Fc Profiling of Polyclonal IgG, IgA and IgM by Light Chain Capturing Coupled with NanoRP-LC-MS The proteoform profile of antibody Fc domains determines antibody effector functions, not only for biopharmaceuticals but also for endogenous antibodies. Endogenous immunoglobulin G (IgG) Fc-proteofor...

Fc Profiling of Polyclonal IgG, IgA and IgM by Light Chain Capturing Coupled with NanoRP-LC-MS #JACSAu pubs.acs.org/doi/10.1021/...

We are thrilled to share that final version of our work is now published in JACS Au doi.org/10.1021/jacs...
Congratulations @ashishchemist.bsky.social
@random-chemist.bsky.social @sohamchakraborty.bsky.social @catalyzer.bsky.social
Faraj, Tom & River
#JACSAu #Catalysis #OlefinCoupling

Accurate Quantification of 45N2O with a Membrane Inlet Mass Spectrometer by Optimizing the Temperature of a Cold Trap Membrane Inlet Mass Spectrometry (MIMS) is extensively applied in the study of nitrogen cycling processes. However, robust methods for the quantitative detection of N2O by this technique are still sca...

Accurate Quantification of 45N2O with a Membrane Inlet Mass Spectrometer by Optimizing the Temperature of a Cold Trap #JACSAu pubs.acs.org/doi/10.1021/...

Commonality of Mechanism in Glycoside Hydrolases, Nucleoside Hydrolases, and Phosphorylases: Importance of Side-Chain Conformation Preorganization A survey of the Protein Data Bank reveals that the arabinofuranosidase class of enzymes broadly restrict their substrate side chains to the gauche,gauche (gg) conformation that provides maximum electrostatic stabilization to oxocarbenium ion-like transition states and so employ the strategy reported previously for the majority of glycoside hydrolases, transglycosidases, and glycosyltransferases acting on pyranosyl substrates. The fructofuranosidases, ribonucleosidases, ribonucleoside phosphorylases, and nucleoside 2′-deoxyribosyltransferases, whose gg conformation is sterically hindered, restrict their substrate side chains to the next most positive charge-stabilizing gauche,trans (gt) conformation. These conclusions are supported by extensive literature studies on the mechanisms of C–N bond cleavage by members of the nucleosidase and nucleoside phosphorylase families and are discussed in terms of Warshel’s concept of the electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites.

Happy to share this latest work from the Crich group in #JACSAu, where we extend our studies on side chain conformational preorganization to encompass furanoside- and nucleoside-processing enzymes! @pubs.acs.org
pubs.acs.org/doi/10.1021/...

Check our latest publication in #JACSAu @ACSPublications with Elliot Chan and @bpsiyork.bsky.social, where we describe how the bacterial protein HU binds DNA at atomic resolution. Thanks to EPSRC for funds and @n8cir.bsky.social and hecbiosim for computational resources. pubs.acs.org/doi/10.1021/...

Graphic design with the text: 'Call for Papers. . JACS Au Open Access. . Continuous Flow Chemistry. . Submit your research'

#CallforPapers: Continuous Flow Chemistry

This #JACSAu Special Issue aims to showcase the multidisciplinary applications of continuous flow chemistry and provide a platform for the latest innovations in the field.

Submit your work by November 30, 2025!

Learn more on ACS Axial: buff.ly/lTWiPqu

From Solution to Gas Phase: Revealing Ligand-Dependent Conformations of Ribonuclease A with Tandem-Trapped Ion Mobility Spectrometry Protein activity depends on motional transitions between conformational states. Modifications or ligand binding can alter the protein dynamics, leading to changes in activity. Established biophysical methods effectively determine protein structures but face challenges when investigating dynamic biological processes that involve steady states of transiently populated conformations. Ion mobility/mass spectrometry shows promise for studying transient protein conformations but characterizes them in a solvent-free environment and does not directly provide detailed structural information. Here, we investigate to what extent subtly different conformational states are retained in their solvent-free environment. We investigate the conformations of unliganded ribonuclease A (RNase A) and RNase A bound to uracil-3′-monophosphate (3′-UMP) and adenosine-5′-monophosphate (5′-AMP) using our tandem-trapped ion mobility spectrometer/tandem mass spectrometer (Tandem-TIMS) in conjunction with molecular dynamics-based computational approaches. RNase A transitions between a closed and an open conformation on the millisecond time scale, with the closed conformation being favored when liganded. A comparison of our experimental and computational results indicates that both ligand-bound and unliganded RNase A maintain approximately 80% of their native contacts in a solvent-free environment. This includes interactions between the ligand and the protein, as well as the ligand’s position within the binding pocket. Furthermore, our experimental data reveal that when solvent-free RNase A is ligand-bound, it maintains a more compact structure, as observed in solution. Additionally, differences between the open and closed conformations─such as the positioning of Loop 1─are mostly preserved in the solvent-free state per our computational analysis, with root-mean-square deviations of about 2 Å. In summary, our findings demonstrate the ability of Tandem-TIMS to characterize subtle structural differences between steady-state protein conformations. This takes on increased significance due to the involvement of transient protein assemblies in cellular signaling and neurodegenerative diseases as well as “hidden” protein states underlying enzyme function that are not directly accessible using established methods.

