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Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force
Authors:M Hendlich  P Lackner  S Weitckus  H Floeckner  R Froschauer  K Gottsbacher  G Casari  M J Sippl
Institution:Department of Biochemistry, University of Salzburg, Austria.
Abstract: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 C beta 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.
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