Solid-state NMR assignment of α-synuclein polymorph prepared from helical intermediate.

Synucleinopathies are neurodegenerative diseases characterized by the accumulation of α-synuclein protein aggregates in the neurons and glial cells. Both ex vivo and in vitro α-synuclein fibrils tend to show polymorphism. Polymorphism results in structure variations among fibrils originating from a single polypeptide/protein. The polymorphs usually have different biophysical, biochemical and pathogenic properties. The various pathologies of a single disease might be associated with distinct polymorphs. Similarly, in the case of different synucleinopathies, each condition might be associated with a different polymorph. Fibril formation is a nucleation-dependent process involving the formation of transient and heterogeneous intermediates from monomers. Polymorphs are believed to arise from heterogeneous oligomer populations because of distinct selection mechanisms in different conditions. To test this hypothesis, we isolated and incubated different intermediates during in vitro fibrillization of α-synuclein to form different polymorphs. Here, we report 13C and 15N chemical shifts and the secondary structure of fibrils prepared from the helical intermediate using solid-state nuclear magnetic spectroscopy.

Assignment of aromatic side-chain spins and characterization of their distance restraints at fast MAS.

The assignment of aromatic side-chain spins has always been more challenging than assigning backbone and aliphatic spins. Selective labeling combined with mutagenesis has been the approach for assigning aromatic spins. This manuscript reports a method for assigning aromatic spins in a fully protonated protein by connecting them to the backbone atoms using a low-power TOBSY sequence. The pulse sequence employs residual polarization and sequential acquisitions techniques to record HN- and HC-detected spectra in a single experiment. The unambiguous assignment of aromatic spins also enables the characterization of 1H-1H distance restraints involving aromatic spins. Broadband (RFDR) and selective (BASS-SD) recoupling sequences were used to generate HN-ΗC, HC-HN and HC-HC restraints involving the side-chain proton spins of aromatic residues. This approach has been demonstrated on a fully protonated U-[13C,15N] labeled GB1 sample at 95-100 kHz MAS.

α-Synuclein Aggregation Intermediates form Fibril Polymorphs with Distinct Prion-like Properties.

α-Synuclein (α-Syn) amyloids in synucleinopathies are suggested to be structurally and functionally diverse, reminiscent of prion-like strains. The mechanism of how the aggregation of the same precursor protein results in the formation of fibril polymorphs remains elusive. Here, we demonstrate the structure-function relationship of two polymorphs, pre-matured fibrils (PMFs) and helix-matured fibrils (HMFs), based on α-Syn aggregation intermediates. These polymorphs display the structural differences as demonstrated by solid-state NMR and mass spectrometry studies and also possess different cellular activities such as seeding, internalization, and cell-to-cell transfer of aggregates. HMFs, with a compact core structure, exhibit low seeding potency but readily internalize and transfer from one cell to another. The less structured PMFs lack transcellular transfer ability but induce abundant α-Syn pathology and trigger the formation of aggresomes in cells. Overall, the study highlights that the conformational heterogeneity in the aggregation pathway may lead to fibril polymorphs with distinct prion-like behavior.

Mechanism of selective polarization exchange amongst chemically similar and distinct protons during weak rf irradiation at fast magic angle spinning.

Band Selective Spectral Spin-Diffusion (BASS-SD) is a method to obtain selective 1H-1H contacts between chemically similar protons within a distance range of 5-6 Å in fully protonated proteins. BASS-SD combines low-amplitude proton spinlock radio frequency (rf) pulses with fast MAS frequency to enable selective polarization exchange in fully protonated molecules. The selectivity of transfer is dictated by the bandwidth of the spinlock pulse and has been used to observe selective HN-HN, Hα-Ηα and Hmethyl-Hmethyl correlations. These proton-proton spatial contacts are similar to those observed in perdeuterated samples and serve as useful structural restraints towards de novo protein structure determination. This study employs bimodal Floquet theory to derive the first- and second-order effective Hamiltonians necessary to understand the spin dynamics during BASS-SD. Analytical calculations combined with numerical simulations delineate two different mechanisms for polarization transfer amongst the proton spins. The BASS-SD recoupling condition has been reoptimized to observe selective correlations between chemically different protons (e.g., HN-Hα) while retaining the spatial contacts between chemically similar protons (e.g., HN-HN). The new BASS-SD condition is integrated with simultaneous and sequential acquisition approaches to generate four different types of structural restraints (HN-HN, Hα-Ηα, HN-Hα, Hα-HN) in one experiment. The approach has been demonstrated on microcrystalline U-[13C,15N] labeled GB1 protein at âˆ¼ 95-100 kHz MAS.

Solid-State NMR: Methods for Biological Solids.

In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.

Accuracy of 1H-1H distances measured using frequency selective recoupling and fast magic-angle spinning.

Selective recoupling of protons (SERP) is a method to selectively and quantitatively measure magnetic dipole-dipole interaction between protons and, in turn, the proton-proton distance in solid-state samples at fast magic-angle spinning. We present a bimodal operator-based Floquet approach to describe the numerically optimized SERP recoupling sequence. The description calculates the allowed terms in the first-order effective Hamiltonian, explains the origin of selectivity during recoupling, and shows how different terms are modulated as a function of the radio frequency amplitude and the phase of the sequence. Analytical and numerical simulations have been used to evaluate the effect of higher-order terms and offsets on the polarization transfer efficiency and quantitative distance measurement. The experimentally measured 1H-1H distances on a fully protonated thymol sample are ∼10%-15% shorter than those reported from diffraction studies. A semi-quantitative model combined with extensive numerical simulations is used to rationalize the effect of the third-spin and the role of different parameters in the experimentally observed shorter distances. Measurements at high magnetic fields improve the match between experimental and diffraction distances. The measurement of 1H-1H couplings at offsets different from the SERP-offset has also been explored. Experiments were also performed on a perdeuterated ubiquitin sample to demonstrate the feasibility of simultaneously measuring multiple quantitative distances and to evaluate the accuracy of the measured distance in the absence of multispin effects. The estimation of proton-proton distances provides a boost to structural characterization of small pharmaceuticals and biomolecules, given that the positions of protons are generally not well defined in x-ray structures.