Atomic insights into the effects of pathological mutants through the disruption of hydrophobic core in the prion protein

Juhwan Lee,Wookyung Yu,Iksoo Chang

doi:10.1038/s41598-019-55661-2

Juhwan Lee, Wookyung Yu + Show 1 more

Open Access

https://doi.org/10.1038/s41598-019-55661-2

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Abstract

Destabilization of prion protein induces a conformational change from normal prion protein (PrPC) to abnormal prion protein (PrPSC). Hydrophobic interaction is the main driving force for protein folding, and critically affects the stability and solvability. To examine the importance of the hydrophobic core in the PrP, we chose six amino acids (V176, V180, T183, V210, I215, and Y218) that make up the hydrophobic core at the middle of the H2-H3 bundle. A few pathological mutants of these amino acids have been reported, such as V176G, V180I, T183A, V210I, I215V, and Y218N. We focused on how these pathologic mutations affect the hydrophobic core and thermostability of PrP. For this, we ran a temperature-based replica-exchange molecular dynamics (T-REMD) simulation, with a cumulative simulation time of 28 μs, for extensive ensemble sampling. From the T-REMD ensemble, we calculated the protein folding free energy difference between wild-type and mutant PrP using the thermodynamic integration (TI) method. Our results showed that pathological mutants V176G, T183A, I215V, and Y218N decrease the PrP stability. At the atomic level, we examined the change in pair-wise hydrophobic interactions from valine-valine to valine-isoleucine (and vice versa), which is induced by mutation V180I, V210I (I215V) at the 180th–210th (176th–215th) pair. Finally, we investigated the importance of the π-stacking between Y218 and F175.

Highlights

Destabilization of prion protein induces a conformational change from normal prion protein (PrPC) to abnormal prion protein (PrPSC)
The subcellular location of PrP is highly dependent on the proteinase K (PK) resistance and aggregation ability[14]
Previous studies on the effect of N-glycosylation on the subcellular localization of PrP reported that the wild-type and monoglycosylated mutant (N181D and N197D) are anchored to the plasma membrane[40], but the T183A mutant and unglycosylated mutant (N181D/N197D) exist in the cytoplasme[15,40]

Summary

Introduction

Destabilization of prion protein induces a conformational change from normal prion protein (PrPC) to abnormal prion protein (PrPSC). From the T-REMD ensemble, we calculated the protein folding free energy difference between wild-type and mutant PrP using the thermodynamic integration (TI) method. A previous review about these programs reported that all computational methods predict a correct trend, but the correlation coefficients between the calculated and experimental change in protein stability (ΔΔG) range from 0.26 to 0.5926. This method is useful to tracks the interaction partners of wild-type and mutant amino acids at the same time This sequential change of the λ value allowed us to compare the stability between wild-type and mutant PrP. We calculated the protein folding free energy differences of six pathogenic mutants using thermodynamic cycle (Fig. S2) with a cumulative simulation time of 113.4 μs, and compared them with experimental results

Methods

Results

Conclusion