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Vuksanovic N, Clasman JR, Imperiali B, Allen KN. Specificity determinants revealed by the structure of glycosyltransferase Campylobacter concisus PglA. Protein Sci 2024; 33:e4848. [PMID: 38019455 PMCID: PMC10731488 DOI: 10.1002/pro.4848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 11/30/2023]
Abstract
In selected Campylobacter species, the biosynthesis of N-linked glycoconjugates via the pgl pathway is essential for pathogenicity and survival. However, most of the membrane-associated GT-B fold glycosyltransferases responsible for diversifying glycans in this pathway have not been structurally characterized which hinders the understanding of the structural factors that govern substrate specificity and prediction of resulting glycan composition. Herein, we report the 1.8 Å resolution structure of Campylobacter concisus PglA, the glycosyltransferase responsible for the transfer of N-acetylgalatosamine (GalNAc) from uridine 5'-diphospho-N-acetylgalactosamine (UDP-GalNAc) to undecaprenyl-diphospho-N,N'-diacetylbacillosamine (UndPP-diNAcBac) in complex with the sugar donor GalNAc. This study identifies distinguishing characteristics that set PglA apart within the GT4 enzyme family. Computational docking of the structure in the membrane in comparison to homologs points to differences in interactions with the membrane-embedded acceptor and the structural analysis of the complex together with bioinformatics and site-directed mutagenesis identifies donor sugar binding motifs. Notably, E113, conserved solely among PglA enzymes, forms a hydrogen bond with the GalNAc C6″-OH. Mutagenesis of E113 reveals activity consistent with this role in substrate binding, rather than stabilization of the oxocarbenium ion transition state, a function sometimes ascribed to the corresponding residue in GT4 homologs. The bioinformatic analyses reveal a substrate-specificity motif, showing that Pro281 in a substrate binding loop of PglA directs configurational preference for GalNAc over GlcNAc. This proline is replaced by a conformationally flexible glycine, even in distant homologs, which favor substrates with the same stereochemistry at C4, such as glucose. The signature loop is conserved across all Campylobacter PglA enzymes, emphasizing its importance in substrate specificity.
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Affiliation(s)
| | | | - Barbara Imperiali
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Karen N. Allen
- Department of ChemistryBoston UniversityBostonMassachusettsUSA
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Shi WJ, Zhao R, Zhu JQ, Wan XH, Wang LB, Li H, Qin S. Complete genome analysis of pathogenic Metschnikowia bicuspidata strain MQ2101 isolated from diseased ridgetail white prawn, Exopalaemon carinicauda. BMC Microbiol 2023; 23:120. [PMID: 37120526 PMCID: PMC10148492 DOI: 10.1186/s12866-023-02865-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/18/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Metschnikowia bicuspidata is a pathogenic yesst that can cause disease in many different economic aquatic animal species. In recent years, there was a new disease outbreak in ridgetail white prawn (Exopalaemon carinicauda) in coastal areas of Jiangsu Province China that was referred to as zombie disease by local farmers. The pathogen was first isolated and identified as M. bicuspidata. Although the pathogenicity and pathogenesis of this pathogen in other animals have been reported in some previous studies, research on its molecular mechanisms is still very limited. Therefore, a genome-wide study is necessary to better understand the physiological and pathogenic mechanisms of M. bicuspidata. RESULT In this study, we obtained a pathogenic strain, MQ2101, of M. bicuspidata from diseased E. carinicauda and sequenced its whole genome. The size of the whole genome was 15.98 Mb, and it was assembled into 5 scaffolds. The genome contained 3934 coding genes, among which 3899 genes with biological functions were annotated in multiple underlying databases. In KOG database, 2627 genes were annotated, which were categorized into 25 classes including general function prediction only, posttranslational modification, protein turnover, chaperones, and signal transduction mechanisms. In KEGG database, 2493 genes were annotated, which were categorized into five classes, including cellular processes, environmental information processing, genetic information processing, metabolism and organismal systems. In GO database, 2893 genes were annotated, which were mainly classified in cell, cell part, cellular processes and metabolic processes. There were 1055 genes annotated in the PHI database, accounting for 26.81% of the total genome, among which 5 genes were directly related to pathogenicity (identity ≥ 50%), including hsp90, PacC, and PHO84. There were also some genes related to the activity of the yeast itself that could be targeted by antiyeast drugs. Analysis based on the DFVF database showed that strain MQ2101 contained 235 potential virulence genes. BLAST searches in the CAZy database showed that strain MQ2101 may have a more complex carbohydrate metabolism system than other yeasts of the same family. In addition, two gene clusters and 168 putative secretory proteins were predicted in strain MQ2101, and functional analysis showed that some of the secretory proteins may be directly involved in the pathogenesis of the strain. Gene family analysis with five other yeasts revealed that strain MQ2101 has 245 unique gene families, including 274 genes involved in pathogenicity that could serve as potential targets. CONCLUSION Genome-wide analysis elucidated the pathogenicity-associated genes of M. bicuspidate while also revealing a complex metabolic mechanism and providing putative targets of action for the development of antiyeast drugs for this pathogen. The obtained whole-genome sequencing data provide an important theoretical basis for transcriptomic, proteomic and metabolic studies of M. bicuspidata and lay a foundation for defining its specific mechanism of host infestation.
