Application of Nuclear Magnetic Resonance Method in Protein Research

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Proteins and Proteomics".

Deadline for manuscript submissions: closed (31 August 2022) | Viewed by 9554

Special Issue Editors


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Guest Editor
Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
Interests: solid-state NMR; protein structure; conformational dynamics; membrane protein; ion channel; intramembrane protease; transporter

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Guest Editor
Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
Interests: NMR; protein structure and dynamics; protein folding; protein–protein interactions; antibody and nanobody; membrane protein; chaperones

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Guest Editor
Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
Interests: NMR; structure biology; high-throughput screening; protein–ligand interaction; virus protein structure

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Guest Editor
Institute for Protein Science and Phage Research, Xi'an Jiaotong University, Xi'an 710061, China
Interests: solution NMR; cryo-EM; drug discovery; antibiotics; phage–host interaction; phage therapy

Special Issue Information

Dear Colleagues,

Nuclear magnetic resonance (NMR) is one of the three major methods used to study protein structure at an atomic resolution. Recently, there has been a revolution in structural biology involving cryogenic-electron microscopy. However, the molecular mechanisms and biological roles for most proteins could not be perfectly illustrated with these frozen static structures. In addition to its high-resolution structure, NMR enables the studies of protein dynamics under the more physiological conditions intimately related to the biological mechanism of proteins. With special labeling schemes and advanced data acquisition methods, the size limit of protein solution NMR studies has been largely extended. In the last decade, magic angle spinning (MAS) solid-state NMR has been successfully used in protein studies due to the ultra-fast spinning and new detection methodology development. Because it is no longer limited by molecular size or lack of long-range order, NMR may be a promising technique for protein studies in complex biological environments, such as protein in lipid membranes, in cells or large biomolecular complexes spanning from well-defined protein complexes to highly dynamical membrane-less organelles. Additionally, NMR is used extensively in drug discovery, such as in high-throughput screening and protein–ligand interaction. 

This Special Issue aims to highlight recent advances in all aspects of NMR-based protein study methodology and applications. It shall broadly contain reviews and original scientific contributions, including solution and solid-state NMR pulse sequence development, data analysis, as well as domain-specific applications such as protein structure determinations, drug discovery, chemical biology, and protein biological function investigations. Submissions of original research articles, short communications, perspectives, and comprehensive review articles are all welcome.

Prof. Dr. Chaowei Shi
Prof. Dr. Lichun He
Prof. Dr. Yan Li
Prof. Dr. Bing Liu
Guest Editors

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Keywords

  • NMR spectroscopy
  • advances in NMR techniques
  • protein structure
  • protein dynamics
  • protein–ligand interaction
  • large biomolecular complexes
  • membrane proteins
  • structure-based drug discovery
  • in-cell NMR
  • drug discovery
  • 19F NMR
  • chemical biology

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Published Papers (3 papers)

