1
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Yapici I, Tokur AG, Sever B, Ciftci H, Basak AN, DeMirci H. Structural Insights into the Dynamics of Water in SOD1 Catalysis and Drug Interactions. Int J Mol Sci 2025; 26:4228. [PMID: 40362464 PMCID: PMC12071975 DOI: 10.3390/ijms26094228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2025] [Revised: 03/09/2025] [Accepted: 03/12/2025] [Indexed: 05/15/2025] Open
Abstract
Superoxide dismutase 1 (SOD1) is a crucial enzyme that protects cells from oxidative damage by converting superoxide radicals into H2O2 and O2. This detoxification process, essential for cellular homeostasis, relies on a precisely orchestrated catalytic mechanism involving the copper cation, while the zinc cation contributes to the structural integrity of the enzyme. This study presents the 2.3 Å crystal structure of human SOD1 (PDB ID: 9IYK), revealing an assembly of six homodimers and twelve distinct active sites. The water molecules form a complex hydrogen-bonding network that drives proton transfer and sustains active site dynamics. Our structure also uncovers subtle conformational changes that highlight the intrinsic flexibility of SOD1, which is essential for its function. Additionally, we observe how these dynamic structural features may be linked to pathological mutations associated with amyotrophic lateral sclerosis (ALS). By advancing our understanding of hSOD1's mechanistic intricacies and the influence of water coordination, this study offers valuable insights for developing therapeutic strategies targeting ALS. Our structure's unique conformations and active site interactions illuminate new facets of hSOD1 function, underscoring the critical role of structural dynamics in enzyme catalysis. Moreover, we conducted a molecular docking analysis using SOD1 for potential radical scavengers and Abelson non-receptor tyrosine kinase (c-Abl, Abl1) inhibitors targeting misfolded SOD1 aggregation along with oxidative stress and apoptosis, respectively. The results showed that CHEMBL1075867, a free radical scavenger derivative, showed the most promising docking results and interactions at the binding site of hSOD1, highlighting its promising role for further studies against SOD1-mediated ALS.
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Affiliation(s)
- Ilkin Yapici
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Türkiye; (I.Y.); (A.G.T.)
| | - Arda Gorkem Tokur
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Türkiye; (I.Y.); (A.G.T.)
| | - Belgin Sever
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskisehir 26470, Türkiye;
| | - Halilibrahim Ciftci
- Department of Molecular Biology and Genetics, Burdur Mehmet Akif Ersoy University, Burdur 15030, Türkiye;
| | - Ayse Nazli Basak
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (KUTTAM-NDAL), School of Medicine, Koc University, Istanbul 34450, Türkiye
| | - Hasan DeMirci
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Türkiye; (I.Y.); (A.G.T.)
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA 94025, USA
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2
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Al Adem K, Ferreira J, Villanueva A, Fadl S, El-Sadaany F, Masmoudi I, Gidiya Y, Gurudza T, Cardoso T, Saksena N, Rabeh W. 3-chymotrypsin-like protease in SARS-CoV-2. Biosci Rep 2024; 44:BSR20231395. [PMID: 39036877 PMCID: PMC11300678 DOI: 10.1042/bsr20231395] [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: 01/31/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/23/2024] Open
Abstract
Coronaviruses constitute a significant threat to the human population. Severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, is a highly pathogenic human coronavirus that has caused the coronavirus disease 2019 (COVID-19) pandemic. It has led to a global viral outbreak with an exceptional spread and a high death toll, highlighting the need for effective antiviral strategies. 3-Chymotrypsin-like protease (3CLpro), the main protease in SARS-CoV-2, plays an indispensable role in the SARS-CoV-2 viral life cycle by cleaving the viral polyprotein to produce 11 individual non-structural proteins necessary for viral replication. 3CLpro is one of two proteases that function to produce new viral particles. It is a highly conserved cysteine protease with identical structural folds in all known human coronaviruses. Inhibitors binding with high affinity to 3CLpro will prevent the cleavage of viral polyproteins, thus impeding viral replication. Multiple strategies have been implemented to screen for inhibitors against 3CLpro, including peptide-like and small molecule inhibitors that covalently and non-covalently bind the active site, respectively. In addition, allosteric sites of 3CLpro have been identified to screen for small molecules that could make non-competitive inhibitors of 3CLpro. In essence, this review serves as a comprehensive guide to understanding the structural intricacies and functional dynamics of 3CLpro, emphasizing key findings that elucidate its role as the main protease of SARS-CoV-2. Notably, the review is a critical resource in recognizing the advancements in identifying and developing 3CLpro inhibitors as effective antiviral strategies against COVID-19, some of which are already approved for clinical use in COVID-19 patients.
