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Ortiz-Soto ME, Seibel J. An overview on glycoside hydrolases and glycosyltransferases. Z NATURFORSCH C 2025; 80:1-8. [PMID: 39308024 DOI: 10.1515/znc-2024-2002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
Affiliation(s)
| | - Jürgen Seibel
- Institute of Organic Chemistry, University of Würzburg, Wurzburg, Germany
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2
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Clemente CM, Prieto JM, Martí M. Unlocking Precision Docking for Metalloproteins. J Chem Inf Model 2024; 64:1581-1592. [PMID: 38373276 DOI: 10.1021/acs.jcim.3c01853] [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: 02/21/2024]
Abstract
Metalloproteins play a fundamental role in molecular biology, contributing to various biological processes. However, the discovery of high-affinity ligands targeting metalloproteins has been delayed due, in part, to a lack of suitable tools and data. Molecular docking, a widely used technique for virtual screening of small-molecule ligand interactions with proteins, often faces challenges when applied to metalloproteins due to the particular nature of the ligand metal bond. To address these limitations associated with docking metalloproteins, we introduce a knowledge-driven docking approach known as "metalloprotein bias docking" (MBD), which extends the AutoDock Bias technique. We assembled a comprehensive data set of metalloprotein-ligand complexes from 15 different metalloprotein families, encompassing Ca, Co, Fe, Mg, Mn, and Zn metal ions. Subsequently, we conducted a performance analysis of our MBD method and compared it to the conventional docking (CD) program AutoDock4, applied to various metalloprotein targets within our data set. Our results demonstrate that MBD outperforms CD, significantly enhancing accuracy, selectivity, and precision in ligand pose prediction. Additionally, we observed a positive correlation between our predicted ligand free energies and the corresponding experimental values. These findings underscore the potential of MBD as a valuable tool for the effective exploration of metalloprotein-ligand interactions.
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Affiliation(s)
- Camila M Clemente
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Juan M Prieto
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Marcelo Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
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3
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Tian J, Dong X, Wu T, Wen P, Liu X, Zhang M, An X, Shi D. Revealing the conformational dynamics of UDP-GlcNAc recognition by O-GlcNAc transferase via Markov state model. Int J Biol Macromol 2024; 256:128405. [PMID: 38016609 DOI: 10.1016/j.ijbiomac.2023.128405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023]
Abstract
The O-linked N-acetylglucosamine (O-GlcNAc) glycosylation is a critical post-translational modification and closely linked to various physiological and pathological conditions. The O-GlcNAc transferase (OGT) functions as the only glycosyltransferase of O-GlcNAc glycosylation by transferring GlcNAc from UDP-GlcNAc to serine or threonine residues on protein substrates. The interaction mode of UDP-GlcNAc against OGT has been preliminarily revealed by the crystal structures, yet an atomic-level comprehension for the conformational dynamics of the recognition process remains elusive. Here, we construct the Markov state model based on extensive all-atom molecular dynamics (MD) simulations with an aggregated simulation time of ∼9 μs, and reveal that the UDP-GlcNAc recognition process by OGT encompasses four key metastable states, occurring within an estimated timescale of ∼10 μs. During UDP-GlcNAc recognition process, we find the pyrophosphate moiety (P2O52-) initially anchors to the active pocket via salt bridge and hydrogen bonds, facilitating subsequent binding of the uridine and GlcNAc moieties. Furthermore, the functional roles of K842 involved in the salt bridge with P2O52- were evaluated through extra mutant MD simulations. Overall, our study provides valuable insights into the UDP-GlcNAc recognition mechanism by OGT, which could further aid in mechanistic studies of O-GlcNAc glycosylation and drug development targeting on OGT.
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Affiliation(s)
- Jiaqi Tian
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xin Dong
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Tianshuo Wu
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Pengbo Wen
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xin Liu
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Mengying Zhang
- School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, Jiangsu Province, China
| | - Xiaoli An
- School of Chemical Engineering, Institute of Pharmaceutical Engineering Technology and Application, Sichuan University of Science & Engineering, Xueyuan Street 180, Huixing Road, Zigong 643000, Sichuan, China.
| | - Danfeng Shi
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, Guangdong, China.
