Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates

The Josephin Domain (JD), i.e. the N-terminal domain of Ataxin 3 (At3) protein, is an interesting example of competition between physiological function and aggregation risk. In fact, the fibrillogenesis of Ataxin 3, responsible for the spinocerebbellar ataxia 3, is strictly related to the JD thermodynamic stability. Whereas recent NMR studies have demonstrated that different JD conformations exist, the likelihood of JD achievable conformational states in solution is still an open issue. Marked differences in the available NMR models are located in the hairpin region, supporting the idea that JD has a flexible hairpin in dynamic equilibrium between open and closed states. In this work we have carried out an investigation on the JD conformational arrangement by means of both classical molecular dynamics (MD) and Metadynamics employing essential coordinates as collective variables. We provide a representation of the free energy landscape characterizing the transition pathway from a JD open-like structure to a closed-like conformation. Findings of our in silico study strongly point to the closed-like conformation as the most likely for a Josephin Domain in water.Author Summary: Proteins are fascinating molecular machines capable of organizing themselves into well-defined hierarchical structures through a huge number of conformational changes to accomplish a wide range of cellular functions. Protein conformational changes may be characterized by transitions from a low-energy conformation to another. Computer simulations and in particular molecular modelling may be able to predict protein transition dynamics and kinetics, thus playing a key role in describing protein tendencies towards specific conformational rearrangements. Approaching this problem from an energetic point of view is of great importance especially in case of amyloidogenic proteins, given the intimate interconnection between the functional energy landscape and aggregation risk. In this work we have employed molecular modelling techniques to shed light into conformational dynamics and kinetics of the Josephin Domain, part of the protein Ataxin 3, which is responsible for the spinocerebbellar ataxia 3, also called Machado Joseph Disease. In greater detail, we have employed enhanced sampling approaches to provide an estimation of the free energy landscape characterizing the transition pathway among several known molecular arrangements of the Josephin Domain.