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Affiliation(s)
- Kenana Al Adem
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Juliana C. Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Adrian J. Villanueva
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Farah El-Sadaany
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Imen Masmoudi
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Yugmee Gidiya
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Tariro Gurudza
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Thyago H.S. Cardoso
- OMICS Centre of Excellence, G42 Healthcare, Masdar City, Abu Dhabi, United Arab Emirates
| | - Nitin K. Saksena
- Victoria University, Footscray Campus, Melbourne, VIC. Australia
| | - Wael M. Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
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3
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Guven O, Sever B, Başoğlu-Ünal F, Ece A, Tateishi H, Koga R, Radwan MO, Demir N, Can M, Dilsiz Aytemir M, Inoue JI, Otsuka M, Fujita M, Ciftci H, DeMirci H. Structural Characterization of TRAF6 N-Terminal for Therapeutic Uses and Computational Studies on New Derivatives. Pharmaceuticals (Basel) 2023; 16:1608. [PMID: 38004473 PMCID: PMC10674494 DOI: 10.3390/ph16111608] [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: 08/31/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Tumor necrosis factor receptor-associated factors (TRAFs) are a protein family with a wide variety of roles and binding partners. Among them, TRAF6, a ubiquitin ligase, possesses unique receptor binding specificity and shows diverse functions in immune system regulation, cellular signaling, central nervous system, and tumor formation. TRAF6 consists of an N-terminal Really Interesting New Gene (RING) domain, multiple zinc fingers, and a C-terminal TRAF domain. TRAF6 is an important therapeutic target for various disorders and structural studies of this protein are crucial for the development of next-generation therapeutics. Here, we presented a TRAF6 N-terminal structure determined at the Turkish light source "Turkish DeLight" to be 3.2 Å resolution at cryogenic temperature (PDB ID: 8HZ2). This structure offers insight into the domain organization and zinc-binding, which are critical for protein function. Since the RING domain and the zinc fingers are key targets for TRAF6 therapeutics, structural insights are crucial for future research. Separately, we rationally designed numerous new compounds and performed molecular docking studies using this template (PDB ID:8HZ2). According to the results, 10 new compounds formed key interactions with essential residues and zinc ion in the N-terminal region of TRAF6. Molecular dynamic (MD) simulations were performed for 300 ns to evaluate the stability of three docked complexes (compounds 256, 322, and 489). Compounds 256 and 489 was found to possess favorable bindings with TRAF6. These new compounds also showed moderate to good pharmacokinetic profiles, making them potential future drug candidates as TRAF6 inhibitors.
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Affiliation(s)
- Omur Guven
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey;
| | - Belgin Sever
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan; (B.S.); (H.T.); (R.K.); (M.O.); (M.F.)
