Article
Chemistry, Multidisciplinary
Duong T. Bui, Zhixiong Li, Pavel I. Kitov, Ling Han, Elena N. Kitova, Marlene Fortier, Camille Fuselier, Philippine Granger Joly de Boissel, David Chatenet, Nicolas Doucet, Stephen M. Tompkins, Yves St-Pierre, Lara K. Mahal, John S. Klassen
Summary: Electrospray ionization mass spectrometry (ESI-MS) is a powerful label-free assay for detecting noncovalent biomolecular complexes and quantifying binding thermochemistry. However, the assumption that the ion signals of free and bound species in ESI-MS measurements can quantitatively reflect their relative concentrations is only valid when their response factors are similar.
ACS CENTRAL SCIENCE
(2022)
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, 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)
Review
Cardiac & Cardiovascular Systems
Jared S. Kushner, Guoxia Liu, Robyn J. Eisert, Gary A. Bradshaw, Geoffrey S. Pitt, J. Travis Hinson, Marian Kalocsay, Steven O. Marx
Summary: This review outlines the application of proximity proteomics in cardiovascular research, discussing its principles, concepts, and potential for future research.
CIRCULATION RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Suprama Datta, Da-Yuan Chen, Alexander H. Tavares, Tamara Reyes-Robles, Keun Ah Ryu, Nazimuddin Khan, Tyler J. Bechtel, Jayde M. Bertoch, Cory H. White, Daria J. Hazuda, Kalpit A. Vora, Erik C. Hett, Olugbeminiyi O. Fadeyi, Rob C. Oslund, Andrew Emili, Mohsan Saeed
Summary: Identifying virus-host interactions on the cell surface is crucial for understanding viral entry and pathogenesis. Researchers have developed a platform called ViraMap, which utilizes photocatalysis to study the molecular neighborhood of the SARS-CoV-2 spike protein on human cell surfaces. This study has revealed novel cell surface proteins that contribute to viral entry, providing valuable insights into SARS-CoV-2 infection.
CELL CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Sabine Wittig, Marcelo Ganzella, Marie Barth, Susann Kostmann, Dietmar Riedel, Angel Perez-Lara, Reinhard Jahn, Carla Schmidt
Summary: The protein interactions within synaptic vesicles are complex and can be categorized into specific modules or interactions caused by 'crowding'. Understanding these interactions provides insights into the composition and function of synaptic vesicles.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Rivkah Rogawski, Adi Rogel, Itai Bloch, Maayan Gal, Amnon Horovitz, Nir London, Michal Sharon
Summary: Researchers have developed a method based on native mass spectrometry for analyzing drug uptake and target engagement in cellular contexts. This approach utilizes direct MS for label-free studies of protein-drug binding in human cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Analytical
Martijn M. Vanduijn, Hendrik-Jan Brouwer, Pablo Sanz de la Torre, Jean-Pierre Chervet, Theo M. Luider
Summary: The research team reported an improved electrochemical method that achieves complete reduction of both intermolecular and intramolecular disulfide bridges in a set of monoclonal antibodies. The method utilizes an online electrochemical flow cell to provide information on the pairing of heavy and light chains in the antibodies. The complete reduction of intramolecular disulfide bridges is important for the intact mass of the antibody chain and the confirmation of the protein's amino acid sequence.
ANALYTICAL CHEMISTRY
(2022)
Review
Biochemical Research Methods
Wei Qin, Kelvin F. Cho, Peter E. Cavanagh, Alice Y. Ting
Summary: This article introduces the proximity labeling technology for studying and applying molecular interactions. By fusing baits with promiscuous enzymes, endogenous molecules interacting with them can be tagged and identified by mass spectrometry or nucleic acid sequencing. PL technology has been used to map protein-protein, protein-RNA, and protein-DNA interactions.
