Review
Biochemical Research Methods
Xiaolu Li, Austin Gluth, Tong Zhang, Wei-Jun Qian
Summary: Redox post-translational modifications greatly impact protein structure and function, allowing for the regulation of biological processes. Redox proteomics approaches use mass spectrometry to study these modifications and have contributed to our understanding of redox signaling and regulation. Various strategies, including blocking free thiols and using selective reduction and enrichment techniques, are employed to analyze redox PTMs. This review discusses the principles and recent advances in redox proteomics and highlights its applications in generating novel biological insights.
Article
Biochemistry & Molecular Biology
Tong Zhang, Nicholas J. Day, Matthew Gaffrey, Karl K. Weitz, Kwame Attah, Patrice N. Mimche, Robert Paine, Wei-Jun Qian, My N. Helms
Summary: This study investigates the impact of high levels of oxygen on redox-dependent regulation in the lung, specifically focusing on the role of protein S-glutathionylation (SSG) in oxygen-induced lung injury. Through proteome-wide profiling, it was found that hyperoxia leads to significant alterations in SSG levels in various proteins. Additionally, overexpression of the beta-subunit of the epithelial sodium channel (Scnn1b) appears to protect against lung injury caused by hyperoxia. These findings highlight the importance of redox regulation in oxygen-induced lung injury and provide insights into potential protective mechanisms.
Article
Nanoscience & Nanotechnology
Pablo Martin-Baniandres, Wei-Hsuan Lan, Stephanie Board, Mercedes Romero-Ruiz, Sergi Garcia-Manyes, Yujia Qing, Hagan Bayley
Summary: Electro-osmosis in an anion-selective alpha-hemolysin nanopore is utilized for capturing, unfolding, and transporting polypeptides with more than 1,200 residues. By monitoring the ionic current at a single-molecule resolution, this method enables the mapping of post-translational modifications in polypeptide chains. The application of nanopore technology holds potential for identifying full-length proteoforms.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Ogonna Nwajiobi, Sriram Mahesh, Xavier Streety, Monika Raj
Summary: In this study, a chemical technology termed as STaR was used to selectively triazenation reaction of secondary amines using arene diazonium salts under biocompatible conditions, achieving highly selective, rapid, and robust tagging of Kme peptides. The efficient decoupling of the triazene-conjugate to afford unmodified starting components under mild conditions was highlighted, establishing a unique chemoselective bioconjugation strategy for the selective enrichment of Kme PTMs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Alexander W. Rookyard, Jana Paulech, Stine Thyssen, Kiersten A. Liddy, Max Puckeridge, Desmond K. Li, Melanie Y. White, Stuart J. Cordwell
Summary: This study investigated reversible and irreversible protein oxidation modifications during myocardial ischemia/reperfusion using mass spectrometry, identifying Cys as a major target for redox regulation associated with changes in cellular redox environment.
ANTIOXIDANTS & REDOX SIGNALING
(2021)
Article
Biochemistry & Molecular Biology
Daniel Salas-Lloret, Roman Gonzalez-Prieto
Summary: Ubiquitination and SUMOylation are dynamic post-translational modifications that regulate cellular processes. The understanding of these modifications has been increased by the development of mass spectrometry-based approaches. This translated article provides a concise overview of the basic mechanisms of ubiquitination and SUMOylation, as well as recent MS-based approaches for specific target identification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Rachel E. Lacoursiere, Dania Hadi, Gary S. Shaw
Summary: Ubiquitination is a complex process controlled by a series of enzymes. Recent studies have shown that these enzymes can be further modified through acetylation or phosphorylation, and alterations in these modifications have been observed in different diseases.
Review
Chemistry, Multidisciplinary
Lin-hui Zhai, Kai-feng Chen, Bing-bing Hao, Min-jia Tan
Summary: Protein post-translational modifications (PTMs) are crucial for protein activity regulation and are involved in diseases. PTM regulatory enzymes are important drug targets. Mass spectrometry-based proteomics enables systematic characterization of PTMs for drug target identification, mechanism elucidation and biomarker discovery in personalized therapy.
