Article
Biochemical Research Methods
Rebecca L. Cain, Ian K. Webb
Summary: Electrospray ionization mass spectrometry (ESI-MS) experiments were used to study the solution-like structures of intact proteins, specifically by controlling the protein unfolding process and analyzing folding intermediates. By mixing various pH solutions online with aqueous cytochrome C, the changes in charge states, arrival time distributions (ATDs), and electron capture dissociation (ECD) were measured to detect folding intermediates and unfolded protein structures.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Melanie Cheung See Kit, Ian K. Webb
Summary: Native mass spectrometry is an attractive method for studying protein structure due to its speed, sensitivity, and tolerance to heterogeneity. The use of different length noncovalent cross-linkers in gas-phase ion/ion chemistry allows for the determination of distance restraints and the identification of cross-linked sites. Molecular dynamics simulations reveal the kinetic trapping of multiple native-like solution structures in the gas phase.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Sarah N. Sipe, Emily B. Lancaster, Jamie P. Butalewicz, Christian P. Whitman, Jennifer S. Brodbelt
Summary: The recent discovery of asymmetric trimers in the tautomerase superfamily (TSF) adds structural diversity and reveals the higher stability of asymmetric trimers compared to symmetric ones. Utilizing native mass spectrometry and ultraviolet photodissociation allows for rapid and sensitive differentiation of symmetric and asymmetric trimers. The increased stability of asymmetric trimers may justify their evolution and concomitant diversification of the TSF, aiding in delineating the evolutionary history of the TSF.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Analytical
Kaoru Karasawa, Eva Duchoslav, Takashi Baba
Summary: Plasma electron detachment dissociation (EDD) is a novel electron-activated dissociation (EAD) method for the fast sequencing of oligonucleotides with a high sequence coverage. Phosphorothioate (PS) positions showed extremely high dissociation efficiency, while locked nucleotides were not suitable for EDD.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Muhammad A. Zenaidee, Benqian Wei, Carter Lantz, Hoi Ting Wu, Tyler R. Lambeth, Jolene K. Diedrich, Rachel R. Ogorzalek Loo, Ryan R. Julian, Joseph A. Loo
Summary: Analysis of internal fragments in TD-MS experiments can complement terminal fragments, increase protein sequence coverage, and enable more reliable localization of modification sites.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Jean-Claude Tabet, Yves Gimbert, Annelaure Damont, David Touboul, Francois Fenaille, Amina S. Woods
Summary: This research investigated the production spectra of [M + Na](+) from diterpene diester species and low molecular mass metabolites using electrospray ionization (ESI). The formation of protonated salt structures was proposed to explain observed neutral losses of carboxylic acids, providing insight into sodium retention mechanisms. Furthermore, unexpected consecutive carboxylic acid losses under resonant excitation conditions were shown to have an exothermic character based on quantum calculations. The formation and function of protonated salt structures are expected to aid in better understanding and software-assisted interpretation of tandem mass spectra from small molecules, particularly in the field of metabolomics.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Yinghua Qi, Xuewen Hu, Xiaojie Yang, Shanshan Jia, Hongying Zhong
Summary: A protonation/deprotonation mechanism has been established for interpreting ions in MALDI, showing that negative ions can be generated in different ways. Surface basicity of substrate materials determines the competition between electron-capture dissociation and deprotonation processes, impacting the generation of negative ions. Multiple electron transfers were observed on TiO2, while ZnO generated gaseous micelles composed of metal ions and fatty acid ions.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Irina D. D. Vasileva, Tatiana Yu. Samgina, Zhaowei Meng, Roman A. A. Zubarev, Albert T. T. Lebedev
Summary: In traditional proteomic analysis, disulfide bonds in peptides pose a problem for sequencing, requiring multiple reaction steps. However, this study found that EThcD technology can sequence peptides with disulfide bonds without the need for chemical derivatization.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Chemistry, Multidisciplinary
Conner C. Harper, Daniel D. Brauer, Matthew B. Francis, Evan R. Williams
Summary: This study used charge detection mass spectrometry to dynamically monitor the mass and charge of individual aqueous nanodrops in a size range relevant to gaseous macromolecular ion formation. The results showed the first direct observation of ion emission from aqueous nanodrops in late stages of droplet evaporation, which is important for understanding macromolecular ion formation.
