Underlying Mechanisms of Chromatographic H/D, H/F, cis/trans and Isomerism Effects in GC-MS

Metabolites, Journal Year: 2025, Volume and Issue: 15(1), P. 43 - 43

Published: Jan. 11, 2025

Charge-free gaseous molecules labeled with deuterium 2H (D) atoms elute earlier than their protium-analogs 1H (H) from most stationary GC phases. This effect is known as the chromatographic H/D isotope (hdIEC) and can be calculated by dividing retention times (tR) of protiated (tR(H) ) to those deuterated (tR(D)) analytes: hdIEC = tR(H)/tR(D). Analytes 13C, 15N or 18O have almost identical lack a effect. Derivatives cis- trans-analytes such trans-fatty acids also differ in times. that contain trans-C=C-double bonds gas chromatography-mass spectrometry (GC-MS) cis-C=C-double containing congeners. The cis/trans-effect (ctEC) trans-analytes: ctEC tR(c)/tR(t). In present work, values endogenous exogenous substances were previously reported GC-MS analyses found range each between 1.0009 1.0400. examination suggests H/D-isotope effects cis/trans-effects observed are based on differences inter-molecular interaction strengths analyte derivatives phase columns. atoms, being larger H analytes, attenuate skeleton phase. angulation decreases phase, only parts close enough interact. Other caused hydrogen fluorine (F) stereo-isomerism considered similar mechanism due different orientation side chains.

Language: Английский

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PARPs and ADP-ribosylation-mediated biomolecular condensates: determinants, dynamics, and disease implications

Trends in Biochemical Sciences, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 1, 2025

Language: Английский

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RosettaHDX: Predicting antibody-antigen interaction from hydrogen-deuterium exchange mass spectrometry data

Journal of Structural Biology, Journal Year: 2025, Volume and Issue: 217(1), P. 108166 - 108166

Published: Jan. 5, 2025

Language: Английский

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Dissecting the properties of circulating IgG against streptococcal pathogens through a combined systems antigenomics-serology workflow

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Feb. 24, 2025

Abstract This study showcases an integrative mass spectrometry-based strategy combining systems antigenomics and serology to characterize human antibodies in clinical samples. involves using circulating plasma affinity-enrich antigenic proteins biochemically fractionated pools of bacterial proteins, followed by their identification quantification spectrometry. A selected subset the identified antigens is then expressed recombinantly isolate antigen-specific IgG, characterization structural functional properties these antibodies. We focused on Group streptococcus (GAS), a major pathogen lacking approved vaccine. The data shows that both healthy GAS-infected individuals have IgG against conserved streptococcal including toxins virulence factors. breadth remains relatively constant across but changes considerably GAS bacteremia. Moreover, analysis reveals individual variation titers, subclass distributions, Fc-signaling capacity, despite similar epitope Fc-glycosylation patterns. Finally, we show may cross-react with Streptococcus dysgalactiae (SD), occupies niches causes comparable infections. Collectively, our results highlight complexity GAS-specific antibody responses versatility methodology immune pathogens.

Language: Английский

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HRaDeX: R Package and Web Server for Computing High-Resolution Deuterium Uptake Rates for HDX–MS Data

Journal of Proteome Research, Journal Year: 2025, Volume and Issue: unknown

Published: March 19, 2025

Hydrogen–deuterium exchange monitored by mass spectrometry (HDX–MS) is a well-established and powerful technique used to study protein dynamics stability capturing local global unfolding events in structures. However, this technique, obtaining region-specific information requires proteolytic digestion that breaks the into peptide fragments, causing HDX data reflect averages over these fragments rather than individual amino acids. We propose new computational method provides deuterium uptake kinetic parameters with high resolution, considering trajectories of superimposed peptides. Our algorithm, HRaDeX, available as web server an R package capable processing from single-state comparative HDX–MS studies. Utilizing eight benchmark sets, we demonstrate HRaDeX reaches average root-mean-square error 7.15% reconstitution experimental normalized curves.

Language: Английский

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Unraveling the Atomistic Mechanisms of Temperature-Induced Destabilization in the PqsE-RhlR Complex of Pseudomonas aeruginosa at Mammalian Body Temperature through Classical Molecular Dynamics and Metadynamics.

Journal of Molecular Graphics and Modelling, Journal Year: 2024, Volume and Issue: 135, P. 108931 - 108931

Published: Dec. 24, 2024

Language: Английский

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