Article
Plant Sciences
Yan Song, Shaoyang Liu, Haoxi Ben, Yuanming Zhang, Guangting Han, Arthur J. Ragauskas, Wei Jiang
Summary: Chemically deuterated cellulose fiber has limitations in mechanical properties and enzymatic degradation performance. However, it can promote bacterial growth and be quickly identified by near-infrared technique, potentially serving as anticounterfeiting materials.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Chemistry, Inorganic & Nuclear
Yifeng Guo, Zhe Zhuang, Yongguo Liu, Xuan Yang, Chen Tan, Xiaowen Zhao, Jiajing Tan
Summary: The recent increase in the use of deuterated compounds in pharmaceuticals has created a need for new synthetic tools to easily access D-containing building blocks. Aldehydes, as one of the most important chemical entities in organic synthesis, play a crucial role in assembling structurally diverse molecules. Recent efforts have focused on developing synthetic methods for C1-deuterated aldehydes, which expand and streamline approaches to versatile deuterated compounds. This article aims to provide a timely and comprehensive survey of this emerging topic, divided into four sections based on the synthetic tools used, with specific emphasis on reaction design, mechanistic pathway, and resulting new synthetic paradigms.
COORDINATION CHEMISTRY REVIEWS
(2022)
Article
Chemistry, Analytical
Joseph Anacleto, Cristina Lento, Vladimir Sarpe, Ayesha Maqsood, Banafsheh Mehrazma, David Schriemer, Derek J. Wilson
Summary: Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a rapidly growing technique that provides information about the dynamic structural changes in proteins during biological function. The continuous flow injection setup for time-resolved HDX-MS (CFI-TRESI-HDX) introduced in this work allows for automated, continuous or discrete labeling time measurements from milliseconds to hours, with substantially reduced runtimes compared to conventional systems.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Eric Largy, Matthieu Ranz
Summary: Hydrogen-deuterium exchange mass spectrometry (HDX/MS) is used for studying protein conformation dynamics and characterizing oligonucleotide conformations and their interactions with cations, small molecules, and proteins. OligoR is a web-based application that provides dedicated solutions for processing and visualizing native HDX/MS data of oligonucleotides. It offers a simple and robust approach to deconvoluting bimodal isotope distributions and can be extended to various analytes. The results are presented in interactive data tables and can be exported as publication-quality figures.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Ramin Ekhteiari Salmas, Antoni James Borysik
Summary: The quantification of hydrogen deuterium exchange (HDX) kinetics provides information on the stability of individual amino acids in proteins. The new programming tool HDXmodeller allows for optimization of low-resolution HDX-mass spectrometry (MS) data to understand exchange rates of individual amino acids. The tool also has a unique autovalidation method based on a covariance matrix for quantifying the accuracy of modeled exchange rates.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Jason M. Hogan, Peter S. Lee, Susan C. Wong, Sean M. West, Winse H. Morishige, Christine Bee, Gamze Camdere Tapia, Arvind Rajpal, Pavel Strop, Gavin Dollinger
Summary: This article presents a novel application of mass spectrometry-based carbene chemical footprinting for identification of antibody binding epitopes. The technique allows for high-resolution mapping of epitopes at the single-residue level and has been validated using X-ray crystallography and yeast surface display epitope mapping. The characterized epitopes provide important information for understanding competitive binding results and accelerating the drug discovery process.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Organic
Fei-Fei Sheng, Jian-Guo Gu, Kai-Hui Liu, Hong-Hai Zhang
Summary: This study presents a highly efficient and easily manipulated palladium-catalyzed H/D exchange protocol for the synthesis of beta-deuterated N-protected amino amides, which can be converted to beta-deuterated amino acids by removing protecting groups. The use of pivalic acid as an additive also promoted the successful deuterium labeling of phenylalanine derivatives.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Analytical
Josiah J. Rensner, Young Jin Lee
Summary: This study developed a highly efficient hydrogen-deuterium exchange technique for more accurate metabolite identification in MALDI-MS imaging, while retaining spatial information. By combining deuterium-labeled matrix and D2O vapor, an HDX efficiency of 73-85% was achieved. This method can systematically improve untargeted metabolite annotation through METASPACE annotation.
ANALYTICAL CHEMISTRY
(2022)
Review
Materials Science, Paper & Wood
Yan Song, Xianzhi Meng, Wei Jiang, Barbara R. Evans, Haoxi Ben, Yuanming Zhang, Yunqiao Pu, Sai Venkatesh Pingali, Brian H. Davison, Sai Zhang, Guangting Han, Arthur J. Ragauskas
Summary: Deuterated cellulose has significant applications in neutron scattering studies, providing insights into the structure and interactions of cellulose in plant cell walls.
