From Protein Primary Sequence to the Gamut of Covalent Modifications Using Mass Spectrometry

1996 ◽  
pp. 472-511 ◽  
Author(s):  
A. L. Burlingame ◽  
K. F. Medzihradszky ◽  
K. R. Clauser ◽  
S. C. Hall ◽  
D. A. Maltby ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Primary Sequence ◽  
Covalent Modifications

scholarly journals Structural basis of antigen recognition: crystal structure of duck egg lysozyme

2017 ◽  
Vol 73 (11) ◽  
pp. 910-920 ◽  
Author(s):  
David Brent Langley ◽  
Ben Crossett ◽  
Peter Schofield ◽  
Jenny Jackson ◽  
Mahdi Zeraati ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mass Spectrometry ◽  
Binding Affinity ◽  
Anas Platyrhynchos ◽  
Antigen Recognition ◽  
Pekin Duck ◽  
Structural Basis ◽  
Primary Sequence ◽  
Duck Egg ◽  
Differential Affinity

Duck egg lysozyme (DEL) is a widely used model antigen owing to its capacity to bind with differential affinity to anti-chicken egg lysozyme antibodies. However, no structures of DEL have so far been reported, and the situation had been complicated by the presence of multiple isoforms and conflicting reports of primary sequence. Here, the structures of two DEL isoforms from the eggs of the commonly used Pekin duck (Anas platyrhynchos) are reported. Using structural analyses in combination with mass spectrometry, non-ambiguous DEL primary sequences are reported. Furthermore, the structures and sequences determined here enable rationalization of the binding affinity of DEL for well documented landmark anti-lysozyme antibodies.

scholarly journals Searching for a placental derived ES-62-like molecule to explain rheumatoid arthritis amelioration in pregnancy

2014 ◽  
Vol 6 (1) ◽  
Author(s):  
Craig D. Scoville ◽  
Devon Rasmussen
Keyword(s):  
Rheumatoid Arthritis ◽  
Mass Spectrometry ◽  
Animal Models ◽  
Heavy Chain ◽  
Protein Identification ◽  
Cross Reactivity ◽  
Primary Sequence ◽  
Reduce Disease Activity ◽  
Filarial Nematodes ◽  
In Pregnancy

The majority of women with rheumatoid arthritis (RA) experience disease amelioration during pregnancy for unclear reasons. One possible explanation pursued and described here is whether the placenta produces a protein similar to the immunomodulating protein, ES-62, excreted by filarial nematodes. This protein has also been shown to reduce disease activity in animal models of RA. Eleven human placentas were prepared and a polyclonal anti-ES-62 antiserum was used to identify if any ES-62-like molecule exists from human placental tissues. Any bands identified were then excised from the gel and sent for mass spectrometry and protein identification. The anti-serum showed consistent cross reactivity with the heavy chain from immunoglobulin G (IgG) from the eleven human placentas by mass spectrometry. No primary sequence homology between the heavy chain of IgG and ES-62 was identified. The placenta does not produce an ES-62-like molecule. However the binding of the antiserum to the Fc region of IgG suggests that this may be a possible mechanism for rheumatoid factor production in some patients with chronic filarial infections.

scholarly journals The separation and sequencing of permethylated peptides by mass spectrometry directly coupled to gas-liquid chromatography

1976 ◽  
Vol 157 (3) ◽  
pp. 777-780 ◽  
Author(s):  
J D Priddle ◽  
K Rose ◽  
R E Offord
Keyword(s):  
Mass Spectrometry ◽  
Molecular Weight ◽  
Chemical Ionization ◽  
Chromatographic Retention ◽  
Gas Liquid Chromatography ◽  
Retention Data ◽  
Primary Sequence ◽  
Peptide Derivatives ◽  
Derivatives Of

The use of g.l.c. coupled to mass spectrometry to separate and sequence permethylated acetyl- and trifluoroacetyl-peptides in a single operation is described. Both electron impact and chemical ionization were used to induce fragmentation, and the latter was found to be more sensitive. Chromatographic retention data are presented which suggest that peptide derivatives of molecular weight of at least 750 are accessible to the technique. The application of our methods to the determination of the primary sequence of proteins is discussed.

scholarly journals Mass Spectrometry-Based Methodologies for Targeted and Untargeted Identification of Protein Covalent Adducts (Adductomics): Current Status and Challenges

2019 ◽  
Vol 8 (2) ◽  
pp. 9 ◽  
Author(s):  
Nunes ◽  
Charneira ◽  
Morello ◽  
Rodrigues ◽  
Pereira ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Disease Diagnosis ◽  
Quantitative Information ◽  
Current Status ◽  
Technological Advances ◽  
Wide Range ◽  
Covalent Modifications ◽  
Covalent Adducts ◽  
Pre Treatment ◽  
Protein Covalent

Protein covalent adducts formed upon exposure to reactive (mainly electrophilic) chemicals may lead to the development of a wide range of deleterious health outcomes. Therefore, the identification of protein covalent adducts constitutes a huge opportunity for a better understanding of events underlying diseases and for the development of biomarkers which may constitute effective tools for disease diagnosis/prognosis, for the application of personalized medicine approaches and for accurately assessing human exposure to chemical toxicants. The currently available mass spectrometry (MS)-based methodologies, are clearly the most suitable for the analysis of protein covalent modifications, providing accuracy, sensitivity, unbiased identification of the modified residue and conjugates along with quantitative information. However, despite the huge technological advances in MS instrumentation and bioinformatics tools, the identification of low abundant protein covalent adducts is still challenging. This review is aimed at summarizing the MS-based methodologies currently used for the identification of protein covalent adducts and the strategies developed to overcome the analytical challenges, involving not only sample pre-treatment procedures but also distinct MS and data analysis approaches.

