scholarly journals Functions and Mechanisms of Lysine Glutarylation in Eukaryotes

2021 ◽  
Vol 9 ◽  
Author(s):  
Longxiang Xie ◽  
Yafei Xiao ◽  
Fucheng Meng ◽  
Yongqiang Li ◽  
Zhenyu Shi ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Post Translational Modification ◽  
Computational Tools ◽  
Chromatin Dynamics ◽  
Biochemical Processes ◽  
Development History ◽  
Cellular Processes ◽  
Regulation Of Metabolism ◽  
Recent Developments ◽  
History Of

Lysine glutarylation (Kglu) is a newly discovered post-translational modification (PTM), which is considered to be reversible, dynamic, and conserved in prokaryotes and eukaryotes. Recent developments in the identification of Kglu by mass spectrometry have shown that Kglu is mainly involved in the regulation of metabolism, oxidative damage, chromatin dynamics and is associated with various diseases. In this review, we firstly summarize the development history of glutarylation, the biochemical processes of glutarylation and deglutarylation. Then we focus on the pathophysiological functions such as glutaric acidemia 1, asthenospermia, etc. Finally, the current computational tools for predicting glutarylation sites are discussed. These emerging findings point to new functions for lysine glutarylation and related enzymes, and also highlight the mechanisms by which glutarylation regulates diverse cellular processes.

Recent developments in mass spectrometry-based quantitative phosphoproteomicsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.

2008 ◽  
Vol 86 (2) ◽  
pp. 137-148 ◽  
Author(s):  
Jeffrey C. Smith ◽  
Daniel Figeys
Keyword(s):  
Mass Spectrometry ◽  
Protein Phosphorylation ◽  
Review Process ◽  
Peer Review Process ◽  
Cellular Systems ◽  
Post Translational Modification ◽  
Dynamic Nature ◽  
Cellular Processes ◽  
Recent Developments ◽  
Selection Of

Protein phosphorylation is a reversible post-translational modification that is involved in virtually all eukaryotic cellular processes and has been studied in great detail in recent years. Many developments in mass spectrometry (MS)-based proteomics have been successfully applied to study protein phosphorylation in highly complicated samples. Furthermore, the emergence of a variety of enrichment strategies has allowed some of the challenges associated with low phosphorylation stoichiometry and phosphopeptide copy number to be overcome. The dynamic nature of protein phosphorylation complicates its analysis; however, a number of methods have been developed to successfully quantitate phosphorylation changes in a variety of cellular systems. The following review details some of the most recent breakthroughs in the study of protein phosphorylation, or phosphoproteomics, using MS-based approaches. The majority of the focus is placed on detailing strategies that are currently used to conduct MS-based quantitative phosphoproteomics.

Applications of Mass Spectrometry in Proteomics

2013 ◽  
Vol 66 (7) ◽  
pp. 721 ◽  
Author(s):  
Izabela Sokolowska ◽  
Armand G. Ngounou Wetie ◽  
Alisa G. Woods ◽  
Costel C. Darie
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Protein Identification ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Physiological Processes ◽  
Protein Functions ◽  
Instruments And Techniques ◽  
Accurate Mass Spectrometry

Characterisation of proteins and whole proteomes can provide a foundation to our understanding of physiological and pathological states and biological diseases or disorders. Constant development of more reliable and accurate mass spectrometry (MS) instruments and techniques has allowed for better identification and quantification of the thousands of proteins involved in basic physiological processes. Therefore, MS-based proteomics has been widely applied to the analysis of biological samples and has greatly contributed to our understanding of protein functions, interactions, and dynamics, advancing our knowledge of cellular processes as well as the physiology and pathology of the human body. This review will discuss current proteomic approaches for protein identification and characterisation, including post-translational modification (PTM) analysis and quantitative proteomics as well as investigation of protein–protein interactions (PPIs).

scholarly journals Towards comprehensive and quantitative proteomics for diagnosis and therapy of human disease

2016 ◽  
Author(s):  
Paolo Cifani ◽  
Alex Kentsis
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Human Disease ◽  
Protein Modification ◽  
Functional Characterization ◽  
Exchange Chromatography ◽  
Post Translational Modification ◽  
Biochemical Processes ◽  
Modern Mass

AbbreviationsDDAData Dependent AcquisitionDIAData Independent AcquisitionPRMParallel Reaction MonitoringPTMpost-translational modificationSAXstrong anion exchange (chromatography)SCXStrong cation exchange (chromatography)AbstractDespite superior analytical features, mass spectrometry proteomics remains seldom used for the basic investigation and clinical treatment of human disease. This need is particularly pressing for childhood diseases that can be rare in incidence and variable in presentation. Modern mass spectrometry enables detailed functional characterization of the pathogenic biochemical processes, as achieved by accurate and comprehensive quantification of proteins and their regulatory chemical modifications. Here, we describe how high-accuracy mass spectrometry in combination with high-resolution chromatographic separations can be leveraged to meet these analytical requirements in a mechanism-focused manner. We review the quantification methods capable of producing accurate measurements of protein abundance and post-translational modification stoichiometries. We then discuss how experimental design and chromatographic resolution can be leveraged to achieve comprehensive functional characterization of biochemical processes in complex biological proteomes. Finally, we describe current approaches for quantitative analysis of a common functional protein modification: reversible phosphorylation. In all, current instrumentation and methods of high-resolution chromatography and mass spectrometry proteomics are poised for immediate translation into improved diagnostic and therapeutic strategies for pediatric and adult diseases.

