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Artarini A, Hadianti T, Giri-Rachman EA, Tan MI, Safitri IA, Hidayat NA, Retnoningrum DS, Natalia D. Development of Adenovirus-Based Covid-19 Vaccine Candidate in Indonesia. Mol Biotechnol 2024; 66:222-232. [PMID: 37076664 PMCID: PMC10115376 DOI: 10.1007/s12033-023-00749-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/05/2023] [Indexed: 04/21/2023]
Abstract
Covid-19 pandemic has struck worldwide by end of 2019 and the use of various vaccine platforms was one of the main strategies to end this. To meet the needs for vaccine technology equality among many countries, we developed adenovirus-based Covid-19 vaccine candidate in Indonesia. SARS-CoV-2 Spike gene (S) was constructed into pAdEasy vector. The recombinant serotype 5 Adenovirus (AdV_S) genome was transfected into AD293 cells to produce recombinant adenovirus. Characterization using PCR confirmed the presence of spike gene. Transgene expression analysis showed the expression of S protein in AdV_S infected AD293 and A549 cells. Optimization of viral production showed the highest titer was obtained at MOI of 0.1 and 1 at 4 days. The in vivo study was performed by injecting Balb/c mice with 3.5 × 107 ifu of purified adenovirus. The result showed that S1-specific IgG was increased up to 56 days after single-dose administration of AdV_S. Interestingly, significant increase of S1 glycoprotein-specific IFN-γ ELISpot was observed in AdV_S treated Balb/c mice. In conclusion, the AdV_S vaccine candidate was successfully produced at laboratory scale, immunogenic, and did not cause severe inflammation in Balb/c mice. This study serves as initial step towards manufacturing of adenovirus-based vaccine in Indonesia.
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Affiliation(s)
- Anita Artarini
- School of Pharmacy, Institut Teknologi Bandung, Jln. Ganesha 10, Bandung, 40132, Indonesia.
| | - Tia Hadianti
- School of Pharmacy, Institut Teknologi Bandung, Jln. Ganesha 10, Bandung, 40132, Indonesia
| | | | - Marselina Irasonia Tan
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jln. Ganesha 10, Bandung, 40132, Indonesia
| | - Intan A Safitri
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jln. Ganesha 10, Bandung, 40132, Indonesia
| | - Nurhamidah A Hidayat
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jln. Ganesha 10, Bandung, 40132, Indonesia
| | - Debbie S Retnoningrum
- School of Pharmacy, Institut Teknologi Bandung, Jln. Ganesha 10, Bandung, 40132, Indonesia
| | - Dessy Natalia
- Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jln. Ganesha 10, Bandung, 40132, Indonesia
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Safitri IA, Sugijo Y, Puspasari F, Masduki FF, Ihsanawati, Giri-Rachman EA, Artarini AA, Tan MI, Natalia D. Immunogenicity studies of recombinant RBD SARS-CoV-2 as a COVID-19 vaccine candidate produced in Escherichia coli. Vaccine X 2024; 16:100443. [PMID: 38304876 PMCID: PMC10832452 DOI: 10.1016/j.jvacx.2024.100443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 -related global COVID-19 pandemic has been impacting millions of people since its outbreak in 2020. COVID-19 vaccination has proven highly efficient in reducing illness severity and preventing infection-related fatalities. The World Health Organization has granted emergency use approval to multiple, including protein subunit technology-based, COVID-19 vaccines. Foreseeably, additional COVID-19 subunit vaccine development would be essential to meet the accessible and growing demand for effective vaccines, especially for Low-Middle-Income Countries (LMIC). The SARS-CoV-2 spike protein receptor binding domain (RBD), as the primary target for neutralizing antibodies, holds significant potential for future COVID-19 subunit vaccine development. In this study, we developed a recombinant Escherichia coli-expressed RBD (rRBD) as a vaccine candidate and evaluated its immunogenicity and preliminary toxicity in BALB/c mice. The rRBD induced humoral immune response from day 7 post-vaccination and, following the booster doses, the IgG levels increased dramatically in mice. Interestingly, our vaccine candidate also significantly induced cellular immune response, indicated by the incrased IFN-ɣ-producing cell numbers. We observed no adverse effect or local reactogenicity either in control or treated mice. Taken together, our discoveries could potentially support efficient and cost-effective vaccine antigen production, from which LMICs could particularly benefit.