Article
Biochemical Research Methods
Yoshitomo Hamuro, Stephen J. Coales
Summary: This note discusses the challenges and considerations of observing perturbation of a protein upon binding to a ligand with weak affinity using HDX-MS. The theoretical analysis suggests that the ratio of ligand concentration to dissociation constant can greatly impact the results of the experiment.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Jarrod J. Sandow, Iris Kl Tan, Alan S. Huang, Shashank Masaldan, Jonathan P. Bernardini, Ahmad Z. Wardak, Richard W. Birkinshaw, Robert L. Ninnis, Ziyan Liu, Destiny Dalseno, Daisy Lio, Giuseppi Infusini, Peter E. Czabotar, Andrew Webb, Grant Dewson
Summary: In this study, the dynamic structural mechanisms of BAK activation on a membrane were explored using HDX-MS. It was found that the BH4 domain maintains the inactive conformation of BAK, and the N-terminal region becomes disordered post-activation without affecting its membrane permeabilization. These findings provide new insights into the potential therapeutic targeting opportunities for BAK activation.
Article
Chemistry, Applied
Hannah J. Mckerchar, Cristina Lento, Rachel Z. Bennie, Jennifer M. Crowther, Fabian Dolamore, Jolon M. Dyer, Stefan Clerens, Davide Mercadante, Derek J. Wilson, Renwick C. J. Dobson
Summary: The properties of milk proteins vary between different mammalian species. This study focuses on comparing the dynamics of beta-lactoglobulin (β lg) proteins from goat and cow milk at different pH levels. The dimeric states of the cow β lg B variant homologue exhibit more conformational flexibility than the goat β lg at lower pH, as observed through hydrogen/deuterium exchange experiments and molecular dynamics simulations. Understanding these dynamic differences in β lg homologues is crucial for understanding the variations in milk processing, human digestion, and immunogenicity.
Article
Biochemistry & Molecular Biology
Edward A. Dennis
Summary: Lipids play important roles in chronic diseases, but defining the substrate specificity of lipid metabolism enzymes is challenging. This research focuses on how membranes interact with enzymes to regulate cell signaling and metabolic pathways. By using substrate lipidomics and molecular dynamics simulations, the study reveals the link between enzyme specificity and hydrophobic binding subsites for membrane phospholipid substrates.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Materials Science, Paper & Wood
Yan Song, Wei Jiang, Haoxi Ben, Yuanming Zhang, Guangting Han, Arthur J. Ragauskas
Summary: Preparation of deuterium incorporated cellulose is important for investigating cellulose internal structure and expanding its application fields. The study successfully prepared cellulosic cotton fibers with anti-rehydration deuterium incorporation and characterized the process using nuclear magnetic resonance and spectroscopy. The results showed that the hydrogen-deuterium exchange occurred preferentially in the amorphous cellulose component and increased treatment time led to higher deuterium incorporation. Additionally, the isotope effect did not affect the cellulose microstructure, crystalline index, or degree of polymerization properties significantly.
Article
Biochemical Research Methods
Yoshitomo Hamuro
Summary: In order to make a quantitative argument for a hydrogen/deuterium exchange-mass spectrometry (HDX-MS) experiment, optimization at different stages and extraction of relevant values from medium-resolution data is necessary, while being cautious of potential false results.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Qingbo Shu, Tanxi Cai, Xiulan Chen, Helen He Zhu, Peng Xue, Nali Zhu, Zhensheng Xie, Shasha Wei, Qing Zhang, Lili Niu, Wei-Qiang Gao, Fuquan Yang
JOURNAL OF PROTEOME RESEARCH
(2015)
Article
Biochemical Research Methods
Chengqian Zhang, Zilu Ye, Peng Xue, Qingbo Shu, Yue Zhou, Yanlong Ji, Ying Fu, Jifeng Wang, Fuquan Yang
JOURNAL OF PROTEOME RESEARCH
(2016)
Article
Biochemical Research Methods
Wei Zhang, Qingbo Shu, Zhen Zhao, Jia Fan, Christopher J. Lyon, Adrian M. Zelazny, Ye Hu
CLINICAL PROTEOMICS
(2018)
Article
Multidisciplinary Sciences
Linghai Li, Huina Zhang, Weiyi Wang, Yun Hong, Jifeng Wang, Shuyan Zhang, Shimeng Xu, Qingbo Shu, Juanfen Li, Fuquan Yang, Min Zheng, Zongjie Qian, Pingsheng Liu
SCIENTIFIC REPORTS
(2016)
Article
Biotechnology & Applied Microbiology
Zhiwu An, Qingbo Shu, Hao Lv, Lian Shu, Jifeng Wang, Fuquan Yang, Yan Fu
BIOMED RESEARCH INTERNATIONAL
(2018)
Article
Biochemical Research Methods
Patrick A. Kreitzberg, Marshall Bern, Qingbo Shu, Fuquan Yang, Oliver Serang
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Biochemical Research Methods
Qingbo Shu, Mengjie Li, Lian Shu, Zhiwu An, Jifeng Wang, Hao Lv, Ming Yang, Tanxi Cai, Tony Hu, Yan Fu, Fuquan Yang
MOLECULAR & CELLULAR PROTEOMICS
(2020)
Article
Microbiology
Qingbo Shu, Tara Kenny, Jia Fan, Christopher J. Lyon, Lisa H. Cazares, Tony Y. Hu
Summary: This study introduced six ebolavirus species, emphasizing the importance of species identification and viral burden quantification for timely and effective treatment. The authors developed an IP-MS assay for VP40 antigen detection and quantification, selecting specific regions of VP40 for antibody generation and successfully differentiating four EBV species using this assay.
