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Varga N, Smieško M, Jiang X, Jakob RP, Wagner B, Mühlethaler T, Dätwyler P, Zihlmann P, Rabbani S, Maier T, Schwardt O, Ernst B. Strengthening an Intramolecular Non-Classical Hydrogen Bond to Get in Shape for Binding. Angew Chem Int Ed Engl 2024; 63:e202406024. [PMID: 39072885 DOI: 10.1002/anie.202406024] [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: 04/03/2024] [Revised: 07/03/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
In this research article, we report on the strengthening of a non-classical hydrogen bond (C-H⋅⋅⋅O) by introducing electron withdrawing groups at the carbon atom. The approach is demonstrated on the example of derivatives of the physiological E-selectin ligand sialyl Lewisx (1, sLex). Its affinity is mainly due to a beneficial entropy term, which is predominantly caused by the pre-organization of sLex in its binding conformation. We have shown, that among the elements responsible for the pre-organization, the stabilization by a non-classical hydrogen bond between the H-C5 of l-fucose and the ring oxygen O5 of the neighboring d-galactose moiety is essential and yields 7.4 kJ mol-1. This effect could be further strengthened by replacing l-fucose by 6,6,6-trifluoro-l-fucose leading to an improved non-classical H-bond of 14.9 kJ mol-1, i.e., an improved pre-organization in the bioactive conformation. For a series of glycomimetics of sLex (1), this outcome could be confirmed by high field NMR-shifts of the H-C5Fuc, by X-ray diffraction analysis of glycomimetics co-crystallized with E-selectin as well as by isothermal titration calorimetry. Furthermore, the electron-withdrawing character of the CF3-group beneficially influences the pharmacokinetic properties of sLex mimetics. Thus, acid-stability, a prerequisite for gastrointestinal stability, could be substantially improved.
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Affiliation(s)
- Norbert Varga
- Department of Pharmaceutical Sciences, Molecular Pharmacy, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Martin Smieško
- Department of Pharmaceutical Sciences, Computational Pharmacy, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Xiaohua Jiang
- Department of Pharmaceutical Sciences, Molecular Pharmacy, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Roman P Jakob
- Department Biozentrum, Structural Area Focal Biology, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Beatrice Wagner
- Department of Pharmaceutical Sciences, Molecular Pharmacy, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Tobias Mühlethaler
- Department of Pharmaceutical Sciences, Molecular Pharmacy, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Philipp Dätwyler
- Department of Pharmaceutical Sciences, Molecular Pharmacy, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Pascal Zihlmann
- Department of Pharmaceutical Sciences, Molecular Pharmacy, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Said Rabbani
- Department of Pharmaceutical Sciences, Molecular Pharmacy, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Timm Maier
- Department Biozentrum, Structural Area Focal Biology, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Oliver Schwardt
- Department of Pharmaceutical Sciences, Molecular Pharmacy, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Beat Ernst
- Department of Pharmaceutical Sciences, Molecular Pharmacy, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
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Zhang H, Zhu L, Zhou Z, Wang D, Yang J, Wang S, Lou T. Advancements in the Heterologous Expression of Sucrose Phosphorylase and Its Molecular Modification for the Synthesis of Glycosylated Products. Molecules 2024; 29:4086. [PMID: 39274934 PMCID: PMC11397096 DOI: 10.3390/molecules29174086] [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: 07/16/2024] [Revised: 08/08/2024] [Accepted: 08/26/2024] [Indexed: 09/16/2024] Open
Abstract
Sucrose phosphorylase (SPase), a member of the glycoside hydrolase GH13 family, possesses the ability to catalyze the hydrolysis of sucrose to generate α-glucose-1-phosphate and can also glycosylate diverse substrates, showcasing a wide substrate specificity. This enzyme has found extensive utility in the fields of food, medicine, and cosmetics, and has garnered significant attention as a focal point of research in transglycosylation enzymes. Nevertheless, SPase encounters numerous obstacles in industrial settings, including low enzyme yield, inadequate thermal stability, mixed regioselectivity, and limited transglycosylation activity. In-depth exploration of efficient expression strategies and molecular modifications based on the crystal structure and functional information of SPase is now a critical research priority. This paper systematically reviews the source microorganisms, crystal structure, and catalytic mechanism of SPase, summarizes diverse heterologous expression systems based on expression hosts and vectors, and examines the application and molecular modification progress of SPase in synthesizing typical glycosylated products. Additionally, it anticipates the broad application prospects of SPase in industrial production and related research fields, laying the groundwork for its engineering modification and industrial application.
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Affiliation(s)
- Hongyu Zhang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Leting Zhu
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Zixuan Zhou
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Danyun Wang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Jinshan Yang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Suying Wang
- Tianjin Key Laboratory of Food Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Tingting Lou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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Mandal A, Ahmed J, Singh S, Goyal A. Structure elucidation of a multi-modular recombinant endoglucanase, AtGH9C-CBM3A-CBM3B from Acetivibrio thermocellus ATCC 27405 and its substrate binding analysis. Int J Biol Macromol 2024; 273:133212. [PMID: 38897502 DOI: 10.1016/j.ijbiomac.2024.133212] [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: 01/17/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/21/2024]
Abstract
Cellulases from GH9 family show endo-, exo- or processive endocellulase activity, but the reason behind the variation is unclear. A GH9 recombinant endoglucanase, AtGH9C-CBM3A-CBM3B from Acetivibrio thermocellus was structurally characterized for conformation, binding and dynamics assessment. Modeled AtGH9C-CBM3A-CBM3B depicted (α/α)6-barrel structure with Asp98, Asp101 and Glu489 acting as catalytic triad. CD results revealed 25.2 % α-helix, 18.4 % β-sheet and rest 56.4 % of random coils, corroborating with predictions from PSIPRED and SOPMA. MD simulation of AtGH9C-CBM3A-CBM3B bound cellotetraose showed structural stability and global compactness with lowered RMSD values (1.5 nm) as compared with only AtGH9C-CBM3A-CBM3B (1.8 nm) for 200 ns. Higher fluctuation in RMSF values in far-positioned CBM3B pointed to its redundancy in substrate binding. Docking studies showed maximum binding with cellotetraose (ΔG = -5.05 kcal/mol), with reduced affinity towards ligands with degree of polymerization (DP) lower (DP < 4) or higher than 4 (DP > 4). Processivity index displayed the enzyme to be processive with loop 3 (342-379 aa) possibly blocking the non-reducing end of cellulose chain, resulting in cellotetraose release. SAXS analysis of AtGH9C-CBM3A-CBM3B at 5 mg/mL displayed monodispersed state with fist-and-elbow shape in solution. Negative zeta potential of -24 mV at 5 mg/mL indicated stability and free from aggregation.
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Affiliation(s)
- Ardhendu Mandal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Jebin Ahmed
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Shweta Singh
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India; Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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Xie J, Luo M, Chen Q, Zhang Q, Qin L, Wang Y, Zhao Y, He Y. Hypolipidemic effect and gut microbiota regulation of Gypenoside aglycones in rats fed a high-fat diet. JOURNAL OF ETHNOPHARMACOLOGY 2024; 328:118066. [PMID: 38499259 DOI: 10.1016/j.jep.2024.118066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Gynostemma pentaphyllum (Thunb.) Makino has traditional applications in Chinese medicine to treat lipid abnormalities. Gypenosides (GPs), the main bioactive components of Gynostemma pentaphyllum, have been reported to exert hypolipidemic effects through multiple mechanisms. The lipid-lowering effects of GPs may be attributed to the aglycone portion resulting from hydrolysis of GPs by the gut microbiota. However, to date, there have been no reports on whether gypenoside aglycones (Agl), the primary bioactive constituents, can ameliorate hyperlipidemia by modulating the gut microbiota. AIM OF THE STUDY This study explored the potential therapeutic effects of gypenoside aglycone (Agl) in a rat model of high-fat diet (HFD)-induced hyperlipidemia. METHODS A hyperlipidemic rat model was established by feeding rats with a high-fat diet. Agl was administered orally, and serum lipid levels were analyzed. Molecular techniques, including RT-polymerase chain reaction (PCR) and fecal microbiota sequencing, were used to investigate the effects of Agl on lipid metabolism and gut microbiota composition. RESULTS Agl administration significantly reduced serum levels of total cholesterol (TC), triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C) and mitigated hepatic damage induced by HFD. Molecular investigations have revealed the modulation of key lipid metabolism genes and proteins by Agl. Notably, Agl treatment enriched the gut microbiota with beneficial genera, including Lactobacillus, Akkermansia, and Blautia and promoted specific shifts in Lactobacillus murinus, Firmicutes bacterium CAG:424, and Allobaculum stercoricanis. CONCLUSION This comprehensive study established Agl as a promising candidate for the treatment of hyperlipidemia. It also exhibits remarkable hypolipidemic and hepatoprotective properties. The modulation of lipid metabolism-related genes, along with the restoration of gut microbiota balance, provides mechanistic insights. Thus, Agl has great potential for clinical applications in hyperlipidemia management.
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Affiliation(s)
- Jian Xie
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi, 563000, China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China; 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine Zunyi Medical University, Zunyi, 563000, China; Department of Medical Genetics, Zunyi Medical University, Zunyi, 563000, China.
| | - Mingxia Luo
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi, 563000, China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China; 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine Zunyi Medical University, Zunyi, 563000, China.
| | - Qiuyi Chen
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi, 563000, China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China; 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine Zunyi Medical University, Zunyi, 563000, China.
| | - Qianru Zhang
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi, 563000, China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China; 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine Zunyi Medical University, Zunyi, 563000, China.
| | - Lin Qin
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi, 563000, China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China; 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine Zunyi Medical University, Zunyi, 563000, China.
| | - Yuhe Wang
- Department of Pharmacy, Affiliated Hospital of Zunyi Medical University, Zunyi, 563000, China.
| | - Yongxia Zhao
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi, 563000, China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China; 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine Zunyi Medical University, Zunyi, 563000, China.
| | - Yuqi He
- Guizhou Engineering Research Center of Industrial Key-Technology for Dendrobium Nobile, Zunyi Medical University, Zunyi, 563000, China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563000, China; 2011 Cooperative Inovational Center for Guizhou Traditional Chinese Medicine and Ethnic Medicine Zunyi Medical University, Zunyi, 563000, China.
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Ofman TP, Heming JJA, Nin-Hill A, Küllmer F, Moran E, Bennett M, Steneker R, Klein AM, Ruijgrok G, Kok K, Armstrong ZWB, Aerts JMFG, van der Marel GA, Rovira C, Davies GJ, Artola M, Codée JDC, Overkleeft HS. Conformational and Electronic Variations in 1,2- and 1,5a-Cyclophellitols and their Impact on Retaining α-Glucosidase Inhibition. Chemistry 2024; 30:e202400723. [PMID: 38623783 DOI: 10.1002/chem.202400723] [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: 02/22/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024]
Abstract
Glycoside hydrolases (glycosidases) take part in myriad biological processes and are important therapeutic targets. Competitive and mechanism-based inhibitors are useful tools to dissect their biological role and comprise a good starting point for drug discovery. The natural product, cyclophellitol, a mechanism-based, covalent and irreversible retaining β-glucosidase inhibitor has inspired the design of diverse α- and β-glycosidase inhibitor and activity-based probe scaffolds. Here, we sought to deepen our understanding of the structural and functional requirements of cyclophellitol-type compounds for effective human α-glucosidase inhibition. We synthesized a comprehensive set of α-configured 1,2- and 1,5a-cyclophellitol analogues bearing a variety of electrophilic traps. The inhibitory potency of these compounds was assessed towards both lysosomal and ER retaining α-glucosidases. These studies revealed the 1,5a-cyclophellitols to be the most potent retaining α-glucosidase inhibitors, with the nature of the electrophile determining inhibitory mode of action (covalent or non-covalent). DFT calculations support the ability of the 1,5a-cyclophellitols, but not the 1,2-congeners, to adopt conformations that mimic either the Michaelis complex or transition state of α-glucosidases.
