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Wu F, Cheng Y, Zhou J, Liu X, Lin R, Xiang S, Liu Z, Wang C. Zn 2+ regulates human oxalate metabolism by manipulating oxalate decarboxylase to treat calcium oxalate stones. Int J Biol Macromol 2023; 234:123320. [PMID: 36682657 DOI: 10.1016/j.ijbiomac.2023.123320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/21/2022] [Accepted: 01/14/2023] [Indexed: 01/20/2023]
Abstract
A high concentration of oxalate is associated with an increased risk of kidney calcium oxalate (CaOx) stones, and the degradation of exogenous oxalate mostly depends on oxalate-degrading enzymes from the intestinal microbiome. We found that zinc gluconate supplement to patients with CaOx kidney stones could significantly improve the abundance of oxalate metabolizing bacteria in humans through clinical experiments on patients also subjected to antibiotic treatment. The analysis of clinical samples revealed that an imbalance of Lactobacillus and oxalate decarboxylase (OxDC) was involved in the formation of CaOx kidney stones. Then, we identified that Zn2+ could be used as an external factor to improve the activity of OxDC and promote Lactobacillus in the intestinal flora, and this treatment achieved a therapeutic effect on rats with stones aggravated by antibiotics. Finally, by analyzing the three-dimensional structure of OxDC and completing in vitro experiments, we propose a model of the Zn2+-induced reduction of CaOx kidney stone symptoms in rats by increasing the metabolism of oxalate through the positive effects of Zn2+ on Lactobacillus and OxDC.
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Affiliation(s)
- Fang Wu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yuanyuan Cheng
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Jianfu Zhou
- Department of Urology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xuehua Liu
- Department of Urology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Rongwu Lin
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Songtao Xiang
- Department of Urology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
| | - Caiyan Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
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Gupta S, Kanwar SS. Molecular characterization and in silico analysis of oxalate decarboxylase of Pseudomonas sp. OXDC12. J Biomol Struct Dyn 2023; 41:1495-1509. [PMID: 35007451 DOI: 10.1080/07391102.2021.2024882] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Oxalate decarboxylase (OxDC) is a Mn-dependent hexameric enzyme that is highly important in management of calcium oxalate mediated nephrolithiasis. The present study reported the production and purification of OxDC from Pseudomonas sp. OXDC12 up to 45.3-fold with an overall yield of 7%. The purified OxDC displayed a single band of approximately 40 kDa on SDS-PAGE and 240 kDa on Native-PAGE suggesting it to be a hexameric enzyme. The purified OxDC displayed an optimum activity at 26 °C and pH 4.5 in the presence of substrate sodium oxalate (30 mg/mL) with a Km and Vmax value of 43.9 mM and 8.9 µmol/min, respectively and an activation energy of 52.49 kJ/mol. The enzyme activity was significantly enhanced by adding o-phenylenediamine to the reaction mixture. OxDC exhibited a very low 17 haemolytic activity which suggested a relatively safer therapeutic aspect of the tested OxDC. The structure prediction studies of the OxDC revealed a tertiary structure with α/β chains that formed the β barrel structure, typical of all cupin domains. The Ramachandran plot produced by PROCHECK shows that 90.5% of the residues are in the most favoured region and hence the OxDC model produced was a good one. Docking studies revealed the binding of the metal ions and ligands to cluster of three histidine residues in the N terminal domain that formed the active site pocket of the enzyme. It was suggested that the histidine coordinated Mn2+ ion was critical for substrate recognition and binding and was also directly involved in OxDC catalyses.highlightsOxalate decarboxylase (OxDC) was successfully purified from Pseudomonas sp. OXDC12 up-to 45.3-fold.The Km and Vmax values of the purified OxDC were calculated as 43.9 mM and 8.9 µmol/min, respectively.Genre analysis and structure prediction studies revealed the presence of β barrel structure typical of all cupin domains. The model exhibited a bi-cupin domain that forms the dimer of the homo-hexameric OxDC.Docking experiments revealed that the cluster of three HIS residues in the N terminal domain of the tested enzyme formed the active site pocket for binding of Mn as well as the ligands.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shruti Gupta
