Article
Biochemistry & Molecular Biology
Nikhil J. Pandya, Sonja Meier, Stefka Tyanova, Marco Terrigno, Congwei Wang, A. Mattijs Punt, E. J. Mientjes, Audrey Vautheny, Ben Distel, Thomas Kremer, Ype Elgersma, Ravi Jagasia
Summary: This study investigates the mechanisms and potential therapeutic options for Angelman syndrome. Proteomics analysis reveals changes in protein pathways during different stages of development in an AS mouse model. Restoring UBE3A expression is shown to reverse these changes and provide a promising treatment option. Additionally, a novel UBE3A substrate is discovered, and a protein database is created to support future research.
MOLECULAR PSYCHIATRY
(2022)
Article
Biochemistry & Molecular Biology
Marta L. Mendes, Gunnar Dittmar
Summary: The structure of the 26S proteasome, essential for protein degradation and maintaining cell homeostasis, has been successfully determined using cryo-electron microscopy, revealing at least seven different conformational states. The application of cross-linking mass spectrometry in integrative structural biology studies promises to answer more unanswered questions.
Article
Chemistry, Analytical
Beirong Zhang, Hang Gao, Zhou Gong, Lili Zhao, Bowen Zhong, Zhigang Sui, Zhen Liang, Yukui Zhang, Qun Zhao, Lihua Zhang
Summary: Chemical cross-linking coupled with mass spectrometry (XL-MS) is a crucial technique for the structural analysis of protein complexes. Photo-cross-linking, although heterogenous, is valuable for this analysis. In this study, a photo-cross-linking method using alkynyl-succinimidyl-diazirine (ASD) was demonstrated to enhance structure elucidation for proteins with less lysine and high flexibility. Additionally, enrichment approaches improved cross-link identification coverage. This method can be used for membrane proteome-wide complex analysis and significantly improves XL-MS in functional structure analysis.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Lars Kolbowski, Lutz Fischer, Juri Rappsilber
Summary: Cross-linking mass spectrometry is transitioning to enable structural systems biology, with MS3-based approaches for identifying cross-linked peptides showing potential despite MS2-based methods currently outperforming.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Nicole Strittmatter, Frances M. Richards, Alan M. Race, Stephanie Ling, Daniel Sutton, Anna Nilsson, Yann Wallez, Jennifer Barnes, Gareth Maglennon, Aarthi Gopinathan, Rebecca Brais, Edmond Wong, Maria Paola Serra, James Atkinson, Aaron Smith, Joanne Wilson, Gregory Hamm, Timothy Johnson, Charles R. Dunlop, Brajesh P. Kaistha, Josephine Bunch, Owen J. Sansom, Zoltan Takats, Per E. Andren, Alan Lau, Simon T. Barry, Richard J. A. Goodwin, Duncan Jodrell
Summary: Gemcitabine distribution and metabolism were assessed using a multimodal imaging approach, revealing that active metabolites primarily reached tumor cell compartments, while an ATR inhibitor targeted nonviable tumor regions.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Yuwan Chen, Wen Zhou, Yufei Xia, Weijie Zhang, Qun Zhao, Xinwei Li, Hang Gao, Zhen Liang, Guanghui Ma, Kaiguang Yang, Lihua Zhang, Yukui Zhang
Summary: Current methods for intracellular protein analysis often require the separation of specific organelles or changes to the intracellular environment. We demonstrate a method for in situ cross-linking and analysis of mitochondrial proteins in living cells. By delivering protein cross-linkers into mitochondria using poly(lactic-co-glycolic acid) (PLGA) nanoparticles functionalized with dimethyldioctadecylammonium bromide (DDAB), we identify novel protein-protein interactions and validate the data with structural analysis of mitochondrial respiratory chain proteins.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Fanindra Kumar Deshmukh, Gili Ben-Nissan, Maya A. Olshina, Maria G. Fuzesi-Levi, Caley Polkinghorn, Galina Arkind, Yegor Leushkin, Irit Fainer, Sarel J. Fleishman, Dan Tawfik, Michal Sharon
Summary: Controlled degradation of proteins is crucial for maintaining a healthy proteome. A family of proteins called Catalytic Core Regulators (CCRs) has been discovered to regulate the function of the 20S proteasome through an allosteric mechanism. The physical binding of the PSMB4 subunit attenuates the proteolytic activities of the proteasome. This finding sheds light on a novel allosteric pathway that can be targeted for developing selective 20S proteasome inhibitors and uncoupling the degradation pathways of 20S and 26S proteasomes.