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Affiliation(s)
- Tim P Ofman
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jurriaan J A Heming
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica), Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franques 1-11, E-08028, Barcelona, Spain
| | - Florian Küllmer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Elisha Moran
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Megan Bennett
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Roy Steneker
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Anne-Mei Klein
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijs Ruijgrok
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Ken Kok
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Zach W B Armstrong
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Johannes M F G Aerts
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gijsbert A van der Marel
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica), Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franques 1-11, E-08028, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020, Barcelona, Spain
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, United Kingdom
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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Avcı D, Özge Ö, Sönmez F, Tamer Ö, Başoğlu A, Atalay Y, Kurt BZ. In vitro α-glucosidase, docking and density functional theory studies on novel azide metal complexes. Future Med Chem 2024; 16:1109-1125. [PMID: 38916564 PMCID: PMC11229344 DOI: 10.1080/17568919.2024.2342650] [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: 01/26/2024] [Accepted: 04/04/2024] [Indexed: 06/26/2024] Open
Abstract
Aim: The goal of this study is to synthesize new metal complexes containing N-methyl-1-(pyridin-2-yl)methanimine and azide ligands as α-glucosidase inhibitors for Type 2 diabetes. Materials & methods: The target complexes (12-16) were synthesized by reacting N-methyl-1-(pyridin-2-yl)methanimine (L1) with sodium azide in the presence of corresponding metal salts. The investigation of target protein interactions, vibrational, electronic and nonlinear optical properties for these complexes was performed by molecular docking and density functional theory studies. Results: Among these complexes, complex 13 (IC50 = 0.2802 ± 0.62 μM) containing Hg ion showed the highest α-glucosidase inhibitory property. On the other hand, significant results were detected for complexes containing Cu and Ag ions. Conclusion: Complex 13 may be an alternate anti-diabetic inhibitor according to in vitro/docking results.
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Affiliation(s)
- Davut Avcı
- Sakarya University, Faculty of Science, Department of Physics, 54187, Sakarya, Turkey
| | - Özgen Özge
- Sakarya University, Faculty of Science, Department of Physics, 54187, Sakarya, Turkey
- Cappadocia University, Health Vocational School, Ürgüp, 50400, Nevşehir, Turkey
| | - Fatih Sönmez
- Sakarya University of Applied Sciences, Pamukova Vocational High School, 54055, Sakarya, Turkey
| | - Ömer Tamer
- Sakarya University, Faculty of Science, Department of Physics, 54187, Sakarya, Turkey
| | - Adil Başoğlu
- Sakarya University, Faculty of Science, Department of Physics, 54187, Sakarya, Turkey
| | - Yusuf Atalay
- Sakarya University, Faculty of Science, Department of Physics, 54187, Sakarya, Turkey
| | - Belma Zengin Kurt
- Bezmialem Vakif University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 34093Istanbul, Turkey
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7
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Liu B, Zou X, Zhang Y, Yang Y, Xu H, Tang F, Yu H, Xia F, Liu Z, Zhao J, Shi W, Huang W. Site- and Stereoselective Glycomodification of Biomolecules through Carbohydrate-Promoted Pictet-Spengler Reaction. Angew Chem Int Ed Engl 2024; 63:e202401394. [PMID: 38396356 DOI: 10.1002/anie.202401394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/25/2024]
Abstract
Carbohydrates play pivotal roles in an array of essential biological processes and are consequently involved in many diseases. To meet the needs of glycobiology research, chemical enzymatic and non-enzymatic methods have been developed to generate glycoconjugates with well-defined structures. Herein, harnessing the unique properties of C6-oxidized glycans, we report a straightforward and robust strategy for site- and stereoselective glycomodification of biomolecules with N-terminal tryptophan residues by a carbohydrate-promoted Pictet-Spengler reaction, which is not adapted to typical aldehyde substrates under biocompatible conditions. This method reliably delivers highly homogeneous glycoconjugates with stable linkages and thus has great potential for functional modulation of peptides and proteins in glycobiology research. Moreover, this reaction can be performed at the glycosites of glycopeptides, glycoproteins and living-cell surfaces in a site-specific manner. Control experiments indicated that the protected α-O atom of aldehyde donors and free N-H bond of the tryptamine motif are crucial for this reaction. Mechanistic investigations demonstrated that the reaction exhibited a first-order dependence on both tryptophan and glycan, and deprotonation/rearomatization of the pentahydro-β-carbolinium ion intermediate might be the rate-determining step.
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Affiliation(s)
- Bo Liu
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Xiangman Zou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing, 100049, China
- Key Laboratory of Structure-based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yue Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing, 100049, China
- Key Laboratory of Structure-based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yang Yang
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Hao Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, No. 138 Xianlin Rd, Nanjing, 210023, China
| | - Feng Tang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing, 100049, China
| | - Huixin Yu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing, 100049, China
- Key Laboratory of Structure-based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Fei Xia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing, 100049, China
| | - Zhi Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Jianwei Zhao
- Shenzhen HUASUAN Technology Co., Ltd, Shenzhen, 518055, China
| | - Wei Shi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
| | - Wei Huang
- School of Pharmaceutical Science and Technology, Hangzhou Institute of Advanced Study, Hangzhou, 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai, 201203, China
- University of Chinese Academy of Sciences, No.19 A Yuquan Road, Beijing, 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, No. 138 Xianlin Rd, Nanjing, 210023, China
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8
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Hu C, Wang Y, Wang W, Cui W, Jia X, Mayo KH, Zhou Y, Su J, Yuan Y. A trapped covalent intermediate as a key catalytic element in the hydrolysis of a GH3 β-glucosidase: An X-ray crystallographic and biochemical study. Int J Biol Macromol 2024; 265:131131. [PMID: 38527679 DOI: 10.1016/j.ijbiomac.2024.131131] [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: 01/10/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024]
Abstract
Glycoside hydrolases (GHs) are industrially important enzymes that hydrolyze glycosidic bonds in glycoconjugates. In this study, we found a GH3 β-glucosidase (CcBgl3B) from Cellulosimicrobium cellulans sp. 21 was able to selectively hydrolyze the β-1,6-glucosidic bond linked glucose of ginsenosides. X-ray crystallographic studies of the ligand complex ginsenoside-specific β-glucosidase provided a novel finding that support the catalytic mechanism of GH3. The substrate was clearly identified within the catalytic center of wild-type CcBgl3B, revealing that the C1 atom of the glucose was covalently bound to the Oδ1 group of the conserved catalytic nucleophile Asp264 as an enzyme-glycosyl intermediate. The glycosylated Asp264 could be identified by mass spectrometry. Through site-directed mutagenesis studies with Asp264, it was found that the covalent intermediate state formed by Asp264 and the substrate was critical for catalysis. In addition, Glu525 variants (E525A, E525Q and E525D) showed no or marginal activity against pNPβGlc; thus, this residue could supply a proton for the reaction. Overall, our study provides an insight into the catalytic mechanism of the GH3 enzyme CcBgl3B.
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Affiliation(s)
- Chenxing Hu
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Yibing Wang
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Weiyang Wang
- College of Life Science and Technology, Changchun University of Science & Technology, Changchun, Jilin 130022, China
| | - Wanli Cui
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Xinyue Jia
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Kevin H Mayo
- Department of Biochemistry, Molecular Biology & Biophysics, 6-155 Jackson Hall, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yifa Zhou
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Jiyong Su
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China.
| | - Ye Yuan
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China.
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9
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Lee J, Park JE, Lee D, Seo N, An HJ. Advancements in protein glycosylation biomarkers for ovarian cancer through mass spectrometry-based approaches. Expert Rev Mol Diagn 2024; 24:249-258. [PMID: 38112537 DOI: 10.1080/14737159.2023.2297933] [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: 08/17/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION Ovarian cancer, characterized by metastasis and reduced 5-year survival rates, stands as a substantial factor in the mortality of gynecological malignancies worldwide. The challenge of delayed diagnosis originates from vague early symptoms and the absence of efficient screening and diagnostic biomarkers for early cancer detection. Recent studies have explored the intricate interplay between ovarian cancer and protein glycosylation, unveiling the potential significance of glycosylation-oriented biomarkers. AREAS COVERED This review examines the progress in glycosylation biomarker research, with particular emphasis on advances driven by mass spectrometry-based technologies. We document milestones achieved, discuss encountered limitations, and also highlight potential areas for future research and development of protein glycosylation biomarkers for ovarian cancer. EXPERT OPINION The association of glycosylation in ovarian cancer is well known, but current research lacks desired sensitivity and specificity for early detection. Notably, investigations into protein-specific and site-specific glycoproteomics have the potential to significantly enhance our understanding of ovarian cancer and facilitate the identification of glycosylation-based biomarkers. Furthermore, the integration of advanced mass spectrometry techniques with AI-driven analysis and glycome databases holds the promise for revolutionizing biomarker discovery for ovarian cancer, ultimately transforming diagnosis and improving patient outcomes.
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Affiliation(s)
- Jua Lee
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Ji Eun Park
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
- Asia Glycomics Reference Site, Daejeon, Republic of Korea
| | - Daum Lee
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
- Asia Glycomics Reference Site, Daejeon, Republic of Korea
| | - Nari Seo
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
- Asia Glycomics Reference Site, Daejeon, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
- Asia Glycomics Reference Site, Daejeon, Republic of Korea
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10
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Iqbal H, Ilyas K, Akash MSH, Rehman K, Hussain A, Iqbal J. Real-time fluorescent monitoring of phase I xenobiotic-metabolizing enzymes. RSC Adv 2024; 14:8837-8870. [PMID: 38495994 PMCID: PMC10941266 DOI: 10.1039/d4ra00127c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024] Open
Abstract
This article explores the intricate landscape of advanced fluorescent probes crafted for the detection and real-time monitoring of phase I xenobiotic-metabolizing enzymes. Employing state-of-the-art technologies, such as fluorescence resonance energy transfer, intramolecular charge transfer, and solid-state luminescence enhancement, this article unfolds a multifaceted approach to unraveling the dynamics of enzymatic processes within living systems. This encompassing study involves the development and application of a diverse range of fluorescent probes, each intricately designed with tailored mechanisms to heighten sensitivity, providing dynamic insights into phase I xenobiotic-metabolizing enzymes. Understanding the role of phase I xenobiotic-metabolizing enzymes in these pathophysiological processes, is essential for both medical research and clinical practice. This knowledge can guide the development of approaches to prevent, diagnose, and treat a broad spectrum of diseases and conditions. This adaptability underscores their potential clinical applications in cancer diagnosis and personalized medicine. Noteworthy are the trifunctional fluorogenic probes, uniquely designed not only for fluorescence-based cellular imaging but also for the isolation of cellular glycosidases. This innovative feature opens novel avenues for comprehensive studies in enzyme biology, paving the way for potential therapeutic interventions. The research accentuates the selectivity and specificity of the probes, showcasing their proficiency in distinguishing various enzymes and their isoforms. The sophisticated design and successful deployment of these fluorescent probes mark significant advancements in enzymology, providing powerful tools for both researchers and clinicians. Beyond their immediate applications, these probes offer illuminating insights into disease mechanisms, facilitating early detection, and catalyzing the development of targeted therapeutic interventions. This work represents a substantial leap forward in the field, promising transformative implications for understanding and addressing complex biological processes. In essence, this research heralds a new era in the development of fluorescent probes, presenting a comprehensive and innovative approach that not only expands the understanding of cellular enzyme activities but also holds great promise for practical applications in clinical settings and therapeutic endeavors.
