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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

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Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation.

Helgi I Ingólfsson¹, Azamat Rizuan², Xikun Liu³

¹Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California.

Biophysical Journal

|October 19, 2023

Summary

Molecular dynamics simulations reveal that the protein TDP-43, implicated in neurodegenerative diseases like ALS, dynamically associates with itself and other molecules, driving the formation of cellular condensates.

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Area of Science:

Neuroscience
Biochemistry
Computational Biology

Background:

TDP-43 protein is crucial for mRNA processing and transport.
Cytoplasmic aggregation of TDP-43 is a hallmark of neurodegenerative diseases, including ALS.
The role of TDP-43 accumulation in neurodegeneration remains unclear.

Purpose of the Study:

To investigate the self- and cross-interaction dynamics of TDP-43 using molecular dynamics simulations.
To explore TDP-43 interaction patterns at various resolutions.

Main Methods:

Constructed a full-length molecular model of TDP-43 (414 amino acids).
Employed multi-resolution molecular dynamics simulations (all-atom CHARMM36m and coarse-grained Martini 3).
Simulated single TDP-43 proteins, pairs, and large assemblies to analyze interactions.

Main Results:

TDP-43 exhibits numerous, dynamic interaction preferences.
The protein shows a strong, yet flexible, tendency to associate with itself and other molecules.
These interactions drive the formation of biomolecular condensates.

Conclusions:

Multi-resolution simulations are effective for studying TDP-43 interactions.
TDP-43's dynamic association patterns contribute to condensate formation.
Understanding these dynamics may offer insights into TDP-43's role in neurodegeneration.