Review
Chemistry, Multidisciplinary
Abhijit Saha, Davide Bello, Alberto Fernandez-Tejada
Summary: This review extensively summarizes the recent progress in studying O-GlcNAcylation, highlighting the key aspects of O-GlcNAc enzymes, chemical methods, and functional consequences of the modification. Future research in this field is expected to provide novel chemical strategies and probes for molecular interrogation of O-GlcNAcylation, potentially leading to new mechanisms and therapeutic applications in human health.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Chemistry, Multidisciplinary
Eray Ulas Bozkurt, Irem Niran Cagil, Ebru Sahin Kehribar, Musa Efe Isilak, Urartu Ozgur Safak Seker
Summary: Protein glycosylation, a crucial post-translational modification, plays a fate-determining role and can alter protein properties. We engineered a Campylobacter jejuni N-linked glycosylation machinery to increase the glycosylation rate. By utilizing N-linked glycosylation, we glycosylated a model enzyme, alkaline phosphatase, and found that glycosylation dramatically improves its thermostability, proteolytic stability, tolerance to suboptimal pH, and denaturing conditions.
Article
Biochemistry & Molecular Biology
Alison G. Tebo, Benjamien Moeyaert, Marion Thauvin, Irene Carlon-Andres, Dorothea Boken, Michel Volovitch, Sergi Padilla-Parra, Peter Dedecker, Sophie Vriz, Arnaud Gautier
Summary: Spectrally separated fluorophores enable the observation of multiple targets in living cells simultaneously for a deeper understanding of cell functions. Engineered fluorogen-activating tags based on the FAST system offer orthogonality in recognition and spectral properties, allowing efficient multicolor imaging of proteins in live cells.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Analytical
James W. Dressman, Colin T. McDowell, Xiaowei Lu, Peggi M. Angel, Richard R. Drake, Anand S. Mehta
Summary: N-linked glycosylation plays a crucial role in immune response and cell-to-cell interactions. The current analytical techniques for studying immune cell N-glycosylation have limitations in throughput, structural information, starting materials, and cell purification. This study proposes a rapid antibody array-based approach coupled with MALDI-IMS for analyzing cellular N-glycosylation, which provides a valuable tool for glycoimmunology research and clinical applications.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Patrick M. Killoran, George S. M. Hanson, Sanne J. M. Verhoork, Madeleine Smith, Davide Del Gobbo, Lu-Yun Lian, Christopher R. Coxon
Summary: A method using 4-fluorophenylalanine as a reporter group for F-19 NMR was developed to measure the conformational status of peptidylprolyl bonds in peptide models. This method was applied to study the prolyl bond status in pentapeptide models of the intrinsically disordered region of alpha-synuclein. It was demonstrated that F-19 NMR is a valuable tool for studying proline isomerism under different conditions.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Developmental Biology
Daniel O'Hagan, Robin E. Kruger, Bin Gu, Amy Ralston
Summary: Two strategies for higher throughput production of endogenous protein reporters in mice were presented, utilizing split fluorescent protein mNeonGreen2 and in-frame knock-in of a relatively small protein tag, providing high efficiency and sensitivity for protein reporting, enabling broad downstream applications.
Article
Biochemical Research Methods
Xiaoyang Hou, Yu Wang, Dongbo Bu, Yaojun Wang, Shiwei Sun
Summary: N-linked glycosylation is a crucial protein modification involved in various biological processes. The EMNGly approach, which combines machine learning and deep learning, improves glycosylation site prediction accuracy and outperforms existing techniques.
Review
Biochemistry & Molecular Biology
Veronika Jedlickova, Shekoufeh Ebrahimi Naghani, Helene S. Robert
Summary: This review discusses various types of auxin reporters and biosensors used to monitor auxin distribution and signaling in plants, providing a history of each group and detailing their principles and applications.
