Abstract

contact areas versus atom type in a database of non-homologous protein 25 rue du Docteur Roux structures. The atomic environment is characterized by the surface area 75015 Paris, France accessible to solvent and the surface of contacts with polar and non-polar 2 atoms. Four types of atoms are considered, namely neutral polar atoms from UPR 003 Cancérogénèse et protein backbones and from protein side-chains, non-polar atoms and Mutagénèse Moléculaire et charged atoms. Potential energies �Ej(E) are defined from the preference for Structurale du CNRS an atom of type j to be in a given environment E compared to the expected Boulevard Sébastien Brant value if everything was random; Boltzmann’s law is then used to transform 67400 Illkirch Graffenstaden these preferences into energies. These new potentials very clearly France discriminate misfolded from correct structural models. The performance of these potentials are critically assessed by monitoring the recognition of the native fold among a large number of alternative structural folding types (the hide-and-seek procedure), as well as by testing if the native sequence can be recovered from a large number of randomly shuffled sequences for a given 3D fold (a procedure similar to the inverse folding problem). We suggest that these potentials reflect the atomic short range non-local interactions in proteins. To characterise atomic solvation alone, similar potentials were derived as a function of the percentage of solvent-accessible area alone. These energies were found to agree reasonably well with the solvation formalism of Eisenberg and McLachlan.

Citations