scholarly journals Recent Advances in the Chemical Biology of N-Glycans

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1040
Author(s):  
Asuka Shirakawa ◽  
Yoshiyuki Manabe ◽  
Koichi Fukase

Asparagine-linked N-glycans on proteins have diverse structures, and their functions vary according to their structures. In recent years, it has become possible to obtain high quantities of N-glycans via isolation and chemical/enzymatic/chemoenzymatic synthesis. This has allowed for progress in the elucidation of N-glycan functions at the molecular level. Interaction analyses with lectins by glycan arrays or nuclear magnetic resonance (NMR) using various N-glycans have revealed the molecular basis for the recognition of complex structures of N-glycans. Preparation of proteins modified with homogeneous N-glycans revealed the influence of N-glycan modifications on protein functions. Furthermore, N-glycans have potential applications in drug development. This review discusses recent advances in the chemical biology of N-glycans.

2004 ◽  
Vol 18 (1) ◽  
pp. 13-29 ◽  
Author(s):  
Ke-He Ruan

High resolution Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful tool for determining the solution structures of peptides and small proteins, and their ligand binding functions. Molecular biology mutagenesis is a widely used and powerful approach for identification of the protein functions. We have developed a strategy integrating NMR experiments with mutagenesis studies to advance and extend the approaches used for structure/function relationship studies of proteins, especially for membrane-bound proteins, which play important roles in physiopathological processes. The procedures include the design of the functional protein domain, identification of the solution structure and intermolecular contacts between the protein segment and its ligand. These determinations are resolved by high-resolution 2D NMR spectroscopy, and followed by site-directed mutagenesis of the residues suggested from the NMR experiment for the membrane-bound proteins. The residues important to the protein functions, identified by the mutagenesis, were further used to re-assign the NMR spectra and finalize the docking of the protein with its ligand. A structural model of the protein/ligand interaction can be constructed at an atomic level based on the NMR spectroscopy and mutagenesis results. As an application, the strategy has enhanced our knowledge in the understanding of the structure/function relationship for a membrane-bound G protein coupling receptor, the thromboxane A2receptor (TP receptor), interacting with its ligand, and a microsomal P450, prostacyclin synthase (PGIS), docking with its substrate in the endoplasmic reticulum (ER) membrane. In this review, we have summarized the principles and applications for this newly developed technique.


1961 ◽  
Vol 34 (5) ◽  
pp. 1574-1600 ◽  
Author(s):  
W. P. Slichter

Abstract The remarkable property that we associate with rubberlike elasticity, the high degree of elastic deformability, has long been known to arise from molecular motion. In fact, Joule recognized a century ago that the retractive force in stretched rubber stems from thermal motions of molecules rather than from attractive forces between molecules, a conclusion which was all the more remarkable because Joule had no idea of the polymeric nature of rubber. This review tells of the newest technique for studying molecular motion, nuclear magnetic resonance spectroscopy (NMR), and of its application to studies of rubberlike substances. Appropriately, the most important measurements of rubberlike elasticity have been mechanical—creep, stress relaxation, dynamic response. The visco-elastic properties have been studied theoretically and have been measured profusely. They have told us much about the spectra of relaxation processes, which range over many decades of frequency. However, the mechanical experiments occur at the macroscopic level. Conclusions as to behavior at the molecular level depend upon the soundness of models. Plainly it is also valuable to examine motion directly at the molecular level. There are several techniques that accomplish this end. Infrared spectroscopy and dielectric relaxation studies are two kinds of measurement that directly indicate the motion of atoms and molecules. To these techniques is added nuclear magnetic resonance spectroscopy. This method responds to molecular behavior quite differently from other kinds of measurement, and avoids some of the restrictions encountered in these other techniques. For example, the requirement of a permanent electric dipole moment effectively excludes dielectric measurements for the study of pure natural rubber and other hydrocarbons, yet motion in such substances is readily seen by NMR. On the other hand, there are distinct limitations to the use of nuclear resonance, as we shall note. In this paper, we shall review the phenomenon of nuclear magnetic resonance, with emphasis on its use in studies of molecular motion in elastomers. It would be wrong to say that NMR has achieved the importance of the principal physical techniques used to study elastomers. Indeed, the information on elastomers yielded by NMR consists largely of isolated examples. Still, we shall seek to show that the method is powerful and has great potentialities. For a more detailed review of the fundamental physics than is given here, the reader is referred to the excellent paper by Pake. A comprehensive survey of NMR studies of polymers is given by Powles.


2019 ◽  
Author(s):  
Shenyuan Xu ◽  
Yang Liu ◽  
Ming Tan ◽  
Weiming Zhong ◽  
Dandan Zhao ◽  
...  

AbstractInitial cell attachment of rotavirus (RV) to specific cell surface glycans, which is the essential first step in RV infection, is mediated by the VP8* domain of the spike protein VP4. Recently, human histo-blood group antigens (HBGAs) have been identified as ligands or receptors for human RV strains. RV strains in the P[4] and P[8] genotypes of the P[II] genogroup share common recognition of the Lewis b and H type 1 antigens, while P[6], which is one of the other genotypes in P[II], only recognizes the H type 1 antigen. The molecular basis of receptor recognition by the major human P[8] RVs remains unknown due to lack of experimental structural information. Here, we used nuclear magnetic resonance (NMR) titration experiments and NMR-derived high ambiguity driven docking (HADDOCK) methods to elucidate the molecular basis for P[8] VP8* recognition of the Leb and type 1 HBGAs and for P[6] recognition of H type 1 HBGAs. Unlike P[6] VP8* that recognizes H type 1 HGBAs in a binding surface composed of an α-helix and a β-sheet, referred as “βα binding domain”, the P[8] VP8* binds the type 1 HBGAs requiring the presence of the Lewis epitope in a previously undescribed pocket formed by two β-sheets, referred as “ββ binding domain”. The observation that P[6] and P[8] VP8* domains recognize different glycan structures at distinct binding sites supports the hypothesis that RV evolution is driven, at least in part, by selective pressure driven adaptation to HBGA structural diversity of their natural hosts living in the world. Recognition of the role that HBGAs play in driving RV evolution is essential to understanding RV diversity, host ranges, disease burden and zoonosis and to developing strategies to improve vaccines against RV infections.Author summaryRotaviruses (RV)s are the main cause of severe diarrhea in humans and animals. Significant advances in understanding RV diversity, evolution and epidemiology have been made after discovering that RVs recognize histo-blood group antigens (HBGAs) as host cell receptors. While different RV strains are known to have distinct binding preferences for HBGA receptors, the molecular basis in controlling strain-specific host ranges remains unclear. In this study, we used solution nuclear magnetic resonance to determine the molecular level details for interactions of the human P[8] and P[6] RV VP8* domains with their HBGA receptors. The distinct binding patterns observed between these major human RVs and their respective receptor ligands provides insight into the evolutionary relationships between different P[II] genotypes that ultimately determine host ranges, disease burden, zoonosis and epidemiology, which may impact future strategies for vaccine development against RVs.


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