scholarly journals Leveraging immonium ions for identifying and targeting acyl-lysine modifications in proteomic datasets

2020 ◽  
Author(s):  
John M. Muroski ◽  
Janine Y. Fu ◽  
Hong Hanh Nyugen ◽  
Rachel R. Ogorzalek Loo ◽  
Joseph A. Loo
Keyword(s):  
Protein Modification ◽  
Collision Energy ◽  
Functional Effect ◽  
Lysine Modification ◽  
Strong Indicator ◽  
Chain Acyl ◽  
Domains Of Life ◽  
Immonium Ions ◽  
Insight Into

AbstractAcyl modifications vary greatly in terms of elemental composition and site of protein modification. Developing methods to identify these modifications more confidently can help assess the scope of these modifications in large proteomic datasets. Herein we analyze the utility of acyl-lysine immonium ions for identifying the modifications in proteomic datasets. We demonstrate that the cyclized immonium ion is a strong indicator of acyl-lysine presence when its rank or relative abundance compared to other ions within a spectrum is considered. Utilizing a stepped collision energy method in a shotgun experiment highlights the immonium ion strongly. Implementing an analysis that accounted for features within each MS2 spectra, this method allows peptides with short chain acyl-lysine modifications to be clearly identified in complex lysates. Immonium ions can also be used to validate novel acyl-modifications; in this study we report the first examples of 3-hydroxylpimelyl-lysine modification and validate them using immonium ions. Overall these results solidify the use of the immonium ion as a marker for acyl-lysine modifications in complex proteomic datasets.Statement of SignificanceAcyl-lysine modifications come in a variety of elemental compositions. There is increasing evidence that these modifications can have a functional effect on protein and are present in proteomes across all domains of life. Here we describe a new method that can allow for more confident identification of acyl modifications in proteomes by utilizing the immonium ion of these modifications. Our utilization of these ions allows for more comprehensive insight into the role of acyl modifications at the systems level.

scholarly journals Structural Insight into the Mechanism of N-Linked Glycosylation by Oligosaccharyltransferase

Biomolecules ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 624 ◽  
Author(s):  
Smita Mohanty ◽  
Bharat P Chaudhary ◽  
David Zoetewey
Keyword(s):  
Endoplasmic Reticulum ◽  
Protein Modification ◽  
Cell Communication ◽  
Reticulum Cell ◽  
Enzyme Complex ◽  
Single Polypeptide Chain ◽  
Domains Of Life ◽  
And Function ◽  
Insight Into

Asparagine-linked glycosylation, also known as N-linked glycosylation is an essential and highly conserved post-translational protein modification that occurs in all three domains of life. This modification is essential for specific molecular recognition, protein folding, sorting in the endoplasmic reticulum, cell–cell communication, and stability. Defects in N-linked glycosylation results in a class of inherited diseases known as congenital disorders of glycosylation (CDG). N-linked glycosylation occurs in the endoplasmic reticulum (ER) lumen by a membrane associated enzyme complex called the oligosaccharyltransferase (OST). In the central step of this reaction, an oligosaccharide group is transferred from a lipid-linked dolichol pyrophosphate donor to the acceptor substrate, the side chain of a specific asparagine residue of a newly synthesized protein. The prokaryotic OST enzyme consists of a single polypeptide chain, also known as single subunit OST or ssOST. In contrast, the eukaryotic OST is a complex of multiple non-identical subunits. In this review, we will discuss the biochemical and structural characterization of the prokaryotic, yeast, and mammalian OST enzymes. This review explains the most recent high-resolution structures of OST determined thus far and the mechanistic implication of N-linked glycosylation throughout all domains of life. It has been shown that the ssOST enzyme, AglB protein of the archaeon Archaeoglobus fulgidus, and the PglB protein of the bacterium Campylobactor lari are structurally and functionally similar to the catalytic Stt3 subunit of the eukaryotic OST enzyme complex. Yeast OST enzyme complex contains a single Stt3 subunit, whereas the human OST complex is formed with either STT3A or STT3B, two paralogues of Stt3. Both human OST complexes, OST-A (with STT3A) and OST-B (containing STT3B), are involved in the N-linked glycosylation of proteins in the ER. The cryo-EM structures of both human OST-A and OST-B complexes were reported recently. An acceptor peptide and a donor substrate (dolichylphosphate) were observed to be bound to the OST-B complex whereas only dolichylphosphate was bound to the OST-A complex suggesting disparate affinities of two OST complexes for the acceptor substrates. However, we still lack an understanding of the independent role of each eukaryotic OST subunit in N-linked glycosylation or in the stabilization of the enzyme complex. Discerning the role of each subunit through structure and function studies will potentially reveal the mechanistic details of N-linked glycosylation in higher organisms. Thus, getting an insight into the requirement of multiple non-identical subunits in the N-linked glycosylation process in eukaryotes poses an important future goal.

