Molecular Dynamics Studies on the Buffalo Prion Protein

TL;DR

This study uses molecular modeling and dynamics to explore structural features of buffalo prion protein, revealing specific bonds and loops that may explain buffalo's resistance to prion diseases.

Contribution

The paper provides the first detailed molecular structural analysis of buffalo prion protein, identifying unique bonds and loops linked to disease resistance.

Findings

Buffalo prion protein has unique hydrogen bonds at residue 143.

Strong salt bridge ASP178-ARG164 links the beta2-alpha2 loop.

Presence of specific helices and pi-contacts in buffalo prion protein.

Abstract

It was reported that buffalo is a low susceptibility species resisting to prion diseases, which are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of species. In molecular structures, TSE neurodegenerative diseases are caused by the conversion from a soluble normal cellular prion protein, predominantly with alpha-helices, into insoluble abnormally folded infectious prions, rich in beta-sheets. This paper studies the molecular structure and structural dynamics of buffalo prion protein, in order to reveal the reason why buffalo are resistant to prion diseases. We first did molecular modeling of a homology structure constructed by one mutation at residue 143 from the Nuclear Magnetic Resonance structure of bovine and cattle PrP(124-227); immediately we found for buffalo PrPC(124-227) there are 5 hydrogen bonds at Asn143, but at this position bovine/cattle do not have such hydrogen bonds. Same as that of rabbits, dogs or horses, our molecular dynamics studies also confirmed there is a strong salt bridge ASP178-ARG164 (O-N) keeping the beta2-alpha2 loop linked in buffalo. We also found there is a very strong hydrogen bond SER170-TYR218 linking this loop with the C-terminal end of alpha-helix H3. Other information such as (i) there is a very strong salt bridge HIS187-ARG156 (N-O) linking alpha-helices H2 and H1 (if mutation H187R is made at position 187 then the hydrophobic core of PrPC will be exposed), (ii) at D178, there is a hydrogen bond Y169-D178 and a polar contact R164-D178 for BufPrPC instead of a polar contact Q168-D178 for bovine PrPC, (iii) BufPrPC owns 3-10 helices at 125-127, 152-156 and in the beta2-alpha2 loop respectively, and (iv) in beta2-alpha2 loop there are strong pi-contacts, etc, has been discovered.