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Affiliation(s)
- Intan Aghniya Safitri
- Biology Department, School of Life Science and Technology, Bandung Institute of Technology, Bandung, Indonesia
| | - Yovin Sugijo
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
| | - Fernita Puspasari
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
| | - Fifi Fitriyah Masduki
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
| | - Ihsanawati
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
| | - Ernawati Arifin Giri-Rachman
- Biology Department, School of Life Science and Technology, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
| | - Aluicia Anita Artarini
- Pharmaceutical Biotechnology Laboratory, Pharmaceutics Department, School of Pharmacy, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
| | - Marselina Irasonia Tan
- Biology Department, School of Life Science and Technology, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
| | - Dessy Natalia
- Biochemistry Group, Department of Chemistry, Faculty of Mathematics and Natural Science, Bandung Institute of Technology, Bandung, Indonesia
- Bioscience and Biotechnology Research Centre, Bandung Institute of Technology, Bandung, Indonesia
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Warli SM, Firsty NN, Natalia D, Velaro AJ, Tala ZZ. Urodynamic parameter improvements after mirabegron vs. antimuscarinics agents in non-neurogenic overactive bladder: a systematic review and meta-analysis of treatment effect. Eur Rev Med Pharmacol Sci 2023; 27:3864-3876. [PMID: 37203811 DOI: 10.26355/eurrev_202305_32292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
OBJECTIVE: This review aimed to establish the comparison between mirabegron and antimuscarinic agents through the improvement of the urodynamic study (UDS) parameter among overactive bladder (OAB) populations. MATERIALS AND METHODS: The PRISMA checklist and procedure were utilized to standardize our review of studies from scientific databases published between January 2013 and May 2022 in accordance with the applied eligibility criteria. This study mainly focused on UDS parameter improvement; hence, baseline and follow-up completion were mandatory to be included. The quality of each included study was assessed with the Cochrane risk-of-bias tool in RevMan 5.4.1. RESULTS: We included a total of 5 clinical trials encompassing 430 clinically confirmed OAB individuals. Our meta-analysis demonstrated that the improvement of maximum urinary flow rate (Qmax) was more apparent in the mirabegron arm [mean difference (MD), 1.78 (1.31, 2.26); p<0.05] compared to antimuscarinics arm [MD, 0.02 (-2.53, 2.57); p>0.05) as analyzed in random-effect model (REM) analysis within 95% CI. Similar outcomes were also observed on the other UDS parameters related to the bladder's storage function, e.g., post-void residual (PVR) and detrusor overactivity (DO) cases, with most of the MDs favoring mirabegron. CONCLUSIONS: Mirabegron is superior in improving most of the UDS parameter outcomes compared to the antimuscarinics agents though the current guideline should always refer to symptoms improvement. Emphasizing the role of UDS parameter measurements to objectively confirm a therapeutic effect should be considered in the upcoming studies.
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Affiliation(s)
- S M Warli
- Department of Urology, Universitas Sumatera Utara Hospital - Universitas Sumatera Utara, Medan, Indonesia.
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Shofiyah SS, Yuliani D, Widya N, Sarian FD, Puspasari F, Radjasa OK, Ihsanawati, Natalia D. Isolation, expression, and characterization of raw starch degrading α-amylase from a marine lake Bacillus megaterium NL3. Heliyon 2020; 6:e05796. [PMID: 33426327 PMCID: PMC7776835 DOI: 10.1016/j.heliyon.2020.e05796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/23/2020] [Accepted: 12/18/2020] [Indexed: 01/05/2023] Open
Abstract
A land-locked marine lake Kakaban with its significant ecological paramaters provides a unique habitat for bacteria with novel biotechnology potential that uses a diverse array of catalytic agents, including α-amylase. Aiming at the isolation of raw starch degrading α-amylase from marine biodiversity, a gene encoding BmaN2 from a sea anemone associated bacterium Bacillus megaterium NL3 was cloned and expressed in Escherichia coli ArcticExpress (DE3). It comprises an open reading frame of 1,563 nucleotides encoding BmaN2 of 520 amino acids and belongs to the glycoside hydrolase family 13 subfamily 36 (GH13_36). This α-amylase has a maximum activity at pH 6.0 and 60 °C with a specific activity of 28.7 U mg-1. The BmaN2 activity is enhanced strongly by Ca2+ but inhibited by EDTA. BmaN2 also exhibits high catalytic efficiency on soluble starch with k cat /K M value of 14.1 mL mg-1 s-1. Despite no additional starch-binding domain, BmaN2 is able to hydrolyze various raw starches, such as wheat, corn, cassava, potato, rice, sago, and canna, in which granular wheat is the preferred substrate for BmaN2. These characteristics indicate that BmaN2 is a promising raw starch degrading enzyme within the subfamily GH13_36.
