Using ESI-MS to probe protein structure by site-specific noncovalent attachment of 18-crown-6

2006 ◽  
Vol 17 (9) ◽  
pp. 1209-1215 ◽  
Author(s):  
Tony Ly ◽  
Ryan R. Julian
Keyword(s):  
Protein Structure ◽  
Site Specific ◽  
Esi Ms

scholarly journals Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin

2013 ◽  
Vol 368 (1614) ◽  
pp. 20120334 ◽  
Author(s):  
Austin G. Meyer ◽  
Eric T. Dawson ◽  
Claus O. Wilke
Keyword(s):  
Protein Structure ◽  
Sialic Acid ◽  
Avian Influenza ◽  
Evolutionary Rate ◽  
Solvent Accessibility ◽  
Rate Variation ◽  
Structural Constraints ◽  
Binding Region ◽  
Site Specific ◽  
Sialic Acid Binding

We investigate the causes of site-specific evolutionary-rate variation in influenza haemagglutinin (HA) between human and avian influenza, for subtypes H1, H3, and H5. By calculating the evolutionary-rate ratio, ω = d N /d S as a function of a residue's solvent accessibility in the three-dimensional protein structure, we show that solvent accessibility has a significant but relatively modest effect on site-specific rate variation. By comparing rates within HA subtypes among host species, we derive an upper limit to the amount of variation that can be explained by structural constraints of any kind. Protein structure explains only 20–40% of the variation in ω . Finally, by comparing ω at sites near the sialic-acid-binding region to ω at other sites, we show that ω near the sialic-acid-binding region is significantly elevated in both human and avian influenza, with the exception of avian H5. We conclude that protein structure, HA subtype, and host biology all impose distinct selection pressures on sites in influenza HA.

Site-Specific Interrogation of Protein Structure and Stability

2021 ◽  
pp. 65-87
Author(s):  
Debopreeti Mukherjee ◽  
Ismail A. Ahmed ◽  
Feng Gai
Keyword(s):  
Protein Structure ◽  
Site Specific ◽  
Structure And Stability

Site-specific characterisation of densely O-glycosylated mucin-type peptides using electron transfer dissociation ESI-MS/MS

2011 ◽  
Vol 32 (24) ◽  
pp. 3536-3545 ◽  
Author(s):  
Morten Thaysen-Andersen ◽  
Brendan L. Wilkinson ◽  
Richard J. Payne ◽  
Nicolle H. Packer
Keyword(s):  
Electron Transfer ◽  
Electron Transfer Dissociation ◽  
Site Specific ◽  
Esi Ms

scholarly journals Glycoproteomic measurement of site-specific polysialylation

2019 ◽  
Author(s):  
Ruby Pelingon ◽  
Cassandra L. Pegg ◽  
Lucia F. Zacchi ◽  
Toan K. Phung ◽  
Christopher B. Howard ◽  
...  
Keyword(s):  
Protein Function ◽  
Neurological Diseases ◽  
Polysialic Acid ◽  
Monosaccharide Composition ◽  
Degree Of Polymerization ◽  
Site Specific ◽  
Esi Ms ◽  
Therapeutic Drugs ◽  
Protease Digestion ◽  
Analytical Approaches

AbstractPolysialylation is the enzymatic addition of a highly negatively charged sialic acid polymer to the non-reducing termini of glycans. Polysialylation plays an important role in development, and is involved in neurological diseases, neural tissue regeneration, and cancer. Polysialic acid (PSA) is also a biodegradable and non-immunogenic conjugate to therapeutic drugs to improve their pharmacokinetics. PSA chains vary in length, composition, and linkages, while the specific sites of polysialylation are important determinants of protein function. However, PSA is difficult to analyse by mass spectrometry (MS) due to its high negative charge and size. Most analytical approaches for analysis of PSA measure its degree of polymerization and monosaccharide composition, but do not address the key questions of site specificity and occupancy. Here, we developed a high-throughput LC-ESI-MS/MS glycoproteomics method to measure site-specific polysialylation of glycoproteins. This method measures site-specific PSA modification by using mild acid hydrolysis to eliminate PSA and sialic acids while leaving the glycan backbone intact, together with protease digestion followed by LC-ESI-MS/MS glycopeptide detection. PSA-modified glycopeptides are not detectable by LC-ESI-MS/MS, but become detectable after desialylation, allowing measurement of site-specific PSA occupancy. This method is an efficient analytical workflow for the study of glycoprotein polysialylation in biological and therapeutic settings.Graphical Abstract

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