Determination of Three-Dimensional Structures of Protein Assemblies via Solid-State NMR

Biological assemblies with specific function or pathogenicity are widespread within organisms; however, their insolubility, amorphous properties, and large size are the major obstacles for structure determination via solution NMR spectroscopy and X-ray crystallography. In contrast, solid-state NMR (ssNMR) spectroscopy is not limited by the solubility or crystallinity of the sample and is a potent method to determine the structure of protein assemblies at atomic resolution. High magnetic field, fast magic-angle spinning (MAS), isotope labeling schemes, and improved methodology in ssNMR have enabled resonance assignment and restraints in structure determination among protein assemblies. This review first discusses methods of obtaining structural restraints by ssNMR. Optimization of sample preparation is an effective approach to increase homogeneity in the conformation, thus also improving the resolution of ssNMR spectra. Furthermore, the resolution of C-13 spectra can be further improved by using C-13 sparse labeling strategies with selective labeling of carbon sources during protein expression. Structure characterization by ssNMR is based on structural restraints via multidimensional experiments correlating resonance between C-13 and N-15. Protein secondary structure can be ascertained through chemical shifts involving C-13 alpha, C-13 beta, C-13', and N-15. The backbone torsion angle can be predicted using TALOS+ based on these chemical shifts. Site-specific structural restraints are accessible from 2D experiments such as C-13-C-1(3), e.g., proton-driven spin diffusion (PDSD), dipolar-assisted rotational resonance (DARR), proton-assisted recoupling (PAR) and C-13-N-15, e.g., transferred-echo double-resonance (TEDOR), rotational-echo double-resonance (REDOR). An additional issue is to distinguish inter-molecular and intra-molecular restraints. Preparations of mixed labeled samples (e.g., 50% C-1(3) uniformly labeled subunits and 50% uniformly N-15 labeled subunits) have yielded abundant structural restraints from ssNMR data, facilitating high-resolution structural analysis. Further, hybrid approaches based on ssNMR are discussed. Electron microscopy (EM) is a suitable method to investigate structural features including the diameter of the protein assemblies, which is "invisible" through ssNMR analysis. Scanning transmission electron microscopy (STEM) can help determine the mass-per-length parameters (MPL) of unbranched fibrils, thus confirming the number of subunits in a layer of fibrils. Cryo-EM is a powerful technique to describe the molecular envelope of protein assemblies. Cryo-EM potentially yields the density map and long-range symmetry parameters, while ssNMR provides atomic-level structural details; hence, Cryo-EM and ssNMR are highly complementary methods. X-ray diffraction can help determine the distance (4.5-4.7 angstrom, 1 angstrom = 0.1 nm) along the fibril axis between adjacent polypeptide chains in beta-strand conformation, generally referred to as the "cross-beta" structure. Rosetta has simulated the protein structure in accordance with structural data obtained from protein data bank (PDB) with the same peptide sequence. On combining ssNMR with those methods, more abundant structural information may be obtained, thus shortening the structural calculation cycle. Finally, a detailed description of the ssNMR structural data on amyloid-beta (A beta) fibrils and T355 needles are provided as examples. Various structural characteristics of A beta 40/A beta 42 were reported by several groups, including the trimeric or dimeric conformations, parallel or antiparallel, inregister or out-of-register arrangements of the p-strands, demonstrating the structural polymorphism of A beta 40/A beta 42. Atomicresolution structures of T3SS needles were analyzed on the basis of high-resolution spectra, using C-13 sparse-labeled and ssNMR-Cryo-EM-Rosetta hybrid approaches, indicating that hybrid approaches based on ssNMR are a powerful tool to determine the high-resolution structure of protein assemblies.