title: Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force.
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.
authors.affiliation: Department of Biochemistry, University of Salzburg, Austria.
authors.forename: M
authors.initials: M
authors.lastname: Hendlich
authors.forename: P
authors.initials: P
authors.lastname: Lackner
authors.forename: S
authors.initials: S
authors.lastname: Weitckus
authors.forename: H
authors.initials: H
authors.lastname: Floeckner
authors.forename: R
authors.initials: R
authors.lastname: Froschauer
authors.forename: K
authors.initials: K
authors.lastname: Gottsbacher
authors.forename: G
authors.initials: G
authors.lastname: Casari
authors.forename: M J
authors.initials: MJ
authors.lastname: Sippl
mesh_terms: D000818:Animals; D004268:DNA-Binding Proteins / Q000737:chemistry; D006422:Hemerythrin / Q000737:chemistry; D007147:Immunoglobulin Light Chains; D007135:Immunoglobulin Variable Region; D051379:Mice; D008958:Models, Molecular; D008962:Models, Theoretical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D004268:DNA-Binding Proteins; D006422:Hemerythrin; D007147:Immunoglobulin Light Chains; D007135:Immunoglobulin Variable Region; D011506:Proteins