Molecular dynamics and protein frustration analysis of human fused in Sarcoma protein variants in Amyotrophic Lateral Sclerosis type 6: An In Silico approach

Abstract

Amyotrophic lateral sclerosis (ALS) is the most frequent adult-onset motor neuron disorder. The disease is characterized by degeneration of upper and lower motor neurons, leading to death usually within five years after the onset of symptoms. While most cases are sporadic, 5%-10% of cases can be associated with familial inheritance, including ALS type 6, which is associated with mutations in the Fused in Sarcoma (FUS) gene. This work aimed to evaluate how the most frequent ALS-related mutations in FUS, R521C, R521H, and P525L affect the protein structure and function. We used prediction algorithms to analyze the effects of the non-synonymous single nucleotide polymorphisms and performed evolutionary conservation analysis, protein frustration analysis, and molecular dynamics simulations. Most of the prediction algorithms classified the three mutations as deleterious. All three mutations were predicted to reduce protein stability, especially the mutation R521C, which was also predicted to increase chaperone binding tendency. The protein frustration analysis showed an increase in frustration in the interactions involving the mutated residue 521C. Evolutionary conservation analysis showed that residues 521 and 525 of human FUS are highly conserved sites. The molecular dynamics results indicate that protein stability could be compromised in all three mutations. They also affected the exposed surface area and protein compactness. The analyzed mutations also displayed high flexibility in most residues in all variants, most notably in the interaction site with the nuclear import protein of FUS.

In silico analyses of acetylcholinesterase (AChE) and its genetic variants in interaction with the anti‐Alzheimer drug Rivastigmine

“…11,15 MD have also been proven valuable to characterize protein-ligand interactions, especially when combined with recent post-processing energy calculation methods, such as MM/PBSA and MM/GBSA, which provide relevant mechanistic information on complex interactions over time. 20 In this study, we applied a computational pipeline to investigate the functional and structural effects of common missense mutations on AChE 7 and characterize the impact of these mutations on rivastigmine binding, a widely used drug to treat Alzheimer's disease. This approach favors the design of further experiments and provides structural information that could lead to improvements in AD treatments, especially in the field of precision medicine.…”