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Affiliation(s)
- Hajra Iqbal
- Department of Pharmaceutical Chemistry, Government College University Faisalabad Pakistan
| | - Kainat Ilyas
- Department of Pharmaceutical Chemistry, Government College University Faisalabad Pakistan
| | | | - Kanwal Rehman
- Department of Pharmacy, The Women University Multan Pakistan
| | - Amjad Hussain
- Institute of Chemistry, University of Okara Okara Pakistan
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad, Abbottabad Campus Abbottabad 22044 Pakistan
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11
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Wu J, Liang C, Li Y, Zeng Y, Sun X, Jiang P, Chen W, Xiong D, Jin J, Tang S. Engineering and application of LacI mutants with stringent expressions. Microb Biotechnol 2024; 17:e14427. [PMID: 38465475 PMCID: PMC10926051 DOI: 10.1111/1751-7915.14427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Optimal transcriptional regulatory circuits are expected to exhibit stringent control, maintaining silence in the absence of inducers while exhibiting a broad induction dynamic range upon the addition of effectors. In the Plac /LacI pair, the promoter of the lac operon in Escherichia coli is characterized by its leakiness, attributed to the moderate affinity of LacI for its operator target. In response to this limitation, the LacI regulatory protein underwent engineering to enhance its regulatory properties. The M7 mutant, carrying I79T and N246S mutations, resulted in the lac promoter displaying approximately 95% less leaky expression and a broader induction dynamic range compared to the wild-type LacI. An in-depth analysis of each mutation revealed distinct regulatory profiles. In contrast to the wild-type LacI, the M7 mutant exhibited a tighter binding to the operator sequence, as evidenced by surface plasmon resonance studies. Leveraging the capabilities of the M7 mutant, a high-value sugar biosensor was constructed. This biosensor facilitated the selection of mutant galactosidases with approximately a seven-fold improvement in specific activity for transgalactosylation. Consequently, this advancement enabled enhanced biosynthesis of galacto-oligosaccharides (GOS).
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Affiliation(s)
- Jieyuan Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Chaoning Liang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Yufei Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yueting Zeng
- School of Life SciencesHebei UniversityBaodingChina
| | - Xu Sun
- Beijing Key Laboratory of Plant Resources Research and DevelopmentBeijing Technology and Business UniversityBeijingChina
| | - Peixia Jiang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Dandan Xiong
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jian‐Ming Jin
- Beijing Key Laboratory of Plant Resources Research and DevelopmentBeijing Technology and Business UniversityBeijingChina
| | - Shuang‐Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial ResourcesInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
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12
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Munzone A, Eijsink VGH, Berrin JG, Bissaro B. Expanding the catalytic landscape of metalloenzymes with lytic polysaccharide monooxygenases. Nat Rev Chem 2024; 8:106-119. [PMID: 38200220 DOI: 10.1038/s41570-023-00565-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have an essential role in global carbon cycle, industrial biomass processing and microbial pathogenicity by catalysing the oxidative cleavage of recalcitrant polysaccharides. Despite initially being considered monooxygenases, experimental and theoretical studies show that LPMOs are essentially peroxygenases, using a single copper ion and H2O2 for C-H bond oxygenation. Here, we examine LPMO catalysis, emphasizing key studies that have shaped our comprehension of their function, and address side and competing reactions that have partially obscured our understanding. Then, we compare this novel copper-peroxygenase reaction with reactions catalysed by haem iron enzymes, highlighting the different chemistries at play. We conclude by addressing some open questions surrounding LPMO catalysis, including the importance of peroxygenase and monooxygenase reactions in biological contexts, how LPMOs modulate copper site reactivity and potential protective mechanisms against oxidative damage.
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Affiliation(s)
- Alessia Munzone
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jean-Guy Berrin
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Bastien Bissaro
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France.
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13
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Erkanli ME, El-Halabi K, Kim JR. Exploring the diversity of β-glucosidase: Classification, catalytic mechanism, molecular characteristics, kinetic models, and applications. Enzyme Microb Technol 2024; 173:110363. [PMID: 38041879 DOI: 10.1016/j.enzmictec.2023.110363] [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: 09/25/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 12/04/2023]
Abstract
High-value chemicals and energy-related products can be produced from biomass. Biorefinery technology offers a sustainable and cost-effective method for this high-value conversion. β-glucosidase is one of the key enzymes in biorefinery processes, catalyzing the production of glucose from aryl-glycosides and cello-oligosaccharides via the hydrolysis of β-glycosidic bonds. Although β-glucosidase plays a critical catalytic role in the utilization of cellulosic biomass, its efficacy is often limited by substrate or product inhibitions, low thermostability, and/or insufficient catalytic activity. To provide a detailed overview of β-glucosidases and their benefits in certain desired applications, we collected and summarized extensive information from literature and public databases, covering β-glucosidases in different glycosidase hydrolase families and biological kingdoms. These β-glucosidases show differences in amino acid sequence, which are translated into varying degrees of the molecular properties critical in enzymatic applications. This review describes studies on the diversity of β-glucosidases related to the classification, catalytic mechanisms, key molecular characteristics, kinetics models, and applications, and highlights several β-glucosidases displaying high stability, activity, and resistance to glucose inhibition suitable for desired biotechnological applications.
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Affiliation(s)
- Mehmet Emre Erkanli
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, United States
| | - Khalid El-Halabi
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, United States
| | - Jin Ryoun Kim
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, United States.
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14
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Kaenying W, Tagami T, Suwan E, Pitsanuwong C, Chomngam S, Okuyama M, Kongsaeree P, Kimura A, Kongsaeree PT. Structural and mutational analysis of glycoside hydrolase family 1 Br2 β-glucosidase derived from bovine rumen metagenome. Heliyon 2023; 9:e21923. [PMID: 38034805 PMCID: PMC10685196 DOI: 10.1016/j.heliyon.2023.e21923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/21/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Ruminant animals rely on the activities of β-glucosidases from residential microbes to convert feed fibers into glucose for further metabolic uses. In this report, we determined the structures of Br2, which is a glycoside hydrolase family 1 β-glucosidase from the bovine rumen metagenome. Br2 folds into a classical (β/α)8-TIM barrel domain but displays unique structural features at loop β5→α5 and α-helix 5, resulting in different positive subsites from those of other GH1 enzymes. Br2 exhibited the highest specificity toward laminaritriose, suggesting its involvement in β-glucan hydrolysis in digested feed. We then substituted the residues at subsites +1 and + 2 of Br2 with those of Halothermothrix orenii β-glucosidase. The C170E and C221T mutations provided favorable interactions with glucooligosaccharide substrates at subsite +2, while the A219N mutation probably improved the substrate preference for cellobiose and gentiobiose relative to laminaribiose at subsite +1. The N407Y mutation increased the affinity toward cellooligosaccharides. These results give further insights into the molecular determinants responsible for substrate specificity in GH1 β-glucosidases and may provide a basis for future enzyme engineering applications.
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Affiliation(s)
- Wilaiwan Kaenying
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Takayoshi Tagami
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Eukote Suwan
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok 10900, Thailand
| | - Chariwat Pitsanuwong
- Faculty of Science and Technology, Suan Sunandha Rajabhat University, Bangkok 10300, Thailand
| | - Sinchai Chomngam
- Department of Chemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Masayuki Okuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Palangpon Kongsaeree
- Department of Chemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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15
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Devi S, Carberry AE, Zickuhr GM, Dickson AL, Harrison DJ, da Silva RG. Human 2'-Deoxynucleoside 5'-Phosphate N-Hydrolase 1: Mechanism of 2'-Deoxyuridine 5'-Monophosphate Hydrolysis. Biochemistry 2023; 62:2658-2668. [PMID: 37582341 PMCID: PMC10483697 DOI: 10.1021/acs.biochem.3c00369] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/01/2023] [Indexed: 08/17/2023]
Abstract
The enzyme 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 (DNPH1) catalyzes the N-ribosidic bond cleavage of 5-hydroxymethyl-2'-deoxyuridine 5'-monophosphate to generate 2-deoxyribose 5-phosphate and 5-hydroxymethyluracil. DNPH1 accepts other 2'-deoxynucleoside 5'-monophosphates as slow-reacting substrates. DNPH1 inhibition is a promising strategy to overcome resistance to and potentiate anticancer poly(ADP-ribose) polymerase inhibitors. We solved the crystal structure of unliganded human DNPH1 and took advantage of the slow reactivity of 2'-deoxyuridine 5'-monophosphate (dUMP) as a substrate to obtain a crystal structure of the DNPH1:dUMP Michaelis complex. In both structures, the carboxylate group of the catalytic Glu residue, proposed to act as a nucleophile in covalent catalysis, forms an apparent low-barrier hydrogen bond with the hydroxyl group of a conserved Tyr residue. The crystal structures are supported by functional data, with liquid chromatography-mass spectrometry analysis showing that DNPH1 incubation with dUMP leads to slow yet complete hydrolysis of the substrate. A direct UV-vis absorbance-based assay allowed characterization of DNPH1 kinetics at low dUMP concentrations. A bell-shaped pH-rate profile indicated that acid-base catalysis is operational and that for maximum kcat/KM, two groups with an average pKa of 6.4 must be deprotonated, while two groups with an average pKa of 8.2 must be protonated. A modestly inverse solvent viscosity effect rules out diffusional processes involved in dUMP binding to and possibly uracil release from the enzyme as rate limiting to kcat/KM. Solvent deuterium isotope effects on kcat/KM and kcat were inverse and unity, respectively. A reaction mechanism for dUMP hydrolysis is proposed.
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Affiliation(s)
- Suneeta Devi
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, U.K.
| | - Anna E. Carberry
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, U.K.
| | - Greice M. Zickuhr
- School
of Medicine, University of St Andrews, St Andrews KY16 9TF, U.K.
| | - Alison L. Dickson
- School
of Medicine, University of St Andrews, St Andrews KY16 9TF, U.K.
- NuCana
Plc, Edinburgh EH12 9DT, U.K.
| | - David J. Harrison
- School
of Medicine, University of St Andrews, St Andrews KY16 9TF, U.K.
- NuCana
Plc, Edinburgh EH12 9DT, U.K.
| | - Rafael G. da Silva
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, U.K.
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16
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Pengthaisong S, Piniello B, Davies GJ, Rovira C, Ketudat Cairns JR. Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation. ACS Catal 2023; 13:5850-5863. [PMID: 37180965 PMCID: PMC10167657 DOI: 10.1021/acscatal.3c00620] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/15/2023] [Indexed: 05/16/2023]
Abstract
Retaining glycoside hydrolases use acid/base catalysis with an enzymatic acid/base protonating the glycosidic bond oxygen to facilitate leaving-group departure alongside attack by a catalytic nucleophile to form a covalent intermediate. Generally, this acid/base protonates the oxygen laterally with respect to the sugar ring, which places the catalytic acid/base and nucleophile carboxylates within about 4.5-6.5 Å of each other. However, in glycoside hydrolase (GH) family 116, including disease-related human acid β-glucosidase 2 (GBA2), the distance between the catalytic acid/base and the nucleophile is around 8 Å (PDB: 5BVU) and the catalytic acid/base appears to be above the plane of the pyranose ring, rather than being lateral to that plane, which could have catalytic consequences. However, no structure of an enzyme-substrate complex is available for this GH family. Here, we report the structures of Thermoanaerobacterium xylanolyticum β-glucosidase (TxGH116) D593N acid/base mutant in complexes with cellobiose and laminaribiose and its catalytic mechanism. We confirm that the amide hydrogen bonding to the glycosidic oxygen is in a perpendicular rather than lateral orientation. Quantum mechanics/molecular mechanics (QM/MM) simulations of the glycosylation half-reaction in wild-type TxGH116 indicate that the substrate binds with the nonreducing glucose residue in an unusual relaxed 4C1 chair at the -1 subsite. Nevertheless, the reaction can still proceed through a 4H3 half-chair transition state, as in classical retaining β-glucosidases, as the catalytic acid D593 protonates the perpendicular electron pair. The glucose C6OH is locked in a gauche, trans orientation with respect to the C5-O5 and C4-C5 bonds to facilitate perpendicular protonation. These data imply a unique protonation trajectory in Clan-O glycoside hydrolases, which has strong implications for the design of inhibitors specific to either lateral protonators, such as human GBA1, or perpendicular protonators, such as human GBA2.
