ALS-Linked A315T and A315E Mutations Enhance β-Barrel Formation of the TDP-43_307–319 Hexamer: A REST2 Simulation Study

Abstract

Pathogenic mutations of transactivation response element DNA-binding protein 43 (TDP-43) are closely linked with amyotrophic lateral sclerosis (ALS). It was recently reported that two ALS-linked familial mutants A315T and A315E of TDP-43307–319 peptides can self-assemble into oligomers including tetramers, hexamers, and octamers, among which hexamers were suggested to form the β-barrel structure. However, due to the transient nature of oligomers, their conformational properties and the atomic mechanisms underlying the β-barrel formation remain largely elusive. Herein, we investigated the hexameric conformational distributions of the wild-type (WT) TDP-43307–319 fragment and its A315T and A315E mutants by performing all-atom explicit-solvent replica exchange with solute tempering 2 simulations. Our simulations reveal that each peptide can self-assemble into diverse conformations including ordered β-barrels, bilayer β-sheets and/or monolayer β-sheets, and disordered complexes. A315T and A315E mutants display higher propensity to form β-barrel structures than the WT, which provides atomic explanation for their enhanced neurotoxicity reported previously. Detailed interaction analysis shows that A315T and A315E mutations increase inter-molecular interactions. Also, the β-barrel structures formed by the three different peptides are stabilized by distinct inter-peptide side-chain hydrogen bonding, hydrophobic, and aromatic stacking interactions. This study demonstrates the enhanced β-barrel formation of the TDP-43307–319 hexamer by the pathogenic A315T and A315E mutations and reveals the underlying molecular determinants, which may be helpful for in-depth understanding of the ALS-mutation-induced neurotoxicity of TDP-43 protein.

Simulation-Guided Conformational Space Exploration to Assess Reactive Conformations of a Ribozyme

“…In order to better assess the conformational space exploration starting from the crystallographic structure, we conducted enhanced sampling simulations using REST2, using 24 replicas for a simulation time of 500 ns (see Materials and Methods). The goal of this method is to accelerate the conformational changes of the ribozyme using a ladder of simulations that differ in the rescaling of the molecular interactions involving ribozyme atoms, and it was extensively used to enhance the conformational space exploration of biomolecules, − including RNA. − …”

Dissecting the Effect of ALS Mutation G335D on the Early Aggregation of the TDP-43 Amyloidogenic Core Peptide: Helix-to-β-Sheet Transition and Conformational Shift

“…41 Amber99SB-ILDN force field 42 was used for proteins, and the TIP3P model 43 was used for water molecules, in accordance with recent studies demonstrating that this force field can well simulate the aggregation dynamics and conformational ensembles of fragments of the TDP-43 LCD. 19,28,30,33,37,44,45 For MD simulations, WT or the G335D TDP-43 311−360 dimer was placed in the center of a truncated octahedral box with a minimum distance between the protein to the box wall being 1.2 nm. The shortest distance between two hexagons of the truncated octahedral box is 8.09 nm.…”

“…All simulations were performed using the GROMACS-2018.3 package with the PLUMED2 plugin . Amber99SB-ILDN force field was used for proteins, and the TIP3P model was used for water molecules, in accordance with recent studies demonstrating that this force field can well simulate the aggregation dynamics and conformational ensembles of fragments of the TDP-43 LCD. ,,,,,, …”

A brief history of amyloid aggregation simulations

“…The structured dimers exhibited different β‐strand arrangements; some of them could be assembled to protofibril models that were found to align with experimental data from H/D exchange NMR spectroscopy and atomic force microscopy. In another study published in 2012, Shea together with Guanghong Wei—who was a postdoctoral researcher in Shea's lab in 2004/2005 and continued to work on amyloid aggregation till today 145–147 —and their coworkers investigated $$$ {\mathrm{A}\upbeta}_{25-35} $$$ oligomers ranging from monomers to tetramers 148 . Their key finding was that the monomer primarily adopted a β‐hairpin conformation, while larger aggregates displayed extended structures.…”