Article
Chemistry, Multidisciplinary
Wenshu Zheng, Julian G. Saliba, Xiaojun Wei, Qingbo Shu, Lane M. Pierson, Liyan Mao, Chang Liu, Christopher J. Lyon, Chen-Zhong Li, William C. Wimley, Tony Ye Hu
Summary: Nanopore sensors have been widely used in nucleic acid detection and sequencing, and recent studies have shown their potential in distinguishing high purity peptide mixtures. However, their application in clinical settings is still limited due to the complexity of clinical specimens. In this study, we propose a method to select peptide biomarkers suitable for immunoprecipitation-coupled nanopore assay, and demonstrate its effectiveness in detecting and quantifying pathogen-derived peptides in human serum samples. This assay approach shows promise for diagnosing infectious and chronic diseases using peptide biomarkers.
Article
Biochemical Research Methods
Sudipa Maity, Meredith G. Mayer, Qingbo Shu, Hellmers Linh, Duran Bao, Robert Blair, Yanlin He, Christopher J. Lyon, Tony Y. Hu, Tracy Fischer, Jia Fan
Summary: Neurologic manifestations are common complications of COVID-19, but little is known about the neuropathogenesis of the disease. To understand its impact on the brain, researchers used mass-spectrometry-based proteomics to study cerebrospinal fluid (CSF) proteins from Rhesus Macaque and African Green Monkeys. The results showed significant differences between infected and uninfected monkeys, suggesting altered secretion of CNS factors in response to SARS-CoV-2-induced neuropathology. Dysregulated CSF proteins were found to be associated with neurodegenerative disorders, hemostasis, and innate immune responses, indicating their potential role in neuroinflammatory responses following COVID-19.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Meeting Abstract
Biochemical Research Methods
Qingbo Shu, Jia Fan, Christopher J. Lyon, Tony Hu
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Nanoscience & Nanotechnology
Qingbo Shu, Meena Rajagopal, Jia Fan, Lingpeng Zhan, Xiangxing Kong, Yifan He, Suwatchareeporn Rotcheewaphan, Christopher J. Lyon, Wei Sha, Adrian M. Zelazny, Tony Hu
Summary: Pulmonary disease arising from slow-growing mycobacterial infections is a growing concern in clinical practice. This study developed a novel immunoprecipitation-coupled mass spectrometry assay that can detect and distinguish specific mycobacterial infections, allowing for rapid disease diagnosis.
Article
Medicine, Research & Experimental
Qingbo Shu, Shan Liu, Tonino Alonzi, Sylvia M. LaCourse, Dhiraj Kumar Singh, Duran Bao, Dalton Wamalwa, Li Jiang, Christopher J. Lyon, Grace John-Stewart, Deepak Kaushal, Delia Goletti, Tony Hu
Summary: Using mass spectrometry (MS) to read immunoassays for biomarker-derived peptides can improve sensitivity and specificity, allowing for better identification of tuberculosis cases and differentiation between disease and asymptomatic infection. This approach shows strong potential for infectious disease diagnosis and monitoring changes in Mycobacterium tuberculosis burden for more effective disease control.
Meeting Abstract
Immunology
Daniel L. Moss, Kejing Song, Alanna G. Wanek, Qingbo Shu, Tony Hu, Jay K. Kolls, Ramgopal R. Mettu, Samuel J. Landry
JOURNAL OF IMMUNOLOGY
(2020)