scholarly journals Unraveling the molecular basis of subunit specificity in P pilus assembly by mass spectrometry

2008 ◽  
Vol 105 (35) ◽  
pp. 12873-12878 ◽  
Author(s):  
R. J. Rose ◽  
D. Verger ◽  
T. Daviter ◽  
H. Remaut ◽  
E. Paci ◽  
...  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Gongyu Li ◽  
Kellen DeLaney ◽  
Lingjun Li

Abstract Despite extensive efforts on probing the mechanism of Alzheimer’s disease (AD) and enormous investments into AD drug development, the lack of effective disease-modifying therapeutics and the complexity of the AD pathogenesis process suggest a great need for further insights into alternative AD drug targets. Herein, we focus on the chiral effects of truncated amyloid beta (Aβ) and offer further structural and molecular evidence for epitope region-specific, chirality-regulated Aβ fragment self-assembly and its potential impact on receptor-recognition. A multidimensional ion mobility-mass spectrometry (IM-MS) analytical platform and in-solution kinetics analysis reveal the comprehensive structural and molecular basis for differential Aβ fragment chiral chemistry, including the differential and cooperative roles of chiral Aβ N-terminal and C-terminal fragments in receptor recognition. Our method is applicable to many other systems and the results may shed light on the potential development of novel AD therapeutic strategies based on targeting the D-isomerized Aβ, rather than natural L-Aβ.


Author(s):  
Rojeet Shrestha ◽  
Zhen Chen ◽  
Yusuke Miura ◽  
Yusuke Yamamoto ◽  
Toshihiro Sakurai ◽  
...  

Background Triglyceride-rich lipoproteins are considered to be independent predictors of atherosclerotic cardiovascular disease. The molecular basis of its atherogenicity is uncertain. Here, we aim to identify molecular species of phosphatidylcholine hydroperoxides (PCOOH) in triglyceride-rich lipoproteins. For comparison, copper-oxidized triglyceride-rich lipoproteins were investigated as well. Methods A fasting EDTA blood sample was collected from six healthy human volunteers to isolate two major triglyceride-rich lipoproteins fractions – very low-density lipoproteins (VLDL) and intermediate-density lipoproteins (IDL) using sequential ultracentrifugation. Triglyceride-rich lipoproteins and plasma samples were studied for PCOOH by liquid chromatography (LC) coupled with Orbitrap mass spectrometry. Results Twelve molecular species of PCOOH in triglyceride-rich lipoproteins and/or plasma were identified using the following criteria: (1) high-resolution mass spectrometry (MS) with mass accuracy within 5 ppm, (2) retention time in LC and (3) fragmentation pattern in MS2 and MS3. PC36:4-OOH was most often detected in VLDL, IDL and plasma. The ratio of total PCOOH to phosphatidylcholine progressively increased with the duration of oxidation in both VLDL and IDL. Conclusion This study demonstrated the presence of 12 molecular species of PCOOH in native triglyceride-rich lipoproteins. The frequent detection of PCOOH in triglyceride-rich lipoproteins provides a molecular basis of the atherogenicity of triglyceride-rich lipoproteins. PCOOH in triglyceride-rich lipoproteins might serve as a molecular basis of the atherogenicity of triglyceride-rich lipoproteins.


2021 ◽  
Vol 22 (22) ◽  
pp. 12584
Author(s):  
Alican Güran ◽  
Yanlong Ji ◽  
Pan Fang ◽  
Kuan-Ting Pan ◽  
Henning Urlaub ◽  
...  

β-adrenergic receptor (β-AR) stimulation represents a major mechanism of modulating cardiac output. In spite of its fundamental importance, its molecular basis on the level of cell signalling has not been characterised in detail yet. We employed mass spectrometry-based proteome and phosphoproteome analysis using SuperSILAC (spike-in stable isotope labelling by amino acids in cell culture) standardization to generate a comprehensive map of acute phosphoproteome changes in mice upon administration of isoprenaline (ISO), a synthetic β-AR agonist that targets both β1-AR and β2-AR subtypes. Our data describe 8597 quantitated phosphopeptides corresponding to 10,164 known and novel phospho-events from 2975 proteins. In total, 197 of these phospho-events showed significantly altered phosphorylation, indicating an intricate signalling network activated in response to β-AR stimulation. In addition, we unexpectedly detected significant cardiac expression and ISO-induced fragmentation of junctophilin-1, a junctophilin isoform hitherto only thought to be expressed in skeletal muscle. Data are available via ProteomeXchange with identifier PXD025569.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Christopher W. Davies ◽  
Simon E. Vidal ◽  
Lilian Phu ◽  
Jawahar Sudhamsu ◽  
Trent B. Hinkle ◽  
...  