Article
Biochemistry & Molecular Biology
Mariela Gonzalez-Avendano, Simon Zuniga-Almonacid, Ian Silva, Boris Lavanderos, Felipe Robinson, Roberto Rosales-Rojas, Fabio Duran-Verdugo, Wendy Gonzalez, Monica Caceres, Oscar Cerda, Ariela Vergara-Jaque
Summary: The PPI-MASS web server provides an interactive platform for filtering protein sets based on biological features to identify protein-protein interactions with pharmacological potential. Users can manipulate filters to identify candidate proteins to establish physical contacts with a target protein, offering a powerful tool for the future design of associated therapies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Tara K. Bartolec, Xabier Vazquez-Campos, Alexander Norman, Clement Luong, Marcus Johnson, Richard J. Payne, Marc R. Wilkins, Joel P. Mackay, Jason K. K. Low
Summary: Significant advances in cryoelectron microscopy have expanded our ability to create structural models of proteins and protein complexes. Cross-linking mass spectrometry (XL-MS) is demonstrated to be a powerful tool for high-throughput experimental assessment of protein structures and interactions. The combination of XL-MS data with AlphaFold2 predictions offers opportunities to explore the structural proteome and interactome in depth.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
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)
Review
Biochemistry & Molecular Biology
Isabell Bludau
Summary: This article summarizes the advantages and limitations of mass spectrometry-based interactome screening methods, with a focus on the applicability of hypothesis-driven and discovery-driven data analysis concepts in large-scale protein-protein interaction studies. Hypothesis-driven complex- or network-centric analysis approaches are highlighted as promising strategies for comparative research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Oliver J. Hale, Helen J. Cooper
Summary: This study demonstrates a mass spectrometry analysis method for the direct analysis of intact oligomeric membrane proteins from tissue. By characterizing protein assembly directly from sheep eye lens sections without sample pre-treatment, our approach allows for simultaneous analysis of soluble protein assemblies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Plant Sciences
Silke von Horsten, Lars-Oliver Essen
Summary: Phytochrome activity is regulated not only by light but also by post-translational modifications such as phosphorylation. PAPP5 is a phosphatase responsible for the dephosphorylation of plant phytochromes, and its activation by arachidonic acid leads to conformational changes in the TPR region. Molecular dynamics analysis shows that a C-terminal motif in PAPP5 is associated with restricting the orientation of the TPR region relative to the catalytic PP2A domain when complexed with a phyB phosphopeptide. These findings suggest a high degree of conservation in the activation mode of PPP-type protein phosphatases between plants and mammals.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Khanh Vu Huu, Rene Zangl, Jan Hoffmann, Alicia Just, Nina Morgner
Summary: The study investigates the assembly process of F-1 complex from Acetobacterium woodii using laser induced liquid bead ion desorption mass spectrometry. The results indicate that nucleotide binding is crucial for in vitro assembly of F-1, while ATP hydrolysis is less critical. The study also proposes a model for the assembly pathway of a functional F-1 complex, correlating the results with activity measurements.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Jiangfeng Zhao, Nils Hellwig, Bardya Djahanschiri, Radhika Khera, Nina Morgner, Ingo Ebersberger, Jingkang Wang, Hartmut Michel
Summary: This study presents the results of phylogenetic and functional studies on the PACE family transporter PA2880 from Pseudomonas aeruginosa. It demonstrates that PA2880 mainly exists as a dimer in solution and its dimeric state is essential for its proper function. Furthermore, electrogenicity studies reveal that the chlorhexidine/H+ antiport process is electrogenic and the function of several highly conserved residues was investigated.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Herman K. H. Fung, Shelley Grimes, Alexis Huet, Robert L. Duda, Maria Chechik, Joseph Gault, Carol Robinson, Roger W. Hendrix, Paul J. Jardine, James F. Conway, Christoph G. Baumann, Alfred A. Antson
Summary: Many cellular processes rely on substrate rotation or translocation by a multi-subunit, ring-type NTPase. Researchers have reconstituted a cos packaging system and provided a detailed description of its biochemical and structural properties, revealing similarities and differences in its mechanism and regulation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Di Wu, Carol Robinson
Summary: Oligomerization and glycosylation play important roles in the stability and efficacy of therapeutic glycoproteins, but the interplay between these two attributes is often difficult to define. In this study, a native top-down mass spectrometry approach was used to assess the glycosylation status of therapeutic cytokine and hormone assemblies and to relate interfacial glycan occupancy to complex stability. The study found that interfacial O-glycan stabilizes tumor necrosis factor-alpha trimer, while interferon-beta 1a dimerization is independent of glycosylation. Furthermore, a unique distribution of N-glycans on the follicle-stimulating hormone alpha subunit was discovered, and the interfacial N-glycan was found to interact extensively with the beta subunit to regulate dimer assembly.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Marie-Theres Hutchison, Giovanni Bellomo, Alexey Cherepanov, Elke Stirnal, Boris Fuertig, Christian Richter, Verena Linhard, Elina Gurewitsch, Moreno Lelli, Nina Morgner, Thomas Schrader, Harald Schwalbe
Summary: This study investigates the aggregation process of A beta 42 protein, which is directly related to the pathogenesis of Alzheimer's disease. Real-time solution NMR spectroscopy is used to track the A beta 42 aggregation kinetics and analyze the impact of low-molecular-weight inhibitors. The findings reveal the differential effects of low-molecular-weight inhibitors on early-stage aggregation.
