Josephin Domain Conformational Dynamics explored by Coarse-Grained Molecular Modeling and Enhanced Sampling targeting novel Insight into the Onset and Evolution of Ataxia-3 Pathology  

Ataxin-3 misfolding and aggregation process is responsible of a pathological condition known as Spinocerebellar Ataxia-3, a polyglutamine inherited neurodegenerative disease.The pathology is characterized by progressive challenges in movement and balance.This disorder is associated with mutations at the ATAXN3 gene, located to chromosome 14q32.1, that result in the expansion of the Polyglutamminic tail (PolyQ) in the encoded At-3 protein.Extensive research is conducted on protein aggregation pathway, although the underlying molecular mechanisms are not understood yet.In general variation in pH, temperature and interactions with specific properties substrates can influence protein misfolding. Previous studies demonstrate how At-3-N-terminal region called Josephin Domain(JD) has a leading role in At-3 fiber formation for its amyloidogenic propensity.Therefore, understanding the connection between JD structural characteristics and aggregation tendency could enhance the knowledge of the pathology and facilitate the development of a cure. Experimental techniques are not able to simultaneously achieve high resolution on spatial and temporal scales, being limited in their understanding of the dynamics at molecular scale. On the other hand, computational molecular modelling has proven to be valuable in exploring protein molecular dynamics and mechanisms of action with atomistic resolution.In literature, studies succeeded to investigate the JD conformational dynamics by means of all atom(AA) MD simulations, however, the high computational cost limits the time scale investigation to hundreds of nanoseconds.The results obtained are a validation of the coarse-grained (CG) method which demonstrates to be able to illustrate the conformational dynamics of JD, affirming the capacity of coarse-grained MD in capturing biologically relevant conformations.In literature the CG approach has emerged has a modelling technique with a trade of between computational efficiency and the ability to capture essential molecular behaviours. This approach showed the potential to overcome the limitations, in terms of simulation time, imposed by the AA approach in the study of molecular systems.The aim of the work is to investigate the JD conformational dynamics by CG molecular modelling simulations at the microsecond time scale to provide a description of the domain conformational changes understanding their influence in the At-3 aggregation pathway and pave the way to the investigation of the whole protein. The study leads to further investigation into how the PolyQ tail and JD may contribute independently or synergistically in the aggregation process of At-3.The findings contribute to the methodological advancements in MD simulations and form a robust foundation for the subsequent stages of the research, allowing a comprehensive understanding of JD's role in neurodegenerative pathology.Additionally, JD conformational arrangement is investigated by metadynamics, a powerful method for enhancing the sampling in MD simulations, ensuring a more comprehensive and accurate understanding in JD conformational behavior.In general this work explored the possibility to introduce a CG approach to model the JD to investigate the conformational dynamics of the JD domain and how this can be related to the At-3 aggregation process.This result is promising for further investigation, employing CG modelling, of the whole At-3 protein providing the basis for a deeper understanding of how the PolyQ tail drives the aggregation process.