scholarly journals The development of a molecular toolbox to examine the role of protein O-mannosylation in actinobacteria

2021 ◽  
Author(s):  
Nakita Buenbrazo
Keyword(s):  
Functional Role ◽  
Protein Modification ◽  
Cell Function ◽  
Protein Glycosylation ◽  
Covalent Attachment ◽  
Cell Defense ◽  
Domains Of Life ◽  
Cell Processes

Protein glycosylation is the most abundant and diverse protein modification that occurs in all domains of life. It is defined as the covalent attachment of a carbohydrate moiety to a specific amino acid on a target protein. The functional role of this attachment is implicated in and spans various cell processes from cell signaling, cell defense, and pathogenesis – to name a few. A specific type of protein glycosylation, called protein O-mannosylation (POM) is a process found to be conserved from bacteria to man. In humans, POM is required for healthy cell function, and the absence of POM can cause fatal diseases. Certain prokaryotic species possess a related POM system, but it is poorly understood. It is our hypothesis that the analysis of the POM system in simpler organisms can aid in the characterization of this process and the functional role of the mannosylated proteins that are produced. However, the protocols to prove this theory do not yet exist. This thesis establishes a collection of developed protocols that can be used to characterize the POM systems from gram-positive species Corynebacterium glutamicum and Cellulomonas fimi. In addition the first ever evidence of a C. fimi glycoprotein being glycosylated by the endogenous C. glutamicum POM system is provided.

scholarly journals The development of a molecular toolbox to examine the role of protein O-mannosylation in actinobacteria

2021 ◽  
Author(s):  
Nakita Buenbrazo
Keyword(s):  
Functional Role ◽  
Protein Modification ◽  
Cell Function ◽  
Protein Glycosylation ◽  
Covalent Attachment ◽  
Cell Defense ◽  
Domains Of Life ◽  
Cell Processes

Protein glycosylation is the most abundant and diverse protein modification that occurs in all domains of life. It is defined as the covalent attachment of a carbohydrate moiety to a specific amino acid on a target protein. The functional role of this attachment is implicated in and spans various cell processes from cell signaling, cell defense, and pathogenesis – to name a few. A specific type of protein glycosylation, called protein O-mannosylation (POM) is a process found to be conserved from bacteria to man. In humans, POM is required for healthy cell function, and the absence of POM can cause fatal diseases. Certain prokaryotic species possess a related POM system, but it is poorly understood. It is our hypothesis that the analysis of the POM system in simpler organisms can aid in the characterization of this process and the functional role of the mannosylated proteins that are produced. However, the protocols to prove this theory do not yet exist. This thesis establishes a collection of developed protocols that can be used to characterize the POM systems from gram-positive species Corynebacterium glutamicum and Cellulomonas fimi. In addition the first ever evidence of a C. fimi glycoprotein being glycosylated by the endogenous C. glutamicum POM system is provided.

