α-Synuclein Monomer Conformations Studied by in Silico and in Vitro FRET

Abstract

The pathological aggregation of α-synuclein (AS), a 140-aa presynaptic protein, is cytotoxic to motor neurons in the brain and thus constitutes a major factor in the etiology of Parkinson's disease (PD). AS is intrinsically unstructured and adopts no preferred fold in solution. Since low molecular weight oligomers of AS are considered to be the most toxic species in PD it is important to study the conformers of monomeric AS. In our current investigation we combine classical molecular dynamics (MD) simulations with experimental FRET measurements to determine distance relations in the N-terminus and the NAC region of AS. With extended MD simulations (∼ 90μs) we first generated ensemble structures of monomeric AS molecules. From these trajectories snapshots were extracted and the appropriate amino acids mutated at eight different FRET label positions respectively. The FRET pair consists of a tryptophan as the donor and a coumarine dye attached to a cysteine as the acceptor. QM calculations were carried out to parameterize the coumarine dye for the AMBER 99SB force field and to determine transition dipole moments. From the AS MD simulations with the attached FRET labels instantaneous donor-acceptor distances rDA and values of the orientation factor κ2 can be extracted. Applying Forster's theory energy transfer efficiencies are calculated and compared to the experimental findings. With the directly available values rDA and κ2 we get an improved structural characterization of the disordered AS ensemble.M. Hoefling, N.Lima, D.Haenni, C.A. M.Seidel, B.Schuler, H.Grubmuller, PLoSONE 6(5): e19791. doi:10.1371/journal.pone.0019791.A.Grupi, E.Haas, JMB, 405:1267-1283 (2011).M.J.Roberti, C.W.Bertoncini, R.Klement, E.A.Jares-Erijman, T.M.Jovin, Nature Methods, 4(4):345–351 (2007).