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Affiliation(s)
- Wen-Jun Shi
- Key Laboratory of Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, No. 17, Chunhui Road, Yantai, Shandong Province, 264003, People's Republic of China
- Institute of Oceanology & Marine Fisheries, No. 31, Jiaoyu Road, Nantong, Jiangsu, 226007, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Ran Zhao
- Institute of Oceanology & Marine Fisheries, No. 31, Jiaoyu Road, Nantong, Jiangsu, 226007, People's Republic of China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Jian-Qiang Zhu
- Institute of Oceanology & Marine Fisheries, No. 31, Jiaoyu Road, Nantong, Jiangsu, 226007, People's Republic of China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, People's Republic of China
| | - Xi-He Wan
- Institute of Oceanology & Marine Fisheries, No. 31, Jiaoyu Road, Nantong, Jiangsu, 226007, People's Republic of China.
| | - Li-Bao Wang
- Institute of Oceanology & Marine Fisheries, No. 31, Jiaoyu Road, Nantong, Jiangsu, 226007, People's Republic of China
| | - Hui Li
- Institute of Oceanology & Marine Fisheries, No. 31, Jiaoyu Road, Nantong, Jiangsu, 226007, People's Republic of China
| | - Song Qin
- Key Laboratory of Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, No. 17, Chunhui Road, Yantai, Shandong Province, 264003, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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3
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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Tvaroška I. Glycosyltransferases as targets for therapeutic intervention in cancer and inflammation: molecular modeling insights. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-021-02026-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kulkarni PU, Shah H, Vyas VK. Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-based Drug Design and Discovery. Mini Rev Med Chem 2021; 22:1096-1107. [PMID: 34620049 DOI: 10.2174/1389557521666211007115250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 11/22/2022]
Abstract
Quantum mechanics (QM) is physics based theory which explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to availability of many protein crystal structures; it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however the rest is defined through molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.
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Affiliation(s)
- Prajakta U Kulkarni
- School of Pharmacy, ITM (SLS) Baroda University, Vadodara 391510, Gujarat. India
| | - Harshil Shah
- Department of Pharmaceutical Chemistry, Sardar Patel College of Pharmacy, Bakrol, Anand 388315, Gujarat. India
| | - Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad 382481, Gujarat. India
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Mendoza F, Masgrau L. Computational modeling of carbohydrate processing enzymes reactions. Curr Opin Chem Biol 2021; 61:203-213. [PMID: 33812143 DOI: 10.1016/j.cbpa.2021.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 12/14/2022]
Abstract
Carbohydrate processing enzymes are of biocatalytic interest. Glycoside hydrolases and the recently discovered lytic polysaccharide monooxygenase for their use in biomass degradation to obtain biofuels or valued chemical entities. Glycosyltransferases or engineered glycosidases and phosphorylases for the synthesis of carbohydrates and glycosylated products. Quantum mechanics-molecular mechanics (QM/MM) methods are highly contributing to establish their different chemical reaction mechanisms. Other computational methods are also used to study enzyme conformational changes, ligand pathways, and processivity, e.g. for processive glycosidases like cellobiohydrolases. There is still a long road to travel to fully understand the role of conformational dynamics in enzyme activity and also to disclose the variety of reaction mechanisms these enzymes employ. Additionally, computational tools for enzyme engineering are beginning to be applied to evaluate substrate specificity or aid in the design of new biocatalysts with increased thermostability or tailored activity, a growing field where molecular modeling is finding its way.