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Affiliation(s)
- Salila Pengthaisong
- School
of Chemistry, Institute of Science, Suranaree
University of Technology, Nakhon
Ratchasima 30000, Thailand
- Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Beatriz Piniello
- Departament
de Quımica Inorgánica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Gideon J. Davies
- Department
of Chemistry, University of York, Heslington, York YO10
5DD, U.K.
| | - Carme Rovira
- Departament
de Quımica Inorgánica i Orgànica (Secció
de Química Orgànica) and Institut de Química
Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avancats (ICREA), 08010 Barcelona, Spain
| | - James R. Ketudat Cairns
- School
of Chemistry, Institute of Science, Suranaree
University of Technology, Nakhon
Ratchasima 30000, Thailand
- Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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17
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Kaenying W, Choengpanya K, Tagami T, Wattana-Amorn P, Lang W, Okuyama M, Li YK, Kimura A, Kongsaeree PT. Crystal structure and identification of amino acid residues for catalysis and binding of GH3 AnBX β-xylosidase from Aspergillus niger. Appl Microbiol Biotechnol 2023; 107:2335-2349. [PMID: 36877249 DOI: 10.1007/s00253-023-12445-z] [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: 12/06/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 03/07/2023]
Abstract
β-Xylosidases catalyze the hydrolysis of xylooligosaccharides to xylose in the final step of hemicellulose degradation. AnBX, which is a GH3 β-xylosidase from Aspergillus niger, has a high catalytic efficiency toward xyloside substrates. In this study, we report the three-dimensional structure and the identification of catalytic and substrate binding residues of AnBX by performing site-directed mutagenesis, kinetic analysis, and NMR spectroscopy-associated analysis of the azide rescue reaction. The structure of the E88A mutant of AnBX, determined at 2.5-Å resolution, contains two molecules in the asymmetric unit, each of which is composed of three domains, namely an N-terminal (β/α)8 TIM-barrel-like domain, an (α/β)6 sandwich domain, and a C-terminal fibronectin type III domain. Asp288 and Glu500 of AnBX were experimentally confirmed to act as the catalytic nucleophile and acid/base catalyst, respectively. The crystal structure revealed that Trp86, Glu88 and Cys289, which formed a disulfide bond with Cys321, were located at subsite -1. Although the E88D and C289W mutations reduced catalytic efficiency toward all four substrates tested, the substitution of Trp86 with Ala, Asp and Ser increased the substrate preference for glucoside relative to xyloside substrates, indicating that Trp86 is responsible for the xyloside specificity of AnBX. The structural and biochemical information of AnBX obtained in this study provides invaluable insight into modulating the enzymatic properties for the hydrolysis of lignocellulosic biomass. KEY POINTS: • Asp288 and Glu500 of AnBX are the nucleophile and acid/base catalyst, respectively • Glu88 and the Cys289-Cys321 disulfide bond are crucial for the catalytic activity of AnBX • The W86A and W86S mutations in AnBX increased the preference for glucoside substrates.
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Affiliation(s)
- Wilaiwan Kaenying
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Khuanjarat Choengpanya
- Interdisciplinary Graduate Program in Genetic Engineering, Faculty of Graduate School, Kasetsart University, Bangkok, 10900, Thailand
- Program in Basic Science, Maejo University Phrae Campus, Phrae, 54140, Thailand
| | - Takayoshi Tagami
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Pakorn Wattana-Amorn
- Department of Chemistry, Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Weeranuch Lang
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Masayuki Okuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Yaw-Kuen Li
- Department of Applied Chemistry, College of Science, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Prachumporn T Kongsaeree
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Genetic Engineering, Faculty of Graduate School, Kasetsart University, Bangkok, 10900, Thailand.
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18
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Özge Ö, Avcı D, Sönmez F, Tamer Ö, Dege N, Başoğlu A, Atalay Y, Kurt BZ. Synthesis, DFT calculations, α‐glucosidase inhibitor activity, and docking studies on Schiff base metal complexes containing isothiocyanate. Appl Organomet Chem 2023. [DOI: 10.1002/aoc.7084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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19
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Molecular cloning and production of recombinant Pcal_0672, a family GH57 glycoside hydrolase from Pyrobaculum calidifontis. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01338-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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20
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Zhou HY, Chen Q, Zhang YF, Chen DD, Yi XN, Chen DS, Cheng XP, Li M, Wang HY, Chen KQ, Liu ZQ, Zheng YG. Improving the catalytic activity of β-glucosidase from Coniophora puteana via semi-rational design for efficient biomass cellulose degradation. Enzyme Microb Technol 2023; 164:110188. [PMID: 36584665 DOI: 10.1016/j.enzmictec.2022.110188] [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: 09/09/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
In order to improve the degradation activity of β-glucosidase (CpBgl) from Coniophora puteana, the structural modification was conducted. The enzyme activity of mutants CpBgl-Q20C and CpBgl-A240S was increased by 65.75% and 58.58%, respectively. These mutants exhibited maximum activity under the same conditions as wild-type CpBgl (65 ℃ and pH 5.0), slightly improved stabilities compared that of the wild-type, and remarkably enhanced activities in the presence of Mn2+ or Fe2+. The Vmax of CpBgl-Q20C and CpBgl-A240S was increased to 138.18 and 125.14 μmol/mg/min, respectively, from 81.34 μmol/mg/min of the wild-type, and the catalysis efficiency (kcat/Km) of CpBgl-Q20C (335.79 min-1/mM) and CpBgl-A240S (281.51 min-1/mM) was significantly improved compared with that of the wild-type (149.12 min-1/mM). When the mutant CpBgl-Q20C were used in the practical degradation of different biomasses, the glucose yields of filter paper, corncob residue, and fungi mycelia residue were increased by 17.68%, 25.10%, and 20.37%, respectively. The spatial locations of the mutation residues in the architecture of CpBgl and their unique roles in the enzyme-substrate binding and catalytic efficiency were probed in this work. These results laid a foundation for evolution of other glycoside hydrolases and the industrial bio-degradation of cellulosic biomass in nature.
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Affiliation(s)
- Hai-Yan Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Qi Chen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Yi-Feng Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Dou-Dou Chen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Xiao-Nan Yi
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - De-Shui Chen
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Xin-Ping Cheng
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Hong-Yan Wang
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Kai-Qian Chen
- Zhejiang Huakang Pharmaceutical Co., LTD., 18 Huagong Road, Huabu Town, Kaihua 324302, People's Republic of China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
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21
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Takeoka M, Hoki Y, Yoshinaka T, Hirano K, Mitsui Y, Doi T, Takemura A, Asano T, Katoh R, Nose A, Kozaki D. Multi-Functional Separation Mode-Ion Chromatography Using L-Pyroglutamic Acid Eluent for Simultaneous Determination of Sugars, Organic Acids, and Ethanol during Multiple Parallel Fermentation of Rice Wine. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2023. [DOI: 10.1080/03610470.2022.2158437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- Marino Takeoka
- Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi, Japan
| | | | - Taichi Yoshinaka
- Department of Brewing, Tsukasa Botan Brewing Company, Limited, Kochi, Japan
| | - Kentarou Hirano
- Department of Brewing, Tsukasa Botan Brewing Company, Limited, Kochi, Japan
| | - Yuta Mitsui
- Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi, Japan
| | | | - Akihiko Takemura
- Department of Brewing, Tsukasa Botan Brewing Company, Limited, Kochi, Japan
| | - Tohru Asano
- Department of Brewing, Tsukasa Botan Brewing Company, Limited, Kochi, Japan
| | | | - Akira Nose
- Department of Nutritional Science, Faculty of Human Ecology, Yasuda Women’s University, Hiroshima, Japan
| | - Daisuke Kozaki
- Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi, Japan
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22
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Paulsen Thoresen P, Lange H, Rova U, Christakopoulos P, Matsakas L. Role and importance of solvents for the fractionation of lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2023; 369:128447. [PMID: 36496118 DOI: 10.1016/j.biortech.2022.128447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Lignocellulosic biomass is one of the most important renewable materials to replace carbon-based fossil resources. Solvent-based fractionation is a promising route for fractionation of biomass into its major components. Processing is governed by the employed solvent-systems properties. This review sheds light on the factors governing both dissolution and potential reactivities of the chemical structures present in lignocellulose, highlighting how proper understanding of the underlying mechanisms and interactions between solute and solvent help to choose proper systems for specific fractionation needs. Structural and chemical differences between the carbohydrate-based structural polymers and lignin require very different solvents capabilities in terms of causing and eventually stabilizing conformational changes and consequent activation of bonds to be cleaved by other active components in the. A consideration of potential depolymerization events during dissolution and energetic aspects of the dissolution process considering the contribution of polymer functionalities allow for a mapping of solvent suitability for biomass fractionation.
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Affiliation(s)
- Petter Paulsen Thoresen
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, 971-87, Sweden
| | - Heiko Lange
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, 971-87, Sweden; Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Ulrika Rova
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, 971-87, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, 971-87, Sweden
| | - Leonidas Matsakas
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, 971-87, Sweden.
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23
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Garg P, Manoj N. Structure of an iminosugar complex of a glycoside hydrolase family 5 lichenase provides insights into the active site. Biochimie 2023; 204:69-77. [PMID: 36084911 DOI: 10.1016/j.biochi.2022.09.001] [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: 10/11/2021] [Revised: 05/23/2022] [Accepted: 09/01/2022] [Indexed: 01/12/2023]
Abstract
TmCel5B is a lichenase belonging to glycoside hydrolase family 5 subfamily 36 (GH5_36). To gain insights into the active site of this subfamily which contains multifunctional endoglycanases, we determined the crystal structure of TmCel5B in complex with an iminosugar, 1-deoxynojiromycin (DNJ). DNJ is bound to the -1 subsite, making a network of non-covalent interactions with the acid/base residue Glu139, the nucleophile Glu259, and with other residues that are conserved across the GH5 family. The catalytic site displayed a Glu-Arg-Glu triad of the catalytic glutamates that is unique to the GH5_36 subfamily. Structural comparison of active sites of GH5_36 homologs revealed divergent residues and loop regions that are likely molecular determinants of homolog-specific properties. Furthermore, a comparative analysis of the binding modes of iminocyclitol complexes of GH5 homologs revealed the structural basis of their binding to GH5 glycosidases, in which the subsite binding location, the interactions of the ligand with specific conserved residues, and the electrostatic interactions of the catalytic glutamates with the ring nitrogen, are crucial.
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Affiliation(s)
- Puneet Garg
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
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24
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Li P, Wang X, Zhang C, Xu D. Processive binding mechanism of Cel9G from Clostridium cellulovorans: molecular dynamics and free energy landscape investigations. Phys Chem Chem Phys 2023; 25:646-657. [DOI: 10.1039/d2cp04830b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The processive binding mechanism of cellulose by Cel9G from C. cellulovorans was investigated by MD and metadynamics simulations.
