The cellular prion protein (PrPC) is a GPI-anchored cell-surface protein. A small subset of PrPC molecules, however, can be integrated into the ER-membrane via a transmembrane domain (TM), which also harbors the most highly conserved regions of PrPC, termed the hydrophobic core (HC). A mutation in HC is associated with prion disease resulting in an enhanced formation of a transmembrane form ((PrP)-Pr-ctm), which has thus been postulated to be a neurotoxic molecule besides PrPSc. To elucidate a possible physiological function of the transmembrane domain, we created a set of mutants carrying microdeletions of 2-8 aminoacids within HC between position 114 and 121. Here, we show that these mutations display reduced propensity for transmembrane topology. In addition, the mutants exhibited alterations in the formation of the Cl proteolytic fragment, which is generated by a-cleavage during normal PrPC metabolism, indicating that HC might function as recognition site for the protease(s) responsible for PrPC alpha-cleavage. Interestingly, the mutant G113V, corresponding to a hereditary form of prion disease in humans, displayed increased (PrP)-Pr-Ctm topology and decreased alpha-cleavage in our in vitro assay. In conclusion, HC represents an essential determinant for transmembrane PrP topology, whereas the high evolutionary conservation of this region is rather based upon preservation of PrPC alpha-cleavage, thus highlighting the biological importance of this cleavage. (C) 2010 Elsevier Inc. All rights reserved.