Evolution and Stability 
Beginning This dissertation has discussed some of the many forces that make small and conflicting contributions to protein stability. It is the sum of these various stabilising and destabilising interactions that gives rise to the final stability of a protein. The total destabilising and the total stabilising energies are both large, and their difference is small. This is one of the reasons that current computational methods struggle to predict protein stability from structure.
Furthermore, our understanding of these many forces is incomplete; as often as not mutations have the opposite effect to that which had been predicted. In addition, the activation energy for folding is an important determinant of both kinetic stability and whether a protein will fold to a global minimum. However, it also clear that great strides have been made, and the search for the solution to The Folding Problem, one of the great remaining questions in biology, is and continues to be, an exciting one.
The chapter by Murphy particularly addresses the important thermodynamic principles behind protein stability. Dill provides a more general overview of the subject, presenting clearly both historical background and recent developments.
Murphy K. In Protein Stability and Folding; Shirley B., Ed.; Methods in Molecular Biology 40; Humana: Totowa, NJ, 1995; Chapter 1.
Dill K. Dominant forces in protein folding. Biochemistry 29, 7133-55 (1990).
Akke M. & Forsen S. Protein stability and electrostatic interactions between solvent exposed charged side chains. Proteins: Struct. Funct. Genet. 8, 23-9 (1990).
Baker D. & Agard D., Kinetics versus thermodynamics in protein folding. Biochemistry, 33, 750509 (1994).
Baker E. & Hubbard R. Hydrogen bonding in globular proteins. Prog. Biophy. Mol. Biol., 44, 97-179 (1984).
Betz S., Disulfide bonds and the stability of globular proteins, Protein Science, 2, 155158 (1993).
Braxton S. In Protein Engineering: Principles and Practice, Cleland J. & Craik C. Eds.; Wiley-Liss, New York, NY,1996; Chapter 11.
Carter P., Winter G., Wilkinson A. & Fersht A., The use of double mutants to detect structural changes in the active site of the tyrosyltRNA synthetase (Bacillus stearothermophilus). Cell, 38, 835840 (1984).
Clarke J. & Fersht A., Engineered disulfide bonds as probes of the folding pathway of barnase: increasing the stability of proteins against the rate of denaturation. Biochemistry, 32, 4322-9 (1993).
Creighton T., (1993) Proteins: Structures & molecular properties, 2nd edition, p 147-148, W. H. Freeman & Co., New York.
Dekker K., Yamagata H., Sakaguchi K. & Udaka S. Xylose (glucose) isomerase gene from the thermophile Thermus thermophilus: cloning, sequencing, and comparison with other thermostable xylose isomerases. J. Bacteriol. 173, 3078-83 (1991).
Dixon M., Nicholson H., Shewchuk L., Baase W. & Matthews B. Structure of a hinge-bending bacteriophage T4 lysozyme mutant, Ile3-->Pro. J Mol Biol 227, 917-33 (1992)
Eriksson A., Baase W., Zhang X., Heinz D., Blaber M., Baldwin E. & Matthews B., Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 255, 178-83 (1992).
Fersht A. The hydrogen bond in molecular recognition. Trends Biochem. Sci. 12, 3214-3219 (1987)
Harpaz Y., Gerstein M. & Chothia C. Volume changes on protein folding. Structure 2, 641-9 (1994).
Hartley, G., (1936) Aqueous solutions of paraffin-chain salts, Hermann & Cie., Paris, as quoted in Tanford, C. (1973) The Hydrophobic Effect: Formation of Micelles and Biological Membranes, p viii, John Wiley & Sons, New York.
Hensel R. In Proteins of Extreme Thermophiles, Kates M., Kushner D. & Matheson A. Eds., The Biochemistry of the Archaea (New Comprehensive Biochemistry): Elsvier, Amsterdam, 1993; Vol.26, Chapter 7.
Horovitz A., Serrano L., Avron B., Bycroft M. & Fersht A., Strength and co-operativity of contributions of surface salt bridges to protein stability. J. Mol. Biol. 216, 1031-44 (1990).
