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

Abstract

Monomer dissociation and subsequent misfolding of the transthyretin (TTR) is one of the most critical causative factors of TTR amyloidosis. TTR amyloidosis causes several human diseases, such as senile systemic amyloidosis and familial amyloid cardiomyopathy/polyneuropathy; therefore, it is important to understand the molecular details of the structural deformation and aggregation mechanisms of TTR. However, such molecular characteristics are still elusive because of the complicated structural heterogeneity of TTR and its highly sensitive nature to various environmental factors. Several nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) studies of TTR variants have recently reported evidence of transient aggregation-prone structural states of TTR. According to these studies, the stability of the DAGH β-sheet, one of the two main β-sheets in TTR, is a crucial determinant of the TTR amyloidosis mechanism. In addition, its conformational perturbation and possible involvement of nearby structural motifs facilitates TTR aggregation. This study proposes aggregation-prone structural ensembles of TTR obtained by MD simulation with enhanced sampling and a multiple linear regression approach. This method provides plausible structural models that are composed of ensemble structures consistent with NMR chemical shift data. This study validated the ensemble models with experimental data obtained from circular dichroism (CD) spectroscopy and NMR order parameter analysis. In addition, our results suggest that the structural deformation of the DAGH β-sheet and the AB loop regions may correlate with the manifestation of the aggregation-prone conformational states of TTR. In summary, our method employing MD techniques to extend the structural ensembles from NMR experimental data analysis may provide new opportunities to investigate various transient yet important structural states of amyloidogenic proteins.

Atomic Mechanisms of Transthyretin Tetramer Dissociation Studied by Molecular Dynamics Simulations

“…During the tetramer dissociation, the close contact of V20–V20 in opposing dimers in both WT and T119M indicates that the “lock” role of V20 should be important for the stability of the tetramer, and breaking of the lock should be the final step for tetramer dissociation. A previous study also reported that the V20I mutation reduced the tetramer stability by changing the interactions of opposing dimers via the side chain of Ile 20, and the A-B loop region was reported to correlate with the manifestation of the aggregation-prone conformation states of TTR …”

“…A previous study also reported that the V20I mutation reduced the tetramer stability by changing the interactions of opposing dimers via the side chain of Ile 20, 61 and the A-B loop region was reported to correlate with the manifestation of the aggregation-prone conformation states of TTR. 62 Water Plays a Role in Driving the Dissociation of the TTR Tetramer. As the hydrophobic channel forms (in the first step for tetramer dissociation), water molecules can diffuse into the channel during tetramer dissociation, as shown in the representative snapshots in Figure 7a and 7b.…”

NMR spectroscopic investigations of transition metal complexes in organometallic and bioinorganic chemistry

“…While NMR spectroscopy has been extensively utilized to analyze proteins' structures and dynamics as well as protein-protein interactions in biological systems. 188,189 In the case of metalloproteins, ligand environments surrounded by metal centers could be deduced using the uniform 15 N-isotope labeling method combined with heteronuclear double-resonance and 2D experiments. 190 Isotope-labeling methods can also be applied to investigate the paramagnetic centers of metalloproteins, which broaden NMR signals and complicate the analysis.…”

“…Despite its low sensitivity, 15 N NMR spectroscopy often plays a crucial role in bioinorganic and organometallic chemistry. While NMR spectroscopy has been extensively utilized to analyze proteins' structures and dynamics as well as protein–protein interactions in biological systems 188,189 . In the case of metalloproteins, ligand environments surrounded by metal centers could be deduced using the uniform 15 N‐isotope labeling method combined with heteronuclear double‐resonance and 2D experiments 190 .…”

Molecular Mechanisms of Cardiac Amyloidosis

“…These eight β-strand chains form two four-β-stranded anti-parallel sheets, DAGH and CBEF β-sheets, respectively [ 24 , 28 ]. Yang et al showed various transient structural states of TTR by using nuclear magnetic resonance experimental data analysis and molecular dynamics studies [ 29 ]. Structural deformation of the DAGH β-sheet and the AB loop regions may correlate with the development of the aggregation-prone conformational states of TTR.…”