scholarly journals ProteoSushi: a software tool to biologically annotate and quantify modification-specific, peptide-centric proteomics datasets

2020 ◽  
Author(s):  
Robert W. Seymour ◽  
Sjoerd van der Post ◽  
Arshag D. Mooradian ◽  
Jason M. Held
Keyword(s):  
Large Scale ◽  
Software Tool ◽  
Subcellular Location ◽  
Ease Of Use ◽  
Protein Domain ◽  
Biological Information ◽  
Mass Spectrometry Analysis ◽  
Proteomic Profiling ◽  
Post Translational Modification ◽  
Spectrometry Analysis

AbstractLarge-scale proteomic profiling of protein post-translational modifications has provided important insights into the regulation of cell signaling and disease. These modification-specific proteomics workflows nearly universally enrich modified peptides prior to mass spectrometry analysis, but protein-centric proteomic software tools have many limitations evaluating and interpreting these peptide-centric datasets. We therefore developed ProteoSushi, a software tool tailored to the analysis of each modified site in peptide-centric proteomic datasets that is compatible with any post-translational modification or chemical label. ProteoSushi uses a unique approach to assign identified peptides to shared proteins and genes, minimizing redundancy by prioritizing shared assignments based on UniProt annotation score and optional user-supplied protein/gene lists. ProteoSushi simplifies quantitation by summing or averaging intensities, merging overlapping peptide charge states, missed cleavages, peptide spectral matches, and variable modifications into a single value for each modified site. ProteoSushi annotates each PTM site with the most up-to-date biological information available from UniProt, such as functional roles or known modifications, the protein domain in which the site resides, the protein’s subcellular location and function and more. ProteoSushi has a graphical user interface for ease of use. ProteoSushi’s flexibility and combination of features streamlines peptide-centric data processing and knowledge mining of large modification-specific proteomics datasets.

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.

Abstract 416: Sarcomere Disassembly After Unloading is Regulated by Ubiquitination and Acetylation of Capz and α-actinin

2020 ◽  
Vol 127 (Suppl_1) ◽  
Author(s):  
Christopher Solís ◽  
R John Solaro ◽  
Chad M Warren ◽  
Brenda Russell
Keyword(s):  
Ventricular Myocytes ◽  
Mass Spectrometry Analysis ◽  
Actin Binding ◽  
Mechanical Forces ◽  
Post Translational Modification ◽  
Spectrometry Analysis ◽  
Time Period ◽  
Omecamtiv Mecarbil ◽  
Myocyte Contractility ◽  
Sarcomere Assembly

Cardiac function mainly depends on the total myocyte mass in the ventricles. Assembly and disassembly of sarcomeres occurs to adjust this mass to altered mechanical demand. In the heart, hypertrophic cardiomyopathy results from myofibrillar assembly controlled by post-translational modification of proteins directed by signaling pathways. More is known about assembly on loading than disassembly on unloading. Here, the hypothesis tested is that unloading of mechanical forces affects acetylation (Ac) and ubiquitination (Ub) of the actin-binding proteins, α-actinin and CapZ. Omecamtiv mecarbil (0.5 μM) and mavacamten (1 μM) were used to increase (load) and decrease (unload) cardiomyocyte tension, respectively, via their action on myosin ATPase. Mavacamten decreased myocyte contractility in rat ventricular myocytes (NRVMs) and caused significant sarcomere disassembly by 6 h and 70% atrophy by 24 h. Assembly was preserved with omecamtiv mecarbil (0.5 μM) over the 24 h time period. Post-translational modification was determined in loaded and unloaded NRVMs at 6 h of drug treatment. Bottom-up mass spectrometry analysis showed single residues in α-actinin and CapZ that were acetylated or ubiquitinated. Acetylation levels appeared to increase in the mavacamten-treated samples while these levels are preserved in untreated and omecamtiv mecarbil-treated samples. Ac and Ub in the Z-discs were quantified on immunofluorescent images. The Z-discs colocalized oligo-Ub (K-48 oligo-Ub linkage) and Ac in untreated samples; this Z-disc localization of Ub and Ac was diminished with unloading. Fluorescence recovery after photobleaching (FRAP) measurements of the dynamics of α-actinin and CapZ after reduced cell tension with mavacamten (1 μM) and omecamtiv mercabil (0.5 μM) are ongoing. Overall, results suggest sarcomere assembly is regulated by mechanical forces through a mechanism involving Ac and Ub of myofibrillar proteins. These findings could have consequences for cardiac heart disease with abnormal sarcomeric proteostasis.

scholarly journals Co-Localization of Crotamine with Internal Membranes and Accentuated Accumulation in Tumor Cells

Molecules ◽  
2018 ◽  
Vol 23 (4) ◽  
pp. 968 ◽  
Author(s):  
Nicole Mambelli-Lisboa ◽  
Juliana Mozer Sciani ◽  
Alvaro Rossan Brandão Prieto da Silva ◽  
Irina Kerkis
Keyword(s):  
Molecular Mass ◽  
Tumor Cells ◽  
Large Scale ◽  
Time Lapse ◽  
Mass Spectrometry Analysis ◽  
Molecular Probe ◽  
Spastic Paralysis ◽  
Spectrometry Analysis ◽  
Hind Limbs ◽  
Wide Range