scholarly journals Developments in tandem ion mobility mass spectrometry

2020 ◽  
Vol 48 (6) ◽  
pp. 2457-2466
Author(s):  
Charles Eldrid ◽  
Konstantinos Thalassinos
Keyword(s):  
Mass Spectrometry ◽  
Ion Mobility ◽  
Biological Systems ◽  
Molecular Shape ◽  
Ion Mobility Mass Spectrometry ◽  
Tandem Ms ◽  
Future Directions ◽  
Recent Developments ◽  
History Of

Ion Mobility (IM) coupled to mass spectrometry (MS) is a useful tool for separating species of interest out of small quantities of heterogenous mixtures via a combination of m/z and molecular shape. While tandem MS instruments are common, instruments which employ tandem IM are less so with the first commercial IM–MS instrument capable of multiple IM selection rounds being released in 2019. Here we explore the history of tandem IM instruments, recent developments, the applications to biological systems and expected future directions.

scholarly journals Protein Persulfidation in Plants: Function and Mechanism

Antioxidants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 1631
Author(s):  
Peng Wang ◽  
Hua Fang ◽  
Rong Gao ◽  
Weibiao Liao
Keyword(s):  
Oxidative Stress ◽  
Stress Responses ◽  
Growth And Development ◽  
Protective Mechanism ◽  
Post Translational Modification ◽  
Biochemical Processes ◽  
Cellular Processes ◽  
Growth Development ◽  
Almost All ◽  
And Function

As an endogenous gaseous transmitter, the function of hydrogen sulfide (H2S) has been extensively studied in plants. Once synthesized, H2S may be involved in almost all life processes of plants. Among them, a key route for H2S bioactivity occurs via protein persulfidation, in which process oxidizes cysteine thiol (R-SH) groups into persulfide (R-SSH) groups. This process is thought to underpin a myriad of cellular processes in plants linked to growth, development, stress responses, and phytohormone signaling. Multiple lines of emerging evidence suggest that this redox-based reversible post-translational modification can not only serve as a protective mechanism for H2S in oxidative stress, but also control a variety of biochemical processes through the allosteric effect of proteins. Here, we collate emerging evidence showing that H2S-mediated persulfidation modification involves some important biochemical processes such as growth and development, oxidative stress, phytohormone and autophagy. Additionally, the interaction between persulfidation and S-nitrosylation is also discussed. In this work, we provide beneficial clues for further exploration of the molecular mechanism and function of protein persulfidation in plants in the future.

Dicarbonyl derived post-translational modifications: chemistry bridging biology and aging-related disease

2020 ◽  
Vol 64 (1) ◽  
pp. 97-110
Author(s):  
Christian Sibbersen ◽  
Mogens Johannsen
Keyword(s):  
Mass Spectrometry ◽  
Future Research ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Dicarbonyl Compounds ◽  
Protein Targets ◽  
Post Translational Modifications ◽  
Reactive Protein ◽  
Glycation End Products ◽  
Direct Mass Spectrometry

Abstract In living systems, nucleophilic amino acid residues are prone to non-enzymatic post-translational modification by electrophiles. α-Dicarbonyl compounds are a special type of electrophiles that can react irreversibly with lysine, arginine, and cysteine residues via complex mechanisms to form post-translational modifications known as advanced glycation end-products (AGEs). Glyoxal, methylglyoxal, and 3-deoxyglucosone are the major endogenous dicarbonyls, with methylglyoxal being the most well-studied. There are several routes that lead to the formation of dicarbonyl compounds, most originating from glucose and glucose metabolism, such as the non-enzymatic decomposition of glycolytic intermediates and fructosyl amines. Although dicarbonyls are removed continuously mainly via the glyoxalase system, several conditions lead to an increase in dicarbonyl concentration and thereby AGE formation. AGEs have been implicated in diabetes and aging-related diseases, and for this reason the elucidation of their structure as well as protein targets is of great interest. Though the dicarbonyls and reactive protein side chains are of relatively simple nature, the structures of the adducts as well as their mechanism of formation are not that trivial. Furthermore, detection of sites of modification can be demanding and current best practices rely on either direct mass spectrometry or various methods of enrichment based on antibodies or click chemistry followed by mass spectrometry. Future research into the structure of these adducts and protein targets of dicarbonyl compounds may improve the understanding of how the mechanisms of diabetes and aging-related physiological damage occur.