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, India
| | - Shamsher Singh Kanwar
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, India
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Hollow Hierarchical Cu-BTC as Nanocarriers to Immobilize Lipase for Electrochemical Biosensor. J Inorg Organomet Polym Mater 2022. [DOI: 10.1007/s10904-022-02434-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Giri P, Pagar AD, Patil MD, Yun H. Chemical modification of enzymes to improve biocatalytic performance. Biotechnol Adv 2021; 53:107868. [PMID: 34774927 DOI: 10.1016/j.biotechadv.2021.107868] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/23/2022]
Abstract
Improvement in intrinsic enzymatic features is in many instances a prerequisite for the scalable applicability of many industrially important biocatalysts. To this end, various strategies of chemical modification of enzymes are maturing and now considered as a distinct way to improve biocatalytic properties. Traditional chemical modification methods utilize reactivities of amine, carboxylic, thiol and other side chains originating from canonical amino acids. On the other hand, noncanonical amino acid- mediated 'click' (bioorthogoal) chemistry and dehydroalanine (Dha)-mediated modifications have emerged as an alternate and promising ways to modify enzymes for functional enhancement. This review discusses the applications of various chemical modification tools that have been directed towards the improvement of functional properties and/or stability of diverse array of biocatalysts.
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Affiliation(s)
- Pritam Giri
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Mahesh D Patil
- Department of Nanomaterials and Application Technology, Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, PO Manauli, S.A.S. Nagar, Mohali 140306, Punjab, India
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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The structure and properties of MFG-E8 and the In vitro assessment of its toxic effects on myoblast cells. Protein Expr Purif 2020; 178:105720. [PMID: 32771447 DOI: 10.1016/j.pep.2020.105720] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/09/2020] [Accepted: 07/28/2020] [Indexed: 01/25/2023]
Abstract
Four high-molecular-weight protein fractions of milk fat globule membrane (MFGM) were isolated from bovine milk. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), MALDI-TOF/TOF™ and Liquid chromatography electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) were used to measure the molecular sizes of the MFGM. Fourier transform infrared spectroscopy (FT-IR) and circular dichroism (CD) were performed to determine the conformations of the MFGM. The results showed that the main protein (98.33%) in MFGM protein fraction 2 was Milk fat globule epidermal growth factor-VIII (MFG-E8), with a molecular weight of 47.82 kDa. The secondary structural component measurements showed that the MFG-E8 consisted of 5% helix, 70% sheet and 25% random coil, and the results matched well with the prediction by SSPro 5.1 bioinformatic analysis. The thermograms analysis revealed that Td and△H of MFG-E8 were 60.50°Cand 132.29 kJ/mol. The in vitro digestibility of MFG-E8 showed that it can be enzymatically hydrolyzed in the stomach and relatively stable in the intestinal fluid. The in vitro C2C12 and Caco2 cell activity tests indicated that MFG-E8 promoted the proliferation of C2C12 myoblast cells without cytotoxicity. The biological functional properties of MFG-E8 may be related to the fact that MFG-E8 possesses a high level of β-sheet structure. Our results suggested that MFG-E8 possesses broad prospects not only for use in functional food products but also as a source of natural anti-sarcopenia drugs.
