Exploration of the Misfolding Mechanism of Transthyretin Monomer: Insights from Hybrid-Resolution Simulations and Markov State Model Analysis

Abstract

Misfolding and aggregation of transthyretin (TTR) is widely known to be responsible for a progressive systemic disorder called amyloid transthyretin (ATTR) amyloidosis. Studies suggest that TTR aggregation is initiated by a rate-limiting dissociation of the homo-tetramer into its monomers, which can rapidly misfold and self-assemble into amyloid fibril. Thus, exploring conformational change involved in TTR monomer misfolding is of vital importance for understanding the pathogenesis of ATTR amyloidosis. In this work, microsecond timescale hybrid-resolution molecular dynamics (MD) simulations combined with Markov state model (MSM) analysis were performed to investigate the misfolding mechanism of the TTR monomer. The results indicate that a macrostate with partially unfolded conformations may serve as the misfolded state of the TTR monomer. This misfolded state was extremely stable with a very large equilibrium probability of about 85.28%. With secondary structure analysis, we found the DAGH sheet in this state to be significantly destroyed. The CBEF sheet was relatively stable and sheet structure was maintained. However, the F-strand in this sheet was likely to move away from E-strand and reform a new β-sheet with the H-strand. This observation is consistent with experimental finding that F and H strands in the outer edge drive the misfolding of TTR. Finally, transition pathways from a near native state to this misfolded macrostate showed that the conformational transition can occur either through a native-like β-sheet intermediates or through partially unfolded intermediates, while the later appears to be the main pathway. As a whole, we identified a potential misfolded state of the TTR monomer and elucidated the misfolding pathway for its conformational transition. This work can provide a valuable theoretical basis for understanding of TTR aggregation and the pathogenesis of ATTR amyloidosis at the atomic level.

Aggregation-Prone Structural Ensembles of Transthyretin Collected With Regression Analysis for NMR Chemical Shift

“…It was previously shown that the TTR (105-115) peptide originating from the β-stand G is highly amyloidogenic (Gustavsson et al, 1991). A recent MD study reported a consistent result in which destabilization of the edge at the DAGH β-sheet, namely the β-stands D and H, is responsible for the amyloidogenic propensity of TTR (Zhou et al, 2019;Childers and Daggett, 2020). Furthermore, a series of computational studies have suggested that the DAGH β-sheet may experience structural deformation to reconstruct aggregation-prone α-sheet-like structures (Steward et al, 2008;Childers and Daggett, 2019).…”

Structural and thermodynamic characterization of a highly amyloidogenic dimer of transthyretin involved in a severe cardiomyopathy

“…2 , E and F ). This region has been proposed as one of the great importance through molecular dynamic studies to amyloidogenic propensity of TTR when destabilized ( 59 , 60 ).…”

Molecular Insights into the Inhibitory Role of α-Crystallin against γD-Crystallin Aggregation

“…The Chapman–Kolmogorov (C–K) test was further performed to ensure that the constructed MSM is really Markovian. The C–K test is calculated according to the following equation: T ( n τ ) ≈ T ( τ ) n where T (τ) is the transition probability matrix with selected lag time τ and n is an integer number of steps . The C–K compares MD trajectories at increasing time steps to the probability of the protein remaining in a specific state predicted by the constructed MSM.…”

“…where T(τ) is the transition probability matrix with selected lag time τ and n is an integer number of steps. 74 The C−K compares MD trajectories at increasing time steps to the probability of the protein remaining in a specific state predicted by the constructed MSM. The MSM-reweighted free energy surface (FES) along the first two PC dimensions was also computed.…”