Detecting early stage structural changes in wild type, pathogenic and non-pathogenic prion variants using Markov state model

Abstract

The conversion of prion protein from normal to scrapie followed by the aggregation and deposition of this scrapie form leads to various neurodegenerative diseases. A few studies carried out by researchers suggest that E219K prion mutant (glutamate to lysine mutation at residue position 219) is more stable than wild type protein. However a similar point mutation E200K (glutamate to lysine mutation at residue position 200) is pathogenic. In this study we have carried out detailed atomistic simulation of the wild type, pathogenic mutant E200K and E219K mutant which provides more stability. The aim of the study was to detect the early structural changes present in all the three variants which might be responsible for the stability or for their conversion from PrPC to PrPSc. MSM based analyses have been carried out to find out the differences between WT, E200K and E219K systems. Markov state model (MSM) analysis was able to predict the intermediate states which helped to understand the effect of same mutation at two different locations. The MSM analysis was able to show that the extra stability of E219K mutant may be a result of the increase in number of native contacts, strong salt bridges and less random motions. While pathogenicity of E200K mutant can be attributed to loss of some crucial salt-bridge interactions, increased random motions between helix 2 and helix 3.

Fig. 1. Starting structure used for simulation with mutant residue represented as ball and stick. (A) Wild type. (B) E200K. (C) E219K.

Fig. 2. Comparison of chemical shift values between experimental and simulated ensemble structure for all the three variants.

Fig. 3. (A) Correlation plot between various parameters. Upper triangle represents the correlation value between different parameters. Lower triangle shows clusters where blue colour is wild type, red colour E200K variant and yellow colour is for E219K variant. (B) PCA cluster using defined list of parameters (RMSD, RGY, SASA, native contacts, hydrogen bonds, and important contacts). Blue colour is for wild type, orange colour is for E200K variant and green colour is for E219K variant.

Fig. 4. Markov state model analysis for wild type. (A) Free energy landscape along first two time independent component. (B) Projection of independent component. (C) Free energy landscape along first two time independent component showing three major states (red, blue and green) along with their representative structure. (D) Free energy landscape along first two time independent component showing pathway followed to reach unstable state (green colour) from stable state (red colour).

Fig. 5. Markov state model analysis for E200K variant. (A) Free energy landscape along first two time independent component. (B) Projection of independent component. (C) Free energy landscape along first two time independent component showing three major states (red, blue and green) along with their representative structure. (D) Free energy landscape along first two time independent component showing pathway followed to reach unstable state (green colour) from stable state (red colour).

Fig. 6. Markov state model analysis for E219K variant (A) free energy landscape along first two time independent component. (B) Projection of independent component. (C) Free energy landscape along first two time independent component showing three major states (red, blue and green) along with their representative structure. (D) Free energy landscape along first two time independent component showing pathway followed to reach unstable state (green colour) from stable state (red colour).

Fig. 7. Figure showing residue-wise native contacts for MSM states (A) residue-wise native contacts for state 1 for all the three variants (B) residue-wise native contacts for state 2 for all the three variants (C) residue-wise native contacts for state 3 for all the three protein variants.

Fig. 8. Figure showing electrostatic potential for all the three protein variant. Red is negatively charged surface and blue being positively charged surface. (A) Wild type. (B) E200K. (C) E219K.