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Affiliation(s)
- Fernanda Mendoza
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Sede Concepción, Talcahuano, 4260000, Chile
| | - Laura Masgrau
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Institut de Biotecnología i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain; Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018, Barcelona, Spain.
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7
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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Enzymatic Synthesis of Glycans and Glycoconjugates. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 175:231-280. [PMID: 33052414 DOI: 10.1007/10_2020_148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycoconjugates have great potential to improve human health in a multitude of different ways and fields. Prominent examples are human milk oligosaccharides and glycosaminoglycans. The typical choice for the production of homogeneous glycoconjugates is enzymatic synthesis. Through the availability of expression and purification protocols, recombinant Leloir glycosyltransferases are widely applied as catalysts for the synthesis of a wide range of glycoconjugates. Extensive utilization of these enzymes also depends on the availability of activated sugars as building blocks. Multi-enzyme cascades have proven a versatile technique to synthesize and in situ regenerate nucleotide sugar.In this chapter, the functions and mechanisms of Leloir glycosyltransferases are revisited, and the advantage of prokaryotic sources and production systems is discussed. Moreover, in vivo and in vitro pathways for the synthesis of nucleotide sugar are reviewed. In the second part, recent and prominent examples of the application of Leloir glycosyltransferase are given, i.e., the synthesis of glycosaminoglycans, glycoconjugate vaccines, and human milk oligosaccharides as well as the re-glycosylation of biopharmaceuticals, and the status of automated glycan assembly is revisited.
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9
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Baráth M, Jakubčinová J, Konyariková Z, Kozmon S, Mikušová K, Bella M. Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2. Beilstein J Org Chem 2020; 16:1853-1862. [PMID: 32802202 PMCID: PMC7404141 DOI: 10.3762/bjoc.16.152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/09/2020] [Indexed: 12/02/2022] Open
Abstract
A series of ten novel ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones bearing a 1-O-phosphono moiety and three different substituents at C-2 has been prepared. Due to the structural similarities of these scaffolds to the native substrate of mycobacterial galactofuranosyltransferase GlfT2 in the transition state, we evaluated these compounds by computational methods, as well as in an enzyme assay for the possible inhibition of the mycobacterial galactan biosynthesis. Our data show that despite favorable docking scores to the active site of GlfT2, none of these compounds serve as efficient inhibitors of the enzymes involved in the mycobacterial galactan biosynthesis.
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Affiliation(s)
- Marek Baráth
- Institute of Chemistry Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia
| | - Jana Jakubčinová
- Institute of Chemistry Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia
| | - Zuzana Konyariková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, SK-842 15 Bratislava, Slovakia
| | - Stanislav Kozmon
- Institute of Chemistry Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia
| | - Katarína Mikušová
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, SK-842 15 Bratislava, Slovakia
| | - Maroš Bella
- Institute of Chemistry Slovak Academy of Sciences, Dúbravská cesta 9, SK-845 38 Bratislava, Slovakia
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Tvaroška I, Selvaraj C, Koča J. Selectins-The Two Dr. Jekyll and Mr. Hyde Faces of Adhesion Molecules-A Review. Molecules 2020; 25:molecules25122835. [PMID: 32575485 PMCID: PMC7355470 DOI: 10.3390/molecules25122835] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/27/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
Selectins belong to a group of adhesion molecules that fulfill an essential role in immune and inflammatory responses and tissue healing. Selectins are glycoproteins that decode the information carried by glycan structures, and non-covalent interactions of selectins with these glycan structures mediate biological processes. The sialylated and fucosylated tetrasaccharide sLex is an essential glycan recognized by selectins. Several glycosyltransferases are responsible for the biosynthesis of the sLex tetrasaccharide. Selectins are involved in a sequence of interactions of circulated leukocytes with endothelial cells in the blood called the adhesion cascade. Recently, it has become evident that cancer cells utilize a similar adhesion cascade to promote metastases. However, like Dr. Jekyll and Mr. Hyde’s two faces, selectins also contribute to tissue destruction during some infections and inflammatory diseases. The most prominent function of selectins is associated with the