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Affiliation(s)
- Sofi Siti Shofiyah
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
- Marine Science Program Study, Faculty of Marine Science, OSO University, Pontianak, 78113, Indonesia
| | - Dewi Yuliani
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Nurul Widya
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Fean D. Sarian
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Fernita Puspasari
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Ocky Karna Radjasa
- Center for Tropical Coastal and Marine Studies, Diponegoro University, Widya Puraya, Semarang, 50275, Indonesia
- Indonesian Institute of Sciences, Gatot Subroto 10, Jakarta, Indonesia
| | - Ihsanawati
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Dessy Natalia
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
- University Center of Excellence for Nutraceuticals, Biosciences and Biotechnology Research Center, Bandung, Indonesia
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Naully PG, Nurainy N, Restiawaty E, Natalia D, Retnoningrum DS, Niloperbowo W, Giri-Rachman EA. Integration Stability of sHBsAg-Multi Expression Cassettes in Pichia pastoris GS115 during Methanol Induction. HAYATI J Biosci 2020. [DOI: 10.4308/hjb.27.4.283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Hepatitis B is the major health problem worldwide including in Indonesia. Vaccination is the best prevention strategy for the disease. For the purpose of vaccine development and to decrease drug import, production of Hepatitis B Virus (HBV) small surface antigen (sHBsAg) from Indonesian HBV subtype is needed. The recombinant protein production can be conducted by integrating multi expression cassettes of sHBsAg gene in Pichia pastoris chromosome using gene replacement method. Such integration method turns out to allow loss of foreign gene from chromosome by excisional recombination-mediated looping out. This research was aimed to determine integration stability of four copies of sHBsAg expression cassette in P. pastoris GS115 chromosome inducted with 2% methanol in FM22 medium. The methanol induction was conducted twice at 63-h and 75-h. Integration stability determination was conducted qualitatively using PCR and quantitatively using qPCR absolute quantification. A band of 208 bp with similar intensity was observed after amplification of genomic DNA. All samples generated the same Ct value of around 22 with four copies of sHBsAg gene per genome. The result from this experiment shows that integration of four copies of sHBsAg expression cassette in P. pastoris GS115 chromosome is stable during methanol induction.
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Purkan P, Ihsanawati I, Natalia D, Syah YM, Retnoningrum DS, Siswanto I. Molecular Analysis of katG Encoding Catalase-Peroxidase from Clinical Isolate of Isoniazid-Resistant Mycobacterium tuberculosis. J Med Life 2018; 11:160-167. [PMID: 30140323 PMCID: PMC6101688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Isoniazid (INH) is a drug for the treatment of tuberculosis in patients infected with Mycobacterium tuberculosis. The katG enzyme, or catalase-peroxidase, activates the pro-drug INH that is coded by the katG gene in M. tuberculosis. Mutations of the katG gene in M. tuberculosis are a major INH resistance mechanism. The M. tuberculosis clinical isolate R2 showed INH resistance at a high level of 10 µg/mL. However, the molecular basis for the resistance is unclear. The identification of a mutation in the katG gene of the clinical isolate R2 showed four mutations, i.e., C1061T, G1261 A, G1388T, G2161A, which correspond to the amino acid substitutions T354I, G421S, R463L, and V721M, respectively. The mutant katG gene, along with the wild-type were cloned, expressed and purified. The mutant enzyme showed 86.5% of catalase and 45% of peroxidase activities in comparison to the wild type. The substitutions of T354I and G421S in mutant katG R2 created significant instability in the adduct triad complex (Trp107-Tyr229-Met255), a part of the active site of the catalase-peroxidase enzyme in the model structure analysis. The events could be based on the high resistance of the clinical isolate R2 toward INH as the molecular basis.
