scholarly journals Norovirus–glycan interactions — how strong are they really?

2021 ◽  
Author(s):  
Thomas Peters ◽  
Robert Creutznacher ◽  
Thorben Maass ◽  
Alvaro Mallagaray ◽  
Patrick Ogrissek ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Nmr Spectroscopy ◽  
Major Capsid Protein ◽  
Atomic Resolution ◽  
Blood Group Antigens ◽  
Binding Affinities ◽  
Biophysical Techniques ◽  
Capsid Protein Vp1 ◽  
Short Essay ◽  
Source Of Error

Infection with human noroviruses requires attachment to histo blood group antigens (HBGAs) via the major capsid protein VP1 as a primary step. Several crystal structures of VP1 protruding domain dimers, so called P-dimers, complexed with different HBGAs have been solved to atomic resolution. Corresponding binding affinities have been determined for HBGAs and other glycans exploiting different biophysical techniques, with mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy being most widely used. However, reported binding affinities are inconsistent. At the extreme, for the same system MS detects binding whereas NMR spectroscopy does not, suggesting a fundamental source of error. In this short essay, we will explain the reason for the observed differences and compile reliable and reproducible binding affinities. We will then highlight how a combination of MS techniques and NMR experiments affords unique insights into the process of HBGA binding by norovirus capsid proteins.

scholarly journals Protein Secondary Structure Affects Glycan Clustering in Native Mass Spectrometry

Life ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 554
Author(s):  
Hao Yan ◽  
Julia Lockhauserbäumer ◽  
Gergo Peter Szekeres ◽  
Alvaro Mallagaray ◽  
Robert Creutznacher ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Dissociation Constants ◽  
Protein Secondary Structure ◽  
Binding Pocket ◽  
Native Mass Spectrometry ◽  
Resonance Spectroscopy ◽  
Blood Group Antigens ◽  
Binding Affinities ◽  
Native Ms ◽  
Capsid Protein Vp1

Infection by the human noroviruses (hNoV), for the vast majority of strains, requires attachment of the viral capsid to histo blood group antigens (HBGAs). The HBGA-binding pocket is formed by dimers of the protruding domain (P dimers) of the capsid protein VP1. Several studies have focused on HBGA binding to P dimers, reporting binding affinities and stoichiometries. However, nuclear magnetic resonance spectroscopy (NMR) and native mass spectrometry (MS) analyses yielded incongruent dissociation constants (KD) for the binding of HBGAs to P dimers and, in some cases, disagreed on whether glycans bind at all. We hypothesized that glycan clustering during electrospray ionization in native MS critically depends on the physicochemical properties of the protein studied. It follows that the choice of a reference protein is crucial. We analysed carbohydrate clustering using various P dimers and eight non-glycan binding proteins serving as possible references. Data from native and ion mobility MS indicate that the mass fraction of β-sheets has a strong influence on the degree of glycan clustering. Therefore, the determination of specific glycan binding affinities from native MS must be interpreted cautiously.

scholarly journals Protein secondary structure affects glycan clustering in native mass spectrometry

2021 ◽  
Author(s):  
Hao Yan ◽  
Julia Lockhauserb&aumlumer ◽  
Gergo Peter Szekeres ◽  
Alvaro Mallagaray ◽  
Robert Creutznacher ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Dissociation Constants ◽  
Protein Secondary Structure ◽  
Binding Pocket ◽  
Native Mass Spectrometry ◽  
Resonance Spectroscopy ◽  
Blood Group Antigens ◽  
Binding Affinities ◽  
Native Ms ◽  
Capsid Protein Vp1

Infection with human noroviruses (hNoV) for the vast majority of strains requires attachment of the viral capsid to histo blood group antigens (HBGA). The HBGA binding pocket is formed by dimers of the protruding domain (P dimers) of the capsid protein VP1. Several studies have focused on HBGA binding to P dimers, reporting binding affinities and stoichiometries. However, nuclear magnetic resonance spectroscopy (NMR) and native mass spectrometry (MS) analyses yielded incongruent dissociation constants (KD) for binding of HBGAs to P dimers and, in some cases, disagreed whether glycans bind at all. We hypothesized that glycan clustering during electrospray ionization in native MS critically depends on the physicochemical properties of the protein studied. It follows that the choice of the reference protein is crucial. We analyzed carbohydrate clustering using various P dimers and eight non-glycan binding proteins serving as possible references. Data from native and ion mobility MS indicate that the mass fraction of β-sheet has a strong influence on the degree of glycan clustering. Therefore, the determination of specific glycan binding affinities from native MS must be interpreted cautiously.