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Affiliation(s)
- Penghui Li
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Chunchun Zhang
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Sichuan, Chengdu, 610064, P. R. China
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25
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Chen W, Dong Y, Zheng L, Lai Y, Li F, Zhou L, Wang B, You M, He W. An inducible gene from glycoside hydrolase one family of Plutella xylostella decreases larval survival when feeding on host plant. Front Physiol 2022; 13:1013092. [PMID: 36338470 PMCID: PMC9632345 DOI: 10.3389/fphys.2022.1013092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022] Open
Abstract
Glycoside hydrolase family 1 (GH1) members exhibit a broad substrate spectrum and play important roles in insect-plant interactions, such as the defensive β-glucosidase and β-thioglucosidase (so-called myrosinase). However, knowledge about the expression profiling and function of glycoside hydrolase family 1 members in a specialist pest of crucifers Plutella xylostella is still limited. In this study, 13 putative glycoside hydrolase family 1 members of P. xylostella were identified based on the sequence characteristics, while no myrosinase activity was detectable in P. xylostella using gas chromatography-mass spectrometry (GC-MS). Expression profiling of these glycoside hydrolase family 1 members identified the midgut-specific gene Px008848 that is induced by host plant. Further experiments revealed that the in vitro expressed Px008848 protein had β-glucosidase activity and the survival rate of the larvae feeding on wounded Arabidopsis thaliana leaves declined when leaves were treated with purified Px008848 protein. When CRISPR/Cas9-based homozygous mutant larvae of Px008848 and wild-type larvae were respectively transferred onto the A. thaliana, the larval survival rate of the mutant larvae was significantly higher than that of the wild-type individuals. Our work showed that certain insect glycoside hydrolase family 1 gene may have negative effect on the development of larvae feeding on the host plant, which broadened our understandings on the evolutionary function of this gene family in the insect-plant interaction.
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Affiliation(s)
- Wei Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Ganzhou Key Laboratory of Greenhouse Vegetable/College of Life Sciences, Gannan Normal University, Ganzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhong Dong
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Ganzhou Key Laboratory of Greenhouse Vegetable/College of Life Sciences, Gannan Normal University, Ganzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ling Zheng
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yingfang Lai
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Feifei Li
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li Zhou
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Beibei Wang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Minsheng You
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Minsheng You, ; Weiyi He,
| | - Weiyi He
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Minsheng You, ; Weiyi He,
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26
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Yadav V, Ahmed J, Thakur A, Vishwakarma P, Singh S, Kaur P, Goyal A. Structural insights of a putative β-1,4-xylosidase (PsGH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans. Int J Biol Macromol 2022; 221:751-762. [PMID: 36099997 DOI: 10.1016/j.ijbiomac.2022.09.072] [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: 06/28/2022] [Revised: 08/29/2022] [Accepted: 09/08/2022] [Indexed: 11/26/2022]
Abstract
Structural and conformational insights of a putative β-1,4-xylosidase (PsGH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans were investigated by computational and Circular Dichroism (CD) analyses. PsGH43F was cloned and expressed in E. coli BL21 (DE3) cells and the purified enzyme gave the size ~50 kDa on SDS-PAGE analysis. Multiple Sequence Alignment of PsGH43F sequence followed by superposition of modeled structure with homologous structures displayed the presence of three conserved catalytic amino acid residues, Asp33, Asp149 and Glu212. The secondary structure analysis by CD showed 2.72 % α-helix and 36.06 % β-strands. The homology modeled structure of PsGH43F displayed a 5-bladed β-propeller fold for catalytic module at N-terminal and a β-sandwich structure for CBM6 at the C-terminal. Ramachandran plot displayed 99.5 % of residues in the allowed regions. MD simulation of PsGH43F revealed the compactness and stability of the structure. Molecular docking studies of PsGH43F with xylo-oligosaccharides revealed its maximum binding affinity for xylobiose. MD simulation of PsGH43F-xylobiose complex confirmed the increased structural and conformational stability in presence of substrate. The Hydrodynamic diameter analysis of PsGH43F by DLS was in the range, 0.25-0.28 μm.
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Affiliation(s)
- Vishwanath Yadav
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Jebin Ahmed
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Abhijeet Thakur
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India; Department of Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Poorvi Vishwakarma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Shubha Singh
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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27
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Polsinelli I, Salomone-Stagni M, Benini S. Erwinia tasmaniensis levansucrase shows enantiomer selection for (S)-1,2,4-butanetriol. Acta Crystallogr F Struct Biol Commun 2022; 78:289-296. [PMID: 35924596 PMCID: PMC9350837 DOI: 10.1107/s2053230x2200680x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/01/2022] [Indexed: 11/12/2022] Open
Abstract
Levansucrases are biotechnologically interesting fructosyltransferases due to their potential use in the enzymatic or chemo-enzymatic synthesis of glycosides of non-natural substrates relevant to pharmaceutical applications. The structure of Erwinia tasmaniensis levansucrase in complex with (S)-1,2,4-butanetriol and its biochemical characterization suggests the possible application of short aliphatic moieties containing polyols with defined stereocentres in fructosylation biotechnology. The structural information revealed that (S)-1,2,4-butanetriol mimics the natural substrate. The preference of the protein towards a specific 1,2,4-butanetriol enantiomer was assessed using microscale thermophoresis binding assays. Furthermore, the results obtained and the structural comparison of levansucrases and inulosucrases suggest that the fructose binding modes could differ in fructosyltransferases from Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Ivan Polsinelli
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Universita 5, 39100 Bolzano, Italy
| | - Marco Salomone-Stagni
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Universita 5, 39100 Bolzano, Italy
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Universita 5, 39100 Bolzano, Italy
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28
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Influence of Association on Binding of Disaccharides to YKL-39 and hHyal-1 Enzymes. Int J Mol Sci 2022; 23:ijms23147705. [PMID: 35887053 PMCID: PMC9317946 DOI: 10.3390/ijms23147705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 07/01/2022] [Accepted: 07/09/2022] [Indexed: 12/04/2022] Open
Abstract
Disaccharide complexes have been shown experimentally to be useful for drug delivery or as an antifouling surface biofilm, and are promising drug-encapsulation and delivery candidates. Although such complexes are intended for medical applications, to date no studies at the molecular level have been devoted to the influence of complexation on the enzymatic decomposition of polysaccharides. A theoretical approach to this problem has been hampered by the lack of a suitable computational tool for binding such non-covalent complexes to enzymes. Herein, we combine quantum-mechanical calculations of disaccharides complexes with a nonstandard docking GaudiMM engine that can perform such a task. Our results on four different complexes show that they are mostly stabilized by electrostatic interactions and hydrogen bonds. This strong non-covalent stabilization demonstrates the studied complexes are some excellent candidates for self-assembly smart materials, useful for drug encapsulation and delivery. Their advantage lies also in their biocompatible and biodegradable character.
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29
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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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30
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A Comparison of the Transglycosylation Capacity between the Guar GH27 Aga27A and Bacteroides GH36 BoGal36A α-Galactosidases. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12105123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The transglycosylation behavior and capacity of two clan GH-D α-galactosidases, BoGal36A from the gut bacterium Bacteroides ovatus and Aga27A from the guar plant, was investigated and compared. The enzymes were screened for the ability to use para-nitrophenyl-α-galactoside (pNP-Gal), raffinose and locust bean gum (LBG) galactomannan as glycosyl donors with the glycosyl acceptors methanol, propanol, allyl alcohol, propargyl alcohol and glycerol using mass spectrometry. Aga27A was, in general, more stable in the presence of the acceptors. HPLC analysis was developed and used as a second screening method for reactions using raffinose or LBG as a donor substrate with methanol, propanol and glycerol as acceptors. Time-resolved reactions were set up with raffinose and methanol as the donor and acceptor, respectively, in order to develop an insight into the basic transglycosylation properties, including the ratio between the rate of transglycosylation (methyl galactoside synthesis) and rate of hydrolysis. BoGal36A had a somewhat higher ratio (0.99 compared to 0.71 for Aga27A) at early time points but was indicated to be more prone to secondary (product) hydrolysis in prolonged incubations. The methyl galactoside yield was higher when using raffinose (48% for BoGal36A and 38% for Aga27A) compared to LBG (27% for BoGal36A and 30% for Aga27A).
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Li P, Shi M, Wang X, Xu D. QM/MM investigation of the catalytic mechanism of processive endoglucanase Cel9G from Clostridium cellulovorans. Phys Chem Chem Phys 2022; 24:11919-11930. [PMID: 35514276 DOI: 10.1039/d2cp00593j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Carbohydrate degradation catalyzed by glucoside hydrolases (GHs) is a major mechanism in biomass conversion. GH family 9 endoglucanase (Cel9G) from Clostridium cellulovorans, a typical multimodular enzyme, contains a catalytic domain closely linked to a family 3c carbohydrate-binding module (CBM3c). Unlike the conventional behavior proposed for other carbohydrate-binding modules, CBM3c has a direct impact on catalytic activity. In this work, extensive molecular dynamics (MD) simulations were employed to clarify the functional role of CBM3c. Furthermore, the detailed catalytic mechanism of Cel9G was investigated at the atomistic level using the combined quantum mechanical and molecular mechanical (QM/MM) method. Based on these simulations, owing to the rigidity of the peptide linker, CBM3c may affect the enzymatic activity via direct interactions with alpha helix 4 of GH9, especially with the K123 and H125 residues. In addition, using cellohexaose as a substrate, the QM/MM MD simulations confirmed that this enzyme can cleave the β-1,4-glycosidic linkage via an inverting mechanism. An oxocarbenium ion-like transition state was located with a barrier height of 19.6 kcal mol-1. Furthermore, the G(-1) pyranose unit preferentially adopted a distorted 1S5/4H5 conformer in the enzyme-substrate complex. For the cleavage of the glycosidic bond, we were able to identify a plausible route (1S5/4H5 → [4H5/4E]# → 4C1) from the reactant to the product at the G(-1) site.
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Affiliation(s)
- Penghui Li
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, 610064, P. R. China.
| | - Mingsong Shi
- State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Xin Wang
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, 610064, P. R. China.
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, Sichuan, 610064, P. R. China.
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Gomes M, Rondelez Y, Leibler L. Lessons from Biomass Valorization for Improving Plastic-Recycling Enzymes. Annu Rev Chem Biomol Eng 2022; 13:457-479. [PMID: 35378043 DOI: 10.1146/annurev-chembioeng-092120-091054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Synthetic polymers such as plastics exhibit numerous advantageous properties that have made them essential components of our daily lives, with plastic production doubling every 15 years. The relatively low cost of petroleum-based polymers encourages their single use and overconsumption. Synthetic plastics are recalcitrant to biodegradation, and mismanagement of plastic waste leads to their accumulation in the ecosystem, resulting in a disastrous environmental footprint. Enzymes capable of depolymerizing plastics have been reported recently that may provide a starting point for eco-friendly plastic recycling routes. However, some questions remain about the mechanisms by which enzymes can digest insoluble solid substrates. We review the characterization and engineering of plastic-eating enzymes and provide some comparisons with the field of lignocellulosic biomass valorization. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Margarida Gomes
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Yannick Rondelez
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
| | - Ludwik Leibler
- Laboratoire Gulliver (UMR 7083), CNRS, ESPCI Paris, PSL Research University, Paris, France; ;
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McGregor NGS, Overkleeft HS, Davies GJ. Detecting and identifying glycoside hydrolases using cyclophellitol-derived activity-based probes. Methods Enzymol 2022; 664:103-134. [PMID: 35331370 DOI: 10.1016/bs.mie.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ability to detect active enzymes in a complex mixture of folded proteins (e.g., secretome, cell lysate) generally relies on observations of catalytic ability, necessitating the development of an activity assay that is compatible with the sample and selective for the enzyme(s) of interest. Deconvolution of the contributions of different enzymes to an observed catalytic ability further necessitates an often-challenging protein separation. The advent of broadly reactive activity-based probes (ABPs) for retaining glycoside hydrolases (GHs) has enabled an alternative, often complementary, assay for active GHs. Using activity-based protein profiling (ABPP) techniques, many retaining glycoside hydrolases can be separated, detected, and identified with high sensitivity and selectivity. This chapter outlines ABPP methods for the detection and identification of retaining glycoside hydrolases from microbial sources, including protein sample preparation from bacterial lysates and fungal secretomes, enzyme labeling and detection via fluorescence, and enzyme identification using affinity-based enrichment coupled to peptide sequencing following isobaric labeling.
