NMR refinement of under-determined loop regions of the E200K variant of the human prion protein using database-derived distance constraints

Abstract

<p>Computational studies and research conducted in order to facilitate the understanding of the conversion of the normal cellular prion (PrP[Superscript c]) to the scrapie prion (PrP[Superscript Sc]) in prion diseases, are usually based on the structures determined by NMR. This is mainly attributed to the difficulties involved in crystallizing the prion protein. Due to insufficient experimental restraints, a biologically critical loop region in PrP[Superscript c] (residues 167-171), which is the potential binding site for the hypothized Protein X, is under-determined in most mammalian species. In this research, we show that by adding information about distance constraints derived from a database of high-resolution protein structures, this under-determined loop and some other secondary structural elements of the E200K variant of human PrP[Superscript c] can be refined into more generally realistic and acceptable structures within an ensemble, with improved quality and increased accuracy. In particular, the ensemble becomes more compact after the refinement with database derived distances constraints and the percentage of residues in the most favorable region of the Ramachandran diagram is increased to about 90% in the refined structures from the 80 to 85% range in the previously reported structures. In NMR structures, a model with 90% or more residues lying in the most favorable regions of the Ramachandran plot, is considered a good quality model. Our results not only provide a significantly improved model of structures of the Human prion protein, that would hence facilitate insights into its conversion in the spongiform encephalopathies, but also demonstrate the strong potential for using databases of known protein structures for structure determination and refinement.</p>