NATURE COMMUNICATIONS
(2023)
Review
Medical Laboratory Technology
Amandine Amalric, Amandine Bastide, Aurore Attina, Armelle Choquet, Jerome Vialaret, Sylvain Lehmann, Alexandre David, Christophe Hirtz
Summary: Despite significant progress in targeted therapies, cancer recurrence remains a major cause of mortality worldwide. Identification of accurate biomarkers through molecular profiling in healthy and cancer patient samples can improve cancer diagnosis and advance personalized medicine.
CRITICAL REVIEWS IN CLINICAL LABORATORY SCIENCES
(2022)
Article
Oncology
Keshava K. Datta, Parthiban Periasamy, Sonali V. Mohan, Rebekah Ziegman, Harsha Gowda
Summary: The study identified mechanisms by which cancer cells adapt and survive in oxygen-poor environments, providing novel avenues for treatment. Cancer cells in hypoxic environments are resistant to chemotherapy and radiation, and identifying proteins and pathways regulating their survival could improve anticancer therapy efficacy. The study's proteomic profiling revealed metabolic reprogramming and novel phosphorylation changes, indicating potential vulnerabilities that can be targeted for therapeutic purposes.
Review
Biochemical Research Methods
Vilmos Kertesz, John F. Cahill
Summary: Mass spectrometry has become the primary tool for routine quantitative analysis of biomolecules, and is increasingly used to reveal the spatial distribution of proteins, metabolites, and pharmaceuticals in tissue. However, most spatially resolved MS measurements are qualitative due to potential biases. As demand for quantitative MS imaging and profiling data increases in pharmacological and clinical fields, various technologies now exist to provide different levels of spatial and quantitative information.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Brandon T. Ruotolo
Summary: Recent advancements have made it possible to comprehensively understand protein structure, oligomeric state, sequence, and modification status, providing new possibilities for treating human diseases. Mass spectrometry (MS) tools, especially those associated with ion mobility (IM) separation, have played a crucial role in this progress. However, the application of collision cross section (CCS) values in native proteomics still has limitations.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Multidisciplinary Sciences
Dusan Zivkovic, Angelique Sanchez Dafun, Thomas Menneteau, Adrien Schahl, Sandrine Lise, Christine Kervarrec, Ana Toste Rego, Paula C. A. da Fonseca, Matthieu Chavent, Charles Pineau, Odile Burlet-Schiltz, Julien Marcoux, Marie-Pierre Bousquet
Summary: During spermatogenesis, the proteasome plays a crucial role in regulating cell division processes. The s20S proteasome becomes highly active during meiosis, mainly through 19S activation and PA200 binding. The proteasome population shifts from c20S to s20S during differentiation, and s20S interacts with components of the meiotic synaptonemal complex. In vitro, s20S shows higher trypsin- and chymotrypsin-like activities and displays structural differences between alpha 4 and alpha 4s.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Analytical
Holly-May Lewis, Catia Costa, Veronique Dartois, Firat Kaya, Mark Chambers, Janella de Jesus, Vladimir Palitsin, Roger Webb, Melanie J. Bailey
Summary: This study combines elemental imaging and a new method for spatially resolved lipidomics to investigate the relationship between metals, drugs, and lipids in different areas of tissues. The method was applied to rabbit lung tissues with tuberculosis infection and demonstrated the association between ion accumulation, lipid profiles, and local drug distribution.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Haitang Zhang, Jianken Chen, Guifan Zeng, Xiaohong Wu, Junhao Wang, Jiyuan Xue, Yu-hao Hong, Yu Qiao, Shi-Gang Sun
Summary: Graphite anodes in practical applications often suffer from Li plating, causing capacity fade and safety hazards. This study monitored the secondary gas evolution behavior during Li plating process using OEMS, and detected the local microscale Li plating on graphite anode in situ for early safety warnings. The distribution of irreversible capacity loss under Li plating conditions was accurately quantified using TMS. The effect of typical VC/FEC additives on Li plating was recognized based on OEMS/TMS results, and it was found that these additives could reduce the loss of dead Li capacity.
