Thermodynamic studies, proteins

Irback A, Sjunnesson F. Folding thermodynamics of three beta-sheet peptides a model study. Proteins 2004 56 110-6. 

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

Poklar, N., N. Petrovcic, M. Oblak, and G. Vesnaver. 1999. Thermodynamic stability of ribonuclease A in alkylurea solutions and preferential solvation changes accompanying its thermal denaturation a calorimetric and spectroscopic study. Protein Sci 8 832-840. 

The Ki for HSA binding to racemic warfarin has been reported for 3-6 pM by various techniques, including frontal analysis and equilibrium dialysis, and is temperature- and pH-dependent. See Loun, B., Hage, D.S. Chiral separation mechanisms in protein-based HPLC columns. 1. Thermodynamic studies of (R)- and (S)-warfarin binding to immobilized human serum albumin. Anal. Chem. 1994, 66, 3814-3822. 

The substantial free energy available in the binding of hemes into natural proteins is frequently harnessed to fold or stabilize the final protein structure as observed in the differences in the apo- (77) and holo-structures (73) of cytochrome 6562 shown in Fig. 2. Although detailed thermodynamic studies of natural heme proteins are beginning... 

Many of the same models and techniques have been used to study the transitions in these two types of biopolymers, and we will present some common background information first. Then we will specialize and present the results of important thermodynamic studies in proteins and nucleic acids separately. However, common to both reports is the observation that the application of thermodynamic measurements and a thermodynamic analysis to carefully but widely chosen systems allows one to gain insights into structural details that complement molecular structure determinations obtained from instrumental techniques such as spectroscopy and X-ray crystallography. 

Comparison of results on thermodynamic studies of protein denaturation and hydrocarbon dissolution in water shows a number of surprising similarities and differences between these two processes. The most surprising result is the close correspondence of the temperature of convergence of the enthalpy and entropy functions for the denaturation of proteins, Tx, and the temperature 7s for the dissolution of hydrocarbons in water. 

The chapter written by Ramos and coworkers reviews various computational techniques used to study protein-protein interactions, with particular attention given to thermodynamic characteristics of mutated proteins and their interactions. 

The large dependence of enthalpy with temperature is indicative of a specihc interaction, even though that the affinities of these monomeric interactions between TRAF2 and receptors are rather low. As suggested from thermodynamic studies of protein-DNA interactions, a non-specific weak complex held together by electrostatic forces often exhibits little temperature dependence of enthalpy (Ladbury, 1995). 

In view of the coordination pattern in protein-bound methylcobalamin (see below), the thermodynamic studies on the effect of the coordination of the dimethylbenzimidazole base to the a-side of the cobalt center on the homolytic and heterolytic (Co/3-C)-bond dissociation energy in (4) (thermodynamic effect of the trans hgand or trans influence ) were extended to corresponding investigations with CojS-methyl-imidazolylcobamides, such as (9), where imidazole replaces the dimethylbenzimidazole these studies showed this change of the nature of the axial base to have httle effect on the two relevant bond-dissociation energies of the corresponding methylcobamide. ... 

Barratt, J.O., Thrombin and calcium chloride in relation to coagulation, Biochem. J. 9, 511-543, 1915 Van der Meer, C., Effect of calcium chloride on choline esterase. Nature 171, 78-79, 1952 Bhat, R. and Ahluwalia, J.C., Effect of calcium chloride on the conformation of proteins. Thermodynamic studies of some model compounds, Int. J. Pept. Protein Res. 30,145-152,1987 Furihata, C., Sudo, K., and Matsushima, T, Calcium chloride inhibits stimulation of replicative DNA... 

To study protein folding theoretically, simulation methods have proved indispensable. The folding transition is ultimately governed by statistical thermodynamics and hence it is paramount to use sampling methods that are able to reproduce the canonical Boltzmann distribution. Common sampling techniques are molecular dynamics (MD), Langevin or Brownian dynamics (BD) and Monte Carlo (MC). 

Kinetics and thermodynamics are always complementary for process study. While kinetics describes the rate of the process, thermodynamics analyzes its feasibility. As kinetic mechanisms describe the sequential search with the end state being a single protein having a particular function, a thermodynamic study involves... 

There are now well over 200 publications in which microcalorimetry has specifically been used to study protein-hgand interactions of a variety of types. A fist of these studies is readily available by a MEDLINE search or from ITC equipment suppliers. Since the studies are too numerous to review here, perhaps a recent one might serve as a representative example of the technique and of its application. In this example [40] we determined the thermodynamic parameters associated with the binding of the reversible inhibitor 2 -CMP (2 -cytidine monophosphate) to RNAse-A (ribonuclease A). We were specifically interested in the binding under conditions that were relatively physiological, i.e., at body temperature and in a buffer that contained multiple ions at roughly cellular concentrations. 

Tizzano B, Palladino P, De Capua A, Marasco D, Rossi F, Benedetti E, Pedone C, Ragone R, Ruvo M (2005) The human prion protein alpha 2 helix a thermodynamic study of its conformational preferences. Proteins Struct Funct Bioinform 59 72... 

Battistel, E., Luisi, P.L. and Rialdi, G., Thermodynamic study of globular protein stability in microemulsions, Journal of Physical Chemistry, 1988, 92, 6680-6685. 

The first systematic experimental evidence for the unusual behavior of proteins with respect to temperature and pressure came from the kinetic studies of Suzuki [2] and thermodynamic studies by Hawley [4]. The mathematical implications and assumptions that are usually made in the analysis of the data have recently been discussed [79]. Of particular... 

So far there have been relatively few applications of electrophoresis at elevated hydrostatic pressures. However, this method has several advantages over other methods such as optical methods it is a simple and direct means of studying dissociation and denaturation processes, and of describing the thermodynamics of protein-ligand interactions. These qualitative and quantitative studies can be performed using small amounts of pure proteins or complex protein mixtures. In addition, this technique permits separation and subsequent isolation of the different protein conformational states or subunits. 

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