The Conformational Ensembles of α-Synuclein and Tau: Combining Single-Molecule FRET and Simulations

Intrinsically disordered proteins (IDPs) are increasingly recognized for their important roles in a range of biological contexts, both in normal physiological function and in a variety of devastating human diseases. However, their structural characterization by traditional biophysical methods, for the purposes of understanding their function and dysfunction, has proved challenging. Here, we investigate the model IDPs α-Synuclein (αS) and tau, that are involved in major neurodegenerative conditions including Parkinson’s and Alzheimer’s diseases, using excluded volume Monte Carlo simulations constrained by pairwise distance distributions from single-molecule fluorescence measurements. Using this, to our knowledge, novel approach we find that a relatively small number of intermolecular distance constraints are sufficient to accurately determine the dimensions and polymer conformational statistics of αS and tau in solution. Moreover, this method can detect local changes in αS and tau conformations that correlate with enhanced aggregation. Constrained Monte Carlo simulations produce ensembles that are in excellent agreement both with experimental measurements on αS and tau and with all-atom, explicit solvent molecular dynamics simulations of αS, with much lower configurational sampling requirements and computational expense.Abbreviations used: AAMD, all-atom molecular dynamics; ECMC, experimentally constrained Monte Carlo; ET_eff, energy transfer efficiency; (sm)FRET, (single molecule) Förster resonance energy transfer; IDP, intrinsically disordered protein; LJ, Lennard-Jones; MC, Monte Carlo; MD, molecular dynamics; PRE, paramagnetic relaxation enhancement; SAX(N)S, small-angle x-ray (neutron) scattering; UMC, unconstrained Monte Carlo     

Comparison of Monte Carlo Simulations of Cytochrome b<Subscript>6</Subscript>f with Experiment Using Latin Hypercube Sampling

We have programmed a Monte Carlo simulation of the Q-cycle model of electron transport in cytochrome b₆f complex, an enzyme in the photosynthetic pathway that converts sunlight into biologically useful forms of chemical energy. Results were compared with published experiments of Kramer and Crofts (Biochim. Biophys. Acta 1183:72–84, 1993). Rates for the simulation were optimized by constructing large numbers of parameter sets using Latin hypercube sampling and selecting those that gave the minimum mean square deviation from experiment. Multiple copies of the simulation program were run in parallel on a Beowulf cluster. We found that Latin hypercube sampling works well as a method for approximately optimizing very noisy objective functions of 15 or 22 variables. Further, the simplified Q-cycle model can reproduce experimental results in the presence or absence of a quinone reductase (Q_i) site inhibitor without invoking ad hoc side-reactions.     

Intracellular Screening of a Peptide Library to Derive a Potent Peptide Inhibitor of α-Synuclein Aggregation

Aggregation of α-synuclein (α-syn) into toxic fibrils is a pathogenic hallmark of Parkinson disease (PD). Studies have focused largely on residues 71–82, yet most early-onset mutations are located between residues 46 and 53. A semirationally designed 209,952-member library based entirely on this region was constructed, containing all wild-type residues and changes associated with early-onset PD. Intracellular cell survival screening and growth competition isolated a 10-residue peptide antagonist that potently inhibits α-syn aggregation and associated toxicity at a 1:1 stoichiometry. This was verified using continuous growth measurements and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide cytotoxicity studies. Atomic force microscopy and circular dichroism on the same samples showed a random-coil structure and no oligomers. A new region of α-syn for inhibitor targeting has been highlighted, together with the approach of using a semirational design and intracellular screening. The peptides can then be used as candidates for modification in drugs capable of slowing or even preventing the onset of PD.     

Genetic Variants of the α-Synuclein Gene SNCA Are Associated with Multiple System Atrophy

Background

Multiple system atrophy (MSA) is a progressive neurodegenerative disorder characterized by parkinsonism, cerebellar ataxia and autonomic dysfunction. Pathogenic mechanisms remain obscure but the neuropathological hallmark is the presence of α-synuclein-immunoreactive glial cytoplasmic inclusions. Genetic variants of the α-synuclein gene, SNCA, are thus strong candidates for genetic association with MSA. One follow-up to a genome-wide association of Parkinson''s disease has identified association of a SNP in SNCA with MSA.

Methodology/Findings

We evaluated 32 SNPs in the SNCA gene in a European population of 239 cases and 617 controls recruited as part of the Neuroprotection and Natural History in Parkinson Plus Syndromes (NNIPPS) study. We used 161 independently collected samples for replication. Two SNCA SNPs showed association with MSA: rs3822086 (P = 0.0044), and rs3775444 (P = 0.012), although only the first survived correction for multiple testing. In the MSA-C subgroup the association strengthened despite more than halving the number of cases: rs3822086 P = 0.0024, OR 2.153, (95% CI 1.3–3.6); rs3775444 P = 0.0017, OR 4.386 (95% CI 1.6–11.7). A 7-SNP haplotype incorporating three SNPs either side of rs3822086 strengthened the association with MSA-C further (best haplotype, P = 8.7×10⁻⁴). The association with rs3822086 was replicated in the independent samples (P = 0.035).