initial stage of the leukocyte adhesion cascade, in which selectin binding enables tethering and rolling. The first adhesive event occurs through specific non-covalent interactions between selectins and their ligands, with glycans functioning as an interface between leukocytes or cancer cells and the endothelium. Targeting these interactions remains a principal strategy aimed at developing new therapies for the treatment of immune and inflammatory disorders and cancer. In this review, we will survey the significant contributions to and the current status of the understanding of the structure of selectins and the role of selectins in various biological processes. The potential of selectins and their ligands as therapeutic targets in chronic and acute inflammatory diseases and cancer will also be discussed. We will emphasize the structural characteristic of selectins and the catalytic mechanisms of glycosyltransferases involved in the biosynthesis of glycan recognition determinants. Furthermore, recent achievements in the synthesis of selectin inhibitors will be reviewed with a focus on the various strategies used for the development of glycosyltransferase inhibitors, including substrate analog inhibitors and transition state analog inhibitors, which are based on knowledge of the catalytic mechanism.
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Affiliation(s)
- Igor Tvaroška
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovak Republic
- Correspondence: (I.T.); (J.K.); Tel.: +421-948-535-601 (I.T.); +420-731-682-606 (J.K.)
| | - Chandrabose Selvaraj
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Jaroslav Koča
- Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
- Correspondence: (I.T.); (J.K.); Tel.: +421-948-535-601 (I.T.); +420-731-682-606 (J.K.)
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Jakubčinová J, Kozmon S, Šesták S, Baráth M. Novel 1‐ O‐Sulfono‐α‐ d‐Fructofuranosyl Sulfones as Possible Inhibitors of Human GnT‐I Enzyme. ChemistrySelect 2020. [DOI: 10.1002/slct.202001098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jana Jakubčinová
- Institution of ChemistrySlovak Academy of Sciences Dúbravská cesta 9 84538 Bratislava Slovakia
| | - Stanislav Kozmon
- Institution of ChemistrySlovak Academy of Sciences Dúbravská cesta 9 84538 Bratislava Slovakia
| | - Sergej Šesták
- Institution of ChemistrySlovak Academy of Sciences Dúbravská cesta 9 84538 Bratislava Slovakia
| | - Marek Baráth
- Institution of ChemistrySlovak Academy of Sciences Dúbravská cesta 9 84538 Bratislava Slovakia
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12
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Kóňa J. How inverting β-1,4-galactosyltransferase-1 can quench a high charge of the by-product UDP3−in catalysis: a QM/MM study of enzymatic reaction with native and UDP-5′ thio galactose substrates. Org Biomol Chem 2020; 18:7585-7596. [DOI: 10.1039/d0ob01490g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The function of Asp252 in the catalysis of β-1,4-galactosyltransferase-1 may be the stabilization of a high charge of the by-product UDP3−by a substrate-assisted proton transfer reaction.
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Affiliation(s)
- J. Kóňa
- Institute of Chemistry
- Center for Glycomics
- Slovak Academy of Sciences
- 84538 Bratislava
- Slovak Republic
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13
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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: 59] [Impact Index Per Article: 11.8] [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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14
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Turupcu A, Poliak P, Margreitter C, Oostenbrink C, Staudacher E. UDP-N-acetyl-α-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase from the snail Biomphalaria glabrata - structural reflections. Glycoconj J 2019; 37:15-25. [PMID: 31396754 PMCID: PMC6994419 DOI: 10.1007/s10719-019-09886-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/02/2019] [Accepted: 07/18/2019] [Indexed: 11/26/2022]
Abstract
UDP-GalNAc:polypeptide GalNAc transferase (ppGalNAcT; EC 2.4.1.41) is the initiating enzyme for mucin-type O-glycosylation in animals. Members of this highly conserved glycosyltransferase family catalyse a single glycosidic linkage. They transfer an N-acetylgalactosamine (GalNAc) residue from an activated donor (UDP-GalNAc) to a serine or threonine of an acceptor polypeptide chain. A ppGalNAcT from the freshwater snail Biomphalaria glabrata is the only characterised member of this enzyme family from mollusc origin. In this work, we interpret previously published experimental characterization of this enzyme in the context of in silico models of the enzyme and its acceptor substrates. A homology model of the mollusc ppGalNAcT is created and various substrate peptides are modelled into the active site. We hypothesize about possible molecular interpretations of the available experimental data and offer potential explanations for observed substrate and cofactor specificity. Here, we review and synthesise the current knowledge of Bge-ppGalNAcT, supported by a molecular interpretation of the available data.