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Affiliation(s)
- P Purkan
- Department of Chemistry, Faculty of Sciences and Technology, Airlangga University; Surabaya, Indonesia
| | - I Ihsanawati
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Bandung, Indonesia
| | - D Natalia
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Bandung, Indonesia
| | - YM Syah
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Bandung, Indonesia
| | - DS Retnoningrum
- School of Pharmacy, Bandung Institute of Technology, Bandung, Indonesia
| | - I Siswanto
- Department of Chemistry, Faculty of Sciences and Technology, Airlangga University; Surabaya, Indonesia
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Puspasari F, Putri RD, Aisyah, Damayanti RRR, Yuwita A, Alisjahbana B, Handali S, Ihsanawati, Natalia D. Construction and expression of a synthetic gene encoding nonstructural glycoprotein NS1 of dengue 2 virus in Pichia pastoris. Asian Pac J Trop Biomed 2017. [DOI: 10.1016/j.apjtb.2017.07.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Sarian FD, Janeček Š, Pijning T, Ihsanawati, Nurachman Z, Radjasa OK, Dijkhuizen L, Natalia D, van der Maarel MJEC. A new group of glycoside hydrolase family 13 α-amylases with an aberrant catalytic triad. Sci Rep 2017; 7:44230. [PMID: 28287181 PMCID: PMC5347038 DOI: 10.1038/srep44230] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/31/2017] [Indexed: 11/09/2022] Open
Abstract
α-Amylases are glycoside hydrolase enzymes that act on the α(1→4) glycosidic linkages in glycogen, starch, and related α-glucans, and are ubiquitously present in Nature. Most α-amylases have been classified in glycoside hydrolase family 13 with a typical (β/α)8-barrel containing two aspartic acid and one glutamic acid residue that play an essential role in catalysis. An atypical α-amylase (BmaN1) with only two of the three invariant catalytic residues present was isolated from Bacillus megaterium strain NL3, a bacterial isolate from a sea anemone of Kakaban landlocked marine lake, Derawan Island, Indonesia. In BmaN1 the third residue, the aspartic acid that acts as the transition state stabilizer, was replaced by a histidine. Three-dimensional structure modeling of the BmaN1 amino acid sequence confirmed the aberrant catalytic triad. Glucose and maltose were found as products of the action of the novel α-amylase on soluble starch, demonstrating that it is active in spite of the peculiar catalytic triad. This novel BmaN1 α-amylase is part of a group of α-amylases that all have this atypical catalytic triad, consisting of aspartic acid, glutamic acid and histidine. Phylogenetic analysis showed that this group of α-amylases comprises a new subfamily of the glycoside hydrolase family 13.
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Affiliation(s)
- Fean D Sarian
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, Indonesia.,Aquatic Biotechnology and Bioproduct Engineering, Engineering and Technology institute Groningen (ENTEG), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, SK-84551 Bratislava, Slovakia.,Department of Biology, Faculty of Natural Sciences, University of SS. Cyril and Mehtodius, Nam. J. Herdu 2, SK-91701 Trnava, Slovakia
| | - Tjaard Pijning
- X-Ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Ihsanawati
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, Indonesia
| | - Zeily Nurachman
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, Indonesia
| | - Ocky K Radjasa
- Department of Marine Science, Faculty of Fishery and Marine Science, Diponegoro University, Semarang 50275, Central Java, Indonesia
| | - Lubbert Dijkhuizen
- Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Dessy Natalia
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung, 40132, Indonesia
| | - Marc J E C van der Maarel
- Aquatic Biotechnology and Bioproduct Engineering, Engineering and Technology institute Groningen (ENTEG), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Natalia D, Suprijatna E, Muryani R. Pengaruh penggunaan limbah industri jamu dan bakteri asam laktat (Lactobacillus sp.) sebagai sinbiotik untuk aditif pakan terhadap performans ayam petelur periode layer. JIIP 2016. [DOI: 10.21776/ub.jiip.2016.026.03.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Natalia D, Syah YM, Retnoningrum DS, Kusuma HS. Mutation of katG in a clinical isolate of Mycobacterium tuberculosis: effects on catalase-peroxidase for isoniazid activation. Ukr Biochem J 2016; 88:71-81. [PMID: 29235814 DOI: 10.15407/ubj88.05.071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Mutations in katG gene are often associated with isoniazid (INH) resistance in Mycobacterium tuberculosis strain. This research was perfomed to identify the katG mutation in clinical isolate (L8) that is resistant to INH at 1 μg/ml. In addition to characterize the catalase-peroxidase of KatG L8 and perform the ab initio structural study of the protein to get a more complete understanding in drug activation and the resistance mechanism. The katG gene was cloned and expressed in Escherichia coli, then followed by characterization of catalase-peroxidase of KatG. The structure modelling was performed to know a basis of alterations in enzyme activity. A substitution of A713G that correspond to Asn238Ser replacement was found in the L8 katG. The Asn238Ser modification leads to a decline in the activity of catalase-peroxidase and INH oxidation of the L8 KatG protein. The catalytic efficiency (Kcat/KM) of mutant KatGAsn238Ser respectively decreases to 41 and 52% for catalase and peroxidase. The mutant KatGAsn238Ser also shows a decrease of 62% in INH oxidation if compared to a wild type KatG (KatGwt). The mutant Asn238Ser might cause instability in the substrate binding site of KatG, because of removal of a salt bridge connecting the amine group of Asn238 to the carboxyl group of Glu233, which presents in KatGwt. The lost of the salt bridge in the substrate binding site in mutant KatGAsn238Ser created changes unfavorable for enzyme activities, which in turn emerge as INH resistance in the L8 isolate of M. tuberculosis.