ACTA PHARMACOLOGICA SINICA
(2022)
Article
Biochemistry & Molecular Biology
Nicolas Campolo, Mauricio Mastrogiovanni, Michele Mariotti, Federico M. Issoglio, Dario Estrin, Per Hagglund, Tilman Grune, Michael J. Davies, Silvina Bartesaghi, Rafael Radi
Summary: Glutamine synthetase (GS) is an important enzyme that plays a crucial role in nitrogen metabolism. This study investigated the oxidative inactivation of human GS by peroxynitrite (ONOO-) in vitro. The results showed that ONOO- exposure led to a dose-dependent loss of GS activity and various oxidative modifications of the enzyme. Multiple tyrosine nitration sites and dityrosine cross-links were identified, but nitration of specific tyrosine residues alone was not responsible for enzyme inactivation. In addition, ONOO- induced GS aggregation and activity loss, with thiol oxidation being a key modification to elicit aggregation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Jiena Liu, Qin Wang, Yujuan Kang, Shouping Xu, Da Pang
Summary: Breast cancer is the most common malignant tumor in women worldwide, and post-translational modifications (PTMs) of proteins play important roles in tumorigenesis and progression. However, the study of non-histone modifications, particularly those other than phosphorylation, has been relatively limited. This review aims to explore the functions and impact of these PTMs in breast cancer, and emphasizes the importance of developing novel therapeutic drugs targeting PTMs and biological markers for breast cancer detection.
CELL AND BIOSCIENCE
(2022)
Review
Cell Biology
Rohan Gupta, Mehar Sahu, Devesh Srivastava, Swati Tiwari, Rashmi K. Ambasta, Pravir Kumar
Summary: Post-translational modifications play a crucial role in the pathogenesis of neurodegenerative diseases by regulating protein homeostasis and signaling cascades, leading to enhanced neuroprotection and potentially reversing misfolded protein accumulation.
AGEING RESEARCH REVIEWS
(2021)
Article
Biotechnology & Applied Microbiology
Ian C. C. Nova, Justas Ritmejeris, Henry Brinkerhoff, Theo J. R. Koenig, Jens H. H. Gundlach, Cees Dekker
Summary: Drawing peptides through a nanopore allows for the detection of individual phosphorylation sites; Current methods cannot measure single molecules or differentiate between closely spaced phosphorylation sites; We can detect cancer-associated post-translational modifications at the single-molecule level by controlling the peptide's movement through a nanopore; With individual reads of single molecules, we can discriminate peptide sequences with one or two closely spaced phosphates with 95% accuracy.
NATURE BIOTECHNOLOGY
(2023)
Review
Plant Sciences
Heng Zhou, Jingjing Huang, Patrick Willems, Frank Van Breusegem, Yanjie Xie
Summary: Reactive electrophilic species are widely present in plant cells and play a role in specific redox-regulated signaling events. Redox signaling is known to regulate gene expression during various biological processes, including plant growth, development, and stress responses. Recent data has shown that transcription factors are a major target of cysteine thiol-based oxidative post-translational modifications, which can affect their activity and transmit redox information to the nucleus. This review discusses the progress made in characterizing these modifications, their biochemical properties, and their effects on plant transcription factors, as well as the underlying mechanism of redox regulation and the challenges that remain in understanding the redox regulation of plant gene expression.
TRENDS IN PLANT SCIENCE
(2023)
Review
Biotechnology & Applied Microbiology
Ruiqin Zhang, Chenghao Cao, Jiahua Bi, Yanjun Li
Summary: This article systematically summarizes the issues of protein engineering and post-translational modifications of fungal cellulases, pointing out the current challenges and opportunities, providing reference for further improvement of cellulase properties.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Review
Multidisciplinary Sciences
Ji Min Lee, Henrik M. Hammaren, Mikhail M. Savitski, Sung Hee Baek
Summary: Post-translational modifications (PTMs) on specific amino acids control the stability of target proteins. These PTM-regulated degrons act as signals for protein degradation or stabilization. This review summarizes the current knowledge of PTM-mediated protein stability regulation to enhance the identification of novel drug targets.
NATURE COMMUNICATIONS
(2023)
Article
Critical Care Medicine
Geremy Clair, Lisa M. Bramer, Ravi Misra, Matthew D. McGraw, Soumyaroop Bhattacharya, Joseph A. Kitzmiller, Song Feng, Vincent G. Danna, Gautam Bandyopadhyay, Harsh Bhotika, Heidie L. Huyck, Gail H. Deutsch, Thomas J. Mariani, James P. Carson, Jeffrey A. Whitsett, Gloria S. Pryhuber, Joshua N. Adkins, Charles Ansong
Summary: This study provides a comprehensive analysis of the human lung proteome during development, revealing distinct molecular substages of alveolar development and evidence of post-transcriptional control in early postnatal development. The study also supports the extensive remodeling of the lung proteome during development and the concept of immune system maturation as an inherent part of normal lung development.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2022)
Review
Agricultural Engineering
Sivasamy Sethupathy, Garbriel Murillo Morales, Lu Gao, Hongliang Wang, Bin Yang, Jianxiong Jiang, Jianzhong Sun, Daochen Zhu
Summary: As an abundant aromatic biopolymer, lignin holds great potential for producing various chemicals and biofuels through biorefinery activities, contributing to a sustainable circular economy. However, lignin valorization faces challenges such as its heterogeneous nature, intrinsic recalcitrance, strong smell, dark color, difficulties in lignocellulosic fractionation, and high bond dissociation enthalpies in its functional groups. Despite these constraints, recent research and development have shown promising applications of lignin-based hydrogels, surfactants, 3D printing materials, electrodes, and fine chemicals production. This review summarizes the main limitations and possible solutions for industrial lignin valorization, and provides future perspectives based on its abundance and potential applications reported in scientific literature.