Article
Chemistry, Organic
Terrence-Thang H. Nguyen, Connor J. O'Brien, Minh L. N. Tran, Steven H. Olson, Nicholas S. Settineri, Stanley B. Prusiner, Nick A. Paras, Jay Conrad
Summary: The development of a water-soluble iridium catalyst enables the trifluoromethylation of polar small molecules and peptides in DMSO solution or aqueous media, providing up to 60% CF3- peptide. This reaction was optimized in a microtiter plate format under ambient air, using commercial Langlois reagent as a CF3 radical source and blue LEDs for excitation.
Article
Biochemical Research Methods
Soumya Mukherjee, Andris Jankevics, Florian Busch, Markus Lubeck, Yang Zou, Gary Kruppa, Albert J. R. Heck, Richard A. Scheltema, Karli R. Reiding
Summary: Ion mobility enables spatial separation of ions in the gas phase, providing information about their size. The timsTOF Pro device can physically separate N-glycopeptides from nonmodified peptides and produce high-quality fragmentation spectra. This method allows for the effective selection of analytes of interest based on the clear cluster in the mobiologram formed by the glycan moieties enlarging the size of glycopeptides.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Biochemical Research Methods
Wouter van Bergen, Johannes F. Hevler, Wei Wu, Marc P. Baggelaar, Albert J. R. Heck
Summary: Most drugs target proteins, and determining the exact drug binding sites on proteins is crucial for understanding their effects. A strategy called PhosID-ABPP was developed to identify drug binding sites using immobilized metal-affinity chromatography and phosphonate affinity tags. This method successfully identified over 500 unique binding sites of the drug PF-06672131. PhosID-ABPP also revealed differences in binding sites between intact cells and cell lysates, and captured a previously elusive binding site on the epidermal growth factor receptor.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Cardiac & Cardiovascular Systems
Gunasekaran Subramaniam, Katharina Schleicher, Duangnapa Kovanich, Anna Zerio, Milda Folkmanaite, Ying-Chi Chao, Nicoletta C. Surdo, Andreas Koschinski, Jianshu Hu, Arjen Scholten, Albert J. R. Heck, Maria Ercu, Anastasiia Sholokh, Kyung Chan Park, Enno Klussmann, Viviana Meraviglia, Milena Bellin, Sara Zanivan, Svenja Hester, Shabaz Mohammed, Manuela Zaccolo
Summary: In this study, previously unrecognized cAMP nanodomains associated with beta-adrenergic stimulation were identified using an integrated phosphoproteomics approach and network analysis. The composition and function of one of these nanodomains were validated. The findings reveal a mechanism that explains the negative long-term clinical outcome observed in patients with heart failure treated with PDE3 inhibitors.
CIRCULATION RESEARCH
(2023)
Article
Biochemical Research Methods
Shelley Jager, Dario A. T. Cramer, Albert J. R. Heck
Summary: Alpha-1-antitrypsin (A1AT) has been suggested as a potential biomarker for distinguishing healthy and diseased individuals. However, the variability of the SERPINA1 gene in the general population may affect A1AT expression and serum protein levels, which are often overlooked in proteomics studies. This study found significant differences in allele-specific protein serum levels of A1AT among heterozygous donors, suggesting the importance of considering these factors when analyzing A1AT as a potential serum biomarker.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Anjusha Mathew, Frans Giskes, Alexandros Lekkas, Jean-Francois Greisch, Gert B. Eijkel, Ian G. M. Anthony, Kyle Fort, Albert J. R. Heck, Dimitris Papanastasiou, Alexander A. Makarov, Shane R. Ellis, Ron M. A. Heeren
Summary: We discuss the design, development, and evaluation of an Orbitrap/time-of-flight (TOF) mass spectrometry-based instrument with integrated UV photodissociation (UVPD) and time/mass-to-charge ratio (m/z)-resolved imaging for studying the higher-order molecular structure of macromolecular assemblies (MMAs). The instrument combines a bespoke TOF analyzer with an ultrahigh mass range hybrid quadrupole-Orbitrap MS. It employs a 193nm excimer laser for photofragmenting MMA ions and uses microchannel plates (MCPs)-Timepix (TPX) quad and MCPs-phosphorscreen-TPX3CAM assemblies as axial and orthogonal imaging detectors. The instrument can operate in four different modes to measure UVPD-generated fragment ions with high-mass resolution or image them in a mass-resolved manner to reveal the relative positions of the UVPD fragments post-dissociation. This information is crucial for understanding the molecular structure and dissociation dynamics of MMAs in the gas phase.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Medicine, Research & Experimental
Dario A. T. Cramer, Vojtech Franc, Anna-Katharina Heidenreich, Michaela Hook, Mahdi Adibzadeh, Dietmar Reusch, Albert J. R. Heck, Markus Haberger
Summary: This article focuses on the characterization of high molecular weight species (HMWs) in complex antibody formats, such as bispecifics, and their impact on activity. The study presents a multi-method approach for the identification, analysis, and understanding of HMW by-products, which is important for the development and evaluation of therapeutic bispecific antibodies.