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Natalia D, Jumadila O, Anggraini ID, Meutia F, Puspasari F, Hasan K. Alkyl hydroperoxide reductase from Bacillus aquimaris
MKSC 6.2 protects Esherichia coli
from oxidative stress. J Basic Microbiol 2015; 56:834-7. [DOI: 10.1002/jobm.201500406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/03/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Dessy Natalia
- Division of Biochemistry Research; Faculty of Mathematics and Natural Sciences; Institut Teknologi Bandung; Bandung Indonesia
- Bioscience and Biotechnology Research Center; Institut Teknologi Bandung; Bandung Indonesia
| | - Ozi Jumadila
- Division of Biochemistry Research; Faculty of Mathematics and Natural Sciences; Institut Teknologi Bandung; Bandung Indonesia
| | - Irika Devi Anggraini
- Division of Biochemistry Research; Faculty of Mathematics and Natural Sciences; Institut Teknologi Bandung; Bandung Indonesia
| | - Febrina Meutia
- Division of Biochemistry Research; Faculty of Mathematics and Natural Sciences; Institut Teknologi Bandung; Bandung Indonesia
| | - Fernita Puspasari
- Bioscience and Biotechnology Research Center; Institut Teknologi Bandung; Bandung Indonesia
| | - Khomaini Hasan
- Bioscience and Biotechnology Research Center; Institut Teknologi Bandung; Bandung Indonesia
- Biochemistry Laboratory, Faculty of Medicine; Universitas Jenderal Achmad Yani; Cimahi West Java Indonesia
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Azhar M, Natalia D, Syukur S, . V, . J. Gene Fragments that Encodes Inulin Hydrolysis Enzyme from Genomic Bacillus licheniformis: Isolation by PCR Technique Using New Primers. ACTA ACUST UNITED AC 2015. [DOI: 10.3923/ijbc.2015.59.69] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Azhar M, Syukur S, Natalia D, - V, - J. SKRINING DAN IDENTIFIKASI BAKTERI PENDEGRADASI INULIN DARI SUMBER AIR PANAS PADANG BALIMBIANG DI SOLOK. J Ris Kim 2015. [DOI: 10.25077/jrk.v5i1.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
ABSTRACT Thermophilic bacteria and thermotolerant bacteria are potential sources of thermostable of inulin degradating enzyme, an enzyme which converts inulin into fructose and FOS prebiotics. Isolation and identification of 16S rDNA gene inulin degradation bacteria from hot springs of Padang Balimbiang in Solok have been undertaken. Screening of inulin degradation bacteria was done using direct and undirect methods on medium with inulin or inulin-RBB as a sole carbon source. One inulin degradation bacteria have been obtained from 21 isolates. The isolate was designated as UBCT-030. The isolate is able to grow at temperature 23 °C to 60 °C. According to 16S rDNA gene analysis, phisiology and morphology bacteria on UBCT-030 isolate was identified as Bacillus subtilis. Keywords: inulinase bacteria, hot springs, Bacillus subtilis, inulin, 16S rDNA gene
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Natalia D, Vidilaseris K, Ismaya WT, Puspasari F, Prawira I, Hasan K, Fibriansah G, Permentier HP, Nurachman Z, Subroto T, Dijkstra BW, Soemitro S. Effect of introducing a disulphide bond between the A and C domains on the activity and stability of Saccharomycopsis fibuligera R64 α-amylase. J Biotechnol 2014; 195:8-14. [PMID: 25533400 DOI: 10.1016/j.jbiotec.2014.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 11/26/2014] [Accepted: 12/08/2014] [Indexed: 11/30/2022]
Abstract
Native enzyme and a mutant containing an extra disulphide bridge of recombinant Saccharomycopsis fibuligera R64 α-amylase, designated as Sfamy01 and Sfamy02, respectively, have successfully been overexpressed in the yeast Pichia pastoris KM71H. The purified α-amylase variants demonstrated starch hydrolysis resulting in a mixture of maltose, maltotriose, and glucose, similar to the wild type enzyme. Introduction of the disulphide bridge shifted the melting temperature (TM) from 54.5 to 56 °C and nearly tripled the enzyme half-life time at 65 °C. The two variants have similar kcat/KM values. Similarly, inhibition by acarbose was only slightly affected, with the IC50 of Sfamy02 for acarbose being 40 ± 3.4 μM, while that of Sfamy01 was 31 ± 3.9 μM. On the other hand, the IC50 of Sfamy02 for EDTA was 0.45 mM, nearly two times lower than that of Sfamy01 at 0.77 mM. These results show that the introduction of a disulphide bridge had little effect on the enzyme activity, but made the enzyme more susceptible to calcium ion extraction. Altogether, the new disulphide bridge improved the enzyme stability without affecting its activity, although minor changes in the active site environment cannot be excluded.