Plasminogen Activation In Vivo upon Intravenous Infusion of DDAVP

1992 ◽  
Vol 67 (01) ◽  
pp. 111-116 ◽  
Author(s):  
Marcel Levi ◽  
Jan Paul de Boer ◽  
Dorina Roem ◽  
Jan Wouter ten Cate ◽  
C Erik Hack
Keyword(s):  
Monoclonal Antibodies ◽  
Plasminogen Activator ◽  
Plasma Levels ◽  
Fold Increase ◽  
Fibrinolytic System ◽  
Plasminogen Activation ◽  
Plasminogen Activator Activity ◽  
Insight Into

SummaryInfusion of desamino-d-arginine vasopressin (DDAVP) results in an increase in plasma plasminogen activator activity. Whether this increase results in the generation of plasmin in vivo has never been established.A novel sensitive radioimmunoassay (RIA) for the measurement of the complex between plasmin and its main inhibitor α2 antiplasmin (PAP complex) was developed using monoclonal antibodies preferentially reacting with complexed and inactivated α2-antiplasmin and monoclonal antibodies against plasmin. The assay was validated in healthy volunteers and in patients with an activated fibrinolytic system.Infusion of DDAVP in a randomized placebo controlled crossover study resulted in all volunteers in a 6.6-fold increase in PAP complex, which was maximal between 15 and 30 min after the start of the infusion. Hereafter, plasma levels of PAP complex decreased with an apparent half-life of disappearance of about 120 min. Infusion of DDAVP did not induce generation of thrombin, as measured by plasma levels of prothrombin fragment F1+2 and thrombin-antithrombin III (TAT) complex.We conclude that the increase in plasminogen activator activity upon the infusion of DDAVP results in the in vivo generation of plasmin, in the absence of coagulation activation. Studying the DDAVP induced increase in PAP complex of patients with thromboembolic disease and a defective plasminogen activator response upon DDAVP may provide more insight into the role of the fibrinolytic system in the pathogenesis of thrombosis.

On Metaphysics and the Political: A Polemics of Reading Baudelaire in the 1930s

2019 ◽  
Vol 58 (2) ◽  
pp. 249-259
Author(s):  
Joseph Acquisto
Keyword(s):  
Twentieth Century ◽  
Political Crisis ◽  
The Political ◽  
Modern Poetry ◽  
Progressive Politics ◽  
The World ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

This essay examines a polemic between two Baudelaire critics of the 1930s, Jean Cassou and Benjamin Fondane, which centered on the relationship of poetry to progressive politics and metaphysics. I argue that a return to Baudelaire's poetry can yield insight into what seems like an impasse in Cassou and Fondane. Baudelaire provides the possibility of realigning metaphysics and politics so that poetry has the potential to become the space in which we can begin to think the two of them together, as opposed to seeing them in unresolvable tension. Or rather, the tension that Baudelaire animates between the two allows us a new way of thinking about the role of esthetics in moments of political crisis. We can in some ways see Baudelaire as responding, avant la lettre, to two of his early twentieth-century readers who correctly perceived his work as the space that breathes a new urgency into the questions of how modern poetry relates to the world from which it springs and in which it intervenes.

Dažu vācu muzikālo tradīciju pārnese latviešu kultūrtelpā 18. gadsimta II pusē

Letonica ◽  
2020 ◽  
Author(s):  
Māra Grudule
Keyword(s):  
18Th Century ◽  
Musical Instrument ◽  
German Society ◽  
Original Form ◽  
Musical Life ◽  
Popular Songs ◽  
Death Of Jesus ◽  
Musical Traditions ◽  
Insight Into

The article gives insight into a specific component of the work of Baltic enlightener Gotthard Friedrich Stender (1714–1796) that has heretofore been almost unexplored — the transfer of German musical traditions to the Latvian cultural space. Even though there are no sources that claim that Stender was a composer himself, and none of his books contain musical notation, the texts that had been translated by Stender and published in the collections “Jaunas ziņģes” (New popular songs, 1774) and “Ziņģu lustes” (The Joy of singing, 1785, 1789) were meant for singing and, possibly, also for solo-singing with the accompaniment of some musical instrument. This is suggested, first, by how the form of the translation corresponds to the original’s form; second, by the directions, oftentimes attached to the text, that indicate the melody; and third, by the genres of the German originals cantata and song. Stender translated several compositions into Latvian including the text of the religious cantata “Der Tod Jesu” (The Death of Jesus, 1755) by composer Karl Heinrich Graun (1754–1759); songs by various composers that were widely known in German society; as well as a collection of songs by the composer Johann Gottlieb Naumann (1741–1801) that, in its original form, was published together with notation and was intended for solo-singing (female vocals) with the accompaniment of a piano. This article reveals the context of German musical life in the second half of the 18th century and explains the role of music as an instrument of education in Baltic-German and Latvian societies.

