Article
Biochemistry & Molecular Biology
Sarah E. Anderson, James E. Longbotham, Patrick T. O'Kane, Fatima S. Ugur, Danica Galonic Fujimori, Milan Mrksich
Summary: By using a new assay, the study explored the binding preferences of the PHD1 domain of histone demethylase KDMSA for H3 ligands, revealing tolerance for H3Q5 mutations and a high-affinity interaction with Q5-serotonylated H3. This work demonstrates the value of PI-SAMDI and fluorescence polarization in investigating protein-ligand binding.
ACS CHEMICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Che-Fan Huang, Cara J. Gottardi, Milan Mrksich
Summary: Phosphorylation plays a crucial role in cellular signaling, and dysregulation of phosphorylation can lead to diseases. However, while most studies focus on kinases, the role of phosphatases is often overlooked. This study demonstrates that basic amino acids adjacent to phosphotyrosines can restrict the activity of tyrosine phosphatases, providing insights into the mechanisms underlying disease-associated mutations and potential treatment strategies.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Qingwen Zhou, Yixuan Xie, Matthew Lam, Carlito B. Lebrilla
Summary: Glycomic profiling methods were used to study the effect of metabolic inhibitors on glycan production, with kifunensine being the most effective in converting nearly 95% of glycans to high mannose types. Other inhibitors also had an impact on glycan structures. Future research could utilize these inhibitors to investigate cellular behavior associated with alterations in glycosylation in various biological systems.
Article
Chemistry, Analytical
Laure Bar, Christophe Nguyen, Mathieu Galibert, Francisco Santos-Schneider, Gudrun Aldrian, Jerome Dejeu, Remy Lartia, Liliane Coche-Guerente, Franck Molina, Didier Boturyn
Summary: Antibodies are not only important for clinical diagnostics and biopharmaceutical analysis, but also as drugs for treating various diseases. The identification of antibody-epitope binding sites, particularly for designing monoclonal antibody mimics like rituximab, is crucial for medical and bioanalytical applications. Rituximab, a monoclonal antibody used to treat cancers and autoimmune disorders, binds to targeted cells via the recognition of the CD20 epitope, with its binding area located on the surface of rituximab.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Weiwei Tang, Jun-Jie Shi, Wei Liu, Xu Lu, Bin Li
Summary: A matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) assisted genome mining strategy was applied to discover a glycosyltransferase (GT) named PgGT1 from the root of Platycodon grandiflorum. PgGT1 was found to catalyze the synthesis of platycoside E (PE) by sequentially attaching two beta-1,6-linked glucosyl residues to the glucosyl residue at the C3 position of platycodin D (PD). The study also revealed the crucial roles of residues S273, E274, and H350 in stabilizing the sugar donor and positioning the glucose for optimal glycosylation. These findings provide insights into the biosynthetic pathway of PE and have potential implications in industrial biotransformation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Yuning Wang, Yu Liu, Shouzhi Yang, Jia Yi, Xiaoyu Xu, Kun Zhang, Baohong Liu, Kun Qian
Summary: A multifunctional self-assembled AuNPs array (MSANA)-based LDI-MS platform was developed for direct amino acids analysis and metabolic profiling in patient CSF samples. The platform demonstrated high selectivity and micromolar sensitivity for capturing and analyzing aromatic amino acids. It also exhibited excellent reproducibility (RSD < 10%) compared to the widely used direct matrix spotting approach (RSD < 44%). The platform was successfully used for metabolic profiling of CSF, enabling the discrimination of medulloblastoma patients from non-tumor controls within minutes. Overall, the MSANA-based LDI-MS platform shows potential clinical values for large-scale metabolic diagnostics and pathogenic mechanism study.
Article
Physics, Applied
Carlos Sebastian-Vicente, Pablo Remacha-Sanz, Eva Elizechea-Lopez, Angel Garcia-Cabanes, Mercedes Carrascosa
Summary: Photovoltaic optoelectronic tweezers are proven to be an efficient tool for manipulation and assembly of micro/nano-objects, relying on strong electric fields produced by certain ferroelectric materials. Research efforts are focused on the fabrication of combinatorial structures made up of multiple types of particles, with three different methods established to tackle this challenge successfully.
