Article
Biochemical Research Methods
James R. Lloyd, Amy Hogan, Vasileios Paschalis, Jeddidiah Bellamy-Carter, Andrew Bottley, Graham B. Seymour, Christopher J. Hayes, Neil J. Oldham
Summary: Protein-ligand interactions are crucial for cell functionality, and carbene footprinting technique can provide valuable information about these interactions, such as binding sites and conformational changes. The application of carbene footprinting to the interaction between eIF4A helicase and hippuristanol has demonstrated the potential of this technique in studying protein-ligand interactions using labeling methods.
Article
Biochemical Research Methods
Yoko Ino, Yutaro Yamaoka, Kiho Tanaka, Kei Miyakawa, Mayuko Nishi, Yasuyoshi Hatayama, Hirokazu Kimura, Yayoi Kimura, Akihide Ryo
Summary: Peptide tag systems are widely used for protein detection and purification. We developed a novel tag system called HiP4 with a specific epitope sequence that overlaps with the conventional 6x histidine tag. By using this system, we developed a TAP-MS system for comprehensive protein interactome analysis, which showed low background and high selectivity in identifying novel protein interactions.
Article
Physics, Atomic, Molecular & Chemical
Xiaoyan Liu, He Zhu, Yanan Li, Hongqiang Qin, Mingliang Ye
Summary: In this study, a MALDI-TOF MS based approach was used for screening high-yield strains of recombinant proteins. By analyzing the affinity tag containing peptide released from host strains expressing target proteins, identification and quantification of strains could be achieved.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2022)
Article
Oncology
Madison T. Wright, Lars Plate
Summary: The endoplasmic reticulum (ER) plays a crucial role in processing the human proteome, with mass spectrometry technology being key in understanding protein quality control mechanisms. There are still unexplored areas in ER proteostasis where mass spectrometry can be utilized to expand our understanding of protein quality control processes in diverse diseases.
EXPERIMENTAL CELL RESEARCH
(2021)
Article
Biochemical Research Methods
Hauh-Jyun Candy Chen, Yan-Ling Liao
Summary: Although malondialdehyde and methylglyoxal have the same molecular formula, they have different chemistry in forming protein adducts. The major lysine adduct of malondialdehyde in hemoglobin is the N-propenal type, while that of methylglyoxal is N6-(1-carboxyethyl)lysine. This Letter provides evidence that the methylglyoxal-like hemoglobin adducts are not derived from malondialdehyde. This Letter also discusses the quantification of malondialdehyde-induced post-translational modifications in human hemoglobin by different mass spectrometry-based methods.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Alicia L. Richards, Manon Eckhardt, Nevan J. Krogan
Summary: Quantitative mass spectrometry (MS) techniques have enabled unbiased mapping of global changes in protein-protein interactions mediated by diseases, which can reveal disease mechanisms and identify new therapeutic targets.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Logan G. Johnson, Chaoyu Zhai, Edward M. Steadham, Leah M. Reever, Kenneth J. Prusa, Mahesh N. Nair, Elisabeth Huff-Lonergan, Steven M. Lonergan
Summary: The tenderness of fresh pork is closely related to postmortem proteolysis. This study used liquid chromatography and mass spectrometry to evaluate the differences in myofibrillar sub-proteome between pork chops with different tenderness values. The results showed that different tenderness values were associated with distinct myofibrillar sub-proteomes.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Biochemical Research Methods
Jorn Dietze, Alienke van Pijkeren, Anna-Sophia Egger, Mathias Ziegler, Marcel Kwiatkowski, Ines Heiland
Summary: Stable isotope labelling combined with high-resolution mass spectrometry is increasingly used for analyzing metabolite and protein modification dynamics. Correcting for naturally occurring stable isotopes, known as isotopologue correction, is crucial for accurately estimating these dynamics. While tools exist for isotopologue correction in mass spectrometry data, they are mainly tailored for low molecular weight metabolites, prompting the development of PICor for complex isotope labelling experiments in proteomics or metabolomics.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Mehar Un Nissa, Nevil Pinto, Arijit Mukherjee, Panga Jaipal Reddy, Biplab Ghosh, Zhi Sun, Saicharan Ghantasala, Chetanya Chetanya, Sanjyot Vinayak Shenoy, Robert L. Moritz, Mukunda Goswami, Sanjeeva Srivastava
Summary: Proteomic studies on Labeo rohita provided a comprehensive organ-based protein profiling, identifying a large number of proteins and global post-translational modifications. These findings offer important insights for basic and applied research in aquaculture field.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Clemens Schimek, Matthias Kubek, David Scheich, Mathias Fink, Cecile Brocard, Gerald Striedner, Monika Cserjan-Puschmann, Rainer Hahn
Summary: This research aimed to design a purification strategy for isolating and characterizing Fab antibody fragments and related impurities. By establishing a three-dimensional chromatography method and performing mass spectrometry analysis, four different Fab molecules were successfully characterized, facilitating strain selection and optimization of cultivation conditions.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Cell Biology
Devanarayanan Siva Sankar, Joern Dengjel
Summary: Autophagy is a crucial cellular degradation process that helps in maintaining cellular homeostasis through the clearance of damaged organelles and harmful substances. Protein-protein interaction networks play a key role in regulating autophagy, contributing to the degradation process and maintaining cellular function.