ABCs of the Revolution

2020 ◽  
Vol 17 (3) ◽  
pp. 278-291
Author(s):  
Egor A. Yesyunin
Keyword(s):  
Civil War ◽  
Second World War ◽  
World War ◽  
Special Significance ◽  
Development History ◽  
The People ◽  
Red Army ◽  
History Of ◽  
Second World ◽  
The Revolution

The article is devoted to the satirical agitation ABCs that appeared during the Civil War, which have never previously been identified by researchers as a separate type of agitation art. The ABCs, which used to have the narrow purpose of teaching children to read and write before, became a form of agitation art in the hands of artists and writers. This was facilitated by the fact that ABCs, in contrast to primers, are less loaded with educational material and, accordingly, they have more space for illustrations. The article presents the development history of the agitation ABCs, focusing in detail on four of them: V.V. Mayakovsky’s “Soviet ABC”, D.S. Moor’s “Red Army Soldier’s ABC”, A.I. Strakhov’s “ABC of the Revolution”, and M.M. Cheremnykh’s “Anti-Religious ABC”. There is also briefly considered “Our ABC”: the “TASS Posters” created by various artists during the Second World War. The article highlights the special significance of V.V. Mayakovsky’s first agitation ABC, which later became a reference point for many artists. The authors of the first satirical ABCs of the Civil War period consciously used the traditional form of popular prints, as well as ditties and sayings, in order to create images close to the people. The article focuses on the iconographic connections between the ABCs and posters in the works of D.S. Moor and M.M. Cheremnykh, who transferred their solutions from the posters to the ABCs.

Mass Spectrometry for Proteomics and Recent Developments in ESI, MALDI and other Ionization Methodologies

2019 ◽  
Vol 16 (4) ◽  
pp. 267-276
Author(s):  
Qurat ul Ain Farooq ◽  
Noor ul Haq ◽  
Abdul Aziz ◽  
Sara Aimen ◽  
Muhammad Inam ul Haq
Keyword(s):  
Mass Spectrometry ◽  
Electrospray Ionization ◽  
New Technologies ◽  
Protein Complexes ◽  
Imaging Techniques ◽  
Desorption Electrospray Ionization ◽  
High Throughput Analysis ◽  
Enhanced Sensitivity ◽  
Recent Developments ◽  
The Way

Background: Mass spectrometry is a tool used in analytical chemistry to identify components in a chemical compound and it is of tremendous importance in the field of biology for high throughput analysis of biomolecules, among which protein is of great interest. Objective: Advancement in proteomics based on mass spectrometry has led the way to quantify multiple protein complexes, and proteins interactions with DNA/RNA or other chemical compounds which is a breakthrough in the field of bioinformatics. Methods: Many new technologies have been introduced in electrospray ionization (ESI) and Matrixassisted Laser Desorption/Ionization (MALDI) techniques which have enhanced sensitivity, resolution and many other key features for the characterization of proteins. Results: The advent of ambient mass spectrometry and its different versions like Desorption Electrospray Ionization (DESI), DART and ELDI has brought a huge revolution in proteomics research. Different imaging techniques are also introduced in MS to map proteins and other significant biomolecules. These drastic developments have paved the way to analyze large proteins of >200kDa easily. Conclusion: Here, we discuss the recent advancement in mass spectrometry, which is of great importance and it could lead us to further deep analysis of the molecules from different perspectives and further advancement in these techniques will enable us to find better ways for prediction of molecules and their behavioral properties.

scholarly journals N-Terminomics Strategies for Protease Substrates Profiling

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4699
Author(s):  
Mubashir Mintoo ◽  
Amritangshu Chakravarty ◽  
Ronak Tilvawala
Keyword(s):  
Mass Spectrometry ◽  
Protease Activity ◽  
Viral Infections ◽  
Mass Spectrometry Analysis ◽  
Post Translational Modification ◽  
Spectrometry Analysis ◽  
Physiological Conditions ◽  
Inflammatory Conditions ◽  
Biological Mixtures

Proteases play a central role in various biochemical pathways catalyzing and regulating key biological events. Proteases catalyze an irreversible post-translational modification called proteolysis by hydrolyzing peptide bonds in proteins. Given the destructive potential of proteolysis, protease activity is tightly regulated. Dysregulation of protease activity has been reported in numerous disease conditions, including cancers, neurodegenerative diseases, inflammatory conditions, cardiovascular diseases, and viral infections. The proteolytic profile of a cell, tissue, or organ is governed by protease activation, activity, and substrate specificity. Thus, identifying protease substrates and proteolytic events under physiological conditions can provide crucial information about how the change in protease regulation can alter the cellular proteolytic landscape. In recent years, mass spectrometry-based techniques called N-terminomics have become instrumental in identifying protease substrates from complex biological mixtures. N-terminomics employs the labeling and enrichment of native and neo-N-termini peptides, generated upon proteolysis followed by mass spectrometry analysis allowing protease substrate profiling directly from biological samples. In this review, we provide a brief overview of N-terminomics techniques, focusing on their strengths, weaknesses, limitations, and providing specific examples where they were successfully employed to identify protease substrates in vivo and under physiological conditions. In addition, we explore the current trends in the protease field and the potential for future developments.

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