The Role of Industry-Academia Collaborative Research in Mineral Exploration

2020 ◽  
Author(s):  
James Marlatt
Keyword(s):  
Collaborative Research ◽  
New Technologies ◽  
Mineral Exploration ◽  
Board Members ◽  
Technological Innovations ◽  
Development Programs ◽  
The University ◽  
Insight Into ◽  
Economic Mineral

ABSTRACT Many people may not be aware of the extent of Kurt Kyser's collaboration with mineral exploration companies through applied research and the development of innovative exploration technologies, starting at the University of Saskatchewan and continuing through the Queen's Facility for Isotope Research. Applied collaborative, geoscientific, industry-academia research and development programs can yield technological innovations that can improve the mineral exploration discovery rates of economic mineral deposits. Alliances between exploration geoscientists and geoscientific researchers can benefit both parties, contributing to the pure and applied geoscientific knowledge base and the development of innovations in mineral exploration technology. Through a collaboration that spanned over three decades, we gained insight into the potential for economic uranium deposits around the world in Canada, Australia, USA, Finland, Russia, Gabon, Namibia, Botswana, South Africa, and Guyana. Kurt, his research team, postdoctoral fellows, and students developed technological innovations related to holistic basin analysis for economic mineral potential, isotopes in mineral exploration, and biogeochemical exploration, among others. In this paper, the business of mineral exploration is briefly described, and some examples of industry-academic collaboration innovations brought forward through Kurt's research are identified. Kurt was a masterful and capable knowledge broker, which is a key criterion for bringing new technologies to application—a grand, curious, credible, patient, and attentive communicator—whether talking about science, business, or life and with first ministers, senior technocrats, peers, board members, first nation peoples, exploration geologists, investors, students, citizens, or friends.

Gender Differences in Empathy During Adolescence: Does Emotional Self-Awareness Matter?

2021 ◽  
pp. 003329412097663
Author(s):  
Cristina Trentini ◽  
Renata Tambelli ◽  
Silvia Maiorani ◽  
Marco Lauriola
Keyword(s):  
Gender Differences ◽  
Reactivity Index ◽  
Self Awareness ◽  
Emotional States ◽  
Personal Distress ◽  
Full Knowledge ◽  
Emotional Concern ◽  
Insight Into ◽  
Tas 20

Empathy refers to the capacity to experience emotions similar to those observed or imagined in another person, with the full knowledge that the other person is the source of these emotions. Awareness of one's own emotional states is a prerequisite for self-other differentiation to develop. This study investigated gender differences in empathy during adolescence and tested whether emotional self-awareness explained these differences. Two-hundred-eleven adolescents (108 girls and 103 boys) between 14 and 19 years completed the Interpersonal Reactivity Index (IRI) and the Toronto Alexithymia Scale (TAS-20) to assess empathy and emotional self-awareness, respectively. Overall, girls obtained higher scores than boys on IRI subscales like emotional concern, personal distress, and fantasy. Regarding emotional self-awareness, we found gender differences in TAS-20 scores, with girls reporting greater difficulty identifying feelings and less externally oriented thinking than boys. Difficulty identifying feelings explained the greatest personal distress experienced by girls. Lower externally oriented thinking accounted for girls’ greater emotional concern and fantasy. These findings offer an insight into the role of emotional self-awareness–which is essential for self-other differentiation–as an account for gender differences in empathic abilities during adolescence. In girls, difficulty identifying feelings can impair the ability to differentiate between ones’ and others’ emotions, leading them to experience self-focused and aversive responses when confronted with others’ suffering. Conversely, in boys, externally oriented thinking can mitigate personal distress when faced with others’ discomfort.