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4
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Clemente CM, Capece L, Martí MA. Best Practices on QM/MM Simulations of Biological Systems. J Chem Inf Model 2023; 63:2609-2627. [PMID: 37100031 DOI: 10.1021/acs.jcim.2c01522] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
During the second half of the 20th century, following structural biology hallmark works on DNA and proteins, biochemists shifted their questions from "what does this molecule look like?" to "how does this process work?". Prompted by the theoretical and practical developments in computational chemistry, this led to the emergence of biomolecular simulations and, along with the 2013 Nobel Prize in Chemistry, to the development of hybrid QM/MM methods. QM/MM methods are necessary whenever the problem we want to address involves chemical reactivity and/or a change in the system's electronic structure, with archetypal examples being the studies of an enzyme's reaction mechanism and a metalloprotein's active site. In the last decades QM/MM methods have seen an increasing adoption driven by their incorporation in widely used biomolecular simulation software. However, properly setting up a QM/MM simulation is not an easy task, and several issues need to be properly addressed to obtain meaningful results. In the present work, we describe both the theoretical concepts and practical issues that need to be considered when performing QM/MM simulations. We start with a brief historical perspective on the development of these methods and describe when and why QM/MM methods are mandatory. Then we show how to properly select and analyze the performance of the QM level of theory, the QM system size, and the position and type of the boundaries. We show the relevance of performing prior QM model system (or QM cluster) calculations in a vacuum and how to use the corresponding results to adequately calibrate those derived from QM/MM. We also discuss how to prepare the starting structure and how to select an adequate simulation strategy, including those based on geometry optimizations as well as free energy methods. In particular, we focus on the determination of free energy profiles using multiple steered molecular dynamics (MSMD) combined with Jarzynski's equation. Finally, we describe the results for two illustrative and complementary examples: the reaction performed by chorismate mutase and the study of ligand binding to hemoglobins. Overall, we provide many practical recommendations (or shortcuts) together with important conceptualizations that we hope will encourage more and more researchers to incorporate QM/MM studies into their research projects.
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Affiliation(s)
- Camila M Clemente
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Luciana Capece
- Departamento de Química Inorgánica Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química de los Materiales, Ambiente y Energía (INQUIMAE) CONICET, Pabellòn 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA) e Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón 2 de Ciudad Universitaria, Ciudad de Buenos Aires C1428EHA, Argentina
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5
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Kóňa J. How inverting β-1,4-galactosyltransferase-1 can quench a high charge of the by-product UDP 3- in catalysis: a QM/MM study of enzymatic reaction with native and UDP-5' thio galactose substrates. Org Biomol Chem 2020; 18:7585-7596. [PMID: 32945815 DOI: 10.1039/d0ob01490g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
The catalysis of inverting glycosyltransferases consists of several biophysical and biochemical processes during which the transfer of a sugar residue from the purine phosphate donor substrate to an acceptor substrate occurs with stereo-inversion of the anomeric C1 center at a product. During catalysis a highly charged phosphate by-product (UDP3-) is formed and a mechanism of how the enzyme stabilizes it back to the UDP2- form is not known. Using methods of molecular modeling (hybrid DFT-QM/MM calculations) we proposed and validated a catalytic mechanism of bovine inverting β-1,4-galactosyltransferase-1 (β4Gal-T1) with native (UDP-galactose) and thio donor substrates (UDP-5' thio galactose). We focused on three aspects of the mechanism not yet investigated: (i) the formation of an oxocarbenium ion intermediate, which was only found for the retaining glycosyltransferases for the time being; (ii) the mechanism of stabilization of a highly charged phosphate by-product (UDP3-) back to its standard in vivo form (UDP2-); (iii) explanation for why in experimental measurements the rate of catalysis with the thio donor substrate is only 8% of the rate of that with the natural substrate. To understand the differences in the interaction patterns between the complexes enzyme : UDP-Gal and enzyme : UDP-5S-Gal, fragmented molecular orbital (FMO) decomposition energy analysis was carried out at the DFT level.
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Affiliation(s)
- J Kóňa
- Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovak Republic.