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Affiliation(s)
- Aysegül Turupcu
- Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Peter Poliak
- Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
- Department of Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, SK-812 37, Bratislava, Slovakia
| | - Christian Margreitter
- Randall Centre for Cell & Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 9RT, UK
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Erika Staudacher
- Department of Chemistry, Glycobiology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
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15
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Brás NF, Fernandes PA, Ramos MJ. Understanding the Rate‐Limiting Step of Glycogenolysis by Using QM/MM Calculations on Human Glycogen Phosphorylase. ChemMedChem 2018; 13:1608-1616. [DOI: 10.1002/cmdc.201800218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/02/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Natércia F. Brás
- REQUIMTE/UCIBIO, Departamento de Química e Bioquímica Faculdade de Ciências Universidade do Porto Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - Pedro A. Fernandes
- REQUIMTE/UCIBIO, Departamento de Química e Bioquímica Faculdade de Ciências Universidade do Porto Rua do Campo Alegre s/n 4169-007 Porto Portugal
| | - Maria J. Ramos
- REQUIMTE/UCIBIO, Departamento de Química e Bioquímica Faculdade de Ciências Universidade do Porto Rua do Campo Alegre s/n 4169-007 Porto Portugal
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16
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Trnka T, Tvaroška I, Koča J. Automated Training of ReaxFF Reactive Force Fields for Energetics of Enzymatic Reactions. J Chem Theory Comput 2017; 14:291-302. [DOI: 10.1021/acs.jctc.7b00870] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Igor Tvaroška
- Institute
of Chemistry, Slovak Academy of Sciences, 845 38 Bratislava, Slovak Republic
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17
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Bella M, Yan S, Šesták S, Kozmon S, Lin CH, Mucha J, Koóš M. Synthesis of a β- d
-Psicofuranosyl Sulfone and Inhibitory-Activity Evaluation Against N
-Acetylglucosaminyltransferase I. European J Org Chem 2017. [DOI: 10.1002/ejoc.201701102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Maroš Bella
- Department of Glycochemistry; Institute of Chemistry; Slovak Academy of Sciences; Dúbravská cesta 9 84538 Bratislava Slovakia
| | - Shi Yan
- Department of Chemistry; University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
| | - Sergej Šesták
- Department of Glycobiology; Institute of Chemistry; Slovak Academy of Sciences; Dúbravská cesta 9 84538 Bratislava Slovakia
| | - Stanislav Kozmon
- Department of Structure and Function of Saccharides; Institute of Chemistry; Slovak Academy of Sciences; Dúbravská cesta 9 84538 Bratislava Slovakia
| | - Chun-Hung Lin
- Institute of Biological Chemistry; Academia Sinica 128; Academia Road Sec. 2 115 Nankang Taipei Taiwan
| | - Ján Mucha
- Department of Glycobiology; Institute of Chemistry; Slovak Academy of Sciences; Dúbravská cesta 9 84538 Bratislava Slovakia
| | - Miroslav Koóš
- Department of Glycochemistry; Institute of Chemistry; Slovak Academy of Sciences; Dúbravská cesta 9 84538 Bratislava Slovakia
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18
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A water-assisted nucleophilic mechanism utilized by BphD, the meta-cleavage product hydrolase in biphenyl degradation. J Mol Graph Model 2017; 76:448-455. [DOI: 10.1016/j.jmgm.2017.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 11/22/2022]
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19
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Recognition of EGF-like domains by the Notch-modifying O-fucosyltransferase POFUT1. Nat Chem Biol 2017; 13:757-763. [DOI: 10.1038/nchembio.2381] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/21/2017] [Indexed: 01/17/2023]
