Atomic Mechanisms of Transthyretin Tetramer Dissociation Studied by Molecular Dynamics Simulations

Abstract

The dissociation of the transthyretin (TTR) tetramer into a monomer is closely related to various TTR amyloidoses in humans. While the tetramer dissociation has been reported to be the rate-limiting step for TTR aggregation, few details are known about the mechanism. Here, molecular dynamics (MD) simulations were performed by combining conventional MD and biased metadynamics to investigate the mechanism for the wild-type (WT) and mutant (T119M) structures. Both were found to have a great deal in common. Conventional MD simulations reveal that interfacial hydrophobic interactions contribute significantly to stabilize the tetramer. Interfacial residues including L17, V20, L110, and V121 with close contacts form a hydrophobic channel. Metadynamics simulations indicate that the mouth opening of the hydrophobic channel is the first and the most difficult step for dissociation. Interactions of V20 between opposing dimers lock four monomers into the tetramer, and disruption of the interactions is found to be involved in the final step. During the dissociation, an increasing extent of solvation was observed by calculating the radial distribution functions of water around interfacial hydrophobic residues, suggesting that water plays a role in driving the tetramer dissociation. Moreover, compared to T119, residue M119 has a longer side chain that extends into the hydrophobic channel, making solvation more difficult, consistent with a higher energy barrier for dissociation of the T119M tetramer. This result provides a good explanation for the protective role of the T119M mutation. Overall, this study can provide atomic-level insights to better understand the pathogenesis of TTR amyloidosis and guide rational drug design in the future.

Probing the Dissociation Pathway of a Kinetically Labile Transthyretin Mutant

“…Tetramer dissociation via the strong dimer intermediate has been previously inferred and studied using Cys-cross-linked dimer constructs, 7,38 by surfaceinduced dissociation in the gas phase by native mass spectrometry, 14 and MD-based free energy calculations. 10,11 Our observation of dimer-mediated dissociation of A25T F under equilibrium conditions at neutral pH is fully consistent with these previously reported results. Numerical simulations have suggested that the dimer-mediated formation of the tetramer (dimer of dimers) can reduce the amounts of protein trapped as assembly intermediates and is employed by all homotetrameric proteins surveyed.…”

“…The enhanced propensity of A25T to dissociate, which occurs on a time scale of minutes compared to days for the WT TTR tetramer, is related to perturbations propagated from the site of mutation to both the weak and strong dimer interfaces, where amide resonances of affected residues are either broadened or shifted. In particular, the amide cross-peaks of L17, V20, L110, and V121, which are located in the subunit interfaces and play a key role in mediating the dissociation of the tetramer to form dimers in MD simulations, 10 are broadened in the TROSY spectrum of A25T (Figure 2D), suggesting enhanced conformational dynamics (Figure 2A−C).…”

“…Several mechanisms for TTR tetramer dissociation and reassembly have been proposed, involving dimeric or trimeric intermediates, − and dissociation pathways via a strong dimer intermediate have been simulated by molecular dynamics (MD). , Previous experimental studies of dissociation pathways have been carried out in the presence of detergent or denaturant to destabilize TTR, , by using cross-linking to shift equilibria, or by relying on surface-induced gas phase dissociation to drive tetramer dissociation . Direct experimental observation of weakly populated dissociative intermediates in solutions that are free of detergent or denaturant has not been possible for WT TTR.…”

Molecular mechanisms and emerging therapies in wild-type transthyretin amyloid cardiomyopathy

“…Molecular dynamics simulations have investigated the dissociation process of TTR by constructing the free energy surface of the system [ 26 , 27 ]. The analysis revealed that tetramer dissociation is a multistep process, and the first step in disrupting the native tetramer is most difficult since the largest energy barrier occurs in the transition [ 28 ]. The energy barriers of TTRwt and the TTR variant (T119M) are comparable; however the T119M system has a higher barrier, providing evidence of the protective function of T119M.…”

Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry

“…Zhou et al. interrogate dissociation mechanisms of the transthyretin (TTR) tetramer into a monomer, through conventional and meta-dynamics simulations, providing guidance for understanding TTR-related amyloidosis and potential therapeutic avenues . Chen et al use Gaussian and amino acid-based network models to study allosteric signaling and communication mechanisms in opioid receptors .…”