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Affiliation(s)
- Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | | | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom.
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Horikoshi S, Saburi W, Yu J, Matsuura H, Cairns JRK, Yao M, Mori H. Substrate specificity of glycoside hydrolase family 1 β-glucosidase AtBGlu42 from Arabidopsis thaliana and its molecular mechanism. Biosci Biotechnol Biochem 2022; 86:231-245. [PMID: 34965581 DOI: 10.1093/bbb/zbab200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/13/2021] [Indexed: 11/15/2022]
Abstract
Plants possess many glycoside hydrolase family 1 (GH1) β-glucosidases, which physiologically function in cell wall metabolism and activation of bioactive substances, but most remain uncharacterized. One GH1 isoenzyme AtBGlu42 in Arabidopsis thaliana has been identified to hydrolyze scopolin using the gene deficient plants, but no enzymatic properties were obtained. Its sequence similarity to another functionally characterized enzyme Os1BGlu4 in rice suggests that AtBGlu42 also acts on oligosaccharides. Here, we show that the recombinant AtBGlu42 possesses high kcat/Km not only on scopolin, but also on various β-glucosides, cellooligosaccharides, and laminarioligosaccharides. Of the cellooligosaccharides, cellotriose was the most preferred. The crystal structure, determined at 1.7 Å resolution, suggests that Arg342 gives unfavorable binding to cellooligosaccharides at subsite +3. The mutants R342Y and R342A showed the highest preference on cellotetraose or cellopentaose with increased affinities at subsite +3, indicating that the residues at this position have an important role for chain length specificity.
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Affiliation(s)
- Shu Horikoshi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Wataru Saburi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Jian Yu
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Hideyuki Matsuura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - James R Ketudat Cairns
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Min Yao
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Haruhide Mori
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Transglycosylation by β-mannanase TrMan5A variants and enzyme synergy for synthesis of allyl glycosides from galactomannan. Process Biochem 2022. [DOI: 10.1016/j.procbio.2021.11.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Naidoo KJ, Bruce-Chwatt T, Senapathi T, Hillebrand M. Multidimensional Free Energy and Accelerated Quantum Library Methods Provide a Gateway to Glycoenzyme Conformational, Electronic, and Reaction Mechanisms. Acc Chem Res 2021; 54:4120-4130. [PMID: 34726899 DOI: 10.1021/acs.accounts.1c00477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Enzyme reactions are complex to simulate accurately, and none more so than glycoenzymes (glycosyltransferase and glycosidases). A rigorous sampling of the protein frame and the conformationally plural carbohydrate substrate coupled with an unbiased treatment of the electron dynamics is needed to discover the true reaction landscapes. Here, we demonstrate the effectiveness of two computational methods ported in libraries that we have developed. The first is a flat histogram free energy method called FEARCF capable of multidimensional sampling and rapidly converging to a complete coverage of phase space. The second, the Quantum Supercharger Library (QSL), is a method that accelerates the computation of the ab initio electronic wave function as well as the integral derivatives on graphical processing units (GPUs). These QSL accelerated computations form the core components needed for direct quantum dynamics and QM/MM dynamics when coupled with legacy codes such as GAMESS and NWCHEM, making state of the art hyper-parallel electronic computations in chemistry and chemical biology possible. The combination of QSL (acceleration of ab initio QM computation) and FEARCF (multidimensional hyper-parallel reaction dynamics) makes the simulation of ab initio QM/MM reaction dynamics of enzyme catalysis feasible. Enzymes that process carbohydrates pose an added challenge as their pyranose ring substrates span multidimensional conformational space whose sampling is an intimate function of the catalytic mechanism. Here, we use the pairing of FEARCF and QSL to simulate the catalytic effect of the glycoenzyme β-N-acetylglucosamine transferase (OGT). The reaction mechanism is discovered from a variable three bond reaction surface using SCCDFTB. The role of the OGT in distorting the pyranose ring of β-N-acetylglucosamine (GlcNAc) away from the equilibrium 4C1 chair conformation toward the E3 envelope needed for the transition state is discovered from its pucker free energy hypersurfaces (or free energy volume, FEV). A complete GlcNAc ring pucker HF 6-31g FEV is constructed from ab initio QM dynamics in vacuum and ab initio QM/MM dynamics in the OGT catalytic domain. The OGT is shown to clearly lower the pathway toward the transition state E3 ring conformer as well as stabilize it by 1.63 kcal/mol. Illustrated here is the use of QSL accelerated ab initio QM/MM dynamics that thoroughly explores carbohydrate catalyzed reactions through a FEARCF multidimensional sampling of the interdependence between reaction and conformational space. This demonstrates how experimentally inaccessible molecular and electronic mechanisms that underpin enzyme catalysis can be discovered by directly modeling the dynamics of these complex reactions.
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Affiliation(s)
- Kevin J Naidoo
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Science, University of Cape Town, Rondebosch 7701, South Africa
| | - Tomás Bruce-Chwatt
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Tharindu Senapathi
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Malcolm Hillebrand
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
- Nonlinear Dynamics and Chaos Group, Department of Mathematics, University of Cape Town, Rondebosch 7701, South Africa
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Mészáros Z, Nekvasilová P, Bojarová P, Křen V, Slámová K. Reprint of: Advanced glycosidases as ingenious biosynthetic instruments. Biotechnol Adv 2021; 51:107820. [PMID: 34462167 DOI: 10.1016/j.biotechadv.2021.107820] [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: 11/25/2020] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 11/27/2022]
Abstract
Until recently, glycosidases, naturally hydrolyzing carbohydrate-active enzymes, have found few synthetic applications in industry, being primarily used for cleaving unwanted carbohydrates. With the establishment of glycosynthase and transglycosidase technology by genetic engineering, the view of glycosidases as industrial biotechnology tools has started to change. Their easy production, affordability, robustness, and substrate versatility, added to the possibility of controlling undesired side hydrolysis by enzyme engineering, have made glycosidases competitive synthetic tools. Current promising applications of engineered glycosidases include the production of well-defined chitooligomers, precious galactooligosaccharides or specialty chemicals such as glycosylated flavonoids. Other synthetic pathways leading to human milk oligosaccharides or remodeled antibodies are on the horizon. This work provides an overview of the synthetic achievements to date for glycosidases, emphasizing the latest trends and outlining possible developments in the field.
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Affiliation(s)
- Zuzana Mészáros
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic; Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 1903/3, CZ-16628 Praha 6, Czech Republic
| | - Pavlína Nekvasilová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, CZ-12843, Praha 2, Czech Republic
| | - Pavla Bojarová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Vladimír Křen
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Kristýna Slámová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic.
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Chen A, Wang D, Ji R, Li J, Gu S, Tang R, Ji C. Structural and Catalytic Characterization of TsBGL, a β-Glucosidase From Thermofilum sp. ex4484_79. Front Microbiol 2021; 12:723678. [PMID: 34659150 PMCID: PMC8517440 DOI: 10.3389/fmicb.2021.723678] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
Beta-glucosidase is an enzyme that catalyzes the hydrolysis of the glycosidic bonds of cellobiose, resulting in the production of glucose, which is an important step for the effective utilization of cellulose. In the present study, a thermostable β-glucosidase was isolated and purified from the Thermoprotei Thermofilum sp. ex4484_79 and subjected to enzymatic and structural characterization. The purified β-glucosidase (TsBGL) exhibited maximum activity at 90°C and pH 5.0 and displayed maximum specific activity of 139.2μmol/min/mgzne against p-nitrophenyl β-D-glucopyranoside (pNPGlc) and 24.3μmol/min/mgzen against cellobiose. Furthermore, TsBGL exhibited a relatively high thermostability, retaining 84 and 47% of its activity after incubation at 85°C for 1.5h and 90°C for 1.5h, respectively. The crystal structure of TsBGL was resolved at a resolution of 2.14Å, which revealed a classical (α/β)8-barrel catalytic domain. A structural comparison of TsBGL with other homologous proteins revealed that its catalytic sites included Glu210 and Glu414. We provide the molecular structure of TsBGL and the possibility of improving its characteristics for potential applications in industries.
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Affiliation(s)
- Anke Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Dan Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Rui Ji
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Shaohua Gu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Rong Tang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
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Gorantla JN, Maniganda S, Pengthaisong S, Ngiwsara L, Sawangareetrakul P, Chokchaisiri S, Kittakoop P, Svasti J, Ketudat Cairns JR. Chemoenzymatic and Protecting-Group-Free Synthesis of 1,4-Substituted 1,2,3-Triazole-α-d-glucosides with Potent Inhibitory Activity toward Lysosomal α-Glucosidase. ACS OMEGA 2021; 6:25710-25719. [PMID: 34632227 PMCID: PMC8495876 DOI: 10.1021/acsomega.1c03928] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
α-Glucosyl triazoles have rarely been tested as α-glucosidase inhibitors, partly due to inefficient synthesis of their precursor α-d-glucosylazide (αGA1). Glycosynthase enzymes, made by nucleophile mutations of retaining β-glucosidases, produce αGA1 in chemical rescue experiments. Thermoanaerobacterium xylanolyticus glucosyl hydrolase 116 β-glucosidase (TxGH116) E441G nucleophile mutant catalyzed synthesis of αGA1 from sodium azide and pNP-β-d-glucoside (pNPGlc) or cellobiose in aqueous medium at 45 °C. The pNPGlc and azide reaction product was purified by Sephadex LH-20 column chromatography to yield 280 mg of pure αGA1 (68% yield). αGA1 was successfully conjugated with alkynes attached to different functional groups, including aryl, ether, amine, amide, ester, alcohol, and flavone via copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry reactions. These reactions afforded the 1,4-substituted 1,2,3-triazole-α-d-glucoside derivatives AGT2-14 without protection and deprotection. Several of these glucosyl triazoles exhibited strong inhibition of human lysosomal α-glucosidase, with IC50 values for AGT4 and AGT14 more than 60-fold lower than that of the commercial α-glucosidase inhibitor acarbose.