Article
Multidisciplinary Sciences
Jodie Scache, Vincent Rigolot, Cedric Lion, Marlene Mortuaire, Tony Lefebvre, Christophe Biot, Anne-Sophie Vercoutter-Edouart
Summary: Sialylation of cell surface glycans is important for cell-cell interaction and communication with the microenvironment. A method called metabolic oligosaccharide engineering (MOE) can be used to study sialylation by incorporating unnatural monosaccharides into sialylated glycoconjugates and detecting them with a bioorthogonal ligation of a molecular probe. Among the bioorthogonal reactions, copper-catalyzed azide-alkyne cycloaddition (CuAAC) is the only ligation that allows both reactive tags to be switched on the chemical reporter or on the probe, making it a flexible and adaptable reaction. This study compared the efficiency of different chemical reporters in labeling sialoglycoproteins in human colon cell lines and found that switching the bioorthogonal tags greatly impacted the metabolic incorporation of the analogs. ManNAz was found to be the most versatile reporter for studying sialylation in these cells.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Thomas J. Kleist, I. Winnie Lin, Sophia Xu, Grigory Maksaev, Mayuri Sadoine, Elizabeth S. Haswell, Wolf B. Frommer, Michael M. Wudick
Summary: The interaction between physical forces and membrane proteins is crucial for environmental sensing and acclimation. We developed genetically encoded osmolality sensors by fusing fluorescent protein spectral variants to mechanosensitive ion channels. These sensors reported changes in osmolality through the emission ratio of fluorescent protein domains.
Article
Biochemical Research Methods
Vasilisa V. Krasitskaya, Maxim K. Efremov, Ludmila A. Frank
Summary: NanoLuc (NLuc) is a small-sized luciferase generated from Oplophorus gracilirostris with long-lasting bright bioluminescence triggered by furimazine. NLuc has been widely used as a reporter in various analytical systems. However, the fusion of NLuc with non-protein biospecific molecules has limitations, thus requiring chemical conjugation to produce biospecific luciferase derivatives. In this study, a combination of genetic engineering and chemical conjugation was used to obtain NLuc derivatives with activity comparable to intact NLuc.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Leonardo Barneschi, Emanuele Marsili, Laura Pedraza-Gonzalez, Daniele Padula, Luca De Vico, Danil Kaliakin, Alejandro Blanco-Gonzalez, Nicolas Ferre, Miquel Huix-Rotllant, Michael Filatov, Massimo Olivucci
Summary: In this study, quantum chemical models were used to investigate the fluorescence properties of a set of Archaerhodopsin reporters. It was found that the fluorescence intensity is directly proportional to the stability of an exotic excited-state diradical intermediate. This finding is significant for the search for novel fluorescent rhodopsin variants and the understanding of electrostatic changes that enhance light emission.
NATURE COMMUNICATIONS
(2022)
Article
Food Science & Technology
Shan-shan Wu, Wei Han, Yan-fen Cheng, Shao-jun Yun, Ming-chang Chang, Fei-er Cheng, Jin-ling Cao, Cui-ping Feng
Summary: This study investigated the effects of TGase-catalyzed glycosylation and cross-linking on the physicochemical and functional properties of Lentinus edodes protein fraction. The results showed that glycosylation and TGase-catalyzed glycosylation decreased certain properties but increased others. TGase-catalyzed glycosylation promoted the generation of cross-linked polymers and improved the processing characteristics of the Lentinula edodes protein fraction.
Article
Chemistry, Multidisciplinary
Yonglei Wu, Yijie Chen, Haolin Chen, Chenjie Yang, Xizhong Shen, Chunhui Deng, Nianrong Sun, Hao Wu
Summary: By analyzing serum N-glycan patterns of 50 Crohn's disease patients and 50 healthy controls, eight N-glycans with significant differences were identified for CD diagnosis. This research is expected to benefit future glycan-based disease detection beyond Crohn's disease.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Fei Ding, Shuangye Zhang, Qian Chen, Xiaodong Xie, Zhifeng Xi, Zhilei Ge, Xiaolei Zuo, Xiurong Yang, Itamar Willner, Chunhai Fan, Qian Li, Qiang Xia
Summary: This study presents a DNA-based programmable atom-like nanoparticle for urinalysis. Through rational spatial organization, these nanoparticles exhibit high stability in interaction with membrane proteins, enabling reverse assessment of protein expression levels.