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
Chemistry, Multidisciplinary
Tarick J. El-Baba, Corinne A. Lutomski, Sean A. Burnap, Jani R. Bolla, Lindsay A. Baker, Andrew J. Baldwin, Weston B. Struwe, Carol V. Robinson
Summary: In this study, the impact of glycans on mediating ACE2 dimerization and interactions with Spike was investigated. The researchers found that glycans play a regulatory role in ACE2 dimerization and that positive cooperativity drives ACE2 to complex with multiple Spike trimers. These findings are important for developing strategies to neutralize the virus.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Correction
Biochemistry & Molecular Biology
Rei Matsuoka, Roman Fudim, Sukkyeong Jung, Chenou Zhang, Andre Bazzone, Yurie Chatzikyriakidou, Carol V. Robinson, Norimichi Nomura, So Iwata, Michael Landreh, Laura Orellana, Oliver Beckstein, David Drew
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Review
Pharmacology & Pharmacy
Hsin-Yung Yen, Ali Jazayeri, Carol Robinson
Summary: GPCRs are important drug targets due to their involvement in physiological processes. Mass spectrometry techniques, such as HDX-MS and native-MS, provide opportunities to investigate GPCR pharmacology and discover new drugs. This review highlights the potential of MS techniques for in-depth investigations of GPCR biology.
PHARMACOLOGICAL REVIEWS
(2023)
Article
Multidisciplinary Sciences
Benjamin J. Hardy, Alvaro Martin Hermosilla, Dinesh K. Chinthapalli, Carol V. Robinson, J. L. Ross Anderson, Paul Curnow
Summary: In this study, a minimal diheme membrane cytochrome was computationally designed and produced in live bacteria. The synthetic construct mimics a four-helix bundle found in respiratory complexes and has no sequence homology to natural polypeptides. This artificial membrane metalloprotein has the potential to function as an electron transfer module in both synthetic protocells and living systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Gabriela Dias Noske, Yun Song, Rafaela Sachetto Fernandes, Rod Chalk, Haitem Elmassoudi, Lizbe Koekemoer, C. David J. Owen, Tarick V. El-Baba, Carol Robinson, Glaucius Oliva, Andre Schutzer Godoy
Summary: The main protease of SARS-CoV-2, M-pro, is responsible for cleaving the viral polyprotein and is crucial for enzyme dimerization and activity. N-terminal cleavage is not critical for dimerization, and different types of inhibitors can affect the oligomeric states. This study provides insights into the maturation process of M-pro and how it can be targeted by inhibitors.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Kenneth R. R. Durbin, Matthew T. T. Robey, Lilien N. N. Voong, Ryan T. T. Fellers, Corinne A. A. Lutomski, Tarick J. J. El-Baba, Carol V. V. Robinson, Neil L. L. Kelleher
Summary: Native mass spectrometry has become an important technique for determining the composition of protein complexes. However, there is a lack of software tools for comprehensive analysis of native mass spectrometry data. In this study, we introduce ProSight Native as an informatics platform that can determine the complete composition of protein complexes. We demonstrated its features by successfully determining the composition of a homotetrameric membrane complex and a heterodimer complex with associated ligands.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Pamela Ornelas, Thomas Bausewein, Janosch Martin, Nina Morgner, Stephan Nussberger, Werner Kuehlbrandt
Summary: The TOM complex is the main entry point for precursor proteins into mitochondria. It consists of two beta-barrels, three receptor subunits, and three short transmembrane subunits. Tom20 acts as a dynamic gatekeeper guiding preproteins into the TOM complex.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Hongmiao Hu, Anne-Marie M. van Roon, George E. Ghanim, Bilal Ahsan, Abraham O. Oluwole, Sew-Yeu Peak-Chew, Carol V. Robinson, Thi Hoang Duong Nguyen
Summary: Shelterin and nucleosomes interact at mammalian telomeres, but the mechanism is not yet understood. Cryo-electron microscopy was used to study the structure of a human telomeric nucleosome bound to the shelterin factor TRF1. The study revealed that TRF1 binds to unwrapped nucleosomal DNA ends by engaging both the DNA and the histone octamer, resulting in a shift in the nucleosomal DNA. Phosphorylation of TRF1 and a noncanonical DNA binding surface on TRF1 were found to be crucial for its association with telomeric nucleosomes. These findings provide important insights into shelterin-chromatin interactions and its roles at telomeres.
Article
Multidisciplinary Sciences
Luke Smithers, Oksana Degtjarik, Dietmar Weichert, Chia-Ying Huang, Coilin Boland, Katherine Bowen, Abraham Oluwole, Corinne Lutomski, Carol V. Robinson, Eoin M. Scanlan, Meitian Wang, Vincent Olieric, Moran Shalev-Benami, Martin Caffrey
Summary: This study investigates the structural changes of the enzyme apolipoprotein N-acyltransferase (Lnt) during its reaction. The study confirms the ping-pong mechanism of Lnt and explains the molecular basis for its ability to bind different substrates.