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Li C, Huang Z, Dong L, Liu X. Improvement of enzymological properties of pepsin by chemical modification with chitooligosaccharides. Int J Biol Macromol 2018; 118:216-227. [DOI: 10.1016/j.ijbiomac.2018.06.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 04/22/2018] [Accepted: 06/11/2018] [Indexed: 10/28/2022]
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Cai XH, Lin RH, Wu J, He JB, Wu YC, Wang XY. Adsorption of ethylenediaminetetraacetic dianhydride modified oxalate decarboxylase on calcium oxalate. Biotech Histochem 2018; 93:220-229. [DOI: 10.1080/10520295.2017.1420820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- XH Cai
- Key Laboratory of New Techniques for Chemical and Biological Conversion Process, College of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, Guangxi, PR China
- Guangxi Colleges and Universities Key Laboratory of Utilization of Microbial and Botanical Resources, College of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, Guangxi, PR China
| | - RH Lin
- Key Laboratory of New Techniques for Chemical and Biological Conversion Process, College of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, Guangxi, PR China
- Guangxi Colleges and Universities Key Laboratory of Utilization of Microbial and Botanical Resources, College of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, Guangxi, PR China
| | - J Wu
- Guangxi Colleges and Universities Key Laboratory of Utilization of Microbial and Botanical Resources, College of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, Guangxi, PR China
| | - JB He
- Guangxi Colleges and Universities Key Laboratory of Utilization of Microbial and Botanical Resources, College of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, Guangxi, PR China
| | - YC Wu
- Key Laboratory of New Techniques for Chemical and Biological Conversion Process, College of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, Guangxi, PR China
| | - XY Wang
- Key Laboratory of New Techniques for Chemical and Biological Conversion Process, College of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, Guangxi, PR China
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Long H, Cai X, Yang H, He J, Wu J, Lin R. Optimization of monomethoxy polyethyleneglycol-modified oxalate decarboxylase by response surface methodology. J Biol Phys 2017; 43:445-459. [PMID: 28780598 PMCID: PMC6104902 DOI: 10.1007/s10867-017-9461-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 06/30/2017] [Indexed: 10/19/2022] Open
Abstract
In order to improve the stability of oxalate decarboxylase (Oxdc), response surface methodology (RSM), based on a four-factor three-level Box-Behnken central composite design was used to optimize the reaction conditions of oxalate decarboxylase (Oxdc) modified with monomethoxy polyethyleneglycol (mPEG5000). Four independent variables such as the ratio of mPEG-aldehyde to Oxdc, reaction time, temperature, and reaction pH were investigated in this work. The structure of modified Oxdc was identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Fourier transform infrared (FTIR) spectroscopy, the stability of the modified Oxdc was also investigated. The optimal conditions were as follows: the mole ratio of mPEG-aldehyde to Oxdc of 1:47.6, time of 13.1 h, temperature at 29.9 °C, and the reaction pH of 5.3. Under optimal conditions, experimental modified rate (MR = 73.69%) and recovery rate (RR = 67.58%) were matched well with the predicted value (MR = 75.11%) and (RR = 69.17%). SDS-PAGE and FTIR analysis showed that mPEG was covalently bound to the Oxdc. Compared with native Oxdc, the modified Oxdc (mPEG-Oxdc) showed higher thermal stability and better tolerance to trypsin or different pH treatment. This work will provide a further theoretical reference for enzyme modification and conditional optimization.
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Affiliation(s)
- Han Long
- Guangxi Colleges and Universities Key Laboratory of Utilization of Microbial and Botanical Resources, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, 530006, Guangxi, People's Republic of China
| | - XingHua Cai
- Guangxi Colleges and Universities Key Laboratory of Utilization of Microbial and Botanical Resources, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, 530006, Guangxi, People's Republic of China
| | - Hui Yang
- Key Laboratory of New Techniques for Chemical and Biological Conversion Process, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, 530006, Guangxi, People's Republic of China
| | - JunBin He
- Guangxi Colleges and Universities Key Laboratory of Utilization of Microbial and Botanical Resources, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, 530006, Guangxi, People's Republic of China
| | - Jia Wu
- Guangxi Colleges and Universities Key Laboratory of Utilization of Microbial and Botanical Resources, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, 530006, Guangxi, People's Republic of China
| | - RiHui Lin
- Guangxi Colleges and Universities Key Laboratory of Utilization of Microbial and Botanical Resources, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, 530006, Guangxi, People's Republic of China.
- Key Laboratory of New Techniques for Chemical and Biological Conversion Process, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, 530006, Guangxi, People's Republic of China.
- Guangxi Key Laboratory Cultivation Base for Polysaccharide Materials and their Modification, Guangxi University for Nationalities, Nanning, 530006, China.
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