Conclusions/Significance

We report a genetic association between MSA and α-synuclein which has replicated in independent samples. The strongest association is with the cerebellar subtype of MSA.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00211224","term_id":"NCT00211224"}}NCT00211224. [{"type":"clinical-trial","attrs":{"text":"NCT00211224","term_id":"NCT00211224"}}NCT00211224]     

Comparative Analysis of MPTP Neurotoxicity in Mice with a Constitutive Knockout of the α-Synuclein Gene

Molecular Biology - Aggregated forms of α-synuclein are core components of pathohistological inclusions known as Lewy bodies in substantia nigra (SN) neurons of patients with Parkinson’s...     

State-dependent Lipid Interactions with the A2a Receptor Revealed by MD Simulations Using In Vivo-Mimetic Membranes

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Simulations of the Ion Current to a Probe in Plasma with Allowance for Ionization and Ion–Neutral Collisions: II. Cylindrical Probe

The ion current to a cylindrical probe is considered with allowance for volume ionization, ion–neutral collisions, and the ion orbital moment. A model based on the molecular dynamics method and applicable in a wide range of plasma parameters (r_p/λ_D= 0.01–100, r_i/λ_D= 0.002–200, ν_i/ω_0i= 0.01–0.05, and T_i/T_e = 0?0.01) is proposed A convenient representation of the dependence of the relative ion current density on the Langmuir coefficient β² and a technique for determining the plasma density from simulation results are offered.     

Fluorescence Resonance Energy Transfer (FRET) Indicates That Association with the Type I Ryanodine Receptor (RyR1) Causes Reorientation of Multiple Cytoplasmic Domains of the Dihydropyridine Receptor (DHPR) α1S Subunit

The skeletal muscle dihydropyridine receptor (DHPR) in the t-tubular membrane serves as the Ca²⁺ channel and voltage sensor for excitation-contraction (EC) coupling, triggering Ca²⁺ release via the type 1 ryanodine receptor (RyR1) in the sarcoplasmic reticulum (SR). The two proteins appear to be physically linked, and both the α_1S and β_1a subunits of the DHPR are essential for EC coupling. Within α_1S, cytoplasmic domains of importance include the I-II loop (to which β_1a binds), the II-III and III-IV loops, and the C terminus. However, the spatial relationship of these domains to one another has not been established. Here, we have taken the approach of measuring FRET between fluorescent proteins inserted into pairs of α_1S cytoplasmic domains. Expression of these constructs in dyspedic (RyR1 null) and dysgenic (α_1S null) myotubes was used to test for function and targeting to plasma membrane/SR junctions and to test whether the presence of RyR1 caused altered FRET. We found that in the absence of RyR1, measureable FRET occurred between the N terminus and C terminus (residue 1636), and between the II-III loop (residue 626) and both the N and C termini; the I-II loop (residue 406) showed weak FRET with the II-III loop but not with the N terminus. Association with RyR1 caused II-III loop FRET to decrease with the C terminus and increase with the N terminus and caused I-II loop FRET to increase with both the II-III loop and N terminus. Overall, RyR1 appears to cause a substantial reorientation of the cytoplasmic α_1S domains consistent with their becoming more closely packed.     

Standardization and Prevalence of the Booster Phenomenon: Evaluation Using a Two-Step Skin Test with 43 kDa Glycoprotein in Individuals from an Endemic Region of Paracoccidioidomycosis

Background

We estimated the occurrence rate of the booster phenomenon by using an intradermal test with 43 kDa glycoprotein in an endemic area of paracoccidioidomycosis in the central-west region of Brazil.

Methods

Individuals who had a negative result on a survey performed by using an intradermal test with 43 kDa glycoprotein in an endemic area of paracoccidioidomycosis underwent a second intradermal test after 10–15 days to determine the presence or absence of the booster phenomenon. Statistical analyses were performed using the Chi-square test, Chi-square for linear trend test, Student’s t test, and binomial test; p < 0.05 was considered significant.

Results

For the first time, we reported the occurrence of the booster phenomenon to an intradermal reaction caused by 43 kDa glycoprotein at a rate of 5.8–8.4%, depending on the test’s cutoff point. This suggests that a cutoff point should be considered for the booster phenomenon in intradermal tests with 43 kDa glycoprotein: a difference of 6–7 mm between readings according to the first and second tests, depending on the purpose of the evaluation.

Conclusion

The results indicate that the prevalence of paracoccidioidal infection in endemic areas is underestimated, as the booster phenomenon has not been considered in epidemiological surveys for this infection.