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20
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Blanco Capurro JI, Hopkins CW, Pierdominici Sottile G, González Lebrero MC, Roitberg AE, Marti MA. Theoretical Insights into the Reaction and Inhibition Mechanism of Metal-Independent Retaining Glycosyltransferase Responsible for Mycothiol Biosynthesis. J Phys Chem B 2017; 121:471-478. [PMID: 27935720 DOI: 10.1021/acs.jpcb.6b10130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding enzymatic reactions with atomic resolution has proven in recent years to be of tremendous interest for biochemical research, and thus, the use of QM/MM methods for the study of reaction mechanisms is experiencing a continuous growth. Glycosyltransferases (GTs) catalyze the formation of glycosidic bonds, and are important for many biotechnological purposes, including drug targeting. Their reaction product may result with only one of the two possible stereochemical outcomes for the reacting anomeric center, and therefore, they are classified as either inverting or retaining GTs. While the inverting GT reaction mechanism has been widely studied, the retaining GT mechanism has always been controversial and several questions remain open to this day. In this work, we take advantage of our recent GPU implementation of a pure QM(DFT-PBE)/MM approach to explore the reaction and inhibition mechanism of MshA, a key retaining GT responsible for the first step of mycothiol biosynthesis, a low weight thiol compound found in pathogens like Mycobacterium tuberculosis that is essential for its survival under oxidative stress conditions. Our results show that the reaction proceeds via a front-side SNi-like concerted reaction mechanism (DNAN in IUPAC nomenclature) and has a 17.5 kcal/mol free energy barrier, which is in remarkable agreement with experimental data. Detailed analysis shows that the key reaction step is the diphosphate leaving group dissociation, leading to an oxocarbenium-ion-like transition state. In contrast, fluorinated substrate analogues increase the reaction barrier significantly, rendering the enzyme effectively inactive. Detailed analysis of the electronic structure along the reaction suggests that this particular inhibition mechanism is associated with fluorine's high electronegative nature, which hinders phosphate release and proper stabilization of the transition state.
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Affiliation(s)
- Juan I Blanco Capurro
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
| | - Chad W Hopkins
- Department of Physics, University of Florida , Gainesville, Florida 32611, United States
| | - Gustavo Pierdominici Sottile
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes , Sáenz Peña 352, Bernal B1876BXD, Argentina
| | - Mariano C González Lebrero
- Departamento de Quimica Inorgánica, Anlı́tica y Quı́mica Fı́sica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina.,Insituto de Quimica Inorgánica, Materiales Ambiente y Energı́a (INQUIMAE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad Universitaria , Intendente Guiraldes 2160, C1428EGA, Ciudad Autónoma de Buenos Aires, Argentina
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21
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Mendoza F, Lluch JM, Masgrau L. Computational insights into active site shaping for substrate specificity and reaction regioselectivity in the EXTL2 retaining glycosyltransferase. Org Biomol Chem 2017; 15:9095-9107. [DOI: 10.1039/c7ob01937h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
QM(DFT)/MM calculations and molecular dynamics simulations on wild-type retaining α1,4-N-acetylhexosaminyltransferase (EXTL2) and Arg293Ala, Asp246Ala, Arg293Ala/Asp246Ala and Asp246Glu mutants are used to understand the role of these two residues.
