Aggregated form of α-synuclein
in the brain has been found
to be the major component of Lewy bodies that are hallmarks of Parkinson′s
disease (PD), the second most devastating neurodegenerative disorder.
We have carried out room-temperature all-atom molecular dynamics (MD)
simulations of an ensemble of widely different α-synuclein1–95 peptide monomer conformations in aqueous solution.
Attempts have been made to obtain a generic understanding of the local
conformational motions of different repeat unit segments, namely R1–R7,
of the peptide and the correlated properties of the solvent at the
interface. The analyses revealed relatively greater rigidity of the
hydrophobic R6 unit as compared to the other repeat units of the peptide.
Besides, water molecules around R6 have been found to be less structured
and weakly interacting with the peptide. These are important observations
as the R6 unit with reduced conformational motions can act as the
nucleation site for the aggregation process, while less structured
weakly interacting water around it can become displaced easily, thereby
facilitating the hydrophobic collapse of the peptide monomers and
their association during the nucleation phase at higher concentrations.
In addition, we demonstrated presence of doubly coordinated highly
ordered as well as triply coordinated relatively disordered water
molecules at the interface. We believe that while the ordered water
molecules can favor water-mediated interactions between different
peptide monomers, the randomly ordered ones on the other hand are
likely to be expelled easily from the interface, thereby facilitating
direct peptide–peptide interactions during the aggregation
process.
It is believed that water around
an intrinsically disordered protein
or peptide (IDP) in an aqueous environment plays an important role
in guiding its conformational properties and aggregation behavior.
However, despite its importance, only a handful of studies exploring
the correlation between the conformational motions of an IDP and the
microscopic properties of water at its surface are reported. Attempts
have been made in this work to study the dynamic properties of water
present in the vicinity of α-synuclein, an IDP associated with
Parkinson’s disease (PD). Room temperature molecular dynamics
(MD) simulations of eight α-synuclein1–95 peptides
with a wide range of initial conformations have been carried out in
aqueous media. The calculations revealed that due to solid-like caging
motions, the translational and rotational mobility of water molecules
near the surfaces of the peptide repeat unit segments R1 to R7 are
significantly restricted. A small degree of dynamic heterogeneity
in the hydration environment around the repeat units has been observed
with water near the hydrophobic R6 unit exhibiting relatively more
restricted diffusivity. The time scales involving the overall structural
relaxations of peptide–water and water–water hydrogen
bonds near the peptide have been found to be correlated with the time
scale of diffusion of the interfacial water molecules. We believe
that the relatively more hindered dynamic environment near R6 can
help create water-mediated contacts centered around R6 between peptide
monomers at a higher concentration, thereby enhancing the early stages
of peptide aggregation.
Ionic liquids (ILs), depending on
their cation–anion combinations,
are known to influence the conformational properties and activities
of proteins in a nonuniform manner. To obtain microscopic understanding
of such influence, it is important to characterize protein–IL
interactions and explore the modified solvation environment around
the protein. In this work, molecular dynamics (MD) simulations of
the globular protein α-lactalbumin have been carried out in
aqueous IL solutions containing 1-butyl-3-methylimidazolium cations
(BMIM+) in combination with a series of anions with varying
degree of hydrophilicity, namely, hexafluorophosphate (PF6
–), ethyl
sulfate (ETS–), acetate (OAc–),
chloride (Cl–), dicyanamide (DCA–), and nitrate (NO3
–) . The calculations revealed that ILs with hydrophobic
and hydrophilic anions have contrasting influence on conformational
flexibility of the protein. It is further observed that the BMIM+ cations exhibit site-specific orientations at the interface
depending on the hydrophilicity of the anion component. Most importantly,
the results demonstrated enhanced propensity of hydrophilic ILs to
replace relatively weaker protein–water hydrogen bonds by stronger
protein–IL hydrogen bonds at the protein surface as compared
to the hydrophobic ILs. Such breaking of protein–water hydrogen
bonds at a greater extent leads to greater loss of water hydrating
the protein in the presence of hydrophilic ILs, thereby reducing the
protein’s stability.
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