Article
Biochemical Research Methods
Klaas J. van Wijk, Tami Leppert, Zhi Sun, Eric W. Deutsch
Summary: A recent paper in Science Advances suggests that intrachloroplast proteins in Arabidopsis can be polyubiquitinated and transferred to the cytosol for degradation, challenging the existing belief that chloroplast organelles lack polyubiquitination mechanisms. However, a reanalysis of the raw mass spectrometry data revealed discrepancies and issues with the results, including extensive artifactual modifications caused by the use of alkylating agent iodoacetamide. As a result, the conclusions regarding intra-chloroplast polyubiquitination cannot be supported by these data. Recommendations for future research are provided to avoid similar pitfalls.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Asia Al-jabiry, Martin Palmer, James Langridge, Jeddidiah Bellamy-Carter, David Robinson, Neil J. Oldham
Summary: Native mass spectrometry is an important tool in structural biology, allowing researchers to study the nature of higher protein structure in the vacuum of the mass spectrometer. By combining protein chemical modification and CIU, the stabilising role of interactions in gas-phase protein structure can be elucidated.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Oncology
Francesca Piaggio, Michela Croce, Francesco Reggiani, Paola Monti, Cinzia Bernardi, Marianna Ambrosio, Barbara Banelli, Mehmet Dogrusoez, Ralf Jockers, Domenico Bordo, Roberto Puzone, Silvia Viaggi, Domenico Coviello, Francesco B. Lanza, Martina Bartolucci, Andrea Petretto, Carlo Mosci, Rosaria Gangemi, Pieter A. van der Velden, Martine J. Jager, Ulrich Pfeffer, Adriana Amaro
Summary: This study investigated the impact of GNAQ and GNA11 gene mutations on the characteristics and prognosis of uveal melanoma. The results showed that GNA11 mutation was associated with worse prognosis and high-risk cytogenetic, mutational, and molecular tumor characteristics. Additionally, G-proteins encoded by GNAQ and GNA11 had different protein interaction partners, and differential DNA methylation might contribute to different progression risks.
EUROPEAN JOURNAL OF CANCER
(2022)
Article
Chemistry, Multidisciplinary
Tobias Schmidt De Leon, Maria Laura Salum, Yasuyuki Matsushita, Kazuhiko Fukushima, Maria Eugenia Monge, Rosa Erra-Balsells
Summary: Cinnamic acid derivatives, specifically Z-sinapinic acid (ZSA), have been found to be more efficient in carbohydrate analysis in mass spectrometry. The formation of more stable complexes between ZSA and carbohydrates has been observed, providing insights into the matrix-analyte interaction model.
NEW JOURNAL OF CHEMISTRY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Laura L. Kiessling, Erin E. Carlson
ACS CHEMICAL BIOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Mohammad Murshid Alam, Cassie M. Jarvis, Robert Hincapie, Craig S. McKay, Jiri Schimer, Carlos A. Sanhueza, Ke Xu, Roger C. Diehl, M. G. Finn, Laura L. Kiessling
Summary: DC surface lectins recognize glycans not typically present on host tissue to facilitate antigen uptake and presentation. Signal transduction through DC-SIGN depends on the ligand displayed on the VLP, promoting DC maturation and induction of a T(H)1-type immune response.
Editorial Material
Biochemistry & Molecular Biology
Laura L. Kiessling
ACS CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Xiaowei Li, Tania M. Palhano Zanela, Eric S. Underbakke, Yan Zhao
Summary: This study introduces a method to precisely manipulate kinase phosphorylation using synthetic receptors, achieving selective phosphorylation of peptides. The inhibition can block the phosphorylation of specific sites while allowing phosphorylation at other sites, and the receptors can work individually or together to protect substrate sequences.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Jordan S. Ho, Amira Gharbi, Baptiste Schindler, Oznur Yeni, Richard Bredy, Laurent Legentil, Vincent Ferrieres, Laura L. Kiessling, Isabelle Compagnon
Summary: Sequencing glycans is challenging due to their structural diversity. In this study, researchers used infrared multiple photon dissociation spectroscopy with mass spectrometry to differentiate between pyranose- and furanose-linked galactose residues, offering a solution to distinguish between these isomers. By analyzing hexose ammonium adducts, the researchers determined diagnostic MS-IR signatures of galactose anomers in different forms, demonstrating the utility of MS-IR for analyzing unique substructures in bacterial glycans.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Christopher Agnew, Pelin Ayaz, Risa Kashima, Hanna S. Loving, Prajakta Ghatpande, Jennifer E. Kung, Eric S. Underbakke, Yibing Shan, David E. Shaw, Akiko Hata, Natalia Jura
Summary: This study reveals the importance of the heterodimeric complex formed by BMP receptors ALK2 and BMPR2 in ligand-induced receptor signaling. Furthermore, it demonstrates that the type I/type II kinase domain heterodimer serves as the scaffold for assembly of the active tetrameric receptor complexes, enabling phosphorylation of the GS domain and activation of SMADs.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Laura L. Kiessling, Roger C. Diehl
Summary: The text discusses how proteins recognize sugars through CH-π interactions, highlighting the importance of electron-rich aromatic residues in glycan binding.