APPLIED PHYSICS LETTERS
(2022)
Article
Nanoscience & Nanotechnology
Yuning Wang, Kun Zhang, Tongtong Tian, Weilong Shan, Liang Qiao, Baohong Liu
Summary: The use of Au nanoparticle arrays at liquid-liquid interfaces enables accurate quantitative biofluids metabolic profiling, showing potential in advanced metabolite analysis and biomedical diagnostics.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Electrochemistry
Xixia Zhu, Zhongchen Xu, Xiaobing Li, Cunlan Guo
Summary: Understanding the charge migration across peptide chains is crucial for both biology and biomolecular electronics. This study investigated the relation between charge migration in wet electrochemistry and on the solid state by studying ferrocene-labeled peptide self-assembled monolayers on Au substrates. The results showed that the ability of peptides to transmit charge was more influenced by peptide length on the solid state compared to wet electrochemistry. Additionally, altering peptide compositions had different consequences for charge migration in wet electrochemistry and on the solid state.
ELECTROCHIMICA ACTA
(2023)
Review
Chemistry, Multidisciplinary
Limin Wang, Ulrich S. Schubert, Stephanie Hoeppener
Summary: Surface modification using self-assembled monolayers has seen significant advancement in the past decade, with the introduction of new chemical reactions such as nucleophilic substitution, click chemistry, supramolecular modification, photochemical reaction, and others, enhancing the properties of solid substrates like silicon and glass.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Chemistry, Multidisciplinary
Christopher A. Petroff, Giuseppe Cassone, Jiri Sponer, Geoffrey R. Hutchison
Summary: This study presents novel piezoelectric force and touch sensors based on self-assembled monolayers of oligopeptides, which show large piezoelectric voltage response and are easily manufactured. Despite modest piezoelectric charge constants, the devices exhibit immense piezoelectric voltage constants. Additionally, a flexible device prototype with high open-circuit voltages is demonstrated, with potential for further improvements in voltage response through peptide selection and device construction.
ADVANCED MATERIALS
(2021)
Article
Chemistry, Analytical
Yuming Jiang, Alexandre Hutton, Caleb W. Cranney, Jesse G. Meyer
Summary: This article introduces an improved direct infusion and ion mobility method for proteome analysis, and proposes a label-free quantification method DISPA-LFQ, which can rapidly identify and quantify proteins in complex mixtures. This technology has important applications in drug screening, biomarker discovery, and clinical analysis.
ANALYTICAL CHEMISTRY
(2022)
Review
Polymer Science
Shuangyang Li, Qixuan Yu, Hongpeng Li, Meiqi Chen, Ye Jin, Da Liu
Summary: Regenerative medicine is an increasingly popular research topic, focusing on the regeneration of skin, bone, and nerves. The development of a new drug is urgently needed due to the vulnerability and weak self-repair ability of these tissues. Self-assembled peptide hydrogel, a scaffolding material similar to the cytoplasmic matrix, has shown great potential in promoting cell adhesion, migration, proliferation, and division. However, more research is needed to understand the specific mechanisms of self-assembled peptide hydrogels in tissue regeneration.
Article
Biochemistry & Molecular Biology
Dimitry Schmidt, Josef Maier, Hubert Bernauer, Alexander Nesterov-Mueller
Summary: Time-of-flight secondary ion mass spectrometry is used to analyze solid-phase synthesis products in high-density peptide arrays. Specific fragments for individual detection of amino acids and their side chain protecting groups within peptides are compiled. The method shows linear increases in specific signals with increasing number of amino acids in the immobilized peptide, and can distinguish between isomers. The study demonstrates the significant potential of the method for high-throughput screening of functional groups and their accessibility in microreactors on a single microscope slide.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Jonathan S. Weerakkody, Marielle El Kazzy, Elise Jacquier, Pierre-Henri Elchinger, Raphael Mathey, Wai Li Ling, Cyril Herrier, Thierry Livache, Arnaud Buhot, Yanxia Hou
Summary: Electronic nose utilizes a multisensor array to differentiate volatile organic compounds. In this study, a biohybrid surface with hierarchical structures made of self-assembling peptides is used for VOCs detection and discrimination. By a simple design process, the biohybrid sensor array shows sufficient discriminatory capabilities for four VOCs, with benchmarked limit of detection.
