Molecular dynamics studies on the NMR and X-ray structures of rabbit prion proteins

Abstract

Prion diseases, traditionally referred to as transmissible spongiform encephalopathies (TSEs), are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species, manifesting as scrapie in sheep and goats, bovine spongiform encephalopathy (BSE or mad-cow disease) in cattle, chronic wasting disease in deer and elk, and Creutzfeldt-Jakob diseases, Gerstmann-Sträussler-Scheinker syndrome, fatal familial insomnia, and kulu in humans, etc. These neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein (PrP(C)) into insoluble abnormally folded infectious prions (PrP(Sc)), and the conversion of PrP(C) to PrP(Sc) is believed to involve conformational change from a predominantly α-helical protein to one rich in β-sheet structure. Such a conformational change may be amenable to study by molecular dynamics (MD) techniques. For rabbits, classical studies show that they have a low susceptibility to be infected by PrP(Sc), but recently it was reported that rabbit prions can be generated through saPMCA (serial automated Protein Misfolding Cyclic Amplification) in vitro and the rabbit prion is infectious and transmissible. In this paper, we first do a detailed survey on the research advances of rabbit prion protein (RaPrP) and then we perform MD simulations on the NMR and X-ray molecular structures of rabbit prion protein wild-type and mutants. The survey shows to us that rabbits were not challenged directly in vivo with other known prion strains and the saPMCA result did not pass the test of the known BSE strain of cattle. Thus, we might still look rabbits as a prion resistant species. MD results indicate that the three α-helices of the wild-type are stable under the neutral pH environment (but under low pH environment the three α-helices have been unfolded into β-sheets), and the three α-helices of the mutants (I214V and S173N) are unfolded into rich β-sheet structures under the same pH environment. In addition, we found an interesting result that the salt bridges such as ASP201-ARG155, ASP177-ARG163 contribute greatly to the structural stability of RaPrP.

In Vitro Approach To Identify Key Amino Acids in Low Susceptibility of Rabbit Prion Protein to Misfolding

“…Similar studies comparing rabbit wild-type PrP and S173N and I214V mutated forms showed that either mutation significantly altered the salt bridge network and the hydrogen bond network, which increased structural instability. Thus, all these studies point toward distinctive intramolecular interactions being responsible for the stability of rabbit PrP, with a major contribution of the interactions established between the ␤2-␣2 loop and ␣-helices 2 and 3 (16,17,24). Importantly, these studies also reveal that point mutations can cause unpredictable changes in regions away from the mutation site itself.…”

“…The generation of transgenic rabbits expressing ovine PrP and their successful infection with scrapie prions definitively highlighted that the amino acid sequence of rabbit PrP C was responsible for the low susceptibility of rabbits to prion infections (14). Although rabbit PrP C has been studied in detail to identify distinctive structural elements that explain its low susceptibility to prion-like misfolding (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28), the key elements or amino acid residues causing this behavior remain unknown.…”

Structural effects of PrP polymorphisms on intra- and interspecies prion transmission

“…Stabilizing long-range interactions between the β2-α2 loop and α-helix 3 also occur in rabbit PrP, a species generally regarded as resistant to prion infection (reviewed in ref. 20). X-ray crystallographic analyses showed the rabbit β2-α2 loop to be clearly ordered and indicated that hydrophobic interactions between the side chains of V169 and, in this case Y221 (elk PrP numbering) of α-helix 3, contributed to the stability of the β2-α2 loop/α helix 3 epitope (21) (Fig.…”

Molecular dynamics studies on the buffalo prion protein

“…The MD methods employed are the same as the previous studies [Zhang & Zhang, 2013, Zhang & Zhang, 2014, Zhang, 2010. Briefly, all simulations used the ff03 force field of the AMBER 11 package [Case et al, 2010].…”