Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates

PLoS Comput Biol. 2016 Jan 8;12(1):e1004699. doi: 10.1371/journal.pcbi.1004699. eCollection 2016 Jan.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Ataxin-3 / chemistry*
  • Computational Biology / methods*
  • Models, Chemical
  • Molecular Dynamics Simulation*
  • Principal Component Analysis
  • Protein Structure, Tertiary*
  • Thermodynamics

Substances

  • Ataxin-3

Grants and funding

This work was supported by a grant from the Swiss National Supercomputing Centre (CSCS) under project ID S530.The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.