Article
Chemistry, Multidisciplinary
Antonio Angelastro, Alexey Barkhanskiy, Ashley P. Mattey, Edward G. Pallister, Reynard Spiess, William Goundry, Perdita Barran, Sabine L. Flitsch
Summary: A glycoengineering methodology was developed to generate antibody drug conjugates with high drug loading by combining enzymatic galactosylation and oxidation with biorthogonal tandem Knoevenagel-Michael addition chemistry.
Article
Chemistry, Applied
Huimin Mao, Shurui Li, Binru Yin, Xisha Lin, Jingyu Guo, Ting Wang, Josef Voglmeir, Li Liu
Summary: This study demonstrates that intact human milk N-glycome is transferred into bacterial cells and decomposed intracellularly. The principal components responsible for the probiotic function of human milk N-glycome towards B. infantis ATCC 15697 are galactose-containing glycans.
Article
Food Science & Technology
Xisha Lin, Hongliang Yao, Jingyu Guo, Yingying Huang, Wenjiao Wang, Binru Yin, Xiang'an Li, Ting Wang, Chunbao Li, Xinglian Xu, Guanghong Zhou, Josef Voglmeir, Li Liu
Summary: This study investigates the impact of exposure to Neu5Gc-rich red meat on healthy Cmah knock-out mice and the underlying mechanisms. The results indicate that long-term intake of Neu5Gc-rich red meat has no adverse effects on the health of the mice, which may be related to the limited absorption of Neu5Gc regulated by protein glycosylation and the metabolism of Neu5Gc by gut microorganisms.
MOLECULAR NUTRITION & FOOD RESEARCH
(2022)
Article
Chemistry, Analytical
Marius Gramlich, Sandra Maier, Philipp D. Kaiser, Bjoern Traenkle, Teresa R. Wagner, Josef Voglmeir, Dieter Stoll, Ulrich Rothbauer, Anne Zeck
Summary: N-linked glycosylation is a common posttranslational modification of proteins, but it poses challenges for their analytical characterization. A new peptide N-glycanase has been developed that can efficiently work under challenging conditions and has been successfully applied in HDX-MS workflow.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Rui-Rui Guo, Tian-Chan Zhang, Thomas Ole Tandrup Lambert, Ting Wang, Josef Voglmeir, Kasper D. Rand, Li Liu
Summary: This article describes a previously unstudied superacidic bacterial N-glycanase (PNGase H+) from the soil bacterium Rudaea cellulosilytica (Rc), which has significantly improved enzymatic properties compared to previously described variants. PNGase Rc shows faster and more versatile deglycosylation of glycoproteins, making it suitable for N-glycan analysis in different samples.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2022)
Article
Plant Sciences
Jianjun Zhang, Yang Xia, Dinghe Wang, Yamin Du, Yongwu Chen, Congcong Zhang, Juan Mao, Muyang Wang, Yi-Min She, Xinxiang Peng, Li Liu, Josef Voglmeir, Zuhua He, Linchuan Liu, Jianming Li
Summary: This study demonstrates that in rescuing bri1-5 protein degradation, AtEDEM1 plays a predominant role over AtEDEM2, while a mutation in ALG3 eliminates the inhibitory effect of irb1-1 on bri1-5 ERAD.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Mattia Ghirardello, Yao-Yao Zhang, Josef Voglmeir, M. Carmen Galan
Summary: The use of ionic liquid based derivatisation agents in glycoscience, especially in sensitive mass spectrometry applications, is of great importance. They provide enhanced polarity and labelability to glycans, allowing for the monitoring and detection of glycans in complex samples. Additionally, ionic liquid based derivatisation agents can be used for the labelling of live cells, enabling the detection of cancer biomarkers and tuning of cell surface properties.