BIORESOURCE TECHNOLOGY
(2022)
Article
Green & Sustainable Science & Technology
Daochen Zhu, Majjid A. Qaria, Bin Zhu, Jianzhong Sun, Bin Yang
Summary: Lignin is a common and abundant aromatic biopolymer in nature. Due to its complexity and highly polymerized structure, normal microorganisms struggle to degrade lignin. Microbes from extreme environments that can degrade lignin are considered promising candidates for lignin bioprocessing. The heterogeneity of lignin depolymerization products poses challenges for refining and utilizing its potential. Various versatile lignin-degrading enzymes, including lignin peroxidase, laccase, manganese peroxidase, and others, are required for the complex lignin degradation pathways. Extremozymes isolated from extremophiles have shown superior performance in harsh conditions, making them promising for efficient degradation and utilization of lignin. However, studying extremophiles and their enzymes is more challenging due to their unique physiological characteristics and the lack of tailored molecular tools. Integrated transcriptomics, proteomics, and metabolomics analysis are expected to provide insights into lignin biotransformation. Furthermore, heterologous expression of extremophile genes in industrially relevant strains is necessary.
RENEWABLE & SUSTAINABLE ENERGY REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Jongmin Woo, Geremy C. Clair, Sarah M. Williams, Song Feng, Chia-Feng Tsai, Ronald J. Moore, William B. Chrisler, Richard D. Smith, Ryan T. Kelly, Ljiljana Pasa-Tolic, Charles Ansong, Ying Zhu
Summary: Single-cell proteomics (scProteomics) is a powerful tool for studying cell functions in complex biological systems. However, current methods face challenges in identifying and quantifying low-abundance proteins accurately. In this study, we present a method called transferring identification based on FAIMS filtering (TIFF), which combines ion mobility-enhanced mass spectrometry acquisition and peptide identification to improve the sensitivity and accuracy of label-free scProteomics. By filtering out singly charged ions, the TIFF method extends the ion accumulation times for peptide ions. Peptide identities are determined using a three-dimensional MS1 feature matching approach. Using TIFF, we achieved unbiased proteome analysis of over 1,700 proteins in single HeLa cells, with more than 1,100 proteins consistently identified. We also applied the TIFF method to study time-dependent proteome changes in single murine macrophage cells during lipopolysaccharide stimulation.
Article
Energy & Fuels
Zhibin Yang, Zhangyang Xu, Maoqi Feng, John R. Cort, Rafal Gieleciak, Joshua Heyne, Bin Yang
Summary: This study reports the development of a jet fuel blend component using a specific feedstock and chemical process. The blended fuel showed similar operability properties to conventional jet fuel, indicating its potential use as a sustainable aviation fuel.
Article
Biochemistry & Molecular Biology
Nicholas J. Day, Tong Zhang, Matthew J. Gaffrey, Rui Zhao, Thomas L. Fillmore, Ronald J. Moore, George G. Rodney, Wei-Jun Qian
Summary: This study reports a deep redox proteome profiling workflow and demonstrates its application in measuring the changes in thiol oxidation and global protein expression in skeletal muscle from mdx mice. The results show that mdx mice exhibit significantly increased thiol oxidation, particularly in the coagulation system and immune-related pathways, while protein abundance changes are more enriched in pathways associated with bioenergetics.
FREE RADICAL BIOLOGY AND MEDICINE
(2022)
Article
Chemistry, Analytical
Junho Park, Fengchao Yu, James M. Fulcher, Sarah M. Williams, Kristin Engbrecht, Ronald J. Moore, Geremy C. Clair, Vladislav Petyuk, Alexey I. Nesvizhskii, Ying Zhu
Summary: To overcome the issue of ratio compression in isobaric labeling-based multiplexed single-cell proteomics, we developed an improved MS3-based method using a linear ion trap. This method increased proteome coverage for single-cell-level peptides and was applied to study immune activation in single macrophages.
