PubMed · 6924476
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1982. Theoretical model testing: full data utilization.. https://doi.org/10.1177/019394598200400321
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As the three-dimensional structures of more and more proteins are determined by experiment, discovering substantially novel folding motifs becomes ever rarer. The natural question is how many motifs are there and how many have already been found? In order to answer this in at least one plausible and well-defined sense, we have chosen a quantitative measure of conformational similarity, rho (based on optimal rigid body superposition), and a means of generating all possible three-dimensional chain conformations using the discrete cosine transform. How many different folding motifs there are then depends on the specified cutoff in rho and on the flexibility allowed for the model polypeptide chain. For single chain proteins having no more than about 170 residues and which are not beta-barrels, there are only about 128 motifs that differ by rho > 1.0 (an extremely vague level of similarity), of which so far only 100 have been seen experimentally. The remaining 28 can be viewed as very low-resolution models of either undiscovered novel folds or violations of unknown principles of protein folding.
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This study investigates the possibility of inferring the thermodynamic stability relationship of polymorphs from their melting data. Thermodynamic formulas are derived for calculating the Gibbs free energy difference (delta G) between two polymorphs and its temperature slope from mainly the temperatures and heats of melting. This information is then used to estimate delta G, thus relative stability, at other temperatures by extrapolation. Both linear and nonlinear extrapolations are considered. Extrapolating delta G to zero gives an estimation of the transition (or virtual transition) temperature, from which the presence of monotropy or enantiotropy is inferred. This procedure is analogous to the use of solubility data measured near the ambient temperature to estimate a transition point at higher temperature. For several systems examined, the two methods are in good agreement. The qualitative rule introduced this way for inferring the presence of monotropy or enantiotropy is approximately the same as The Heat of Fusion Rule introduced previously on a statistical mechanical basis. This method is applied to 96 pairs of polymorphs from the literature. In most cases, the result agrees with the previous determination. The deviation of the calculated transition temperatures from their previous values (n = 18) is 2% on average and 7% at maximum.