AUTHOR=Guzzo Adrien , Delarue Patrice , Rojas Ana , Nicolaï Adrien , Maisuradze Gia G. , Senet Patrick 

TITLE=Missense Mutations Modify the Conformational Ensemble of the α-Synuclein Monomer Which Exhibits a Two-Phase Characteristic

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=8

YEAR=2021

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2021.786123

DOI=10.3389/fmolb.2021.786123

ISSN=2296-889X

ABSTRACT=<p><italic>α</italic>-Synuclein is an intrinsically disordered protein occurring in different conformations and prone to aggregate in <italic>β</italic>-sheet structures, which are the hallmark of the Parkinson disease. Missense mutations are associated with familial forms of this neuropathy. How these single amino-acid substitutions modify the conformations of wild-type <italic>α</italic>-synuclein is unclear. Here, using coarse-grained molecular dynamics simulations, we sampled the conformational space of the wild type and mutants (A30P, A53P, and E46K) of <italic>α</italic>-synuclein monomers for an effective time scale of 29.7 ms. To characterize the structures, we developed an algorithm, CUTABI (CUrvature and Torsion based of Alpha-helix and Beta-sheet Identification), to identify residues in the <italic>α</italic>-helix and <italic>β</italic>-sheet from <italic>C<sup>α</sup></italic>-coordinates. CUTABI was built from the results of the analysis of 14,652 selected protein structures using the Dictionary of Secondary Structure of Proteins (DSSP) algorithm. DSSP results are reproduced with 93% of success for 10 times lower computational cost. A two-dimensional probability density map of <italic>α</italic>-synuclein as a function of the number of residues in the <italic>α</italic>-helix and <italic>β</italic>-sheet is computed for wild-type and mutated proteins from molecular dynamics trajectories. The density of conformational states reveals a two-phase characteristic with a homogeneous phase (state B, <italic>β</italic>-sheets) and a heterogeneous phase (state HB, mixture of <italic>α</italic>-helices and <italic>β</italic>-sheets). The B state represents 40% of the conformations for the wild-type, A30P, and E46K and only 25% for A53T. The density of conformational states of the B state for A53T and A30P mutants differs from the wild-type one. In addition, the mutant A53T has a larger propensity to form helices than the others. These findings indicate that the equilibrium between the different conformations of the <italic>α</italic>-synuclein monomer is modified by the missense mutations in a subtle way. The <italic>α</italic>-helix and <italic>β</italic>-sheet contents are promising order parameters for intrinsically disordered proteins, whereas other structural properties such as average gyration radius, <italic>R</italic><sub><italic>g</italic></sub>, or probability distribution of <italic>R</italic><sub><italic>g</italic></sub> cannot discriminate significantly the conformational ensembles of the wild type and mutants. When separated in states B and HB, the distributions of <italic>R</italic><sub><italic>g</italic></sub> are more significantly different, indicating that global structural parameters alone are insufficient to characterize the conformational ensembles of the <italic>α</italic>-synuclein monomer.</p>