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Affiliation(s)
- Fernanda Mendoza
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Sede Concepción
- Talcahuano
| | - José M. Lluch
- Institut de Biotecnologia i de Biomedicina (IBB)
- Universitat Autònoma de Barcelona
- 08193 Bellaterra (Cerdanyola del Vallès)
- Barcelona
- Spain
| | - Laura Masgrau
- Institut de Biotecnologia i de Biomedicina (IBB)
- Universitat Autònoma de Barcelona
- 08193 Bellaterra (Cerdanyola del Vallès)
- Barcelona
- Spain
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22
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Janoš P, Trnka T, Kozmon S, Tvaroška I, Koča J. Different QM/MM Approaches To Elucidate Enzymatic Reactions: Case Study on ppGalNAcT2. J Chem Theory Comput 2016; 12:6062-6076. [PMID: 27787999 DOI: 10.1021/acs.jctc.6b00531] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hybrid QM/MM computational studies can provide invaluable insight into the mechanisms of enzymatic reactions that can be exploited for rational drug design. Various approaches are available for such studies. However, their strengths and weaknesses may not be immediately apparent. Using the retaining glycosyltransferase ppGalNAcT2 as a case study, we compare different methodologies used to obtain reaction paths and transition state information. Ab Initio MD using CPMD coupled with the String Method is used to derive the minimum free energy reaction path. The geometrical features of the free energy path, especially around the transition state, agree with the minimum potential energy path obtained by the much less computationally expensive Nudged Elastic Band method. The barrier energy, however, differs by 8 kcal/mol. The free energy surface generated by metadynamics provides a rough overview of the reaction and can confirm the physical relevance of optimized paths or provide an initial guess for path optimization methods. Calculations of enzymatic reactions are usually performed at best at the DFT level of theory. A comparison of widely used functionals with high-level DLPNO-CCSD(T)/CBS data on the potential energy profile serves as a validation of the usability of DFT for this type of enzymatic reaction. The M06-2X meta-hybrid functional in particular matches the DLPNO-CCSD(T)/CBS reference extremely well with errors within 1 kcal/mol. However, even pure-GGA functional OPBE provides sufficient accuracy for this type of study.
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Affiliation(s)
| | | | - Stanislav Kozmon
- Institute of Chemistry, Slovak Academy of Sciences , 845 38 Bratislava, Slovak Republic
| | - Igor Tvaroška
- Institute of Chemistry, Slovak Academy of Sciences , 845 38 Bratislava, Slovak Republic
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23
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Merino P, Delso I, Tejero T, Ghirardello M, Juste-Navarro V. Nucleoside Diphosphate Sugar Analogues that Target Glycosyltransferases. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201600396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Pedro Merino
- Department of Synthesis and Structure of Biomolecules; Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
| | - Ignacio Delso
- NMR Service, Center of Chemistry and Materials of Aragon (CEQMA); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
| | - Tomás Tejero
- Department of Synthesis and Structure of Biomolecules; Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
| | - Mattia Ghirardello
- Department of Synthesis and Structure of Biomolecules; Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
| | - Verónica Juste-Navarro
- Department of Synthesis and Structure of Biomolecules; Institute of Chemical Synthesis and Homogeneous Catalysis (ISQCH); University of Zaragoza, CSIC; Zaragoza, Aragón 50009 Spain
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24
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Hamada Y, Kanematsu Y, Tachikawa M. Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism. Biochemistry 2016; 55:5764-5771. [PMID: 27644888 DOI: 10.1021/acs.biochem.6b00267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an SN1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.
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Affiliation(s)
- Yojiro Hamada
- Division of Materials Science, Graduate School of Nanobioscience, Yokohama City University , Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan
| | - Yusuke Kanematsu
- Division of Materials Science, Graduate School of Nanobioscience, Yokohama City University , Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan.,Graduate School of Information Sciences, Hiroshima City University , Ozuka-Higashi 3-4-1, Asa-Minami-Ku, Hiroshima 731-3194, Japan
| | - Masanori Tachikawa
- Division of Materials Science, Graduate School of Nanobioscience, Yokohama City University , Seto 22-2, Kanazawa-ku, Yokohama 236-0027, Japan
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25
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Mendoza F, Gómez H, Lluch JM, Masgrau L. α1,4-N-Acetylhexosaminyltransferase EXTL2: The Missing Link for Understanding Glycosidic Bond Biosynthesis with Retention of Configuration. ACS Catal 2016. [DOI: 10.1021/acscatal.5b02945] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Fernanda Mendoza
- Institut
de Biotecnologia i de Biomedicina (IBB) and ‡Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Hansel Gómez
- Institut
de Biotecnologia i de Biomedicina (IBB) and ‡Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - José M. Lluch
- Institut
de Biotecnologia i de Biomedicina (IBB) and ‡Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Laura Masgrau
- Institut
de Biotecnologia i de Biomedicina (IBB) and ‡Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
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26
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Su H, Sheng X, Liu Y. Insights into the catalytic mechanism of N-acetylglucosaminidase glycoside hydrolase from Bacillus subtilis: a QM/MM study. Org Biomol Chem 2016; 14:3432-42. [DOI: 10.1039/c6ob00320f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
QM/MM calculations on NagZs fromBacillus subtilisfurther confirm NagZs to be glycoside phosphorylases rather than glycoside hydrolases.