From Solution to Gas Phase: Revealing Ligand-Dependent Conformations of Ribonuclease A with Tandem-Trapped Ion Mobility Spectrometry #JACSAu pubs.acs.org/doi/10.1021/...

LUXendin 492/551/555/615/645/651/762
Fluorescent Exendin4(9–39)

Visualize membrane #GLP1R in fixed/live cell & animals (retro-orbital or s.c. injection)
Also act as GLP1R antagonists

Are pancreatic Pericytes also labeled!?😍

#JACSAu 2022
pubs.acs.org/doi/10.1021/...

LA-ICP-TOFMS Imaging Reveals Significant Influence of Cancer Cell Resistance on Oxaliplatin Compartmentalization in the Tumor Microenvironment Chemoresistance in cancer cells, particularly in refractory types, such as colorectal cancer, poses a major challenge to effective treatment. In particular, the interaction between cancer cells and th...

LA-ICP-TOFMS Imaging Reveals Significant Influence of Cancer Cell Resistance on Oxaliplatin Compartmentalization in the Tumor Microenvironment #JACSAu pubs.acs.org/doi/10.1021/...

Developing a Cell Quenching Method to Facilitate Single Cell Mass Spectrometry Metabolomics Studies Single-cell mass spectrometry (SCMS) has emerged as a powerful tool for analyzing metabolites in individual cells, including live cells. However, cell metabolites have a rapid turnover rate, whereas maintaining metabolites’ profiles of live cells during sample transport, storage, or extended measurements can be challenging. In this study, a cell preparation method, which integrates cell washing by volatile salt solution, rapid liquid nitrogen (LN2) quenching, freeze-drying in vacuum, and freezer storage at −80 °C, to preserve cell metabolites for SCMS measurement is discussed. Experimental results revealed that LN2 quenching preserved the overall cell metabolome, whereas storage at −80 °C for 48 h slightly changed the metabolite profiles in quenched cells. However, metabolites in unquenched cells were changed regardless of low-temperature storage. The influence of omission of quenching and low-temperature storage on cell metabolites and relevant pathways were investigated. Results from this work indicate that cell quenching is necessary, but low-temperature storage time should be minimized to preserve cell metabolites. The method developed in the current work can be readily adopted by SCMS techniques with storage remaining largely unaltered, allowing for extended SCMS studies.

Developing a Cell Quenching Method to Facilitate Single Cell Mass Spectrometry Metabolomics Studies #JACSAu pubs.acs.org/doi/10.1021/...

A Workflow Enabling the Automated Synthesis, Chain-End Degradation, and Rapid Mass Spectrometry Analysis for Molecular Information Storage in Sequence-Defined Oligourethanes The field of molecular information storage has recently expanded to include abiotic sequence-defined polymers. While robust methods have been developed, there is a current bottleneck in the throughput of this work as information density is increased. Herein, we introduce an automated workflow in which a commercial peptide synthesizer composed of a single XYZ liquid-handling robot was adapted to both synthesize and sequence sequence-defined oligourethanes. Our sequencing method was improved to cut down the number of samples required for each oligomer from 13 to one. Additionally, we introduce the use of desorption electrospray ionization mass spectrometry as our analysis method for sequencing, which allowed for simplified and increased speed of data acquisition. Finally, we created a Python script that is able to reconstruct the sequence information from the MS data in an automated fashion. We demonstrate this new workflow by encoding and decoding a quote from the late Maya Angelou: “When you learn, teach, when you get, give”.

A Workflow Enabling the Automated Synthesis, Chain-End Degradation, and Rapid Mass Spectrometry Analysis for Molecular Information Storage in Sequence-Defined Oligourethanes #JACSAu pubs.acs.org/doi/10.1021/...