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Affiliation(s)
- Jaggaiah N. Gorantla
- Center
for Biomolecular Structure, Function and Application, School of Chemistry,
Institute of Science, Suranaree University
of Technology, Nakhon
Ratchasima 30000, Thailand
| | - Santhi Maniganda
- Center
for Biomolecular Structure, Function and Application, School of Chemistry,
Institute of Science, Suranaree University
of Technology, Nakhon
Ratchasima 30000, Thailand
| | - Salila Pengthaisong
- Center
for Biomolecular Structure, Function and Application, School of Chemistry,
Institute of Science, Suranaree University
of Technology, Nakhon
Ratchasima 30000, Thailand
| | - Lukana Ngiwsara
- Laboratory
of Biochemistry, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | | | - Suwadee Chokchaisiri
- Center
for Biomolecular Structure, Function and Application, School of Chemistry,
Institute of Science, Suranaree University
of Technology, Nakhon
Ratchasima 30000, Thailand
| | - Prasat Kittakoop
- Chulabhorn
Graduate Institute, Chemical Sciences Program, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Jisnuson Svasti
- Laboratory
of Biochemistry, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - James R. Ketudat Cairns
- Center
for Biomolecular Structure, Function and Application, School of Chemistry,
Institute of Science, Suranaree University
of Technology, Nakhon
Ratchasima 30000, Thailand
- Laboratory
of Biochemistry, Chulabhorn Research Institute, Bangkok 10210, Thailand
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Wang D, Chen JY, Song J, Li JJ, Klosterman SJ, Li R, Kong ZQ, Subbarao KV, Dai XF, Zhang DD. Cytotoxic function of xylanase VdXyn4 in the plant vascular wilt pathogen Verticillium dahliae. PLANT PHYSIOLOGY 2021; 187:409-429. [PMID: 34618145 PMCID: PMC8418393 DOI: 10.1093/plphys/kiab274] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/22/2021] [Indexed: 05/24/2023]
Abstract
Phytopathogen xylanases play critical roles in pathogenesis, likely due to their ability to degrade plant structural barriers and manipulate host immunity. As an invader of plant xylem vessels, the fungus Verticillium dahliae is thought to deploy complex cell wall degrading enzymes. Comparative genomics analyses revealed that the V. dahliae genome encodes a family of six xylanases, each possessing a glycosyl hydrolase 11 domain, but the functions of these enzymes are undetermined. Characterizing gene deletion mutants revealed that only V. dahliae xylanase 4 (VdXyn4) degraded the plant cell wall and contributed to the virulence of V. dahliae. VdXyn4 displayed cytotoxic activity and induced a necrosis phenotype during the late stages of infection, leading to vein and petiole collapse that depended on the enzyme simultaneously localizing to nuclei and chloroplasts. The internalization of VdXyn4 was in conjunction with that of the plasma membrane complexLeucine-rich repeat (LRR)-receptor-like kinase suppressor of BIR1-1 (SOBIR1)/LRR-RLK BRI1-associated kinase-1 (BAK1), but we could not rule out the possibility that VdXyn4 may also act as an apoplastic effector. Immune signaling (in the SA-JA pathways) induced by VdXyn4 relative to that induced by known immunity effectors was substantially delayed. While cytotoxic activity could be partially suppressed by known effectors, they failed to impede necrosis in Nicotiana benthamiana. Thus, unlike typical effectors, cytotoxicity of VdXyn4 plays a crucial intracellular role at the late stages of V. dahliae infection and colonization, especially following pathogen entry into the xylem; this cytotoxic activity is likely conserved in the corresponding enzyme families in plant vascular pathogens.
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Affiliation(s)
- Dan Wang
- Team of Crop Verticillium wilt, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie-Yin Chen
- Team of Crop Verticillium wilt, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Song
- Team of Crop Verticillium wilt, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun-Jiao Li
- Team of Crop Verticillium wilt, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Steven J. Klosterman
- Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, California, USA
| | - Ran Li
- Team of Crop Verticillium wilt, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi-Qiang Kong
- Team of Crop Verticillium wilt, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Krishna V. Subbarao
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, California, USA
| | - Xiao-Feng Dai
- Team of Crop Verticillium wilt, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan-Dan Zhang
- Team of Crop Verticillium wilt, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Endo-xylanases from Cohnella sp. AR92 aimed at xylan and arabinoxylan conversion into value-added products. Appl Microbiol Biotechnol 2021; 105:6759-6778. [PMID: 34458936 DOI: 10.1007/s00253-021-11495-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/29/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
The genus Cohnella belongs to a group of Gram-positive endospore-forming bacteria within the Paenibacillaceae family. Although most species were described as xylanolytic bacteria, the literature still lacks some key information regarding their repertoire of xylan-degrading enzymes. The whole genome sequence of an isolated xylan-degrading bacterium Cohnella sp. strain AR92 was found to contain five genes encoding putative endo-1,4-β-xylanases, of which four were cloned, expressed, and characterized to better understand the contribution of the individual endo-xylanases to the overall xylanolytic properties of strain AR92. Three of the enzymes, CoXyn10A, CoXyn10C, and CoXyn11A, were shown to be effective at hydrolyzing xylans-derived from agro-industrial, producing oligosaccharides with substrate conversion values of 32.5%, 24.7%, and 10.6%, respectively, using sugarcane bagasse glucuronoarabinoxylan and of 29.9%, 19.1%, and 8.0%, respectively, using wheat bran-derived arabinoxylan. The main reaction products from GH10 enzymes were xylobiose and xylotriose, whereas CoXyn11A produced mostly xylooligosaccharides (XOS) with 2 to 5 units of xylose, often substituted, resulting in potentially prebiotic arabinoxylooligosaccharides (AXOS). The endo-xylanases assay displayed operational features (temperature optima from 49.9 to 50.4 °C and pH optima from 6.01 to 6.31) fitting simultaneous xylan utilization. Homology modeling confirmed the typical folds of the GH10 and GH11 enzymes, substrate docking studies allowed the prediction of subsites (- 2 to + 1 in GH10 and - 3 to + 1 in GH11) and identification of residues involved in ligand interactions, supporting the experimental data. Overall, the Cohnella sp. AR92 endo-xylanases presented significant potential for enzymatic conversion of agro-industrial by-products into high-value products.Key points• Cohnella sp. AR92 genome encoded five potential endo-xylanases.• Cohnella sp. AR92 enzymes produced xylooligosaccharides from xylan, with high yields.• GH10 enzymes from Cohnella sp. AR92 are responsible for the production of X2 and X3 oligosaccharides.• GH11 from Cohnella sp. AR92 contributes to the overall xylan degradation by producing substituted oligosaccharides.
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Ferreira P, Fernandes PA, Ramos MJ. THE CATALYTIC MECHANISM OF THE RETAINING GLYCOSYLTRANSFERASE MANNOSYLGLYCERATE SYNTHASE. Chemistry 2021; 27:13998-14006. [PMID: 34355437 DOI: 10.1002/chem.202101724] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Indexed: 11/07/2022]
Abstract
To protect their intracellular proteins, extremophile microorganisms synthesize molecules called compatible solutes. These molecules are the result of the attachment of a small negatively charged molecule to a sugar molecule. It has been found that these molecules, not only protect the microorganism against osmotic stress, as initially thought, but also against other extreme conditions. The observation that these molecules can confer protection against extreme conditions to isolated enzymes from different organisms made them an exciting prospect for potential biotechnological applications. One of the most widespread compatible solute in hyperthermophile organisms is the molecule 2-O-α-D-mannosyl-D-glycerate (MG). In addition to confer protection to proteins against extreme conditions, MG was found to prevent Alzheimer's β-amyloid aggregation and reduce α-synuclein fibril formation in Parkinson's disease. In this work we studied, using computational methods, the catalytic mechanism of the synthesis of MG by the enzyme mannosylglycerate synthase (MGS) from the thermophilic bacteria Rhodothermus marinus . MGS is a promiscuous enzyme, accepting a variety of sugar donors and acceptors. This feature can be used to synthesize other molecules with potential biotechnological applications beyond MG. The unravelling of the catalytic mechanism with atomistic resolution and the associated free energies and electrostatic profiles of the stationary states obtained in the present work will help future investigations to full explore the potential of MGS.
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Affiliation(s)
- Pedro Ferreira
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Pedro A Fernandes
- LAQV@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Maria J Ramos
- LAQV@REQUIMTE, 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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Pengthaisong S, Hua Y, Ketudat Cairns JR. Structural basis for transglycosylation in glycoside hydrolase family GH116 glycosynthases. Arch Biochem Biophys 2021; 706:108924. [PMID: 34019851 DOI: 10.1016/j.abb.2021.108924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022]
Abstract
Glycosynthases are glycoside hydrolase mutants that can synthesize oligosaccharides or glycosides from an inverted donor without hydrolysis of the products. Although glycosynthases have been characterized from a variety of glycoside hydrolase (GH) families, family GH116 glycosynthases have yet to be reported. We produced the Thermoanaerobacterium xylanolyticum TxGH116 nucleophile mutants E441D, E441G, E441Q and E441S and compared their glycosynthase activities to the previously generated E441A mutant. The TxGH116 E441G and E441S mutants exhibited highest glycosynthase activity to transfer glucose from α-fluoroglucoside (α-GlcF) to cellobiose acceptor, while E441D had low but significant activity as well. The E441G, E441S and E441A variants showed broad specificity for α-glycosyl fluoride donors and p-nitrophenyl glycoside acceptors. The structure of the TxGH116 E441A mutant with α-GlcF provided the donor substrate complex, while soaking of the TxGH116 E441G mutant with α-GlcF resulted in cellooligosaccharides extending from the +1 subsite out of the active site, with glycerol in the -1 subsite. Soaking of E441A or E441G with cellobiose or cellotriose gave similar acceptor substrate complexes with the nonreducing glucosyl residue in the +1 subsite. Combining structures with the ligands from the TxGH116 E441A with α-GlcF crystals with that of E441A or E441G with cellobiose provides a plausible structure of the catalytic ternary complex, which places the nonreducing glucosyl residue O4 2.5 Å from the anomeric carbon of α-GlcF, thereby explaining its apparent preference for production of β-1,4-linked oligosaccharides. This functional and structural characterization provides the background for development of GH116 glycosynthases for synthesis of oligosaccharides and glycosides of interest.
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Affiliation(s)
- Salila Pengthaisong
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand; Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Yanling Hua
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand; Center for Scientific and Technological Equipment, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - James R Ketudat Cairns
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand; Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
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Mészáros Z, Nekvasilová P, Bojarová P, Křen V, Slámová K. Advanced glycosidases as ingenious biosynthetic instruments. Biotechnol Adv 2021; 49:107733. [PMID: 33781890 DOI: 10.1016/j.biotechadv.2021.107733] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 12/22/2022]
Abstract
Until recently, glycosidases, naturally hydrolyzing carbohydrate-active enzymes, have found few synthetic applications in industry, being primarily used for cleaving unwanted carbohydrates. With the establishment of glycosynthase and transglycosidase technology by genetic engineering, the view of glycosidases as industrial biotechnology tools has started to change. Their easy production, affordability, robustness, and substrate versatility, added to the possibility of controlling undesired side hydrolysis by enzyme engineering, have made glycosidases competitive synthetic tools. Current promising applications of engineered glycosidases include the production of well-defined chitooligomers, precious galactooligosaccharides or specialty chemicals such as glycosylated flavonoids. Other synthetic pathways leading to human milk oligosaccharides or remodeled antibodies are on the horizon. This work provides an overview of the synthetic achievements to date for glycosidases, emphasizing the latest trends and outlining possible developments in the field.
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Affiliation(s)
- Zuzana Mészáros
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic; Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague, Technická 1903/3, CZ-16628 Praha 6, Czech Republic
| | - Pavlína Nekvasilová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, CZ-12843, Praha 2, Czech Republic
| | - Pavla Bojarová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Vladimír Křen
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic
| | - Kristýna Slámová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Praha 4, Czech Republic.