scholarly journals Free Chlorine and Peroxynitrite Alter the Capsid Structure of Human Norovirus GII.4 and Its Capacity to Bind Histo-Blood Group Antigens

2021 ◽  
Vol 12 ◽  
Author(s):  
Manon Chassaing ◽  
Guillaume Bastin ◽  
Maëlle Robin ◽  
Didier Majou ◽  
Gaël Belliot ◽  
...  
Keyword(s):  
Blood Group ◽  
Major Capsid Protein ◽  
Free Chlorine ◽  
Blood Group Antigens ◽  
Cross Links ◽  
Two Oxidants ◽  
Capsid Protein Vp1 ◽  
Norovirus Gii ◽  
The Impact ◽  
Natural Life

Human noroviruses (HuNoVs) are one of the leading causes of acute gastroenteritis worldwide. HuNoVs are frequently detected in water and foodstuffs. Free chlorine and peroxynitrite (ONOO−) are two oxidants commonly encountered by HuNoVs in humans or in the environment during their natural life cycle. In this study, we defined the effects of these two oxidants on GII.4 HuNoVs and GII.4 virus-like particles (VLPs). The impact on the capsid structure, the major capsid protein VP1 and the ability of the viral capsid to bind to histo-blood group antigens (HBGAs) following oxidative treatments were analyzed. HBGAs are attachment factors that promote HuNoV infection in human hosts. Overall, our results indicate that free chlorine acts on regions involved in the stabilization of VP1 dimers in VLPs and affects their ability to bind to HBGAs. These effects were confirmed in purified HuNoVs. Some VP1 cross-links also take place after free chlorine treatment, albeit to a lesser extent. Not only ONOO− mainly produced VP1 cross-links but can also dissociate VLPs depending on the concentration applied. Nevertheless, ONOO− has less effect on HuNoV particles.

scholarly journals Mass Spectrometry-Based System for Identifying and Typing Norovirus Major Capsid Protein VP1

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2332
Author(s):  
Pei-Yu Chu ◽  
Hui-Wen Huang ◽  
Michittra Boonchan ◽  
Yu-Chang Tyan ◽  
Kevin Leroy Louis ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Capsid Protein ◽  
Major Capsid Protein ◽  
Ultra Performance Liquid Chromatography ◽  
Clinical Samples ◽  
Structural Protein ◽  
Promising Tool ◽  
Technological Advances ◽  
Primary Diagnostics ◽  
Capsid Protein Vp1

Norovirus-associated diseases are the most common foodborne illnesses worldwide. Polymerase chain reaction-based methods are the primary diagnostics for clinical samples; however, the high mutation rate of norovirus makes viral amplification and genotyping challenging. Technological advances in mass spectrometry (MS) make it a promising tool for identifying disease markers. Besides, the superior sensitivity of MS and proteomic approaches may enable the detection of all variants. Thus, this study aimed to establish an MS-based system for identifying and typing norovirus. We constructed three plasmids containing the major capsid protein VP1 of the norovirus GII.4 2006b, 2006a, and 2009a strains to produce virus-like particles for use as standards. Digested peptide signals were collected using a nano-flow ultra-performance liquid chromatography mass spectrometry (nano-UPLC/MSE) system, and analyzed by ProteinLynx Global SERVER and TREE-PUZZLE software. Results revealed that the LC/MSE system had an excellent coverage rate: the system detected more than 94% of amino acids of 3.61 femtomole norovirus VP1 structural protein. In the likelihood-mapping analysis, the proportions of unresolved quartets were 2.9% and 4.9% in the VP1 and S domains, respectively, which is superior to the 15.1% unresolved quartets in current PCR-based methodology. In summary, the use of LC/MSE may efficiently monitor genotypes, and sensitively detect structural and functional mutations of noroviruses.

