Thermostability of salt bridges versus hydrophobic interactions in proteins probed by statistical potentials

The temperature dependence of the interactions that stabilize protein structures is a long-standing issue, the elucidation of which would enable the prediction and the rational modification of the thermostability of a target protein. It is tackled here by deriving distance-dependent amino acid pair potentials from four datasets of proteins with increasing melting temperatures (Tm). The temperature dependence of the interactions is determined from the differences in the shape of the potentials derived from the four datasets. Note that, here, we use an unusual dataset definition, which is based on the Tm values, rather than on the living temperature of the host organisms. Our results show that the stabilizing weight of hydrophobic interactions (between Ile, Leu, and Val) remains constant as the temperature increases, compared to the other interactions. In contrast, the two minima of the Arg--Glu and Arg--Asp salt bridge potentials show a significant Tm dependence. These two minima correspond to two geometries: the fork--fork geometry, where the side chains point toward each other, and the fork--stick geometry, which involves the N(epsilon) side chain atom of Arg. These two types of salt bridges were determined to be significantly more stabilizing at high temperature. Moreover, a preference for more-compact salt bridges is noticeable in heat-resistant proteins, especially for the fork--fork geometry. The Tm-dependent potentials that have been defined here should be useful for predicting thermal stability changes upon mutation.