Article
Biochemistry & Molecular Biology
Johannes F. Hevler, Pascal Albanese, Alfredo Cabrera-Orefice, Alisa Potter, Andris Jankevics, Jelena Misic, Richard A. Scheltema, Ulrich Brandt, Susanne Arnold, Albert J. R. Heck
Summary: The tricarboxylic acid cycle is a central pathway for energy production in eukaryotic cells and plays a key role in aerobic respiration across all life kingdoms. The 2-oxoglutarate dehydrogenase complex (OGDHC) is a crucial enzyme in this cycle, generating NADH by oxidatively decarboxylating 2-oxoglutarate to succinyl-CoA. We provide evidence that MRPS36 is an important component of eukaryotic OGDHC, supported by cross-linking mass spectrometry data and phylogenetic analyses. We propose that MRPS36 evolved as an E3 adaptor protein, functionally replacing the peripheral subunit-binding domain (PSBD) in eukaryotic E2o.
Article
Andrology
Min Zhang, Riccardo Zenezini Chiozzi, Elizabeth G. Bromfield, Albert J. R. Heck, J. Bernd Helms, Bart M. Gadella
Summary: This study aimed to identify the interacting partners of CRISP2. The interactions of these binding partners were investigated under different conditions. The results suggest that CRISP2 may act as a scaffold for protein complex formation and dissociation to ensure the correct positioning of proteins required for the acrosome reaction and zona pellucida penetration.
Article
Biology
Leire Aguinagalde Salazar, Maurits A. den Boer, Suzanne M. Castenmiller, Seline A. Zwarthoff, Carla de Haas, Piet C. Aerts, Frank J. Beurskens, Janine Schuurman, Albert J. R. Heck, Kok van Kessel, Suzan H. M. Rooijakkers
Summary: In this study, it is found that by modifying the structure of monoclonal antibodies (mAbs), the immune protection and bactericidal effect against Streptococcus pneumoniae can be improved. The modified mAbs effectively activate the complement system and recruit complement component C1 for bacterial clearance, enhancing the antibacterial activity against various serotypes of pneumococci. This study provides an important proof of concept for the future development of antibody therapies against encapsulated bacteria.
