Identifying the Role of NEK1 in Driving Amyotrophic Lateral Sclerosis (ALS) by Molecular Modeling

The gene/protein called NEK1 was first linked to ALS in 2016 and has recently been shown to play a significant role in the disease. Mutations in this gene are considered risk factors for ALS. NEK1 is a kinase enzyme, mostly found in the cytoplasm, particularly around the primary cilium. It is thought to be involved in processes like ciliogenesis, microtubule formation, etc., although how it does this is still unknown. Some mutations in NEK1—mutations observed in ALS patients—introduce premature stop codons near the C-terminus of the protein (see Figure 1A in ref. 1). These mutations were previously believed to lead to a total loss of function. However, it was recently shown that these mutations result in the production of a truncated NEK1 variant (NEK1t) in the tissues of ALS model mice carrying this mutation (Figure 1G). This mutant protein forms aggregate-like structures in the motor neurons of these mice (Figure 1G). Most likely, this leads to protein aggregation-induced toxicity in neurons. Through biochemical and biophysical analyses, the authors showed that this mutant protein indeed loses its solubility (Figure 1I) and eventually forms gel-like aggregates over time. We are curious about the potential structure of this mutant protein and whether it is misfolded. It is likely that due to the truncation at the C-terminus, NEK1t is severely misfolded, which likely drives the aggregation while maintaining some of its activity since the mice are alive, while NEK1 knockout mice are embryonic lethal.
Our group's research program is based-on predicting the functions of proteins whose three-dimensional structures are known using dynamical information obtained from trajectories and to foretell how the shifts in the environmental conditions will change these functions. With the rise of protein structure prediction methods such as AlphaFold (2) it is now possible to get high quality structural predictions of any protein sequence. In this project, we will predict and compare the structure of the NEK1t mutant protein to the wild type. Once the structures are modeled, we will use elastic network models to predict the motions of the proteins and relate thise to the the various functions of the protein (3).
References:
(1) P. Georgiadou, …, U. Sahin, “ALS driven by mutant NEK1 aggregation is accelerated by Pml loss, but clinically reversed through pharmacologic induction of Pml-mediated degradation,” Biorxiv (2024); https://doi.org/10.1101/2024.11.23.622051
(2) J. Jumper et al., “Highly accurate protein structure prediction with AlphaFold,” Nature, 596,  583–589 (2021).
(3) A.R. Atilgan, S.R., Durell, R.L. Jernigan, M.C. Demirel, O. Keskin, I. Bahar, "Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model," Biophys. J., 80, 505-515 (2001).