Synthesis and Caracterization of some New 1H-3-aryl-7-etoxycarbonyl-6-methyl-pyrazolo[5,1-c][1,2,4]triazoles

2008 ◽  
Vol 59 (1) ◽  
pp. 41-44
Author(s):  
Maria-Daniela Sofei ◽  
Maria Ilici ◽  
Valentin Badea ◽  
Carol Csunderlik ◽  
Vasile-Nicolae Bercean
Keyword(s):  
Mass Spectrometry ◽  
Acetic Acid ◽  
Nmr Spectroscopy ◽  
Sodium Acetate ◽  
Glacial Acetic Acid ◽  
Ir And Nmr Spectroscopy

The synthesis of 1H-3-aryl-7-ethoxycarbonyl-6-methyl-pyrazolo[5,1-c][1,2,4]triazoles (2) was carried out by cyclization of 1H-5-arylidenehydrazino-4-ethoxycarbonyl-3-methyl-pyrazoles (1) in the presence of bromine using glacial acetic acid as solvent and sodium acetate as base. The new nine obtained compounds were characterized by IR and NMR spectroscopy and mass spectrometry.

The mechanism of formation of 2,7-dimethyl-2,6-octadiene in the synthesis of 3-methylene-7-methyl-1,6-octadiene

1983 ◽  
Vol 48 (7) ◽  
pp. 1864-1866
Author(s):  
Jan Bartoň ◽  
Ivan Kmínek
Keyword(s):  
Mass Spectrometry ◽  
Nmr Spectroscopy ◽  
Alkali Metal ◽  
Chromatographic Analysis ◽  
Solid Phase ◽  
Reaction Pathway ◽  
Mechanism Of Formation ◽  
Gas Chromatographic Analysis ◽  
C Nmr ◽  
Visual Observations

2,7-Dimethyl-2,6-octadiene is formed in the catalytic solution for the dimerization of 2-methyl-1,3-butadiene to β-myrcene (3-methylene-7-methyl-1,6-octadiene), as revealed by mass spectrometry and 13C NMR spectroscopy. Visual observations together with the results of gas chromatographic analysis of the catalytic solution suggest that the formation of 2,7-dimethyl-2,6-octadiene is associated with the transition of the alkali metal (sodium) from the solid phase into the solution. A reaction pathway is suggested accounting for the formation of 2,7-dimethyl-2,6-octadiene in the system.

A New Dimeric Derivative of Ethoxyquin from Its Reaction with Alkylperoxy Radicals

1993 ◽  
Vol 58 (8) ◽  
pp. 1914-1918 ◽  
Author(s):  
Jaroslav Kříž ◽  
Luděk Taimr
Keyword(s):  
Mass Spectrometry ◽  
Nmr Spectroscopy ◽  
Peroxy Radicals ◽  
Methyl Group ◽  
Alkylperoxy Radicals ◽  
C Nmr

The structure of a new compound formed in the reaction of ethoxyquin with alkylperoxy radicals was resolved by 1H and 13C NMR spectroscopy (including COSY, NOESY, HHC RCT and SSLR INEPT techniques) and confirmed by mass spectrometry. The structure suggest participation of 4-methyl group of ethoxyquin in the deactivation of peroxy radicals. A mechanism of this reaction is proposed.

scholarly journals (2S,3R,6R)-2-[(R)-1-Hydroxyallyl]-4,4-dimethoxy-6-methyltetrahydro-2H-pyran-3-ol

Molbank ◽  
10.3390/m1140 ◽  
2020 ◽  
Vol 2020 (2) ◽  
pp. M1140
Author(s):  
Jack Bennett ◽  
Paul Murphy
Keyword(s):  
Mass Spectrometry ◽  
Nmr Spectroscopy ◽  
Ir Spectroscopy ◽  
13C Nmr ◽  
Conjugate Addition ◽  
13C Nmr Spectroscopy ◽  
One Pot ◽  
1H And 13C Nmr ◽  
Esi Mass Spectrometry ◽  
The One

(2S,3R,6R)-2-[(R)-1-Hydroxyallyl]-4,4-dimethoxy-6-methyltetrahydro-2H-pyran-3-ol was isolated in 18% after treating the glucose derived (5R,6S,7R)-5,6,7-tris[(triethylsilyl)oxy]nona-1,8-dien-4-one with (1S)-(+)-10-camphorsulfonic acid (CSA). The one-pot formation of the title compound involved triethylsilyl (TES) removal, alkene isomerization, intramolecular conjugate addition and ketal formation. The compound was characterized by 1H and 13C NMR spectroscopy, ESI mass spectrometry and IR spectroscopy. NMR spectroscopy was used to establish the product structure, including the conformation of its tetrahydropyran ring.

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