scholarly journals Salicylic Acid Accumulation Controlled by LSD1 Is Essential in Triggering Cell Death in Response to Abiotic Stress

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 962
Author(s):  
Maciej Jerzy Bernacki ◽  
Anna Rusaczonek ◽  
Weronika Czarnocka ◽  
Stanisław Karpiński
Keyword(s):  
Cell Death ◽  
Salicylic Acid ◽  
Abiotic Stress ◽  
Wild Type ◽  
Pr Genes ◽  
Genes Expression ◽  
Salicylic Acid Accumulation ◽  
Cell Death Phenotype ◽  
Insight Into

Salicylic acid (SA) is well known hormonal molecule involved in cell death regulation. In response to a broad range of environmental factors (e.g., high light, UV, pathogens attack), plants accumulate SA, which participates in cell death induction and spread in some foliar cells. LESION SIMULATING DISEASE 1 (LSD1) is one of the best-known cell death regulators in Arabidopsis thaliana. The lsd1 mutant, lacking functional LSD1 protein, accumulates SA and is conditionally susceptible to many biotic and abiotic stresses. In order to get more insight into the role of LSD1-dependent regulation of SA accumulation during cell death, we crossed the lsd1 with the sid2 mutant, caring mutation in ISOCHORISMATE SYNTHASE 1(ICS1) gene and having deregulated SA synthesis, and with plants expressing the bacterial nahG gene and thus decomposing SA to catechol. In response to UV A+B irradiation, the lsd1 mutant exhibited clear cell death phenotype, which was reversed in lsd1/sid2 and lsd1/NahG plants. The expression of PR-genes and the H2O2 content in UV-treated lsd1 were significantly higher when compared with the wild type. In contrast, lsd1/sid2 and lsd1/NahG plants demonstrated comparability with the wild-type level of PR-genes expression and H2O2. Our results demonstrate that SA accumulation is crucial for triggering cell death in lsd1, while the reduction of excessive SA accumulation may lead to a greater tolerance toward abiotic stress.

scholarly journals Theoretical Insight into the Reversal of Chemoselectivity in Diels-Alder Reactions of α,β-Unsaturated Aldehydes and Ketones Catalyzed by Brønsted and Lewis Acids

Organics ◽  
2021 ◽  
Vol 2 (1) ◽  
pp. 38-49
Author(s):  
Lakhdar Benhamed ◽  
Sidi Mohamed Mekelleche ◽  
Wafaa Benchouk
Keyword(s):  
Lewis Acids ◽  
Major Product ◽  
Diels Alder ◽  
Unsaturated Ketone ◽  
Unsaturated Aldehydes ◽  
Aldehydes And Ketones ◽  
Theoretical Insight ◽  
Insight Into ◽  
Good Agreement

Experimentally, a reversal of chemoselectivity has been observed in catalyzed Diels–Alder reactions of α,β-unsaturated aldehydes (e.g., (2E)-but-2-enal) and ketones (e.g., 2-hexen-4-one) with cyclopentadiene. Indeed, using the triflimidic Brønsted acid Tf2NH as catalyst, the reaction gave a Diels–Alder adduct derived from α,β-unsaturated ketone as a major product. On the other hand, the use of tris(pentafluorophenyl)borane B(C6F5)3 bulky Lewis acid as catalyst gave mainly the cycloadduct of α,β-unsaturated aldehyde as a major product. Our aim in the present work is to put in evidence the role of the catalyst in the reversal of the chemoselectivity of the catalyzed Diels–Alder reactions of (2E)-but-2-enal and 2-Hexen-4-one with cyclopentadiene. The calculations were performed at the ωB97XD/6-311G(d,p) level of theory and the solvent effects of dichloromethane were taken into account using the PCM solvation model. The obtained results are in good agreement with experimental outcomes.

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