Article
Chemistry, Analytical
Benjamin P. Zercher, Seoyeon Hong, Addison E. Roush, Yuan Feng, Matthew F. Bush
Summary: The kinetic stability of native-like protein ions in the gas phase was evaluated using time-dependent, tandem ion mobility experiments. Monomeric protein ions exhibited structural changes specific to protein and charge state, while large protein complexes did not show noticeable structural changes on the experimental time scales. Comparisons with energy-dependent experiments revealed that the structures observed in time-dependent experiments remained kinetically trapped and retained some memory of their solution-phase structure. These findings suggest that higher-mass protein ions can exhibit remarkable kinetic stability in the gas phase.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Niklas Geue, Tom S. Bennett, Alexandra-Ana-Maria Arama, Lennart A. I. Ramakers, George F. S. Whitehead, Grigore A. Timco, P. B. Armentrout, Eric J. L. McInnes, Neil A. Burton, Richard E. P. Winpenny, Perdita E. Barran
Summary: This study investigates the disassembly mechanisms and energetics of a series of heterometallic rings and ro-taxanes using ion mobility mass spectrometry and density functional theory. It shows that the stability of these complexes can be tuned by altering the metal composition and end groups.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Analytical
Marek Polak, Michael Palasser, Alan Kadek, Daniel Kavan, Christopher A. Wootton, Marc-Andre Delsuc, Kathrin Breuker, Petr Novak, Maria A. van Agthoven
Summary: Two-dimensional mass spectrometry (2D MS) is a multiplexed tandem mass spectrometry method that uses modulation of precursor ion radii to show the fragmentation patterns of analytes. This study introduces quadrupolar detection in 2D MS and discusses its advantages, as well as adapts existing data processing techniques for accurate frequency-to-mass conversion. The method is applied to the top-down analysis of covalently labeled ubiquitin and the label-free relative quantification of biomolecule isoforms.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Luis A. Macias, Jennifer S. Brodbelt
Summary: Disulfide bridges are post-translational modifications that impact the structure and function of proteins. Traditional collisional activation methods are not efficient in cleaving disulfide bonds, making it difficult to analyze proteins that incorporate this feature. Researchers have evaluated the fragmentation pathways enabled by 193 nm ultraviolet photodissociation and photodissociation coupled to electron transfer for the characterization of protein structures incorporating disulfide bonds.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Monika Kijewska, Dorota Gaszczyk, Remigiusz Bachor, Piotr Stefanowicz, Zbigniew Szewczuk
Summary: Peptide modification with a quaternary ammonium group containing a permanent positive charge increases ionization efficiency for ultra-sensitive detection. The effects of fixed-charge tag type and peptide sequence on fragmentation pathways were investigated, with aspartic acid playing a crucial role in collision-induced dissociation.
