d. Mol. Biol. (1990) 216, 167-180 Identification of Native Protein Folds Amongst a Large Number of Incorrect Models The Calculation of Low Energy Conformations from Potentials of Mean Force Manfred Hendlich, Peter Lackner, Sabine Weitckus, Hannes Floeckner, Rosina Froschauer, Karl Gottsbacher, Georg Casarit and Manfred J. Sippl~: Institute for General Biology, Biochemistry and Biophysics Department of Biochemistry, University of Salzburg Hellbrunnerstrafle 34, A-5020 Salzburg, Austria (Received 28 February 1990; accepted 16 July 1990) 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 Cp 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. 1. Introduction In spite of great efforts the problem of calculating protein conformations from amino acid sequences is still unsolved. It is generally thought that the native conformation of proteins corresponds to the structure of lowest free energy as compared to all conformations that are accessible in the approach to equilibrium (Anfinsen, 1973). The high dimensional state space of protein molecules, the multiple minima problem associated with the optimization of complex molecular energy surfaces and the enor- mous execution times required to calculate free energies are main problems from a methodological point of view. The design of useful free energy functions and the modelling of solvent forces remain major theoretical challenges. Using the methods presently available it is still difficult to identify native protein conformations amongst incorrectly folded models (Novotny et al,, 1984, 1988; Baumann et al., 1989). Potential energy t Present address: Research Institut for Molecular Pathology, Dr Bohr Oasse 7, A-1030 Vienna, Austria. :[:Author to whom correspondence should be addressed. functions used to simulate the energetics of protein molecules yield comparable energies for native folds and completely unrelated hypothetical models so that they cannot be used to discriminate between native and incorrect conformations. At present the most useful parameters in protein modelling seem to be related to the accessibility of polar and apolar groups on the protein surface and to the fraction of buried ionized groups (see e.g. Eisenberg & McLachlan, 1986). Here we report an approach that is able to iden- tify correct native conformations amongst a large number of alternative conformations. The approach is based on the compilation of potentials of mean force from a database of known protein structures. These potentials can be used to calculate the total energy of amino acid chains in different conforma- tions. The work presented is an extention of our previous studies, where we concentrated on the short-range forces in globular proteins and calcu- lated conformational ensembles for identical oligo- peptides found in several proteins using the Boltzmann device (Sippl, 1990). In the present study we include medium- and long-range forces and use the Boltzmann device to identify native conformations of globular proteins amongst a large number of misfolded structures. 167 0022-2836/90/200167-14 $03.00/0 ~) 1990 Academic Press Limited