Decoding Protein Glycosylation by an Integrative Mass Spectrometry-Based De Novo Sequencing Strategy Glycoproteins, representing more than 50% of human proteins and most biopharmaceuticals, are crucial for regulating various biological processes. The complexity of multiple glycosylation sites often leads to incomplete sequence coverage and ambiguous glycan modification profiles. Here, we developed an integrative mass spectrometry-based approach for decoding unknown glycoproteins, which is featured with the combination of deglycosylation-mediated de novo sequencing with glycosylation site characterization. We utilized the enzymatic deglycosylation of N-/ O-glycans to achieve comprehensive sequence coverage. Additionally, EThcD fragmentation enables the identification of high-quality long peptides, facilitating precise protein assembly. We subsequently applied this method to de novo sequencing of the highly glycosylated therapeutic fusion protein Etanercept (Enbrel). We also sequenced three new tumor necrosis factor receptor:Fc-fusion biologics with largely unknown sequences, unveiling subtle distinctions in the primary sequences. Furthermore, we characterized N- and O-glycosylation modifications of these proteins at subunit, glycopeptide, and glycan levels. This strategy bridges the gap between the de novo sequencing and glycosylation modification, providing comprehensive information on the primary structure and glycosylation modifications for glycoproteins. Notably, our method could be a robust solution for accurate sequencing of the glycoproteins and has practical value not only in basic research but also in the biopharmaceutical industry.

Decoding Protein Glycosylation by an Integrative Mass Spectrometry-Based De Novo Sequencing Strateg #JACSAu pubs.acs.org/doi/10.1021/...

Engineered Receptor Capture Combined with Mass Spectrometry Enables High-Throughput Detection and Quantitation of SARS-CoV-2 Spike Protein Mass spectrometry (MS) is a potentially powerful approach for the diagnostic detection of SARS-CoV-2 and other viruses. However, MS detection is compromised when viral antigens are present at low conc...

Engineered Receptor Capture Combined with Mass Spectrometry Enables High-Throughput Detection and Quantitation of SARS-CoV-2 Spike Protein #JACSAu pubs.acs.org/doi/10.1021/...

A Systematic Approach to Discover New Natural Product Scaffolds Using Database-Derived Relative Mass Spectral Defects and Molecular Networking Rapid advances in mass spectrometry (MS) data analysis have accelerated the identification of natural products from complex mixtures such as natural product extracts. However, limitations in MS data in metabolite libraries and dereplication strategies are still lacking for assigning structures to known compounds and searching for unidentified compounds. To overcome these limitations, we present an approach that combines molecular networking with MS database-derived mass defect analysis to preferentially discover new compounds with high structural novelty in the initial stage of a discovery workflow. Specifically, unknown metabolites or clusters generated from molecular networking are assigned to a compound class based on their relative mass defects (RMDs) calculated using open-source databases. If ancillary data such as ultraviolet and MS/MS spectra of the unknown clusters are incongruent with the RMD-assigned compound class, metabolites are considered to have a new skeleton that exhibits a large difference in RMD value due to structural changes. Here, we applied this RMD-assisted method to a desert-derived bacterial strain library and validated it through the discovery of brasiliencin A (1), a new 18-membered macrolide from Nocardia brasiliensis. A putative biosynthetic pathway of brasiliencin A was proposed through whole-genome sequence analysis, and an additional 29 analogs were detected using absolute mass defect filtering (AMDF) based on plausible biosynthetic products. This led to the isolation of three additional macrolides, brasiliencins B–D (2–4). The structures of the brasiliencins (1–4) were fully elucidated through spectroscopic data analysis and quantum chemical calculations including ROE distance and 13C NMR chemical shift calculations, and experimental and theoretical electronic circular dichroism (ECD). Brasiliencin A showed strong activity against Mycobacterium smegmatis and Streptococcus australis (MIC = 31.3 nM and 7.81 μM, respectively) compared to brasiliencin B (MIC = 1000 nM and 62.5 μM, respectively) that differs at a single stereocenter.

A Systematic Approach to Discover New Natural Product Scaffolds Using Database-Derived Relative Mass Spectral Defects and Molecular Networking #JACSAu pubs.acs.org/doi/10.1021/...

New Opportunities to Access Fluorinated Molecules Using Organophotoredox Catalysis via C(sp3)–F Bond Cleavage Fluorinated molecules are of paramount importance because of their unique properties. As a result, the search for innovative approaches to the synthesis of this class of compounds has been relentless ...

Take a look at this great perspective now published in #JACSAu in @acs.org from the groups of Besset & Roy
doi.org/10.1021/jacs...
@cnrs.bsky.social

Native Mass Spectrometry Captures the Conformational Plasticity of Proteins with Low-Complexity Domains Disordered regions are an important functional feature of many multidomain proteins. A prime example is proteins in membraneless organelles, which contain folded domains that engage in specific intera...

Native Mass Spectrometry Captures the Conformational Plasticity of Proteins with Low-Complexity Domains #JACSAu pubs.acs.org/doi/10.1021/...

Congrats on this nice publication of Akkattu Biju now in @acs.org in #JACSAu on N-Heterocyclic-Carbene-Catalyzed Imine Umpolung for the Cross-Coupling of Quinoxalin-2-ones with Isatins
pubs.acs.org/doi/10.1021/...

Take a look at this excellent perspective of @wengeroliver.bsky.social and Björn Pfund on Excited Organic Radicals in Photoredox Catalysis, now available in @acs.org #JACSAu