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DeYong AE, Trinidad JC, Pohl NLB. An identification method to distinguish monomeric sugar isomers on glycopeptides. Analyst 2023; 148:4438-4446. [PMID: 37555458 DOI: 10.1039/d3an01036h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
A one-step protocol for the automated flow synthesis of protected glycosylated amino acids is described using pumps with open-source controls in overall yields of 21-50%. The resulting glycosylated amino acids could be used directly in solid-phase peptide synthesis (SPPS) protocols to quickly produce glycopeptide standards. Access to a variety of stereoisomers of the sugar enabled the development of an LC-MS/MS protocol that can distinguish between peptides modified with carbohydrates having the same exact mass. This method could definitively identify fucose in an O-glycosylation site on the transmembrane protein, Notch1.
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Affiliation(s)
- Ashley E DeYong
- Chemistry, Indiana University, 212 S Hawthorne Dr., Bloomington, IN 47405, USA.
| | - Jonathan C Trinidad
- Chemistry, Indiana University, 212 S Hawthorne Dr., Bloomington, IN 47405, USA.
| | - Nicola L B Pohl
- Chemistry, Indiana University, 212 S Hawthorne Dr., Bloomington, IN 47405, USA.
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2
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Chen M, Zhang J, Qi J, Dong R, Liu H, Wu D, Shao H, Jiang X. Boronic Acid-Decorated Multivariate Photosensitive Metal-Organic Frameworks for Combating Multi-Drug-Resistant Bacteria. ACS NANO 2022; 16:7732-7744. [PMID: 35535857 DOI: 10.1021/acsnano.1c11613] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Metal-organic frameworks (MOFs) are promising photosensitized materials that have displayed great advantages in antibacterial application. However, their bactericidal activity is still limited by the ultrashort diffusion distance of biocidal reactive oxygen species (ROS). Herein, we integrate the bacterial-binding boronic acid ligand and photosensitized porphyrin into one single MOF, synergistically boosting antibiotic capability. The introduction of the boronic acid group with a closed physical gap makes multivariate MOFs more powerful for eradicating multi-drug-resistant (MDR) bacteria. The MOFs that are decorated with boronic acid possess antibacterial efficiencies (10-20 times) higher than those without the targeting ligand. Moreover, the MOFs exhibit excellent biocompatibility. They significantly decrease the inflammatory responses and accelerate the healing of chronic wounds infected with MDR bacteria (nearly 2 times faster). This work provides a strategy to develop multivariate MOFs that target bacteria, which will further inspire specific bacterial-binding therapy in the future.
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Affiliation(s)
- Mian Chen
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
| | - Jiangjiang Zhang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Jie Qi
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Ruihua Dong
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Hongmei Liu
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Decheng Wu
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Huawu Shao
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan 610041, People's Republic of China
| | - Xingyu Jiang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
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Kumar M, Kumar N, Gurawa A, Kashyap S. Stereoselective Synthesis of
α
‐ʟ‐Rhamnopyranosides from ʟ‐Rhamnal Employing Ruthenium‐Catalysis. ChemistrySelect 2022. [DOI: 10.1002/slct.202200963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Manoj Kumar
- Carbohydrate Chemistry Research Laboratory (CCRL) Department of Chemistry Malaviya National Institute of Technology Jaipur (MNIT Jaipur) J. L. N. Marg Jaipur 302 017 INDIA
| | - Nitin Kumar
- Carbohydrate Chemistry Research Laboratory (CCRL) Department of Chemistry Malaviya National Institute of Technology Jaipur (MNIT Jaipur) J. L. N. Marg Jaipur 302 017 INDIA
| | - Aakanksha Gurawa
- Carbohydrate Chemistry Research Laboratory (CCRL) Department of Chemistry Malaviya National Institute of Technology Jaipur (MNIT Jaipur) J. L. N. Marg Jaipur 302 017 INDIA
| | - Sudhir Kashyap
- Carbohydrate Chemistry Research Laboratory (CCRL) Department of Chemistry Malaviya National Institute of Technology Jaipur (MNIT Jaipur) J. L. N. Marg Jaipur 302 017 INDIA
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4
