Article
Chemistry, Analytical
Na Wu, Lingyi Jiao, Matthias Butikofer, Zhihui Zeng, Renato Zenobi
Summary: This study successfully utilized commercially available purified proteins as internal standards for high-mass MALDI-MS analysis, achieving absolute quantification of various high-mass analytes. By systematically evaluating four sample deposition methods and using a sandwich deposition method with saturated sinapinic acid, robust quantitative analysis by high-mass MALDI-MS was performed. Furthermore, combining this quantitative strategy with chemical cross-linking allowed for evaluation of the affinity of protein-protein interactions, providing dissociation constants between 10 nM and 5 mu M for the protein complexes formed.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Sandra Martinez-Jarquin, Alina Begley, Yin-Hung Lai, Giovanni Luca Bartolomeo, Adam Pruska, Christian Rotach, Renato Zenobi
Summary: In this study, a paper-based platform was used for the upconcentration and analysis of small molecules from complex matrices. The aptapaper successfully enriched target analytes and allowed for their detection using mass spectrometry. The method showed high sensitivity and selectivity in the analysis of quinine and serotonin.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Laura Moracai, Sara Crotti, Pietro Traldi, Chiara Cosma, Annunziata Lapolla, Salvatore Pucciarelli, Marco Agostini
Summary: Researchers compared the interactions of Cu(I) and Cu(II) with amylin, finding differences in their structures. The Cu(I) complex with amylin exhibited unique structures, suggesting distinct interaction sites compared to the Cu(II) complex.
JOURNAL OF MASS SPECTROMETRY
(2021)
Article
Chemistry, Multidisciplinary
Yun Zhu, Samantha Schrecke, Shuli Tang, Melanie T. Odenkirk, Thomas Walker, Lauren Stover, Jixing Lyu, Tianqi Zhang, David Russell, Erin S. Baker, Xin Yan, Arthur Laganowsky
Summary: This study reveals the selective modulation of phosphatidylserine (PS) binding to TRAAK by cupric ions, while TREK2 is unaffected. Other ions have no impact on the binding of both channels. Additionally, TRAAK shows stronger binding with Cu2+ and Zn2+ compared to TREK2.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Adam Pruska, Adrien Marchand, Renato Zenobi
Summary: The study introduces a novel method using native mass spectrometry and a temperature-controlled nanoelectrospray ionization source to investigate interactions between proximal DNA domains. Results show changes in T-m and thermodynamic characteristics of proximal DNA domains depending on the number of domains, their position, and order in a single experiment.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Agriculture, Multidisciplinary
Haining Xu, Chunhua Dai, Yingxiu Tang, Xueting Xu, Ekene Christopher Umego, Ronghai He, Haile Ma
Summary: The study utilized ARTP mutagenesis technology to successfully increase the production of Surfactin in Bacillus subtilis, resulting in the mutant strain M45 with higher growth rate and yield. The findings provide a basis for industrial production of Surfactin and shed light on the mutagenesis mechanism.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2022)
Article
Chemistry, Analytical
Deseree J. Reid, Tapasyatanu Dash, Zhihan Wang, Craig A. Aspinwall, Michael T. Marty
Summary: Daptomycin is a cyclic lipopeptide antibiotic that interacts with lipid membranes in a non-specific manner. The interaction strength depends on membrane rigidity, with more rigid membranes showing stronger interactions. More fluid membranes may undergo pore formation to expose daptomycin to oxidation. These findings highlight the complementary use of native mass spectrometry, fast photochemical oxidation of peptides, and membrane conductance experiments in studying antibiotic-membrane interactions.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Debabrata Sengupta, Patrick Melix, Saptasree Bose, Joshua Duncan, Xingjie Wang, Mohammad Rasel Mian, Kent O. Kirlikovali, Faramarz Joodaki, Timur Islamoglu, Taner Yildirim, Randall Q. Snurr, Omar K. Farha
Summary: By synthesizing a new air-stable Cu(I)-based material called NU-2100, hydrogen can be stored at ambient temperatures. NU-2100 exhibits good hydrogen storage capability with a density of 10.4 g/L under ambient conditions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Di Wu, Manman Guo, Carol V. Robinson
Summary: Understanding the impact of genetic variations and post-translational modifications on protein interactions is made possible by using native mass spectrometry (MS). In this study, we characterized the proteoforms of plasma serine protease inhibitors and found that different fucosylation linkages have opposing effects on protein interactions.