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6
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Rodrigo-Unzueta A, Ghirardello M, Urresti S, Delso I, Giganti D, Anso I, Trastoy B, Comino N, Tersa M, D'Angelo C, Cifuente JO, Marina A, Liebau J, Mäler L, Chenal A, Albesa-Jové D, Merino P, Guerin ME. Dissecting the Structural and Chemical Determinants of the "Open-to-Closed" Motion in the Mannosyltransferase PimA from Mycobacteria. Biochemistry 2020; 59:2934-2945. [PMID: 32786405 DOI: 10.1021/acs.biochem.0c00376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The phosphatidyl-myo-inositol mannosyltransferase A (PimA) is an essential peripheral membrane glycosyltransferase that initiates the biosynthetic pathway of phosphatidyl-myo-inositol mannosides (PIMs), key structural elements and virulence factors of Mycobacterium tuberculosis. PimA undergoes functionally important conformational changes, including (i) α-helix-to-β-strand and β-strand-to-α-helix transitions and (ii) an "open-to-closed" motion between the two Rossmann-fold domains, a conformational change that is necessary to generate a catalytically competent active site. In previous work, we established that GDP-Man and GDP stabilize the enzyme and facilitate the switch to a more compact active state. To determine the structural contribution of the mannose ring in such an activation mechanism, we analyzed a series of chemical derivatives, including mannose phosphate (Man-P) and mannose pyrophosphate-ribose (Man-PP-RIB), and additional GDP derivatives, such as pyrophosphate ribose (PP-RIB) and GMP, by the combined use of X-ray crystallography, limited proteolysis, circular dichroism, isothermal titration calorimetry, and small angle X-ray scattering methods. Although the β-phosphate is present, we found that the mannose ring, covalently attached to neither phosphate (Man-P) nor PP-RIB (Man-PP-RIB), does promote the switch to the active compact form of the enzyme. Therefore, the nucleotide moiety of GDP-Man, and not the sugar ring, facilitates the "open-to-closed" motion, with the β-phosphate group providing the high-affinity binding to PimA. Altogether, the experimental data contribute to a better understanding of the structural determinants involved in the "open-to-closed" motion not only observed in PimA but also visualized and/or predicted in other glycosyltransfeases. In addition, the experimental data might prove to be useful for the discovery and/or development of PimA and/or glycosyltransferase inhibitors.
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Affiliation(s)
- Ane Rodrigo-Unzueta
- Instituto Biofisika, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Departamento de Bioquímica, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain
| | - Mattia Ghirardello
- Department of Synthesis and Structure of Biomolecules, Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH), University of Zaragoza-CSIC, 50009 Zaragoza, Spain
| | - Saioa Urresti
- Instituto Biofisika, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Departamento de Bioquímica, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain
| | - Ignacio Delso
- Department of Synthesis and Structure of Biomolecules, Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH), University of Zaragoza-CSIC, 50009 Zaragoza, Spain
| | - David Giganti
- Instituto Biofisika, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Departamento de Bioquímica, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Unité de Microbiologie Structurale (CNRS URA 2185), Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Itxaso Anso
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Beatriz Trastoy
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Natalia Comino
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Montse Tersa
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Cecilia D'Angelo
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Javier O Cifuente
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Alberto Marina
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden.,Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Alexandre Chenal
- Unité de Biochimie des Interactions Macromoléculaires (CNRS UMR 3528), Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - David Albesa-Jové
- Instituto Biofisika, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Departamento de Bioquímica, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Pedro Merino
- Glycobiology Unit, Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain
| | - Marcelo E Guerin
- Instituto Biofisika, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Departamento de Bioquímica, Universidad del País Vasco, Barrio Sarriena s/n, Leioa, Bizkaia 48940, Spain.,Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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7
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Mestrom L, Przypis M, Kowalczykiewicz D, Pollender A, Kumpf A, Marsden SR, Bento I, Jarzębski AB, Szymańska K, Chruściel A, Tischler D, Schoevaart R, Hanefeld U, Hagedoorn PL. Leloir Glycosyltransferases in Applied Biocatalysis: A Multidisciplinary Approach. Int J Mol Sci 2019; 20:ijms20215263. [PMID: 31652818 PMCID: PMC6861944 DOI: 10.3390/ijms20215263] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 01/13/2023] Open
Abstract
Enzymes are nature’s catalyst of choice for the highly selective and efficient coupling of carbohydrates. Enzymatic sugar coupling is a competitive technology for industrial glycosylation reactions, since chemical synthetic routes require extensive use of laborious protection group manipulations and often lack regio- and stereoselectivity. The application of Leloir glycosyltransferases has received considerable attention in recent years and offers excellent control over the reactivity and selectivity of glycosylation reactions with unprotected carbohydrates, paving the way for previously inaccessible synthetic routes. The development of nucleotide recycling cascades has allowed for the efficient production and reuse of nucleotide sugar donors in robust one-pot multi-enzyme glycosylation cascades. In this way, large glycans and glycoconjugates with complex stereochemistry can be constructed. With recent advances, LeLoir glycosyltransferases are close to being applied industrially in multi-enzyme, programmable cascade glycosylations.
