| This work presents the application of computer modeling and all-atom molecular dynamics techniques to the prion protein sequence threaded onto a left-handed beta-helical scaffold.;We use AMBER all atom molecular dynamics (MD) to assess the stability of a model of the prion protein in its disease-causing conformation, PrP Sc. The model is based upon threading the ovine prion sequence onto a template left-handed beta-helical (LHbetaH) 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 at roughly 18 amino acids apart, align approximately on the LHbetaH. 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 LHbetaH as a structural candidate for PrPSc. In comparison to known left handed beta-helical proteins, the resulting model is shown in all-atom MD to 10ns to exhibit similar stability as indicated by a low root mean square deviation and the presence of substantial side-chain to side-chain hydrogen bonding. Both physiological and low pH environments were simulated by adjusting the protonation states of pertinent amino acids. While the presented threading does not show statistically significant differences in the RMSD values between the resistant and susceptible alleles, this study is by no means exhaustive. Further study using other threadings of the ovine prion sequence onto the LHbetaH template could still yield information about the relationship between protein conformation and disease susceptibility.;Polymorphisms have also been shown to exist in other species of the mammalian prion protein. There are over 30 mutations in the human prion resulting in single aminoacid substitutions in the protein sequence that have been linked to the inherited prion diseases. We again use AMBER all-atom molecular dynamics (MD) to assess characteristics associated with stability for a model of the prion protein in its disease causing conformation, PrPSc. The model uses as a template left-handed beta-helical (LHbetaH) structure with 18 residues per helical turn as its foundation. A fragment of the prion protein sequence is threaded onto the LHbetaH backbone based upon the results of a physically motivated scoring function which places amino acids in the sequence at designated locations within the LHbetaH structure. This method is used to study various polymorphisms within the human prion sequence which have been shown to either increase resistance or susceptibility to prion disease, as well as affect characteristics of the disease such as incubation time and disease onset age. The threadings used for each sequence are those with the highest score from the threading software, which also aids in establishing the validity of the scoring function. Results of MD over 10ns of production time are compared for each prion sequence.;Finally, directions for future work on these topics are presented. |