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Affiliation(s)
- Hao Su
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Xiang Sheng
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
| | - Yongjun Liu
- Key Laboratory of Colloid and Interface Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
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27
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Ardèvol A, Rovira C. Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations. J Am Chem Soc 2015; 137:7528-47. [DOI: 10.1021/jacs.5b01156] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Albert Ardèvol
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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28
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Kumari M, Kozmon S, Kulhánek P, Štepán J, Tvaroška I, Koča J. Exploring reaction pathways for O-GlcNAc transferase catalysis. A string method study. J Phys Chem B 2015; 119:4371-81. [PMID: 25731954 DOI: 10.1021/jp511235f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The inverting O-GlcNAc glycosyltransferase (OGT) is an important post-translation enzyme, which catalyzes the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine (UDP-GlcNAc) to the hydroxyl group of the Ser/Thr of cytoplasmic, nuclear, and mitochondrial proteins. In the past, three different catalytic bases were proposed for the reaction: His498, α-phosphate, and Asp554. In this study, we used hybrid quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello molecular dynamics to investigate reaction paths using α-phosphate and Asp554 as the catalytic bases. The string method was used to calculate the free-energy reaction profiles of the tested mechanisms. During the investigations, an additional mechanism was observed. In this mechanism, a proton is transferred to α-phosphate via a water molecule. Our calculations show that the mechanism with α-phosphate acting as the base is favorable. This reaction has a rate-limiting free-energy barrier of 23.5 kcal/mol, whereas reactions utilizing Asp554 and water-assisted α-phosphate have barriers of 41.7 and 40.9 kcal/mol, respectively. Our simulations provide a new insight into the catalysis of OGT and may thus guide rational drug design of transition-state analogue inhibitors with potential therapeutic use.
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Affiliation(s)
- Manju Kumari
- †Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,‡Faculty of Science - National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stanislav Kozmon
- †Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,‡Faculty of Science - National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Kulhánek
- †Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,‡Faculty of Science - National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jakub Štepán
- ‡Faculty of Science - National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Igor Tvaroška
- †Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,§Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovak Republic
| | - Jaroslav Koča
- †Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,‡Faculty of Science - National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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29
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Liang DM, Liu JH, Wu H, Wang BB, Zhu HJ, Qiao JJ. Glycosyltransferases: mechanisms and applications in natural product development. Chem Soc Rev 2015; 44:8350-74. [DOI: 10.1039/c5cs00600g] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glycosylation reactions mainly catalyzed by glycosyltransferases (Gts) occur almost everywhere in the biosphere, and always play crucial roles in vital processes.
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Affiliation(s)
- Dong-Mei Liang
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jia-Heng Liu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Hao Wu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Bin-Bin Wang
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Hong-Ji Zhu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jian-Jun Qiao
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
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30
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Sladek V, Holka F, Tvaroška I. Ab initio modelling of the anomeric and exo anomeric effects in 2-methoxytetrahydropyran and 2-methoxythiane corrected for intramolecular BSSE. Phys Chem Chem Phys 2015; 17:18501-13. [DOI: 10.1039/c5cp02191j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxygen substitution in 2-methoxytetrahydropyran by sulphur in 2-methoxythiane approximately doubles the anomeric effect, which slows down enzymatic processing of 2-methoxythiane.
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Affiliation(s)
- Vladimir Sladek
- Institute of Chemistry
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
| | - Filip Holka
- Faculty of Materials Science and Technology in Trnava
- Slovak University of Technology in Bratislava
- SK-917 24 Trnava
- Slovakia
| | - Igor Tvaroška
- Institute of Chemistry
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
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