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Affiliation(s)
- Dessy Natalia
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Jalan Ganesa No 10, Bandung 40132, Indonesia; Center for Life Sciences, Bandung Institute of Technology, Jalan Ganesa No. 10, Bandung 40132, Indonesia.
| | - Keni Vidilaseris
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Jalan Ganesa No 10, Bandung 40132, Indonesia
| | - Wangsa T Ismaya
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands; Biochemistry Laboratory, Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jalan Singaperbangsa No. 2, Bandung 40133, Indonesia.
| | - Fernita Puspasari
- Center for Life Sciences, Bandung Institute of Technology, Jalan Ganesa No. 10, Bandung 40132, Indonesia
| | - Iman Prawira
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Jalan Ganesa No 10, Bandung 40132, Indonesia
| | - Khomaini Hasan
- Center for Life Sciences, Bandung Institute of Technology, Jalan Ganesa No. 10, Bandung 40132, Indonesia
| | - Guntur Fibriansah
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Hjalmar P Permentier
- Mass Spectrometry Core Facility, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Zeily Nurachman
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Jalan Ganesa No 10, Bandung 40132, Indonesia
| | - Toto Subroto
- Biochemistry Laboratory, Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jalan Singaperbangsa No. 2, Bandung 40133, Indonesia
| | - Bauke W Dijkstra
- Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Soetijoso Soemitro
- Biochemistry Laboratory, Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jalan Singaperbangsa No. 2, Bandung 40133, Indonesia
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Kurniasih SD, Alfi A, Natalia D, Radjasa OK, Nurachman Z. Construction of individual, fused, and co-expressed proteins of endoglucanase and β-glucosidase for hydrolyzing sugarcane bagasse. Microbiol Res 2014; 169:725-32. [PMID: 24598011 DOI: 10.1016/j.micres.2014.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/20/2014] [Accepted: 02/01/2014] [Indexed: 11/30/2022]
Abstract
At least a combination of endoglucanase (EglII) and β-glucosidase (BglZ) is required for hydrolyzing crystalline cellulose. To understand the catalytic efficiency of combination enzymes for converting biomass to sugars, EglII and BglZ were constructed in the form of individual, fused as well as co-expression proteins, and their activities for hydrolyzing sugarcane bagasse were evaluated. The genes, eglII isolated from Bacillus amyloliquefaciens PSM3.1 earlier and bglZ from B. amyloliquefaciens ABBD, were expressed extracellularly in Bacillus megaterium MS941. EglII exhibited both exoglucanase and endoglucanase activities, and BglZ belonging to the glycoside hydrolase 1 family (GH 1) showed β-glucosidase activity. A combination of EglII and BglZ showed activity on substrates Avicel, CMC and sugarcane bagasse. Specifically for hydrolyzing sugarcane bagasse, fused protein (fus-EglII+BglZ), co-expression protein (coex-BglZ+EglII), and mixed-individual protein (mix-EglII+BglZ) produced cellobiose as the main product, along with a small amount of glucose. The amount of reducing sugars released from the hydrolyzing bleached sugarcane bagasse (BSB) using fus-EglII+BglZ and mix-EglII+BglZ was 2.7- and 4.2-fold higher, respectively, than steamed sugarcane bagasse (SSB), indicating the synergetic enzymes worked better on treated sugarcane bagasse. Compared with fus-EglII+BglZ and mix-EglII+BglZ, coex-BglZ+EglII released more mol reducing sugars from SSB, indicating the enzymes were potential for biomass conversion. Additionally, coex-BglZ+EglII acted on BSB 2.5-fold faster than fus-EglII+BglZ. Thus, coex-bglZ+eglII expression system was the best choice to produce enzymes for hydrolyzing sugarcane baggase.