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Affiliation(s)
- Luuk Mestrom
- Department of Biotechnology, Delft University of Technology, Section Biocatalysis, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Marta Przypis
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland.
- Biotechnology Center, Silesian University of Technology, B. Krzywoustego 8, 44-100 Gliwice, Poland.
| | - Daria Kowalczykiewicz
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, B. Krzywoustego 4, 44-100 Gliwice, Poland.
- Biotechnology Center, Silesian University of Technology, B. Krzywoustego 8, 44-100 Gliwice, Poland.
| | - André Pollender
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Antje Kumpf
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
- Microbial Biotechnology, Faculty of Biology & Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780 Bochum, Germany.
| | - Stefan R Marsden
- Department of Biotechnology, Delft University of Technology, Section Biocatalysis, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Isabel Bento
- EMBL Hamburg, Notkestraβe 85, 22607 Hamburg, Germany.
| | - Andrzej B Jarzębski
- Institute of Chemical Engineering, Polish Academy of Sciences, Bałtycka 5, 44-100 Gliwice, Poland.
| | - Katarzyna Szymańska
- Department of Chemical and Process Engineering, Silesian University of Technology, Ks. M. Strzody 7, 44-100 Gliwice, Poland.
| | | | - Dirk Tischler
- Environmental Microbiology, Institute of Biosciences, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
- Microbial Biotechnology, Faculty of Biology & Biotechnology, Ruhr-Universität Bochum, Universitätsstr. 150, 44780 Bochum, Germany.
| | - Rob Schoevaart
- ChiralVision, J.H. Oortweg 21, 2333 CH Leiden, The Netherlands.
| | - Ulf Hanefeld
- Department of Biotechnology, Delft University of Technology, Section Biocatalysis, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Peter-Leon Hagedoorn
- Department of Biotechnology, Delft University of Technology, Section Biocatalysis, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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8
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Si Z, Yang Q, Liang R, Chen L, Chen D, Li Y. Digalactosyldiacylglycerol Synthase Gene MtDGD1 Plays an Essential Role in Nodule Development and Nitrogen Fixation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1196-1209. [PMID: 30986120 DOI: 10.1094/mpmi-11-18-0322-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Little is known about the genes participating in digalactosyldiacylglycerol (DGDG) synthesis during nodule symbiosis. Here, we identified full-length MtDGD1, a synthase of DGDG, and characterized its effect on symbiotic nitrogen fixation in Medicago truncatula. Immunofluorescence and immunoelectron microscopy showed that MtDGD1 was located on the symbiosome membranes in the infected cells. β-Glucuronidase histochemical staining revealed that MtDGD1 was highly expressed in the infection zone of young nodules as well as in the whole mature nodules. Compared with the control, MtDGD1-RNA interference transgenic plants exhibited significant decreases in nodule number, symbiotic nitrogen fixation activity, and DGDG abundance in the nodules, as well as abnormal nodule and symbiosome development. Overexpression of MtDGD1 resulted in enhancement of nodule number and nitrogen fixation activity. In response to phosphorus starvation, the MtDGD1 expression level was substantially upregulated and the abundance of nonphospholipid DGDG was significantly increased in the roots and nodules, accompanied by corresponding decreases in the abundance of phospholipids such as phosphatidylcholine, phosphatidylethanolamine, and phosphatidylinositol. Overall, our results indicate that DGD1 contributes to effective nodule organogenesis and nitrogen fixation by affecting the synthesis and content of DGDG during symbiosis.