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Research

11 pages, 1642 KiB  
Article
Structural Insights into Mouse H-FABP
by Lili Wang, Haoran Zhang, Panjing Lv, Yan Li, Maikun Teng, Yahui Liu and Donghai Wu
Life 2022, 12(9), 1445; https://doi.org/10.3390/life12091445 - 16 Sep 2022
Cited by 1 | Viewed by 2238
Abstract
Intracellular fatty acid-binding proteins are evolutionarily highly conserved proteins. The major functions and responsibilities of this family are the regulation of FA uptake and intracellular transport. The structure of the H-FABP ortholog from mouse (Mus musculus) had not been revealed at [...] Read more.
Intracellular fatty acid-binding proteins are evolutionarily highly conserved proteins. The major functions and responsibilities of this family are the regulation of FA uptake and intracellular transport. The structure of the H-FABP ortholog from mouse (Mus musculus) had not been revealed at the time this study was completed. Thus, further exploration of the structural properties of mouse H-FABP is expected to extend our knowledge of the model animal’s molecular mechanism of H-FABP function. Here, we report the high-resolution crystal structure and the NMR characterization of mouse H-FABP. Our work discloses the unique structural features of mouse H-FABP, offering a structural basis for the further development of small-molecule inhibitors for H-FABP. Full article
(This article belongs to the Special Issue Application of Nuclear Magnetic Resonance Method in Protein Research)
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12 pages, 2729 KiB  
Article
NMR Reveals the Conformational Changes of Cytochrome C upon Interaction with Cardiolipin
by Jianhua Zhan, Guangqing Zhang, Xin Chai, Qinjun Zhu, Peng Sun, Bin Jiang, Xin Zhou, Xu Zhang and Maili Liu
Life 2021, 11(10), 1031; https://doi.org/10.3390/life11101031 - 30 Sep 2021
Cited by 7 | Viewed by 2727
Abstract
Conformational change of cytochrome c (cyt c) caused by interaction with cardiolipin (CL) is an important step during apoptosis, but the underlying mechanism is controversial. To comprehensively clarify the structural transformations of cyt c upon interaction with CL and avoid the unpredictable alias [...] Read more.
Conformational change of cytochrome c (cyt c) caused by interaction with cardiolipin (CL) is an important step during apoptosis, but the underlying mechanism is controversial. To comprehensively clarify the structural transformations of cyt c upon interaction with CL and avoid the unpredictable alias that might come from protein labeling or mutations, the conformation of purified yeast iso–1 cyt c with natural isotopic abundance in different contents of CL was measured by using NMR spectroscopy, in which the trimethylated group of the protein was used as a natural probe. The data demonstrate that cyt c has two partially unfolded conformations when interacted with CL: one with Fe–His33 coordination and the other with a penta–coordination heme. The Fe–His33 coordination conformation can be converted into a penta–coordination heme conformation in high content of CL. The structure of cyt c becomes partially unfolded with more exposed heme upon interaction with CL, suggesting that cyt c prefers a high peroxidase activity state in the mitochondria, which, in turn, makes CL easy to be oxidized, and causes the release of cyt c into the cytoplasm as a trigger in apoptosis. Full article
(This article belongs to the Special Issue Application of Nuclear Magnetic Resonance Method in Protein Research)
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14 pages, 3707 KiB  
Article
Solid-State NMR Studies of the Succinate-Acetate Permease from Citrobacter Koseri in Liposomes and Native Nanodiscs
by Xing-Qi Dong, Jing-Yu Lin, Peng-Fei Wang, Yi Li, Jian Wang, Bing Li, Jun Liao and Jun-Xia Lu
Life 2021, 11(9), 908; https://doi.org/10.3390/life11090908 - 31 Aug 2021
Viewed by 3116
Abstract
The succinate-acetate permease (SatP) is an anion channel with six transmembrane domains. It forms different oligomers, especially hexamers in the detergent as well as in the membrane. Solid-state NMR studies of SatP were carried out successfully on SatP complexes by reconstructing the protein [...] Read more.
The succinate-acetate permease (SatP) is an anion channel with six transmembrane domains. It forms different oligomers, especially hexamers in the detergent as well as in the membrane. Solid-state NMR studies of SatP were carried out successfully on SatP complexes by reconstructing the protein into liposomes or retaining the protein in the native membrane of E. coli., where it was expressed. The comparison of 13C-13C 2D correlation spectra between the two samples showed great similarity, opening the possibility to further study the acetate transport mechanism of SatP in its native membrane environment. Solid-state NMR studies also revealed small chemical shift differences of SatP in the two different membrane systems, indicating the importance of the lipid environment in determining the membrane protein structures and dynamics. Combining different 2D SSNMR spectra, chemical shift assignments were made on some sites, consistent with the helical structures in the transmembrane domains. In the end, we pointed out the limitation in the sensitivity for membrane proteins with such a size, and also indicated possible ways to overcome it. Full article
(This article belongs to the Special Issue Application of Nuclear Magnetic Resonance Method in Protein Research)
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