scholarly journals Native mass spectrometry identifies the HybG chaperone as carrier of the Fe(CN)2CO group during maturation of E. coli [NiFe]-hydrogenase 2

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christian Arlt ◽  
Kerstin Nutschan ◽  
Alexander Haase ◽  
Christian Ihling ◽  
Dirk Tänzler ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Native Mass Spectrometry ◽  
Cysteine Residue ◽  
Catalytic Subunit ◽  
Accessory Proteins ◽  
Catalytic Subunits ◽  
E Coli ◽  
Client Proteins ◽  
Covalent Modifications ◽  
Hydrogenase 2

Abstract[NiFe]-hydrogenases activate dihydrogen. Like all [NiFe]-hydrogenases, hydrogenase 2 of Escherichia coli has a bimetallic NiFe(CN)2CO cofactor in its catalytic subunit. Biosynthesis of the Fe(CN)2CO group of the [NiFe]-cofactor occurs on a distinct scaffold complex comprising the HybG and HypD accessory proteins. HybG is a member of the HypC-family of chaperones that confers specificity towards immature hydrogenase catalytic subunits during transfer of the Fe(CN)2CO group. Using native mass spectrometry of an anaerobically isolated HybG–HypD complex we show that HybG carries the Fe(CN)2CO group. Our results also reveal that only HybG, but not HypD, interacts with the apo-form of the catalytic subunit. Finally, HybG was shown to have two distinct, and apparently CO2-related, covalent modifications that depended on the presence of the N-terminal cysteine residue on the protein, possibly representing intermediates during Fe(CN)2CO group biosynthesis. Together, these findings suggest that the HybG chaperone is involved in both biosynthesis and delivery of the Fe(CN)2CO group to its target protein. HybG is thus suggested to shuttle between the assembly complex and the apo-catalytic subunit. This study provides new insights into our understanding of how organometallic cofactor components are assembled on a scaffold complex and transferred to their client proteins.

scholarly journals Proteome-wide profiling and mapping of post translational modifications in human hearts

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Navratan Bagwan ◽  
Henrik H. El Ali ◽  
Alicia Lundby
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Protein Function ◽  
High Resolution Mass Spectrometry ◽  
Chemical Modifications ◽  
Post Translational Modifications ◽  
Specific Amino Acid ◽  
Covalent Modifications ◽  
Small Chemical ◽  
Resolution Mass

AbstractPost translational modifications (PTMs) are covalent modifications of proteins that can range from small chemical modifications to addition of entire proteins. PTMs contribute to regulation of protein function and thereby greatly increase the functional diversity of the proteome. In the heart, a few well-studied PTMs, such as phosphorylation and glycosylation, are known to play essential roles for cardiac function. Yet, only a fraction of the ~ 300 known PTMs have been studied in a cardiac context. Here we investigated the proteome-wide map of PTMs present in human hearts by utilizing high-resolution mass spectrometry measurements and a suite of PTM identification algorithms. Our approach led to identification of more than 150 different PTMs across three of the chambers in human hearts. This finding underscores that decoration of cardiac proteins by PTMs is much more diverse than hitherto appreciated and provides insights in cardiac protein PTMs not yet studied. The results presented serve as a catalogue of which PTMs are present in human hearts and outlines the particular protein and the specific amino acid modified, and thereby provides a detail-rich resource for exploring protein modifications in human hearts beyond the most studied PTMs.

scholarly journals Emerging Technologies in Mass Spectrometry-Based DNA Adductomics

2019 ◽  
Vol 8 (2) ◽  
pp. 13 ◽  
Author(s):  
Jingshu Guo ◽  
Robert J. Turesky
Keyword(s):  
Mass Spectrometry ◽  
Dna Damage ◽  
Dna Adducts ◽  
Disease Risk ◽  
Scanning Speed ◽  
Molecular Evidence ◽  
Main Transition ◽  
Human Exposure Assessment ◽  
Covalent Modifications

The measurement of DNA adducts, the covalent modifications of DNA upon the exposure to the environmental and dietary genotoxicants and endogenously produced electrophiles, provides molecular evidence for DNA damage. With the recent improvements in the sensitivity and scanning speed of mass spectrometry (MS) instrumentation, particularly high-resolution MS, it is now feasible to screen for the totality of DNA damage in the human genome through DNA adductomics approaches. Several MS platforms have been used in DNA adductomic analysis, each of which has its strengths and limitations. The loss of 2′-deoxyribose from the modified nucleoside upon collision-induced dissociation is the main transition feature utilized in the screening of DNA adducts. Several advanced data-dependent and data-independent scanning techniques originated from proteomics and metabolomics have been tailored for DNA adductomics. The field of DNA adductomics is an emerging technology in human exposure assessment. As the analytical technology matures and bioinformatics tools become available for analysis of the MS data, DNA adductomics can advance our understanding about the role of chemical exposures in DNA damage and disease risk.

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