Abstract

Amyotrophic Lateral Sclerosis (ALS) is strongly associated with TDP43 proteinopathy, where mutations in TARDBP gene alter the protein’s stability, solubility, and RNA related functions. This study examines eight ALS-linked missense mutations located in both the structured RRM domains and the intrinsically disordered C-terminal region, aiming to clarify how single residue substitutions perturb TDP43 structure and behavior. The full length TDP43 model was obtained from the AlphaFold database due to the absence of complete crystallographic structures. Each mutation was manually introduced into the appropriate domain using Molecular Operating Environment (MOE) software. Under appropriate conditions, Molecular Dynamics simulations were performed on wildtype and mutated structures; Wildtype and mutant proteins were then compared with respect to conformational changes, focusing on energetic profiles, surfaces, and electrostatics properties, considering how these variations can be related to effects of mutations found in literature. RRM domain mutations showed localized but mechanistically distinct alterations. D169G increased domain stability through a subtle β-turn rearrangement without affecting nucleic acid binding. K181E and K263E reversed local electrostatics, disrupting the positively charged RNA binding groove. C terminal mutations (Q331K, A315E, M337V, N345K, G298S) produced broader effects, including enhanced aggregation propensity, altered phase behavior, impaired DNA repair interactions, and increased protein half-life. Despite their heterogeneity, all mutations converge toward mechanisms that promote TDP43 misfolding, aggregation, and loss of nuclear function-key drivers of ALS pathology. The conclusions of this study indicate that even minimal local perturbations can result in significant functional consequences, reinforcing the importance of mutation specific structural insights for future therapeutic strategies.