Article
Chemistry, Physical
Haley M. Schramm, Tomoya Tamadate, Christopher J. Hogan, Brian H. Clowers
Summary: This study investigates gas-phase ion-neutral reactions of peptides and reveals the link between gas-phase hydrogen/deuterium exchange and the probabilities of vapor association. The effects of additional charges and structural characteristics on the reactions are also examined.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
News Item
Chemistry, Multidisciplinary
Kathrin Breuker
Article
Chemistry, Analytical
Jovana Vusurovic, Kathrin Breuker
ANALYTICAL CHEMISTRY
(2019)
Article
Biophysics
Sebastian Fuehrer, Simone Trimmel, Kathrin Breuker, Martin Tollinger
BIOMOLECULAR NMR ASSIGNMENTS
(2019)
Article
Biochemistry & Molecular Biology
Markus Hartl, Stella Glasauer, Sabine Gufler, Andrea Raffeiner, Kane Puglisi, Kathrin Breuker, Klaus Bister, Bert Hobmayer
Article
Biochemistry & Molecular Biology
Elisabeth Fuchs, Christoph Falschlunger, Ronald Micura, Kathrin Breuker
NUCLEIC ACIDS RESEARCH
(2019)
Article
Chemistry, Multidisciplinary
Giovanni Calderisi, Heidelinde Glasner, Kathrin Breuker
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Chemistry, Analytical
Matthias Halper, Marc-Andre Delsuc, Kathrin Breuker, Maria A. van Agthoven
ANALYTICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Raphael Bereiter, Maximilian Himmelstoss, Eva Renard, Elisabeth Mairhofer, Michaela Egger, Kathrin Breuker, Christoph Kreutz, Eric Ennifar, Ronald Micura
Summary: The study comprehensively investigates the impact of deazapurine nucleosides on RNA properties, showing that they can significantly decrease thermodynamic stability of base pairing and enhance base pair opening dynamics. The findings by NMR and X-ray crystallography provide a rationale for the reduced pairing strength, marking a major step towards a comprehensive understanding of this important class of nucleoside modifications.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Marc-Andre Delsuc, Kathrin Breuker, Maria A. van Agthoven
Summary: Two-dimensional mass spectrometry (2D MS) is a tandem mass spectrometry method that correlates precursor and fragment ion signals by manipulating ion motions. Phase-corrected absorption mode 2D mass spectrometry improves signal-to-noise ratios and resolving power significantly, making data interpretation easier.
Article
Multidisciplinary Sciences
Laurin Flemmich, Sarah Heel, Sarah Moreno, Kathrin Breuker, Ronald Micura
Summary: Methylation is a common post-transcriptional modification in RNA, where methyltransferases and small organic substances are used as methyl-group donors. A direct link between a riboswitch and site-specific methylation has been uncovered, suggesting that nucleic acid-mediated methylation is an ancient mechanism.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Michael Palasser, Kathrin Breuker
Summary: High-resolution mass spectrometry was used to localize and quantify the modifications of a neomycin-sensing riboswitch aptamer domain. The data showed that the structure of the riboswitch in complex with aminoglycosides was different from that of the free RNA. This study demonstrates the importance of chemical probing and mass spectrometry in studying nucleic acid structures.
Article
Biochemistry & Molecular Biology
Julia Thaler, Egor A. Syroegin, Kathrin Breuker, Yury S. Polikanov, Ronald Micura
Summary: Hydrolysis-resistant RNA-peptide conjugates that mimic peptidyl-tRNAs are important for protein synthesis studies. In this study, a solution to the problem of generating N-formylmethionyl terminus in the conjugates was demonstrated. The structural integrity of the obtained conjugates was verified and their applicability for structural studies was confirmed. This approach opens new avenues for exploring ribosomal translation.
ACS CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Analytical
Marek Polak, Michael Palasser, Alan Kadek, Daniel Kavan, Christopher A. Wootton, Marc-Andre Delsuc, Kathrin Breuker, Petr Novak, Maria A. van Agthoven
Summary: Two-dimensional mass spectrometry (2D MS) is a multiplexed tandem mass spectrometry method that uses modulation of precursor ion radii to show the fragmentation patterns of analytes. This study introduces quadrupolar detection in 2D MS and discusses its advantages, as well as adapts existing data processing techniques for accurate frequency-to-mass conversion. The method is applied to the top-down analysis of covalently labeled ubiquitin and the label-free relative quantification of biomolecule isoforms.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Sarah Viola Heel, Karolina Bartosik, Fabian Juen, Christoph Kreutz, Ronald Micura, Kathrin Breuker
Summary: Understanding how ligands bind to ribonucleic acids (RNA) is crucial in studying RNA recognition and drug development. This study used mass spectrometry (MS) to investigate neomycin B binding to neomycin-sensing riboswitch aptamer constructs. The MS data revealed the binding site and ligand interactions, providing valuable insights for RNA recognition by aminoglycosides.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Eva-Maria Schneeberger, Matthias Halper, Michael Palasser, Sarah Viola Heel, Jovana Vusurovic, Raphael Plangger, Michael Juen, Christoph Kreutz, Kathrin Breuker
NATURE COMMUNICATIONS
(2020)