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Katoh T, Yamamoto K. Innovative Preparation of Biopharmaceuticals Using Transglycosylation Activity of Microbial Endoglycosidases. J Appl Glycosci (1999) 2021; 68:1-9. [PMID: 34354540 PMCID: PMC8113915 DOI: 10.5458/jag.jag.jag-2020_0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/16/2020] [Indexed: 12/02/2022] Open
Abstract
Most functional biopharmaceuticals such as antibodies are glycoproteins carrying N-linked oligosaccharides (N-glycans). In animal cells, these glycans are generally expressed as heterogeneous glycoforms that are difficult to separate into a pure form. The structure of these glycans directly affects several biological aspects of the glycoproteins, especially binding affinity. Therefore, the preparation of glycoproteins with well-defined and homogeneous glycoforms is necessary for functional studies and improved efficacy, particularly for biopharmaceuticals. This review describes the recent remarkable progress in the development and production of biopharmaceutical glycan-modified antibodies, through the use of glycan remodeling using microbial endoglycosidases and sophisticated glycoengineering techniques utilizing microbial enzymatic reaction mechanisms.
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Affiliation(s)
| | - Kenji Yamamoto
- 2 Center for Innovative and Joint Research, Wakayama University
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46
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Nath P, Goyal A. Structure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans. J Mol Model 2021; 27:106. [PMID: 33694107 PMCID: PMC7945971 DOI: 10.1007/s00894-021-04721-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/01/2021] [Indexed: 11/30/2022]
Abstract
Structure and conformational behaviour of a putative β-1,4-glucosidase of glycoside hydrolase family 3 (PsGH3) from Pseudopedobacter saltans was predicted by using in-silico tools. PsGH3 modeled structure constructed using Phyre2 displayed multidomain architecture comprising an N-terminal (β/α)8-fold domain followed by (α/β)6-sandwich domain, PA14 domain, and a C-terminal domain resembling an immunoglobulin fold. Ramachandran plot displayed 99.3% of amino acids in the allowed region and 0.7% residues in the disallowed region. Multiple sequence alignment (MSA) and structure superposition of PsGH3 with other homologues from GH3 family revealed the conserved residues, Asp274 and Glu624 present in loops LA and LB, respectively originating from N-terminal domain act as catalytic residues. The volume and area calculated for PsGH3 displayed a deep active-site conformation comparable with its homologues, β-1,4-glucosidases (GH3) of Kluyveromyces marxianus and Streptomyces venezuelae. Molecular dynamic (MD) simulation of PsGH3 structure for 80 ns suggested stable and compact structure. Molecular docking studies revealed deeper active site conformation of PsGH3 that could house larger cellooligosaccharides up to 7° of polymerization (DP7). The amino acid residues, Ala86, Leu88, Cys275, Pro483, Phe493, Asn417, Asn491, Pro492, and Leu495 created a binding pocket near the catalytic cleft, crucial for ligand binding. MD simulation of PsGH3 in the presence of cellooligosaccharides, viz., cellobiose and celloheptaose showed stability in terms of RMSD, Rg, and SASA values till 80 ns. The calculation of average number of hydrogen bond (H-bond), interaction energy, and binding free energy confirmed the stronger binding affinity of the larger cellooligosaccharides such as celloheptaose in the binding cavity of PsGH3.
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Affiliation(s)
- Priyanka Nath
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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Jafari S, Ryde U, Irani M. QM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues. J Chem Theory Comput 2021; 17:1822-1841. [PMID: 33543623 PMCID: PMC8023669 DOI: 10.1021/acs.jctc.0c01121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Myrosinase from Sinapis alba hydrolyzes glycosidic
bonds of β-d-S-glucosides. The enzyme
shows an enhanced activity in the presence of l-ascorbic
acid. In this work, we employed combined quantum mechanical and molecular
mechanical (QM/MM) calculations and molecular dynamics simulations
to study the catalytic reaction of wild-type myrosinase and its E464A,
Q187A, and Q187E mutants. Test calculations show that a proper QM
region to study the myrosinase reaction must contain the whole substrate,
models of Gln-187, Glu-409, Gln-39, His-141, Asn-186, Tyr-330, Glu-464,
Arg-259, and a water molecule. Furthermore, to make the deglycosylation
step possible, Arg-259 must be charged, Glu-464 must be protonated
on OE2, and His-141 must be protonated on the NE2 atom. The results
indicate that assigning proper protonation states of the residues
is more important than the size of the model QM system. Our model
reproduces the anomeric retaining characteristic of myrosinase and
also reproduces the experimental fact that ascorbate increases the
rate of the reaction. A water molecule in the active site, positioned
by Gln-187, helps the aglycon moiety of the substrate to stabilize
the buildup of negative charge during the glycosylation reaction and
this in turn makes the moiety a better leaving group. The water molecule
also lowers the glycosylation barrier by ∼9 kcal/mol. The results
indicate that the Q187E and E464A mutants but not the Q187A mutant
can perform the glycosylation step. However, the energy profiles for
the deglycosylation step of the mutants are not similar to that of
the wild-type enzyme. The Glu-464 residue lowers the barriers of the
glycosylation and deglycosylation steps. The ascorbate ion can act
as a general base in the reaction of the wild-type enzyme only if
the Glu-464 and His-141 residues are properly protonated.
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Affiliation(s)
- Sonia Jafari
- Department of Chemistry, University of Kurdistan, 66175-416 Sanandaj, Iran
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Mehdi Irani
- Department of Chemistry, University of Kurdistan, 66175-416 Sanandaj, Iran
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Méndez-Líter JA, de Eugenio LI, Nieto-Domínguez M, Prieto A, Martínez MJ. Hemicellulases from Penicillium and Talaromyces for lignocellulosic biomass valorization: A review. BIORESOURCE TECHNOLOGY 2021; 324:124623. [PMID: 33434871 DOI: 10.1016/j.biortech.2020.124623] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/21/2020] [Accepted: 12/23/2020] [Indexed: 05/26/2023]
Abstract
The term hemicellulose groups different polysaccharides with heterogeneous structures, mannans, xyloglucans, mixed-linkage β-glucans and xylans, which differ in their backbone and branches, and in the type and distribution of glycosidic linkages. The enzymatic degradation of these complex polymers requires the concerted action of multiple hemicellulases and auxiliary enzymes. Most commercial enzymes are produced by Trichoderma and Aspergillus species, but recent studies have disclosed Penicillium and Talaromyces as promising sources of hemicellulases. In this review, we summarize the current knowledge on the hemicellulolytic system of these genera, and the role of hemicellulases in the disruption and synthesis of glycosidic bonds. In both cases, the enzymes from Penicillium and Talaromyces represent an interesting alternative for valorization of lignocellulosic biomass in the current framework of circular economy.
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Affiliation(s)
- Juan A Méndez-Líter
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/ Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Laura I de Eugenio
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/ Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Manuel Nieto-Domínguez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/ Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Alicia Prieto
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/ Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María Jesús Martínez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), c/ Ramiro de Maeztu 9, 28040 Madrid, Spain.
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Matsuyama K, Kishine N, Fujimoto Z, Sunagawa N, Kotake T, Tsumuraya Y, Samejima M, Igarashi K, Kaneko S. Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-β-1,3-galactanase from Phanerochaete chrysosporium. J Biol Chem 2020; 295:18539-18552. [PMID: 33093171 PMCID: PMC7939473 DOI: 10.1074/jbc.ra120.016149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/20/2020] [Indexed: 12/27/2022] Open
Abstract
Arabinogalactan proteins (AGPs) are plant proteoglycans with functions in growth and development. However, these functions are largely unexplored, mainly because of the complexity of the sugar moieties. These carbohydrate sequences are generally analyzed with the aid of glycoside hydrolases. The exo-β-1,3-galactanase is a glycoside hydrolase from the basidiomycete Phanerochaete chrysosporium (Pc1,3Gal43A), which specifically cleaves AGPs. However, its structure is not known in relation to its mechanism bypassing side chains. In this study, we solved the apo and liganded structures of Pc1,3Gal43A, which reveal a glycoside hydrolase family 43 subfamily 24 (GH43_sub24) catalytic domain together with a carbohydrate-binding module family 35 (CBM35) binding domain. GH43_sub24 is known to lack the catalytic base Asp conserved among other GH43 subfamilies. Our structure in combination with kinetic analyses reveals that the tautomerized imidic acid group of Gln263 serves as the catalytic base residue instead. Pc1,3Gal43A has three subsites that continue from the bottom of the catalytic pocket to the solvent. Subsite -1 contains a space that can accommodate the C-6 methylol of Gal, enabling the enzyme to bypass the β-1,6-linked galactan side chains of AGPs. Furthermore, the galactan-binding domain in CBM35 has a different ligand interaction mechanism from other sugar-binding CBM35s, including those that bind galactomannan. Specifically, we noted a Gly → Trp substitution, which affects pyranose stacking, and an Asp → Asn substitution in the binding pocket, which recognizes β-linked rather than α-linked Gal residues. These findings should facilitate further structural analysis of AGPs and may also be helpful in engineering designer enzymes for efficient biomass utilization.
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Affiliation(s)
- Kaori Matsuyama
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Naomi Kishine
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Zui Fujimoto
- Advanced Analysis Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Naoki Sunagawa
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Toshihisa Kotake
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama, Japan
| | - Yoichi Tsumuraya
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama, Japan
| | - Masahiro Samejima
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan; Faculty of Engineering, Shinshu University, Nagano, Japan
| | - Kiyohiko Igarashi
- Department of Biomaterial Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan; VTT Technical Research Centre of Finland, Espoo, Finland.
| | - Satoshi Kaneko
- Department of Subtropical Bioscience and Biotechnology, Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa, Japan
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Pedrood K, Sherafati M, Mohammadi-Khanaposhtani M, Asgari MS, Hosseini S, Rastegar H, Larijani B, Mahdavi M, Taslimi P, Erden Y, Günay S, Gulçin İ. Design, synthesis, characterization, enzymatic inhibition evaluations, and docking study of novel quinazolinone derivatives. Int J Biol Macromol 2020; 170:1-12. [PMID: 33352155 DOI: 10.1016/j.ijbiomac.2020.12.121] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022]
Abstract
In this study, novel quinazolinone derivatives 7a-n were synthesized and evaluated against metabolic enzymes including α-glycosidase, acetylcholinesterase, butyrylcholinesterase, human carbonic anhydrase I, and II. These compounds exhibited high inhibitory activities in comparison to used standard inhibitors with Ki values in the range of 19.28-135.88 nM for α-glycosidase (Ki value for standard inhibitor = 187.71 nM), 0.68-23.01 nM for acetylcholinesterase (Ki value for standard inhibitor = 53.31 nM), 1.01-29.56 nM for butyrylcholinesterase (Ki value for standard inhibitor = 58.16 nM), 10.25-126.05 nM for human carbonic anhydrase I (Ki value for standard inhibitor = 248.18 nM), and 13.46-178.35 nM for human carbonic anhydrase II (Ki value for standard inhibitor = 323.72). Furthermore, the most potent compounds against each enzyme were selected in order to evaluate interaction modes of these compounds in the active site of the target enzyme. Cytotoxicity assay of the title compounds 7a-n against cancer cell lines MCF-7 and LNCaP demonstrated that these compounds do not show significant cytotoxic effects.
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Affiliation(s)
- Keyvan Pedrood
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Maedeh Sherafati
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Mohammadi-Khanaposhtani
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | | | - Samanesadat Hosseini
- Department of Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Rastegar
- Cosmetic Products Research Center, Iranian Food and Drug Administration, MOHE, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, 74100 Bartin, Turkey.
| | - Yavuz Erden
- Department of Molecular Biology and Genetics, Faculty of Science, Bartin University, 74100 Bartin, Turkey
| | - Sevilay Günay
- Department of Molecular Biology and Genetics, Faculty of Science, Bartin University, 74100 Bartin, Turkey
| | - İlhami Gulçin
- Department of Chemistry, Faculty of Sciences, Ataturk University, 25240, Erzurum, Turkey
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