ANALYTICAL CHEMISTRY
(2023)
Review
Biotechnology & Applied Microbiology
Jian Fitria, Jian Liu, Bin Yang
Summary: Minerals in biomass have a significant impact on biofuel quality and yield, especially in current thermochemical biomass conversion processes. However, the roles of plant minerals in biochemical conversion have not been extensively studied, despite their known effect of reducing carbohydrate feedstock and sugar yield. This review discusses the challenges posed by plant minerals in a biorefinery, including decreased biomass quality, reduced process efficiency, and lower product quality and quantity from biomass conversion. It highlights the importance of strategically managing the occurrence of minerals in biomass to optimize biofuel production and support the concept of a circular bioeconomy.
BIOFUELS BIOPRODUCTS & BIOREFINING-BIOFPR
(2023)
Article
Biochemical Research Methods
Evan A. Martin, James M. Fulcher, Mowei Zhou, Matthew E. Monroe, Vladislav A. Petyuk
Summary: Top-down proteomics is a developing field that analyzes proteins in their intact form without proteolysis. However, limitations in instrumentation and data interpretation have hindered its progress. TopPICR is a companion R package that extends the capabilities of the popular proteoform identification tool, TopPIC, to label-free proteoform quantification. The pipeline includes several key steps, such as filtering identifications and compiling feature intensities, and the output is compatible with downstream data analysis packages from the Bioconductor project.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Panshak P. P. Dakup, Song Feng, Tujin Shi, Jon M. Jacobs, H. Steven Wiley, Wei-Jun Qian
Summary: Post-translational modifications (PTMs), especially phosphorylation, play a crucial role in regulating protein function. Traditional immunological assays often lack sensitivity and specificity for quantitative measurements of protein phosphorylation. Recent advances in Mass Spectrometry (MS)-based targeted proteomics, such as selected reaction monitoring (SRM) and parallel reaction monitoring (PRM), have greatly improved the accuracy and reliability of phosphoprotein quantification. This quantitative data can be used to build mathematical models of phospho-signaling pathways, providing valuable insights for better diagnosis and treatment of diseases.
Article
Multidisciplinary Sciences
Nathaniel J. Merrill, W. Sean Davidson, Yi He, Ivo Diaz Ludovico, Snigdha Sarkar, Madelyn R. Berger, Jason E. Mcdermott, Linda J. Van Eldik, Donna M. Wilcock, Matthew E. Monroe, Jennifer E. Kyle, Kimberley D. Bruce, Jay W. Heinecke, Tomas Vaisar, Jacob Raber, Joseph F. Quinn, John T. Melchior
Summary: Lipoproteins in cerebrospinal fluid (CSF) resemble plasma high-density lipoproteins (HDLs) and exhibit diverse subpopulations with unique protein combinations related to CNS health.
Meeting Abstract
Biochemical Research Methods
Chia-Feng Tsai, Yi-Ting Wang, Chuan-Chih Hsu, Reta B. Kitata, Rosalie K. Chu, Marija Velickovic, Rui Zhao, Sarai M. Williams, William B. Chrisler, Marda L. Jorgensen, Ronald J. Moore, Ying Zhu, Karin D. Rodland, Richard D. Smith, Clive H. Wasserfall, Tujin Shi, Tao Liu
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Chemistry, Multidisciplinary
Adarsh Kumar, Meenu Jindal, Shivam Rawat, Abhisek Sahoo, Rahul Verma, Devesh Chandra, Sagar Kumar, Bhaskar Thallada, Bin Yang
Summary: Research found that Ni5Co5-AC catalyst on activated carbon showed the best catalytic performance due to its distorted metal alloy spinel structure and optimum particle size, enhancing its catalytic efficiency.
Article
Biochemical Research Methods
Yumi Kwon, Paul D. Piehowski, Rui Zhao, Ryan L. Sontag, Ronald J. Moore, Kristin E. Burnum-Johnson, Richard D. Smith, Wei-Jun Qian, Ryan T. Kelly, Ying Zhu
Summary: Spatial proteomics holds great promise for revealing tissue heterogeneity, but current workflows require large sample amounts that may blur cell-type or microstructure-specific information. In this study, an improved sample preparation method was developed to enhance sample recovery and enable more precise protein analysis by integration with established techniques.
Article
Cell Biology
Michael A. Kochen, Steven S. Andrews, H. Steven Wiley, Song Feng, Herbert M. Sauro
Summary: This article discusses how signaling pathway modeling can assist in identifying effective drugs for treating diseases like cancer, and summarizes recent findings on phosphorylation cycles and regulatory motifs. Additionally, it highlights the urgent need for building scalable signaling network models that can accurately represent their complexity across different cell types and tumors.
CURRENT PATHOBIOLOGY REPORTS
(2022)