Planck-Benzinger thermal work function: thermodynamic characterization of the carboxy-terminus of p53 peptide fragments.

The thermodynamic parameters for six p53 carboxy-terminus peptide fragments as determined by analytical ultracentrifugal analysis were compared over the experimental temperature range of 275-310 K to evaluate the Gibbs free energy change as a function of temperature, ΔG°(T), from 0 to 400 K using our general linear third-order fitting function, ΔG°(T) = α + βT² + γT³. Data obtained at the typical experimental temperature range are not sufficient to accurately describe the variations observed in the oligomerization of these p53 fragments. It is necessary to determine a number of thermodynamic parameters, all of which can be precisely assessed using this general third-order linear fitting function.

Thermodynamic molecular switch in sequence-specific hydrophobic interaction: two computational models compared.

We have shown in our published work the existence of a thermodynamic switch in biological systems wherein a change of sign in DeltaCp(o)(T)reaction leads to a true negative minimum in the Gibbs free energy change of reaction, and hence, a maximum in the related K(eq). We have examined 35 pair-wise, sequence-specific hydrophobic interactions over the temperature range of 273-333 K, based on data reported by Nemethy and Scheraga in 1962. A closer look at a single example, the pair-wise hydrophobic interaction of leucine-isoleucine, will demonstrate the significant differences when the data are analyzed using the Nemethy-Scheraga model or treated by the Planck-Benzinger methodology which we have developed.

Molecular-level thermodynamic switch controls chemical equilibrium in sequence-specific hydrophobic interaction of 35 dipeptide pairs.

Applying the Planck-Benzinger methodology, the sequence-specific hydrophobic interactions of 35 dipeptide pairs were examined over a temperature range of 273-333 K, based on data reported by Nemethy and Scheraga in 1962. The hydrophobic interaction in these sequence-specific dipeptide pairs is highly similar in its thermodynamic behavior to that of other biological systems. The results imply that the negative Gibbs free energy change minimum at a well-defined stable temperature, , where the bound unavailable energy, TdeltaS(o) = 0, has its origin in the sequence-specific hydrophobic interactions, are highly dependent on details of molecular structure.

Misconceptions arising from a sign discrepancy in thermodynamic data for the Gibbs free energy profile of ribonuclease a.

An apparent discrepancy in the data for the Gibbs free energy change as a function of temperature at different pHs, originally published by Brandts in 1965 and repeated by Brandts and Hunt in 1967 with an unexplained change in sign, has lead to close to 40 years of misguided thinking in examining the thermodynamics of protein unfolding, including the frequently promulgated idea of cold denaturation. We have carried out a detailed analysis based on the Planck-Benzinger approach, which is very powerful in clarifying the fundamental aspects of biochemical energetics.