Crotamine is a highly cationic; cysteine rich, cross-linked, low molecular mass cell penetrating peptide (CPP) from the venom of the South American rattlesnake. Potential application of crotamine in biomedicine may require its large-scale purification. To overcome difficulties related with the purification of natural crotamine (nCrot) we aimed in the present study to synthesize and characterize a crotamine analog (sCrot) as well investigate its CPP activity. Mass spectrometry analysis demonstrates that sCrot and nCrot have equal molecular mass and biological function—the capacity to induce spastic paralysis in the hind limbs in mice. sCrot CPP activity was evaluated in a wide range of tumor and non-tumor cell tests performed at different time points. We demonstrate that sCrot-Cy3 showed distinct co-localization patterns with intracellular membranes inside the tumor and non-tumor cells. Time-lapse microscopy and quantification of sCrot-Cy3 fluorescence signalss in living tumor versus non-tumor cells revealed a significant statistical difference in the fluorescence intensity observed in tumor cells. These data suggest a possible use of sCrot as a molecular probe for tumor cells, as well as, for the selective delivery of anticancer molecules into these tumors.

scholarly journals Large-scale identification of protein histidine methylation in human cells

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Sebastian Kapell ◽  
Magnus E Jakobsson
Keyword(s):  
Large Scale ◽  
Human Cells ◽  
System Level ◽  
Mass Spectrometry Analysis ◽  
Regulatory Function ◽  
Lysine Methylation ◽  
Spectrometry Analysis ◽  
Arginine Residues ◽  
Sequence Requirements ◽  
Level Analysis

Abstract Methylation can occur on histidine, lysine and arginine residues in proteins and often serves a regulatory function. Histidine methylation has recently attracted attention through the discovery of the human histidine methyltransferase enzymes SETD3 and METTL9. There are currently no methods to enrich histidine methylated peptides for mass spectrometry analysis and large-scale studies of the modification are hitherto absent. Here, we query ultra-comprehensive human proteome datasets to generate a resource of histidine methylation sites. In HeLa cells alone, we report 299 histidine methylation sites as well as 895 lysine methylation events. We use this resource to explore the frequency, localization, targeted domains, protein types and sequence requirements of histidine methylation and benchmark all analyses to methylation events on lysine and arginine. Our results demonstrate that histidine methylation is widespread in human cells and tissues and that the modification is over-represented in regions of mono-spaced histidine repeats. We also report colocalization of the modification with functionally important phosphorylation sites and disease associated mutations to identify regions of likely regulatory and functional importance. Taken together, we here report a system level analysis of human histidine methylation and our results represent a comprehensive resource enabling targeted studies of individual histidine methylation events.

scholarly journals β-N-Acetylglucosamine (O-GlcNAc) Is a Novel Regulator of Mitosis-specific Phosphorylations on Histone H3

2012 ◽  
Vol 287 (15) ◽  
pp. 12195-12203 ◽  
Author(s):  
Jerry J. Fong ◽  
Brenda L. Nguyen ◽  
Robert Bridger ◽  
Estela E. Medrano ◽  
Lance Wells ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Cycle Progression ◽  
Histone H3 ◽  
Mass Spectrometry Analysis ◽  
Post Translational Modification ◽  
Cycle Progression ◽  
Spectrometry Analysis ◽  
Biochemical Assays ◽  
M Phase ◽  
Nucleocytoplasmic Proteins

O-Linked β-N-acetylglucosamine, or O-GlcNAc, is a dynamic post-translational modification that cycles on and off serine and threonine residues of nucleocytoplasmic proteins. The O-GlcNAc modification shares a complex relationship with phosphorylation, as both modifications are capable of mutually inhibiting the occupation of each other on the same or nearby amino acid residue. In addition to diabetes, cancer, and neurodegenerative diseases, O-GlcNAc appears to play a significant role in cell growth and cell cycle progression, although the precise mechanisms are still not well understood. A recent study also found that all four core nucleosomal histones (H2A, H2B, H3, and H4) are modified with O-GlcNAc, although no specific sites on H3 were reported. Here, we describe that histone H3, a protein highly phosphorylated during mitosis, is modified with O-GlcNAc. Several biochemical assays were used to validate that H3 is modified with O-GlcNAc. Mass spectrometry analysis identified threonine 32 as a novel O-GlcNAc site. O-GlcNAc was detected at higher levels on H3 during interphase than mitosis, which inversely correlated with phosphorylation. Furthermore, increased O-GlcNAcylation was observed to reduce mitosis-specific phosphorylation at serine 10, serine 28, and threonine 32. Finally, inhibiting OGA, the enzyme responsible for removing O-GlcNAc, hindered the transition from G2 to M phase of the cell cycle, displaying a phenotype similar to preventing mitosis-specific phosphorylation on H3. Taken together, these data indicate that O-GlcNAcylation regulates mitosis-specific phosphorylations on H3, providing a mechanistic switch that orchestrates the G2-M transition of the cell cycle.

