Citation: Deng Jing, Ma Tao, Chang Ziwei, Zhao Weijing, Yang Jun. Determination of Three-Dimensional Structures of Protein Assemblies via Solid-State NMR[J]. Acta Physico-Chimica Sinica, ;2020, 36(4): 190501. doi: 10.3866/PKU.WHXB201905019 shu

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

Deng Jing ^1,2,† ,
Ma Tao ^1,2,† ,
Chang Ziwei ¹ ,
Zhao Weijing ¹ ,
Yang Jun ^1,,

1.
Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P. R. China
2.
University of Chinese Academy of Sciences, Beijing 100049, P. R. China

Corresponding author: Yang Jun, yangjun@wipm.ac.cn
Received Date: 2 May 2019
Revised Date: 10 June 2019
Accepted Date: 17 June 2019
Available Online: 24 April 2019
Fund Project: The project was supported by the National Natural Science Foundation of China (21425523, 31770798, 31600613, 21603269)the National Natural Science Foundation of China 21603269the National Natural Science Foundation of China 31600613the National Natural Science Foundation of China 31770798the National Natural Science Foundation of China 21425523

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 ¹³C spectra can be further improved by using ¹³C 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 ¹³C and ¹⁵N. Protein secondary structure can be ascertained through chemical shifts involving ¹³Cα, ¹³Cβ, ¹³C', and ¹⁵N. 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 ¹³C-¹³C, e.g., proton-driven spin diffusion (PDSD), dipolar-assisted rotational resonance (DARR), proton-assisted recoupling (PAR) and ¹³C-¹⁵N, 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% ¹³C uniformly labeled subunits and 50% uniformly ¹⁵N 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 Å, 1 Å = 0.1 nm) along the fibril axis between adjacent polypeptide chains in β-strand conformation, generally referred to as the "cross-β" 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-β (Aβ) fibrils and T3SS needles are provided as examples. Various structural characteristics of Aβ40/Aβ42 were reported by several groups, including the trimeric or dimeric conformations, parallel or antiparallel, in-register or out-of-register arrangements of the β-strands, demonstrating the structural polymorphism of Aβ40/Aβ42. Atomic-resolution structures of T3SS needles were analyzed on the basis of high-resolution spectra, using ¹³C 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.
- Solid-state NMR,
- Protein assembly,
- High resolution structure,
- Type Ⅲ secretion system needle,
- β-amyloid fibril
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沈阳化工大学材料科学与工程学院沈阳 110142