A Coarse Grained Molecular Dynamics Study of the Formation and Structure of Bicelles

Abstract

We use AMBER all atom molecular dynamics (MD) to assess the stability of a model of the prion protein in its disease-causing conformation, PrPsc. The model is based upon threading the ovine prion sequence onto a template left-handed beta-helical (LHBH) structure with 18 residues per turn. Five polymorphisms in the sheep prion protein, VRQ, ARQ, ARH, AHQ, and ARR, have been identified at residues 136, 154, and 171 respectively, which are roughly 18 amino acids apart which thus align approximately on the LHBH. Threading of the sequence was thus done with an emphasis on the locations of these special sites as a means to investigate their possible role in disease susceptibility as well as investigating the overall viability of the LHBH as a structural candidate for PrPsc. In comparison to known left handed beta-helical proteins, the resulting model for VRQ is shown in all atom MD to 10 ns to exhibit similar stability as indicated by a low root mean square deviation, the presence of substantial side-chain to side-chain hydrogen bonding, and volume packing fraction. Interestingly, and in corroboration with experimental data that it is a disease resistant variant, the same model for ARR exhibits much less stability. Each polymorphic site was also investigated individually by comparing results from models with only one site different and showed a good correlation to experimental data regarding the relation of the variants to disease susceptibility.