AbstractThe ubiquitin conjugating enzyme UBE2W catalyzes non-canonical ubiquitination on the N-termini of proteins, although its substrate repertoire remains unclear. To identify endogenous N-terminally-ubiquitinated substrates, we discover four monoclonal antibodies that selectively recognize tryptic peptides with an N-terminal diglycine remnant, corresponding to sites of N-terminal ubiquitination. Importantly, these antibodies do not recognize isopeptide-linked diglycine (ubiquitin) modifications on lysine. We solve the structure of one such antibody bound to a Gly-Gly-Met peptide to reveal the molecular basis for its selective recognition. We use these antibodies in conjunction with mass spectrometry proteomics to map N-terminal ubiquitination sites on endogenous substrates of UBE2W. These substrates include UCHL1 and UCHL5, where N-terminal ubiquitination distinctly alters deubiquitinase (DUB) activity. This work describes an antibody toolkit for enrichment and global profiling of endogenous N-terminal ubiquitination sites, while revealing functionally relevant substrates of UBE2W.


PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5506 ◽  
Author(s):  
Michael Tessler ◽  
Jean P. Gaffney ◽  
Jason M. Crawford ◽  
Eric Trautman ◽  
Nehaben A. Gujarati ◽  
...  

Bioluminescent copepods are often the most abundant marine zooplankton and play critical roles in oceanic food webs. Metridia copepods exhibit particularly bright bioluminescence, and the molecular basis of their light production has just recently begun to be explored. Here we add to this body of work by transcriptomically profiling Metridia lucens, a common species found in temperate, northern, and southern latitudes. In this previously molecularly-uncharacterized species, we find the typical luciferase paralog gene set found in Metridia. More surprisingly, we recover noteworthy putative luciferase sequences that had not been described from Metridia species, indicating that bioluminescence produced by these copepods may be more complex than previously known. This includes another copepod luciferase, as well as one from a shrimp. Furthermore, feeding experiments using mass spectrometry and 13C labelled L-tyrosine and L-phenylalanine firmly establish that M. lucens produces its own coelenterazine luciferin rather than acquiring it through diet. This coelenterazine synthesis has only been directly confirmed in one other copepod species.


2018 ◽  
Vol 14 (5) ◽  
pp. 307-319 ◽  
Author(s):  
Benjamin C. Blum ◽  
Fatemeh Mousavi ◽  
Andrew Emili

Advances in instrumentation and analysis tools are permitting evermore comprehensive interrogation of diverse biomolecules and allowing investigators to move from linear signaling cascades to network models, which more accurately reflect the molecular basis of biological systems and processes.


2020 ◽  
pp. mcp.RA120.002168 ◽  
Author(s):  
Madison T Wright ◽  
Logan Kouba ◽  
Lars Plate

Thyroglobulin (Tg) is a secreted iodoglycoprotein serving as the precursor for T3 and T4 hormones. Many characterized Tg gene mutations produce secretion-defective variants resulting in congenital hypothyroidism (CH). Tg processing and secretion is controlled by extensive interactions with chaperone, trafficking, and degradation factors comprising the secretory proteostasis network. While dependencies on individual proteostasis network components are known, the integration of proteostasis pathways mediating Tg protein quality control and the molecular basis of mutant Tg misprocessing remain poorly understood. We employ a multiplexed quantitative affinity purification–mass spectrometry approach to define the Tg proteostasis interactome and changes between WT and several CH-variants. Mutant Tg processing is associated with common imbalances in proteostasis engagement including increased chaperoning, oxidative folding, and engagement by targeting factors for ER-associated degradation (ERAD). Furthermore, we reveal mutation-specific changes in engagement with N-glycosylation components, suggesting distinct requirements for one Tg variant on dual engagement of both oligosaccharyltransferase complex isoforms for degradation. Modulating dysregulated proteostasis components and pathways may serve as a therapeutic strategy to restore Tg secretion and thyroid hormone biosynthesis.


2017 ◽  
Vol 7 (1) ◽  
Author(s):  
William C. H. Chao ◽  
Benjamin O. Wade ◽  
Céline Bouchoux ◽  
Andrew W. Jones ◽  
Andrew G. Purkiss ◽  
...  

Abstract Sister-chromatid cohesion is established by Eco1-mediated acetylation on two conserved tandem lysines in the cohesin Smc3 subunit. However, the molecular basis of Eco1 substrate recognition and acetylation in cohesion is not fully understood. Here, we discover and rationalize the substrate specificity of Eco1 using mass spectrometry coupled with in-vitro acetylation assays and crystallography. Our structures of the X. laevis Eco2 (xEco2) bound to its primary and secondary Smc3 substrates demonstrate the plasticity of the substrate-binding site, which confers substrate specificity by concerted conformational changes of the central β hairpin and the C-terminal extension.


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