Article
Biochemical Research Methods
Ghassan Al Hamoui Dit Banni, Rouba Nasreddine, Syntia Fayad, Cyril Colas, Axel Marchal, Reine Nehme
Summary: This study utilized MST technology to evaluate the binding affinities of lipases from crude porcine pancreatic extracts to triterpenoid compounds, successfully optimizing experimental conditions. Additionally, the enrichment of the 50 kDa lipase responsible for hydrolysis activity using ammonium sulfate precipitation was confirmed using capillary electrophoresis and HRMS. Complementary binding assays with catalytic activity ones are imperative for accurately explaining enzyme modulation mechanisms.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Dimitris Korovesis, Vanessa P. Gaspar, Hester A. Beard, Suyuan Chen, Rene P. Zahedi, Steven H. L. Verhelst
Summary: Photoaffinity labeling followed by tandem mass spectrometry is a commonly used strategy to identify protein targets and drug binding sites. However, it becomes challenging to identify distinct binding sites for bioactive peptides due to complex fragmentation patterns during tandem mass spectrometry. This study presents the development and application of small cleavable photoaffinity reagents that enable light-induced covalent binding and the identification of drug binding sites in bioactive peptides.
Article
Biochemical Research Methods
Tianyi Zhao, Jinxin Liu, Xi Zeng, Wei Wang, Sheng Li, Tianyi Zang, Jiajie Peng, Yang Yang
Summary: PMI-DB is a freely accessible, comprehensive and accurate resource of PMIs, providing non-interaction samples and supporting deep learning prediction of PMIs, which helps reduce experimental costs and facilitates the construction of more accurate algorithms.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Chemistry, Multidisciplinary
Qiongyu Li, Yixuan Xie, Rachel Rice, Emanual Maverakis, Carlito B. Lebrilla
Summary: Antigen-antibody proximity labeling (AAPL) is a novel method to map the antigen interaction sites as well as interactors of antibody-targeted proteins. Oxidative proteomic analysis can determine the degree of oxidation, the site of oxidation within the targeted antigen, and the interacting proteins that were in close proximity to the targeted antigen.
Article
Chemistry, Multidisciplinary
Nathan D. Donahue, Vinit Sheth, Alex N. Frickenstein, Alyssa Holden, Sandy Kanapilly, Chady Stephan, Stefan Wilhelm
Summary: We have developed a method for absolute quantification of nanoparticle interactions with individual human B cells. Our study demonstrates higher association of positively charged nanoparticles with single B cells compared to neutrally charged nanoparticles. By using dual analyte ICP-MS, we confirmed that a large percentage of single B cells internalized the nanoparticles. This unique workflow has significant implications for the rational design of nanomaterials for cellular interactions.