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Affiliation(s)
- Sari Dewi Kurniasih
- Biochemistry Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132, Indonesia
| | - Almasul Alfi
- Biochemistry Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132, Indonesia
| | - Dessy Natalia
- Biochemistry Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132, Indonesia
| | - Ocky Karna Radjasa
- Research Center for Tropical Marine Biotechnology, Diponegoro University, Jl. Soedarto SH No. 1, Semarang 50275, Indonesia
| | - Zeily Nurachman
- Biochemistry Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132, Indonesia.
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Ismaya WT, Hasan K, Kardi I, Zainuri A, Rahmawaty RI, Permanahadi S, El Viera BV, Harinanto G, Gaffar S, Natalia D, Subroto T, Soemitro S. Chemical modification of Saccharomycopsis fibuligera R64 α-amylase to improve its stability against thermal, chelator, and proteolytic inactivation. Appl Biochem Biotechnol 2013; 170:44-57. [PMID: 23468006 DOI: 10.1007/s12010-013-0164-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 02/21/2013] [Indexed: 10/27/2022]
Abstract
α-Amylase catalyzes hydrolysis of starch to oligosaccharides, which are further degraded to simple sugars. The enzyme has been widely used in food and textile industries and recently, in generation of renewable energy. An α-amylase from yeast Saccharomycopsis fibuligera R64 (Sfamy) is active at 50 °C and capable of degrading raw starch, making it attractive for the aforementioned applications. To improve its characteristics as well as to provide information for structural study ab initio, the enzyme was chemically modified by acid anhydrides (nonpolar groups), glyoxylic acid (GA) (polar group), dimethyl adipimidate (DMA) (cross-linking), and polyethylene glycol (PEG) (hydrophilization). Introduction of nonpolar groups increased enzyme stability up to 18 times, while modification by a cross-linking agent resulted in protection of the calcium ion, which is essential for enzyme activity and integrity. The hydrophilization with PEG resulted in protection against tryptic digestion. The chemical modification of Sfamy by various modifiers has thereby resulted in improvement of its characteristics and provided systematic information beneficial for structural study of the enzyme. An in silico structural study of the enzyme improved the interpretation of the results.
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Affiliation(s)
- Wangsa Tirta Ismaya
- Biochemistry Laboratory, Department of Chemistry, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jalan Singaperbangsa No. 2, 40133 Bandung, Indonesia.
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Puspasari F, Radjasa OK, Noer AS, Nurachman Z, Syah YM, van der Maarel M, Dijkhuizen L, Janeček S, Natalia D. Raw starch-degrading α-amylase from Bacillus aquimaris MKSC 6.2: isolation and expression of the gene, bioinformatics and biochemical characterization of the recombinant enzyme. J Appl Microbiol 2012; 114:108-20. [PMID: 23020612 DOI: 10.1111/jam.12025] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 08/18/2012] [Accepted: 08/29/2012] [Indexed: 11/30/2022]
Abstract
AIMS The aims were to isolate a raw starch-degrading α-amylase gene baqA from Bacillus aquimaris MKSC 6.2, and to characterize the gene product through in silico study and its expression in Escherichia coli. METHODS AND RESULTS A 1539 complete open reading frame of a starch-degrading α-amylase gene baqA from B. aquimaris MKSC 6·2 has been determined by employing PCR and inverse PCR techniques. Bioinformatics analysis revealed that B. aquimaris MKSC 6.2 α-amylase (BaqA) has no starch-binding domain, and together with a few putative α-amylases from bacilli may establish a novel GH13 subfamily most closely related to GH13_1. Two consecutive tryptophans (Trp201 and Trp202, BaqA numbering) were identified as a sequence fingerprint of this novel GH13 subfamily. Escherichia coli cells produced the recombinant BaqA protein as inclusion bodies. The refolded recombinant BaqA protein degraded raw cassava and corn starches, but exhibited no activity with soluble starch. CONCLUSIONS A novel raw starch-degrading B. aquimaris MKSC 6.2 α-amylase BaqA is proposed to be a member of new GH13 subfamily. SIGNIFICANCE AND IMPACT OF THE STUDY This study has contributed to the overall knowledge and understanding of amylolytic enzymes that are able to bind and digest raw starch directly.