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Affiliation(s)
- Zaiyong Si
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Qianqian Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Rongrong Liang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Ling Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Dasong Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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9
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Tanaka M, Nakagawa A, Nishi N, Iijima K, Sawa R, Takahashi D, Toshima K. Boronic-Acid-Catalyzed Regioselective and 1,2- cis-Stereoselective Glycosylation of Unprotected Sugar Acceptors via S Ni-Type Mechanism. J Am Chem Soc 2018; 140:3644-3651. [PMID: 29457892 DOI: 10.1021/jacs.7b12108] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Regio- and 1,2- cis-stereoselective chemical glycosylation of unprotected glycosyl acceptors has been in great demand for the efficient synthesis of natural glycosides. However, simultaneously regulating these selectivities has been a longstanding problem in synthetic organic chemistry. In nature, glycosyl transferases catalyze regioselective 1,2- cis-glycosylations via the SNi mechanism, yet no useful chemical glycosylations based on this mechanism have been developed. In this paper, we report a highly regio- and 1,2- cis-stereoselective SNi-type glycosylation of 1,2-anhydro donors and unprotected sugar acceptors using p-nitrophenylboronic acid (10e) as a catalyst in the presence of water under mild conditions. Highly controlled regio- and 1,2- cis-stereoselectivities were achieved via the combination of boron-mediated carbohydrate recognition and the SNi-type mechanism. Mechanistic studies using the KIEs and DFT calculations were consistent with a highly dissociative concerted SNi mechanism. This glycosylation method was applied successfully to the direct glycosylation of unprotected natural glycosides and the efficient synthesis of a complex oligosaccharide with minimal protecting groups.
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Affiliation(s)
- Masamichi Tanaka
- Department of Applied Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
| | - Akira Nakagawa
- Department of Applied Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
| | - Nobuya Nishi
- Department of Applied Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
| | - Kiyoko Iijima
- Institute of Microbial Chemistry (BIKAKEN) , 3-14-23 Kamiosaki , Shinagawa-ku, Tokyo 141-0021 , Japan
| | - Ryuichi Sawa
- Institute of Microbial Chemistry (BIKAKEN) , 3-14-23 Kamiosaki , Shinagawa-ku, Tokyo 141-0021 , Japan
| | - Daisuke Takahashi
- Department of Applied Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
| | - Kazunobu Toshima
- Department of Applied Chemistry, Faculty of Science and Technology , Keio University , 3-14-1 Hiyoshi , Kohoku-ku, Yokohama 223-8522 , Japan
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Li F, Korenaga T, Nakanishi T, Kikuchi J, Terada M. Chiral Phosphoric Acid Catalyzed Enantioselective Ring Expansion Reaction of 1,3-Dithiane Derivatives: Case Study of the Nature of Ion-Pairing Interaction. J Am Chem Soc 2018; 140:2629-2642. [PMID: 29377689 DOI: 10.1021/jacs.7b13274] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Chiral counterion controlled asymmetric catalysis via an ion-pairing interaction has attracted immense attention in recent years. Despite a number of successful studies, the mechanistic elucidation of the stereocontrolling element in the ion-pairing interaction is rarely conducted and hence its nature is still far from being well understood. Herein we report an in-depth mechanistic case study of a newly developed enantioselective ring expansion reaction of 1,3-dithiane derivatives catalyzed by chiral phosphoric acid (CPA). An unprecedented enantioselective 1,2-sulfur rearrangement/stereospecific nucleophilic addition sequence was proven to be the stereoselective pathway. More importantly, by thorough investigation of the intrinsic nature of the stereospecific nucleophilic addition to the cationic thionium intermediate, we discovered that the key interaction in this process is the nonclassical C-H···O hydrogen bonds formed between the conjugate base of the CPA catalyst and the cationic intermediate. These C-H···O hydrogen bonds not only bind the catalyst to the substrates to form energetically favored states throughout the overall processes but also firmly maintain the relative positions of these fragments as the "fixed" contact ion pair to sustain the chiral information generated at the initial sulfur rearrangement step. This mechanistic case study provides a very clear understanding of the nature of the ion-pairing interaction in organocatalysis. The conclusion encourages the further development of the research field with the focus to design new organocatalysts and cultivate novel organocatalytic transformations.
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Affiliation(s)
- Feng Li
- Department of Chemistry, Graduate School of Science, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Toshinobu Korenaga
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University , 4-3-5 Ueda, Morioka 020-8551, Japan
| | - Taishi Nakanishi
- Department of Chemistry, Graduate School of Science, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Jun Kikuchi
- Department of Chemistry, Graduate School of Science, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
| | - Masahiro Terada
- Department of Chemistry, Graduate School of Science, Tohoku University , Aoba-ku, Sendai 980-8578, Japan
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