Article
Biotechnology & Applied Microbiology
Yen-Hsi Chen, Weihua Tian, Makiko Yasuda, Zilu Ye, Ming Song, Ulla Mandel, Claus Kristensen, Lorenzo Povolo, Andre R. A. Marques, Tomislav Caval, Albert J. R. Heck, Julio Lopes Sampaio, Ludger Johannes, Takahiro Tsukimura, Robert Desnick, Sergey Y. Y. Vakhrushev, Zhang Yang, Henrik Clausen
Summary: Currently available enzyme replacement therapies for lysosomal storage diseases are limited in their effectiveness due to short circulation times and suboptimal biodistribution of the therapeutic enzymes. Researchers have engineered Chinese hamster ovary (CHO) cells to produce glycoengineered enzymes, which have improved circulation time and biodistribution. This glycoengineering approach, known as Long-Acting-GlycoDesign (LAGD), may be widely applicable to lysosomal replacement enzymes to improve their circulatory stability and therapeutic efficacy.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Oncology
Beiping Miao, Zhaoqing Hu, Riccardo Mezzadra, Lotte Hoeijmakers, Astrid Fauster, Shangce Du, Zhi Yang, Melanie Sator-Schmitt, Helena Engel, Xueshen Li, Caroline Broderick, Guangzhi Jin, Raquel Gomez-Eerland, Lisette Rozeman, Xin Lei, Hitoshi Matsuo, Chen Yang, Ingrid Hofland, Dennis Peters, Annegien Broeks, Elke Laport, Annika Fitz, Xiyue Zhao, Mohamed A. A. Mahmoud, Xiujian Ma, Sandrine Sander, Hai-kun Liu, Guoliang Cui, Yu Gan, Wei Wu, Yanling Xiao, Albert J. R. Heck, Wenxian Guan, Scott W. Lowe, Hugo M. Horlings, Cun Wang, Thijn R. Brummelkamp, Christian U. Blank, Ton N. M. Schumacher, Chong Sun
Summary: The dysregulation of immune checkpoint molecules allows cancer cells to escape immune destruction. CD58, an important costimulatory ligand, is found to be positively regulated by CMTM6, which also interacts with PD-L1. The presence of CMTM6 and CD58 on tumor cells significantly affects T cell-tumor interactions and the response to PD-L1-PD-1 blockade.
Article
Biochemical Research Methods
Johannes F. Hevler, Albert J. R. Heck
Summary: Mitochondria, packed with proteins, play important roles in various cellular processes. While many mitochondrial protein complexes have been identified, some protein-protein interactions remain elusive. Cross-linking mass spectrometry (XL-MS) has proven to be a valuable tool for the in-depth characterization of these interactions. In this article, experimental strategies for the analysis of proteome-wide protein-protein interactions in mitochondria using XL-MS are highlighted, along with recent technological advances that can further enhance the in situ characterization of these interactions.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Oncology
Marjolein C. Stip, Mitchell Evers, Maaike Nederend, Chilam Chan, Karli R. Reiding, Mirjam J. Damen, Albert J. R. Heck, Sofia Koustoulidou, Ruud Ramakers, Gerard C. Krijger, Remmert de Roos, Edouard Souteyrand, Annelisa M. Cornel, Miranda P. Dierselhuis, Marco Jansen, Mark de Boer, Thomas Valerius, Geert van Tetering, Jeanette H. W. Leusen, Friederike Meyer-Wentrup
Summary: Researchers engineered an antibody called IgA3.0 ch14.18, which shows promise as a new therapy for neuroblastoma. The antibody has a longer half-life, increased protein stability, and potent tumor-killing abilities.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2023)
Article
Biochemistry & Molecular Biology
Inge Gazi, Karli R. Reiding, Andre Groeneveld, Jan Bastiaans, Thom Huppertz, Albert J. R. Heck
Summary: We monitored the changes in bovine milk IgG over a 28-day period after calving, finding that IgG accounts for over 50% of protein content in colostrum but less than 3% in mature milk. The N-glycosylation profile of bovine milk IgG was found to be highly heterogeneous with over 40 glycoforms, and this profile changed significantly during lactation. We also identified the presence of IgG3 subtype in bovine milk, alongside IgG1 and IgG2. These findings are important for understanding calf's immune development and the nutritional value of bovine milk.
Article
Immunology
Kelly A. Dingess, Max Hoek, Danique M. H. van Rijswijk, Sem Tamara, Maurits A. den Boer, Tim Veth, Mirjam J. A. Damen, Arjan Barendregt, Michelle Romijn, Hannah G. Juncker, Britt J. van Keulen, Gestur Vidarsson, Johannes B. van Goudoever, Albert Bondt, Albert J. R. Heck
Summary: The most abundant immunoglobulin in the human body is IgA and it is found in high concentrations in mucosal lining and biofluids like milk. The structure and clonal repertoire of IgA1-containing molecular assemblies were analyzed using mass spectrometry-based approach in serum and milk from three donors. The results showed that serum IgA1 consists of two distinct structural populations, monomeric IgA1 and dimeric J-chain coupled IgA1, while IgA1 in milk is present only as secretory IgA (SIgA) with various assemblies. The IgA1-Fab repertoires in serum and milk were also found to be different.
CELLULAR & MOLECULAR IMMUNOLOGY
(2023)