ACS CHEMICAL BIOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Mia L. Huang, Laura L. Kiessling
ACS CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Victoria M. Marando, Daria E. Kim, Phillip J. Calabretta, Matthew B. Kraft, Bryan D. Bryson, Laura L. Kiessling
Summary: Researchers proposed a new strategy for chemoselective glycan modification utilizing cellular glycosyltransferases. They successfully synthesized and tested probes of D-arabinofuranose (D-Araf), which can selectively label arabinofuranose-containing glycans for the first time.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Editorial Material
Biochemical Research Methods
Amanda E. Dugan, Amanda L. Peiffer, Laura L. Kiessling
Summary: Interactions between carbohydrates and lectins play a key role in viral infection. Studying glycosylation has been challenging, but recent advancements in methods have allowed for atomic-level information about glycans on viruses and host cells.
Article
Biochemical Research Methods
Elad Deiss-Yehiely, Spencer D. Brucks, Natalie Boehnke, Andrew J. Pickering, Laura L. Kiessling, Paula T. Hammond
Summary: Targeted delivery of nanoparticle drug carriers is crucial for the development of nanomedicine. In this study, the authors investigated the association between modified nanoparticles and ovarian cancer cells using the well-characterized hyaluronic acid-CD44 binding pair. The results demonstrated that functionalizing nanoparticles with high molecular weight hyaluronic acid using the layer-by-layer adsorption method improved cell association.
BIOCONJUGATE CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Azin Saebi, Joseph S. Brown, Victoria M. Marando, Nina Hartrampf, Nicole M. Chumbler, Stephanie Hanna, Mackenzie Poskus, Andrei Loas, Laura L. Kiessling, Deborah T. Hung, Bradley L. Pentelute
Summary: The impermeable outer membrane of Pseudomonas aeruginosa can be bypassed by antibacterial proteins called S-type pyocins. Pyocins are investigated as a potential new class of antimicrobials against Pseudomonas infections due to their properties. In this study, a rapid production method for a pyocin S2 import domain was employed using automated fast-flow peptide synthesis, resulting in milligram quantities of the desired product. These synthetic pyocin domains can be used to understand the import mechanisms of P. aeruginosa and to develop selective antimicrobial agents that can bypass the outer membrane.
ACS CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tania M. Palhano Zanela, Alexzandrea Woudenberg, Karen G. Romero Bello, Eric S. Underbakke
Summary: Pyk2 is a non-receptor tyrosine kinase that undergoes multistage activation mechanism, involving conformational rearrangements, autophosphorylation, and Src recruitment. By employing hydrogen/deuterium exchange mass spectrometry and kinase activity profiling, the conformational dynamics associated with substrate binding and Src-mediated activation loop phosphorylation were mapped. The phosphorylation-induced rearrangements elevate kinase activity above the basal autophosphorylation rate.
Article
Biochemistry & Molecular Biology
Ting Jiang, Guanghua Wan, Haikun Zhang, Yadav Prasad Gyawali, Eric S. Underbakke, Changjian Feng
Summary: Nitric oxide synthase (NOS) is responsible for synthesizing nitric oxide (NO), a critical signaling molecule that regulates various physiological processes. This study investigates the regulatory dynamics of neuronal NOS (nNOS) using cross-linking mass spectrometry (XL MS), focusing on the effects of calmodulin (CaM) and NADP(+) on nNOS conformation. The results show that CaM induces global conformational changes, while NADP(+) primarily affects the NADPH-binding subdomain of nNOS. Furthermore, CaM increases the abundance of intra-nNOS cross-links related to inter-CaM-nNOS cross-links.
Article
Chemistry, Multidisciplinary
Katherine I. Taylor, Jordan S. Ho, Hallie O. Trial, Alan W. Carter, Laura L. Kiessling
Summary: Probes that covalently label protein targets are crucial for identifying ligand-binding sites. Squaramides, as mild electrophiles, exhibit higher selectivity for binding site lysine residues, making them promising for affinity-based chemoproteomic probes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