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Affiliation(s)
- F Puspasari
- Biochemistry Research Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, Indonesia
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Natalia D, Greiner L, Leitner W, Ansorge-Schumacher MB. Stability, activity, and selectivity of benzaldehyde lyase in supercritical fluids. J Supercrit Fluids 2012. [DOI: 10.1016/j.supflu.2011.11.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Natalia D, Kohlmann C, Ansorge-Schumacher MB, Greiner L. Direct spectrophotometric assay for benzaldehyde lyase activity. Biotechnol Res Int 2011; 2011:478925. [PMID: 21804944 PMCID: PMC3142707 DOI: 10.4061/2011/478925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/25/2011] [Accepted: 06/08/2011] [Indexed: 11/20/2022]
Abstract
Benzaldehyde lyase from Pseudomonas fluorescens Biovar I. (BAL, EC 4.1.2.38) is a versatile catalyst for the organic synthesis of chiral α-hydroxy ketones. To allow fast assessment of enzyme activity, a direct spectrophotometric assay is desirable. Here, a new robust and easy-to-handle assay based on UV absorption is presented. The assay developed is based on the ligation of the α-hydroxy ketone (R)-2,2′-furoin from 2-furaldehyde. A robust assay with direct monitoring of the product is facilitated with a convenient concentration working range minimising experimental associated with low concentrations.
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Affiliation(s)
- Dessy Natalia
- ITMC, RWTH Aachen University, Worringerweg 1, 52056 Aachen, Germany
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Puspasari F, Nurachman Z, Noer AS, Radjasa OK, van der Maarel MJEC, Natalia D. Characteristics of raw starch degrading α-amylase from Bacillus aquimaris MKSC 6.2 associated with soft coral Sinularia sp. STARCH-STARKE 2011. [DOI: 10.1002/star.201000127] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Rizal SI, Rizal M, Indrasari W, Natalia D, Boediono A. EMB-011 Effect of number of oocytes retrieved on the fertilization and pregnancy rate in correlation with female age. Reprod Biomed Online 2008. [DOI: 10.1016/s1472-6483(10)61562-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Williamson RA, Natalia D, Gee CK, Murphy G, Carr MD, Freedman RB. Chemically and conformationally authentic active domain of human tissue inhibitor of metalloproteinases-2 refolded from bacterial inclusion bodies. Eur J Biochem 1996; 241:476-83. [PMID: 8917445 DOI: 10.1111/j.1432-1033.1996.00476.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The aggregation of recombinant proteins into inclusion bodies is a major problem for expression in bacterial systems. The inclusion bodies must be solubilized and the denatured protein renatured if an active molecule is to be recovered. We have developed such a procedure for the active N-terminal domain of tissue inhibitor of metalloproteinases-2 [TIMP-2-(1-127)], a small mammalian protein containing three disulfide bonds. Conditions for its renaturation were determined by studying the refolding behaviour of reduced and denatured mammalian-cell-expressed TIMP-(1-127) by intrinsic fluorescence. This strategy allows the development of a refolding protocol before generation of a bacterial expression system, and allows rapid and systematic optimization of each refolding variable by assessing its effect on the rate and extent of the refolding reaction. TIMP-(1-127) was expressed at high levels in Escherichia coli, and refolded from TIMP-2-(1-127) inclusion bodies, by means of the method developed with mammalian-cell-expressed protein, to give a refolding efficiency of 30-40% and a final yield of 11-14 mg purified protein/l culture. The chemical structure and conformation of this material was characterized by electrospray mass spectrometry and two-dimensional 1H-NMR; no significant differences were found between it and the native protein. Mass analysis of uniformly 13C-labeled and 15N-labeled protein was used to help identify a mistranslated TIMP-(1-127) contaminant in the purified refolded sample. This technique provides additional information on the nature of the modification and allows a distinction to be made between those modifications that are cell derived, and those that arise from subsequent handling of the protein.
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Affiliation(s)
- R A Williamson
- Department of Biosciences, University of Kent, Canterbury, UK
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Dunn A, Luz JM, Natalia D, Gamble JA, Freedman RB, Tuite MF. Protein disulphide isomerase (PDI) is required for the secretion of a native disulphide-bonded protein from Saccharomyces cerevisiae. Biochem Soc Trans 1995; 23:78S. [PMID: 7758797 DOI: 10.1042/bst023078s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- A Dunn
- Research School of Biosciences, University of Kent, Canterbury, UK
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