Horovitz A. & Fersht A., Strategy for analysing the co-operativity of intramolecular interactions in peptides and proteins. J. Mol. Biol. 214, 613-7 (1990).
Kellis J., Todd R. & Arnold F., Protein stabilization by engineered metal chelation, Bio/Technology 9, 9945 (1991).
Kuroki R., Taniyama Y., Seko C., Nakamura H., Kikuchi M. & Ikehara M., Design and creation of a Ca2+ binding site in human lysozyme to enhance structural stability. Proc. Natl. Acad. Sci. U.S.A. 86, 6903-7 (1989).
McDonald I. & Thornton J., Satisfying hydrogen bonding potential in proteins. J Mol Biol 238, 777-93 (1994).
Matthews B., Nicholson H. & Becktel W. Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. Proc. Natl. Acad. Sci . U S A, 84, 6663-7 (1987)
Pace C., Evaluating the contribution of hydrogen bonding and hydrophobic bonding to protein folding. Methods Enzymol. 259, 538-554 (1995).
Pace C., Shirley B., McNutt M. & Gajiwala K.,Forces contributing to the conformational stability of proteins. FASEB J., 10, 75-83 (1996).
Pan H., Barbar E., Barany G. &Woodward C.,Extensive nonrandom structure in reduced and unfolded bovine pancreatic trypsin inhibitor. Biochemistry, 34, 13974-81 (1995).
Perutz M. & Raidt H. Sterochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2. Nature, 255, 256-59 (1975).
Perutz M. Electrostatic effects in proteins. Science, 201, 1185-91 (1978).
Serrano L., Day A. & Fersht A. Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability. J. Mol. Biol. 233, 305-12 (1993).
Serrano
L., Matouschek A. & Fersht A.,
(a)The
folding of an enzyme. III. Structure of the transition state for unfolding
of barnase analysed by a protein engineering procedure. J. Mol. Biol.
224, 805-18 (1992).
(b) The
folding of an enzyme. IV. Structure of an intermediate in the refolding
of barnase analysed by a protein engineering procedure. J. Mol. Biol.
224, 819-35 (1992).
Serrano L., Bycroft M. & Fersht A., Aromatic-aromatic interactions and protein stability. Investigation by double-mutant cycles. J. Mol. Biol. 218, 465-75 (1991).
Serrano L., Kellis J., Cann P., Matouschek A. & Fersht A., The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J Mol Biol 224, 783-804 (1992).
Shortle D. & Meeker A., Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation. Proteins 1, 81-9 (1986).
Shortle D., The denatured state (the other half of the folding equation) and its role in protein stability. FASEB J., 10, 27-34 (1996).
Sosnick T. & Trewhella J, Denatured states of ribonuclease A have compact dimensions and residual secondary structure. Biochemistry, 31, 8329-35 (1992).
Sturtevant J., The thermodynamic effects of protein mutations, Curr. Opin. Struct. Biol. 4, 69-78 (1994).
Tanaka A., Flanagan J., and Sturtevant J. Thermal unfolding of staphylococcal nuclease and several mutant forms thereof studied by differential scanning calorimetry. Protein Sci. 2, 567 - 576 (1993).
Tanner J., Hecht R. & Krause K. Determinants of enzyme thermostability observed in the molecular structure of Thermus aquaticus D-glyceraldehyde-3-phosphate dehydrogenase at 25 Angstroms Resolution. Biochemistry 35, 2597-609 (1996).
Vieille C. & Zeikus J., Thermozymes: identifying molecular determinants of protein structural and functional stability. Trends in Biotechnology 14, 183-90 (1996).
Waldburger C., Schildbach J. & Sauer R. Are buried salt bridges important for protein stability and conformational specificity? Nat. Struct. Biol. 2, 122-8 (1995)
Waldburger C., Jonsson T. & Sauer R. Barriers to protein folding: formation of buried polar interactions is a slow step in acquisition of structure. Proc. Natl. Acad. Sci. U.S.A. 93, 2629-34 (1996).
Evolution and Stability Beginning
I would like to acknowledge the assistance of Jane Clark with text preparation and HTML. Any mistakes remaining are mine.