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Koller F, Lassak J. Two RmlC homologs catalyze dTDP-4-keto-6-deoxy-D-glucose epimerization in Pseudomonas putida KT2440. Sci Rep 2021; 11:11991. [PMID: 34099824 PMCID: PMC8184846 DOI: 10.1038/s41598-021-91421-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/26/2021] [Indexed: 11/09/2022] Open
Abstract
l-Rhamnose is an important monosaccharide both as nutrient source and as building block in prokaryotic glycoproteins and glycolipids. Generation of those composite molecules requires activated precursors being provided e. g. in form of nucleotide sugars such as dTDP-β-l-rhamnose (dTDP-l-Rha). dTDP-l-Rha is synthesized in a conserved 4-step reaction which is canonically catalyzed by the enzymes RmlABCD. An intact pathway is especially important for the fitness of pseudomonads, as dTDP-l-Rha is essential for the activation of the polyproline specific translation elongation factor EF-P in these bacteria. Within the scope of this study, we investigated the dTDP-l-Rha-biosynthesis route of Pseudomonas putida KT2440 with a focus on the last two steps. Bioinformatic analysis in combination with a screening approach revealed that epimerization of dTDP-4-keto-6-deoxy-d-glucose to dTDP-4-keto-6-deoxy-l-mannose is catalyzed by the two paralogous proteins PP_1782 (RmlC1) and PP_0265 (RmlC2), whereas the reduction to the final product is solely mediated by PP_1784 (RmlD). Thus, we also exclude the distinct RmlD homolog PP_0500 and the genetically linked nucleoside diphosphate-sugar epimerase PP_0501 to be involved in dTDP-l-Rha formation, other than suggested by certain databases. Together our analysis contributes to the molecular understanding how this important nucleotide-sugar is synthesized in pseudomonads.
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Affiliation(s)
- Franziska Koller
- Department Biology I, Microbiology, Ludwig-Maximilians-Universität München, Planegg/Martinsried, Germany
| | - Jürgen Lassak
- Department Biology I, Microbiology, Ludwig-Maximilians-Universität München, Planegg/Martinsried, Germany.
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Yakovlieva L, Wood TM, Kemmink J, Kotsogianni I, Koller F, Lassak J, Martin NI, Walvoort MTC. A β-hairpin epitope as novel structural requirement for protein arginine rhamnosylation. Chem Sci 2020; 12:1560-1567. [PMID: 34163919 PMCID: PMC8179230 DOI: 10.1039/d0sc05823h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
For canonical asparagine glycosylation, the primary amino acid sequence that directs glycosylation at specific asparagine residues is well-established. Here we reveal that a recently discovered bacterial enzyme EarP, that transfers rhamnose to a specific arginine residue in its acceptor protein EF-P, specifically recognizes a β-hairpin loop. Notably, while the in vitro rhamnosyltransferase activity of EarP is abolished when presented with linear substrate peptide sequences derived from EF-P, the enzyme readily glycosylates the same sequence in a cyclized β-hairpin mimic. Additional studies with other substrate-mimicking cyclic peptides revealed that EarP activity is sensitive to the method used to induce cyclization and in some cases is tolerant to amino acid sequence variation. Using detailed NMR approaches, we established that the active peptide substrates all share some degree of β-hairpin formation, and therefore conclude that the β-hairpin epitope is the major determinant of arginine-rhamnosylation by EarP. Our findings add a novel recognition motif to the existing knowledge on substrate specificity of protein glycosylation, and are expected to guide future identifications of rhamnosylation sites in other protein substrates.
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Affiliation(s)
- Liubov Yakovlieva
- Chemical Biology Group, Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
| | - Thomas M Wood
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Leiden The Netherlands .,Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University Utrecht The Netherlands
| | - Johan Kemmink
- Chemical Biology Group, Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
| | - Ioli Kotsogianni
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Leiden The Netherlands
| | - Franziska Koller
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München Planegg/Martinsried Germany
| | - Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München Planegg/Martinsried Germany
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University Leiden The Netherlands
| | - Marthe T C Walvoort
- Chemical Biology Group, Stratingh Institute for Chemistry, University of Groningen Groningen The Netherlands
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