IDENTIFICATION OF NATIVE PROTEIN FOLDS AMONGST A LARGE NUMBER OF INCORRECT MODELS - THE CALCULATION OF LOW-ENERGY CONFORMATIONS FROM POTENTIALS OF MEAN FORCE

We present an approach that is able to detect native folds amongst a large number of non-native conformations. The method is based on the compilation of potentials of mean force of the interactions of the Cβ atoms of all amino acid pairs from a database of known three-dimensional protein structures. These potentials are used to calculate the conformational energy of amino acid sequences in a number of different folds. For a substantial number of proteins we find that the conformational energy of the native state is lowest amongst the alternatives. Exceptions are proteins containing large prosthetic groups, Fe-S clusters or polypeptide chains that do not adopt globular folds. We discuss briefly potential applications in various fields of protein structural research. © 1990 Academic Press Limited.