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