ADVANCED MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Krysten A. Jones, David J. Li, Elliot Hui, Mark A. Sellmyer, Jennifer A. Prescher
ACS CHEMICAL BIOLOGY
(2015)
Article
Chemistry, Multidisciplinary
William B. Porterfield, Krysten A. Jones, David C. McCutcheon, Jennifer A. Prescher
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2015)
Article
Biochemistry & Molecular Biology
Rachel C. Steinhardt, Colin M. Rathbun, Brandon T. Krull, Jason M. Yu, Yuhang Yang, Brian D. Nguyen, Jake Kwon, David C. McCutcheon, Krysten A. Jones, Filipp Furche, Jennifer A. Prescher
Article
Immunology
Lidia A. Nazarova, Roxanna J. Ochoa, Krysten A. Jones, Naomi S. Morrissette, Jennifer A. Prescher
MICROBES AND INFECTION
(2016)
Article
Chemistry, Multidisciplinary
Krysten A. Jones, William B. Porterfield, Colin M. Rathbun, David C. McCutcheon, Miranda A. Paley, Jennifer A. Prescher
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2017)
Article
Chemistry, Multidisciplinary
Colin M. Rathbun, William B. Porterfield, Krysten A. Jones, Marian J. Sagoe, Monique R. Reyes, Christine T. Hua, Jennifer A. Prescher
ACS CENTRAL SCIENCE
(2017)
Article
Biochemistry & Molecular Biology
Brendan S. Zhang, Krysten A. Jones, David C. McCutcheon, Jennifer A. Prescher
Article
Hematology
Marsilio Adriani, Krysten A. Jones, Toru Uchiyama, Martha R. Kirby, Christopher Silvin, Stacie M. Anderson, Fabio Candotti
Article
Chemistry, Multidisciplinary
Brian F. Fisher, Harrison M. Snodgrass, Krysten A. Jones, Mary C. Andorfer, Jared C. Lewis
ACS CENTRAL SCIENCE
(2019)
Article
Multidisciplinary Sciences
Jerzy Osipiuk, Saara-Anne Azizi, Steve Dvorkin, Michael Endres, Robert Jedrzejczak, Krysten A. Jones, Soowon Kang, Rahul S. Kathayat, Youngchang Kim, Vladislav G. Lisnyak, Samantha L. Maki, Vlad Nicolaescu, Cooper A. Taylor, Christine Tesar, Yu-An Zhang, Zhiyao Zhou, Glenn Randall, Karolina Michalska, Scott A. Snyder, Bryan C. Dickinson, Andrzej Joachimiak
Summary: The study focused on papain-like protease (PLpro) as a potential target for antivirals against SARS-CoV-2, identifying inhibitors and their interactions with the enzyme. The findings demonstrate the potential for developing high-affinity inhibitors through structure-based drug design efforts targeting PLpro.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Nir Drayman, Jennifer K. DeMarco, Krysten A. Jones, Saara-Anne Azizi, Heather M. Froggatt, Kemin Tan, Natalia Ivanovna Maltseva, Siquan Chen, Vlad Nicolaescu, Steve Dvorkin, Kevin Furlong, Rahul S. Kathayat, Mason R. Firpo, Vincent Mastrodomenico, Emily A. Bruce, Madaline M. Schmidt, Robert Jedrzejczak, Miguel A. Munoz-Alia, Brooke Schuster, Vishnu Nair, Kyu-yeon Han, Amornrat O'Brien, Anastasia Tomatsidou, Bjoern Meyer, Marco Vignuzzi, Dominique Missiakas, Jason W. Botten, Christopher B. Brooke, Hyun Lee, Susan C. Baker, Bryan C. Mounce, Nicholas S. Heaton, William E. Severson, Kenneth E. Palmer, Bryan C. Dickinson, Andrzej Joachimiak, Glenn Randall, Savas Tay
Summary: This study identified a drug called masitinib that can inhibit the replication of both SARS-CoV-2 and OC43 virus, and acts by competitively inhibiting 3CLpro. The drug showed strong antiviral effects in in vivo experiments on mice infected with SARS-CoV-2, and was effective against multiple variants in vitro.
Article
Chemistry, Multidisciplinary
Krysten A. Jones, Harrison M. Snodgrass, Ketaki Belsare, Bryan C. Dickinson, Jared C. Lewis
Summary: Ligand-dependent biosensors have been developed to link enzymatic activity with the production of essential phage protein, enabling biocatalyst-dependent phage-assisted continuous evolution and selection. By combining phage-based evolution and library selection technologies, enzyme variants with improved and expanded catalytic properties have been successfully evolved. The genetic diversity resulting from a highly mutated PACS library is enriched for active enzyme variants with altered substrate scope, laying the foundation for engineering biocatalysts with novel substrate scope and reactivity.
ACS CENTRAL SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Simone Rauch, Krysten A. Jones, Bryan C. Dickinson
ACS CENTRAL SCIENCE
(2020)
Review
Nanoscience & Nanotechnology
Krysten A. Jones, Julia Zinkus-Boltz, Bryan C. Dickinson