Application of IOT (Internet of Things) Technology in Chemical Testing with Large-Scale Analysis Instruments

2014 ◽  
Vol 701-702 ◽  
pp. 475-479
Author(s):  
Hong Bo Chen ◽  
Yi Zheng ◽  
Yan Gang Han
Keyword(s):  
Large Scale ◽  
Mass Spectrometry Analysis ◽  
Testing System ◽  
Spectrometry Analysis ◽  
Whole Process ◽  
Large Scale Analysis ◽  
Intelligent Methods ◽  
Internet Of Things Technology ◽  
Chemical Testing ◽  
Standard Development

In the field of chemical testing, it is of great importance to improve the accuracy and efficiency and reduce the risk caused by artificial factor with modern intelligent methods, which are critical to the standard development of testing labs. In this paper, intelligent control during the whole process of chromatography and mass spectrometry analysis with cloud computing technology was realized and discussed in detail. The intelligent testing system could be applied to the chemical analysis labs and spread to other fields.

Prediction and collection of protein–metabolite interactions

2021 ◽  
Author(s):  
Tianyi Zhao ◽  
Jinxin Liu ◽  
Xi Zeng ◽  
Wei Wang ◽  
Sheng Li ◽  
...  
Keyword(s):  
Small Molecule ◽  
Protein Interactions ◽  
Large Scale ◽  
Rapid Development ◽  
Area Under The Curve ◽  
Membrane Receptors ◽  
Mass Spectrometry Analysis ◽  
Spectrometry Analysis ◽  
Cellular Processes ◽  
The Rich

Abstract Interactions between proteins and small molecule metabolites play vital roles in regulating protein functions and controlling various cellular processes. The activities of metabolic enzymes, transcription factors, transporters and membrane receptors can all be mediated through protein–metabolite interactions (PMIs). Compared with the rich knowledge of protein–protein interactions, little is known about PMIs. To the best of our knowledge, no existing database has been developed for collecting PMIs. The recent rapid development of large-scale mass spectrometry analysis of biomolecules has led to the discovery of large amounts of PMIs. Therefore, we developed the PMI-DB to provide a comprehensive and accurate resource of PMIs. A total of 49 785 entries were manually collected in the PMI-DB, corresponding to 23 small molecule metabolites, 9631 proteins and 4 species. Unlike other databases that only provide positive samples, the PMI-DB provides non-interaction between proteins and metabolites, which not only reduces the experimental cost for biological experimenters but also facilitates the construction of more accurate algorithms for researchers using machine learning. To show the convenience of the PMI-DB, we developed a deep learning-based method to predict PMIs in the PMI-DB and compared it with several methods. The experimental results show that the area under the curve and area under the precision-recall curve of our method are 0.88 and 0.95, respectively. Overall, the PMI-DB provides a user-friendly interface for browsing the biological functions of metabolites/proteins of interest, and experimental techniques for identifying PMIs in different species, which provides important support for furthering the understanding of cellular processes. The PMI-DB is freely accessible at http://easybioai.com/PMIDB.

scholarly journals Mass spectrometry analysis of newly emerging coronavirus HCoV-19 spike S protein and human ACE2 reveals camouflaging glycans and unique post-translational modifications

2020 ◽  
Author(s):  
Zeyu Sun ◽  
Keyi Ren ◽  
Xing Zhang ◽  
Jinghua Chen ◽  
Zhengyi Jiang ◽  
...  
Keyword(s):  
Structural Models ◽  
Mass Spectrometry Analysis ◽  
Post Translational Modification ◽  
Complex Type ◽  
Post Translational Modifications ◽  
S Protein ◽  
Spectrometry Analysis ◽  
Glycosylation Sites ◽  
Binding Surface ◽  
Structural Details

AbstractThe pneumonia-causing COVID-19 pandemia has prompt worldwide efforts to understand its biological and clinical traits of newly identified HCoV-19 virus. In this study, post-translational modification (PTM) of recombinant HCoV-19 S and hACE2 were characterized by LC-MSMS. We revealed that both proteins were highly decorated with specific proportions of N-glycan subtypes. Out of 21 possible glycosites in HCoV-19 S protein, 20 were confirmed completely occupied by N-glycans, with oligomannose glycans being the most abundant type. All 7 possible glycosylation sites in hACE2 were completely occupied mainly by complex type N-glycans. However, we showed that glycosylation did not directly contribute to the binding affinity between SARS-CoV spike protein and hACE2. Additionally, we also identified multiple sites methylated in both proteins, and multiple prolines in hACE2 were converted to hydroxylproline. Refined structural models were built by adding N-glycan and PTMs to recently published cryo-EM structure of the HCoV-19 S and hACE2 generated with glycosylation sites in the vicinity of binding surface. The PTM and glycan maps of both HCoV-19 S and hACE2 provide additional structural details to study mechanisms underlying host attachment, immune response mediated by S protein and hACE2, as well as knowledge to develop remedies and vaccines desperately needed nowadays.

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