Article
Chemistry, Analytical
Deseree J. Reid, Tapasyatanu Dash, Zhihan Wang, Craig A. Aspinwall, Michael T. Marty
Summary: In this study, native mass spectrometry (MS) and fast photochemical oxidation of peptides (FPOP) were used to investigate the interactions between the antibiotic daptomycin and different lipid bilayer nanodiscs. The results showed that daptomycin incorporates randomly into bilayers and has stronger interactions with rigid membranes. Pore formation may occur in fluid membranes, exposing daptomycin to oxidation. These findings demonstrate the complementarity of native MS, FPOP, and membrane conductance experiments in understanding antibiotic peptide-membrane interactions.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Justin M. Bradley, Dimitri A. Svistunenko, Geoffrey R. Moore, Nick E. Le Brun
Article
Biochemistry & Molecular Biology
Laura J. Smith, Aleksandra Bochkareva, Matthew D. Rolfe, Debbie M. Hunt, Christina Kahramanoglou, Yvonne Braun, Angela Rodgers, Alix Blockley, Stephen Coade, Kathryn E. A. Lougheed, Nor Azian Hafneh, Sarah M. Glenn, Jason C. Crack, Nick E. Le Brun, Jose W. Saldanha, Vadim Makarov, Irene Nobeli, Kristine Arnvig, Galina V. Mukamolova, Roger S. Buxton, Jeffrey Green
NUCLEIC ACIDS RESEARCH
(2017)
Article
Plant Sciences
Emma L. Bastow, Katrine Bych, Jason C. Crack, Nick E. Le Brun, Janneke Balk
Article
Multidisciplinary Sciences
Bassam K. Kudhair, Andrea M. Hounslow, Matthew D. Rolfe, Jason C. Crack, Debbie M. Hunt, Roger S. Buxton, Laura J. Smith, Nick E. Le Brun, Michael P. Williamson, Jeffrey Green
NATURE COMMUNICATIONS
(2017)
Article
Biochemistry & Molecular Biology
Liang Zhou, Kristine L. Kay, Oliver Hecht, Geoffrey R. Moore, Nick E. Le Brun
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2018)
Article
Chemistry, Multidisciplinary
Jason C. Crack, Chris J. Hamilton, Nick E. Le Brun
CHEMICAL COMMUNICATIONS
(2018)
Article
Chemistry, Multidisciplinary
Stella A. Child, Justin M. Bradley, Tara L. Pukala, Dimitri A. Svistunenko, Nick E. Le Brun, Stephen G. Bell
Review
Biochemistry & Molecular Biology
Jason C. Crack, Nick E. Le Brun
ANTIOXIDANTS & REDOX SIGNALING
(2018)
Article
Chemistry, Multidisciplinary
Jason C. Crack, Nick E. Le Brun
CHEMISTRY-A EUROPEAN JOURNAL
(2019)
Article
Biochemistry & Molecular Biology
Kristine L. Kay, Chris J. Hamilton, Nick E. Le Brun
JOURNAL OF INORGANIC BIOCHEMISTRY
(2019)
Article
Chemistry, Multidisciplinary
Anne Volbeda, Ma Teresa Pellicer Martinez, Jason C. Crack, Patricia Amara, Oceane Gigarel, John T. Munnoch, Matthew I. Flutchings, Claudine Darnault, Nick E. Le Brun, Juan C. Fontecilla-Camps
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Article
Multidisciplinary Sciences
Justin M. Bradley, Dimitri A. Svistunenko, Jacob Pullin, Natalie Hill, Rhona K. Stuart, Brian Palenik, Michael T. Wilson, Andrew M. Hemmings, Geoffrey R. Moore, Nick E. Le Brun
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Salvatore Adinolfi, Rita Puglisi, Jason C. Crack, Clara Iannuzzi, Fabrizio Dal Piaz, Petr V. Konarev, Dmitri I. Svergun, Stephen Martin, Nick E. Le Brun, Annalisa Pastore
FRONTIERS IN MOLECULAR BIOSCIENCES
(2018)
Review
Biochemistry & Molecular Biology
Justin M. Bradley, Geoffrey R. Moore, Nick E. Le Brun
CURRENT OPINION IN CHEMICAL BIOLOGY
(2017)
Article
Chemistry, Multidisciplinary
Kristine L. Kay, Liang Zhou, Leonardo Tenori, Justin M. Bradley, Chloe Singleton, Margaret A. Kihlken, Simone Ciofi-Baffoni, Nick E. Le Brun
CHEMICAL COMMUNICATIONS
(2017)