Thermodynamics of proteins

This text is similar to that of McCammon and Harvey (see below), but also provides a background for force field-based calculations and a more sophisticated discussion. Includes numerous examples of computing the structure, dynamics, and thermodynamics of proteins. The authors provide an interesting chapter on the complementary nature of molecular mechanics calculations and specific experimental techniques. 

FIGURE 3.4 The dependence of AG on temperatnre for the denaturation of chymotrypsinogen. (Adapted from Brandts, J. K, 1964. The thermodynamics of protein denaturation. I. The denaturation of e.hymotryjosinogeti. femrntA of the American Chemical Society m-.429I-430I.)... 

Simonson, T. Brimger, A. T., Thermodynamics of protein-peptide binding in the ribonuclease S system studied by molecular dynamics and free energy calculations.,... 

Livingstone, J.R., R.S. Spolar, and M.T. Record, Jr. 1991. Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area. Biochemistry 30 4237 1244. 

F. Oosawa S. Asakura (1975) Thermodynamics of Protein Polymerization, Academic Press, New York. 

INNATE THERMODYNAMIC QUANTITIES Thermodynamics of protein unfolding, INNATE THERMODYNAMIC QUANTITIES Thermodynamic quantities. 

Work from Sturtevant s laboratory detailed the kinetics and thermodynamics of zinc binding to apocarbonic anhydrase (carbonate dehydratase) selected data are recorded in Table II (Henkens and Sturtevant, 1968 Henkens etal., 1969). The thermodynamic entropy term A5 at pH 7.0 is 88 e.u. (1 e.u. = 1 cal/mol-K), and this is essentially matched by the binding of zinc to the hexadentate ligand cyclohexylenediamine tetraacetate where AS = 82 e.u. At pH 7.0 the enthalpy of zinc-protein association is 9.8 kcal/mol, but this unfavorable term is overwhelmed by the favorable entropic contribution to the free energy (AG = AH - T AS), where —TAS = -26.2 kcal/mol at 298 K (25°C). Hence, the kinetics and thermodynamics of protein-zinc interaction in this example are dominated by very favorable entropy effects. 

It has been known that adsorption kinetics and/or thermodynamics of proteins depend on the electric or electrochemical properties of solid supports on which the proteins are adsorbed. This has led us to elucidate the effects of electrode potential on the adsorption behavior of avidin on the electrode surface. For this purpose, the electrode potential of a Pt electrode was varied systematically in the range of -0.5-+2.0 V in an avidin solution (pH 7.4). Although the data was somewhat scattered, a general trend was observed that the adsorption of avidin is suppressed by the application of a positive potential (+1.0-+2.0 V). This may be originating from the fact that avidin is a basic protein and has net positive charges in the solution of neutral pH. In the potential range tested, no significant acceleration in the adsorption was induced. 

Thermodynamics of Proteins Calculating the Entropy of a Helix-Coil Transition in a Small Antibacterial Peptide using Statistical Mechanics (J. Mol. Bio. 1999, 294, 785-794. "Thermodynamics of the a-Helix-Coil Transition of Amphipathic Peptides in a Membrane Environment Implications for the Peptide-Membrane Binding Equilibrium")... 

Perozzo, R., Folkers, G., and Scapozza, L. (2004). Thermodynamics of protein-ligand interactions history, presence and future aspects. Journal of Receptor and Signal Transduction Research 24, 1-52. 

F. Thermodynamics of Protein—Salt—Water Interactions and Structural... 

Shortcomings in current understanding of the thermodynamics of protein solutions can be illustrated by considering one of the oldest protein concentration methods, precipitation, and one of the newest and most technologically interesting methods for protein separation and purification, aqueous... 

Franks, F., Hatley, R. H. M and Friedman, H. L The thermodynamics of protein stability. Cold destabilization as a general phenomenon. Biophys. Chem. 31, 307-316 (1988). 

Lee, B., Isoenthalpic and isoentropic temperatures and the thermodynamics of protein denaturation. Proc. Natl. Acad. Sci. USA 88, 5154 (1991). 

Lee and Richards (1971) defined the solvent-accessible surface as that described by the center of a solvent molecule rolled about the surface of a solute molecule. This concept and its offspring are the basis of various computations of the contribution of hydration to the thermodynamics of protein folding and the thermodynamics of protein interactions. Ed-sall and McKenzie (1983) reviewed the literature on the thermodynamics of transfer processes used to model hydration and correlated this information with protein structure results analyzed according to the Lee and Richards formalism. Other notable reviews are those by Richards (1977), Nemethy et al. (1981), and Nemethy (1986). 

The applications of the chemistry of amino acids to the biological problem, protein structure and function, and folding and stability are the main focus of this article. The article is divided into hve main sections that include the biological insights on protein structures, chemical applications including protein functions, thermodynamics of proteins, protein interactions, and computational protein design. 

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