. Schellmann, “The thermodynamics of urea solutions and the heat of Formation of the peptide hydrogen bond,” Comptes rendus des travaux du laboratoire Carlsberg, Serie Chimique, Vol. 29, 1955, pp. 223-230.
[11]	J. A. Schellmann (1955), “The stability of hydrogen- bonded peptide structures in Aqueous solution,” Comptes rendus des travaux du laboratoire Carlsberg, Serie Chimique, Vol. 29, 1955, pp. 230-59.
[12]	W. Kauzmann, “Some factors in the interpretation of protein denaturation,”Advances in Protein Chemistry, Vol. 14, 1959, pp. 1-63.
[13]	A. Fersht, “Structure and Mechanism in Protein Science,” W. H. Freeman and Comp. New York, 1999.
[14]	A. Ben-Naim, “Molecular Theory of Water and Aqueous Solutions Part I: Understanding Water,” World Scientific, Singapore, 2009.
[15]	A. Ben-Naim, “Molecular Theory of Water and Aqueous Solutions,” Part II: Hydrophilic Effects in Protein Folding, Self-Assembly and Molecular Recognition,” World Scientific, Singapore, 2011.
[16]	A. Ben-Naim, “Entropy Demystified. The Second Law Reduced to Plain Common Sense,” World Scientific, Singapore, 2007.
[17]	M. Tribus, and McIrvine, “Energy and Information,” Scientific American, Vol. 225, 1971, pp. 179-188.
[18]	A. Ben-Naim, “A Farewell to Entropy. Statistical Mechanics Based on Information,” World Scientific, Singapore, 2008.
[19]	A. Ben-Naim, “Hydrophobic Interactions,” Plenum Press, New York, 1980.
[20]	A. Ben-Naim, “On the role of hydrogen-bonds in protein folding and protein. association, Journal of Physical Chemistry, Vol. 95, 1990, pp. 1444-1473.
[21]	A. Ben-Naim, “Solvent-induced interactions: Hydrophobic and Hydrophilic Phenomena,” Journal of Chemical Physics, Vol. 90, 1989, pp. 7412-7525.
[22]	A. Ben-Naim, “Solvent effects on protein association and protein folding,” Biopolymers, Vol. 29, 1990, pp. 567- 596.
[23]	A. Ben-Naim, “Solvent induced forces in protein folding,” Journal of Chemical Physics, Vol. 94, 1990, pp. 6893-6895.
[24]	A. Ben-Naim, “Strong forces between Hydrophilic Macromolecules; Implications in Biological Systems,” Journal of Chemical Physics, Vol. 93, 1991, pp. 8196- 8210.
[25]	A. Ben-Naim, “Statistical Thermodynamics for Chemists and Biochemists,” Plenum Press, New York, 1992.
[26]	M. Mezei, and A. Ben-Naim, Journal of Chemical Physics, Vol. 92, 1990, pp. 1359-1361.
[27]	S.R. Durell, B.R. Brooks, and A. Ben-Naim, Journal of Physical Chemistry, Vol. 98, 1994, pp. 2198-2202.
[28]	P. Haberfield, J. Kivuls, M. Haddad, and T. Rizzo, “Enthalpies, free energies, and entropies of transfer of phenols from nonpolar solvents to water,” Journal of Physical Chemistry, Vol. 88, 1984, pp. 1913-1916.
[29]	C. B. Anfinsen, “Principles that Govern the Folding of Protein Chains,” Science, New Series, Vol. 181, 1973, pp. 223-230.
[30]	E. Haber, and C. B. Anfinsen, “Studies on the Reduction on Reformation of Protein Disulfide Bonds,” Journal of Biological Chemistry, Vol. 236, 1961, pp. 1361-1363.
[31]	H. Wang, and A. Ben-Naim, Solvation and Solubility of Globular Proteins, Journal of Physical Chemistry B, Vol. 101, 1997, pp. 1077-1086.
[32]	T. E. Creighton, “The problem of how and why proteins adopt folded conformations, Journal of Physical Chemistry, Vol. 89, 1985, pp. 2452-2459.
[33]	G. D. Rose, P. J. Fleming, J. R. Banavar and A. Maritan, “A backbone based Theory of protein folding,” Proceedings of the National Academy of Science, Vol. 103, 2006, pp. 16623-16633.
[34]	K. A. Dill, “Dominant forces in protein folding,” Biochemistry, Vol. 29, 1990, pp. 7133-7155.
[35]	A. Ben-Naim, “Cooperativity and Regulation in Biochemical Processes,” Kluwer Academic/Plenum Publishers, New York, 2001.
[36]	H. Wang and A. Ben-Naim, “A Possible Involvement of Solvent Induced Interactions in Drug Design,” J. Medicinal Chemistry, Vol. 39, 1996, pp 1531-1539.