CARBOHYDRATE RESEARCH
(2022)
Article
Multidisciplinary Sciences
Lucy I. Crouch, Paulina A. Urbanowicz, Arnaud Basle, Zhi-Peng Cai, Li Liu, Josef Voglmeir, Javier M. Melo Diaz, Samuel T. Benedict, Daniel I. R. Spencer, David N. Bolam
Summary: The human colonic microbiota can utilize complex glycans as a source of nutrients. Gut microbes have a diverse array of carbohydrate-active enzymes that can degrade plant N-glycans. The discovery of these enzymes provides a potential tool for modifying plant N-glycans for various applications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Christopher R. B. Swanson, Grayson J. Ford, Ashley P. Mattey, Lea Gourbeyre, Sabine L. Flitsch
Summary: In this study, a protecting group-free chemoenzymatic and biocatalytic cascade was developed to synthesize iminosugars from sugar-derived aminopolyols in two steps. The use of galactose oxidase variant F-2 followed by a chemical or enzymatic reduction allowed for efficient one-pot synthesis of these targets, with a product formation rate of over 70%. Genome mining was utilized to identify bacterial shikimate dehydrogenases as promiscuous iminosugar reductases, which was crucial for the success of this strategy. The cell-free protocols enabled isolation of highly polar iminosugar products from biotransformations in a single step through the development of a gradient-elution cation exchange purification. This two-step pathway provides a short synthetic route that can serve as a cell-free platform for broader iminosugar synthesis.
ACS CENTRAL SCIENCE
(2023)
Review
Chemistry, Multidisciplinary
Max Lubberink, William Finnigan, Sabine L. Flitsch
Summary: Amide bonds are commonly formed in the pharmaceutical industry and there is a growing interest in biocatalytic methods for their synthesis. The use of low water systems and ATP-dependent enzymes have shown promise in driving amide bond formation. A publicly available database, RetroBioCat, has been compiled to provide literature on these methods.
Article
Chemistry, Multidisciplinary
Grayson J. Ford, Christopher R. Swanson, Ruth T. Bradshaw Allen, James R. Marshall, Ashley P. Mattey, Nicholas J. Turner, Pere Clapes, Sabine L. Flitsch
Summary: This study presents a three-component strategy for the stereoselective enzymatic synthesis of amino-diols and amino-polyols. Through biocatalytic aldol reactions and reductive aminations, stereoselective formation of amino-polyols was achieved without the need for intermediates isolation.
Article
Chemistry, Multidisciplinary
Grayson J. Ford, Christopher R. Swanson, Ruth T. Bradshaw Allen, James R. Marshall, Ashley P. Mattey, Nicholas J. Turner, Pere Clapes, Sabine L. Flitsch
Summary: A three-component strategy was developed for the stereoselective enzymatic synthesis of amino-diols and amino-polyols. The strategy utilized a diverse set of prochiral aldehydes, hydroxy ketones, and amines as starting materials, combining biocatalytic aldol reactions and reductive aminations. Stereoselective formation of the desired enantiomers of amino-polyols was observed and confirmed by X-ray crystallography.
Article
Chemistry, Multidisciplinary
Robert J. Young, Sabine L. Flitsch, Michael Grigalunas, Paul D. Leeson, Ronald J. Quinn, Nicholas J. Turner, Herbert Waldmann
Summary: This article reviews the case for focusing on Nature in drug discovery, specifically biomimetic molecules and natural products. It discusses the declining natural product-likeness of licensed drugs and the logic of seeking new bioactive agents with enhanced natural mimicry. The article also explores the potential for computational guidance in designing tailored molecules and emphasizes the advantages of organic/biological structures.
Article
Materials Science, Biomaterials
Joana Silva, Reynard Spiess, Andrea Marchesi, Sabine L. Flitsch, Julie E. Gough, Simon J. Webb
Summary: Despite existing as a mixture of isomers, N-acetylglucosamine (GlcNAc) oximes can still be substrates for beta(1,4)-galactosyltransferase (beta 4GalT1). Combining oxime formation with enzymatic elaboration can be a useful method for the high-throughput surface modification of drug delivery vehicles, such as liposomes, with cell-targeting oligosaccharides. The beta-anomer is consumed preferentially but long reaction times allow this isomer to be replenished by equilibration from the remaining isomers.
JOURNAL OF MATERIALS CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Jin-Min Shi, Ting-Ting Wu, Hui Zhou, Yao-Yao Zhang, Li Liu, Goran Widmalm, Josef Voglmeir
Summary: Galactokinases (GalKs) are a group of structurally conserved proteins found in all life forms. A unique GalK orthologue from the bacterium Solitalea canadensis (ScGalK) has been discovered with relaxed substrate requirements and the ability to convert xylose to xylose-1-phosphate. Further investigation identified a putative Glucose-1-phosphate Uridyltransferase (ScGPUT) in close proximity to the ScGalK gene, which can convert xylose-1-phosphate to uridine diphosphate xylose (UDP-xylose) with the presence of uridine triphosphate (UTP).