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskisehir 26470, Turkey
| | - Faika Başoğlu-Ünal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, European University of Lefke, Northern Cyprus, TR-10, Mersin 99770, Turkey;
| | - Abdulilah Ece
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, Istanbul 34015, Turkey;
| | - Hiroshi Tateishi
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan; (B.S.); (H.T.); (R.K.); (M.O.); (M.F.)
| | - Ryoko Koga
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan; (B.S.); (H.T.); (R.K.); (M.O.); (M.F.)
| | - Mohamed O. Radwan
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan; (B.S.); (H.T.); (R.K.); (M.O.); (M.F.)
| | - Nefise Demir
- Department of Nanoscience and Nanotechnology, Izmir Katip Celebi University, Izmir 35620, Turkey;
| | - Mustafa Can
- Faculty of Engineering and Architecture, Department of Engineering Sciences, Izmir Katip Celebi University, Izmir 35620, Turkey;
| | - Mutlu Dilsiz Aytemir
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, İzmir Katip Çelebi University, Izmir 35620, Turkey;
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara 6100, Turkey
| | - Jun-ichiro Inoue
- Research Platform Office, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan;
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan; (B.S.); (H.T.); (R.K.); (M.O.); (M.F.)
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan; (B.S.); (H.T.); (R.K.); (M.O.); (M.F.)
| | - Halilibrahim Ciftci
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey;
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan; (B.S.); (H.T.); (R.K.); (M.O.); (M.F.)
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan
| | - Hasan DeMirci
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey;
- Koc University Isbank Center for Infectious Diseases (KUISCID), Koc University, Istanbul 34010, Turkey
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA 94025, USA
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4
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Botha S, Fromme P. Review of serial femtosecond crystallography including the COVID-19 pandemic impact and future outlook. Structure 2023; 31:1306-1319. [PMID: 37898125 PMCID: PMC10842180 DOI: 10.1016/j.str.2023.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/30/2023]
Abstract
Serial femtosecond crystallography (SFX) revolutionized macromolecular crystallography over the past decade by enabling the collection of X-ray diffraction data from nano- or micrometer sized crystals while outrunning structure-altering radiation damage effects at room temperature. The serial manner of data collection from millions of individual crystals coupled with the femtosecond duration of the ultrabright X-ray pulses enables time-resolved studies of macromolecules under near-physiological conditions to unprecedented temporal resolution. In 2020 the rapid spread of the coronavirus SARS-CoV-2 resulted in a global pandemic of coronavirus disease-2019. This led to a shift in how serial femtosecond experiments were performed, along with rapid funding and free electron laser beamtime availability dedicated to SARS-CoV-2-related studies. This review outlines the current state of SFX research, the milestones that were achieved, the impact of the global pandemic on this field as well as an outlook into exciting future directions.
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Affiliation(s)
- Sabine Botha
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
| | - Petra Fromme
- Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA; School of Molecular Sciences, Arizona State University, Tempe, AZ 85287-1604, USA.
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5
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Gul M, Ayan E, Destan E, Johnson JA, Shafiei A, Kepceoğlu A, Yilmaz M, Ertem FB, Yapici İ, Tosun B, Baldir N, Tokay N, Nergiz Z, Karakadioğlu G, Paydos SS, Kulakman C, Ferah CK, Güven Ö, Atalay N, Akcan EK, Cetinok H, Arslan NE, Şabanoğlu K, Aşci B, Tavli S, Gümüsboğa H, Altuntaş S, Otsuka M, Fujita M, Teki N Ş, Çi Ftçi H, Durdaği S, Karaca E, Kaplan Türköz B, Kabasakal BV, Kati A, DeMi Rci H. Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source. Sci Rep 2023; 13:8123. [PMID: 37208392 PMCID: PMC10198979 DOI: 10.1038/s41598-023-33989-0] [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: 11/01/2022] [Accepted: 04/21/2023] [Indexed: 05/21/2023] Open
Abstract
High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.
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Affiliation(s)
- Mehmet Gul
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Esra Ayan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Ebru Destan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - J Austin Johnson
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Alaleh Shafiei
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Abdullah Kepceoğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Koç University Surface Science and Technology Center (KUYTAM), Koç University, Istanbul, Türkiye
| | - Merve Yilmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Fatma Betül Ertem
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - İlkin Yapici
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Bilge Tosun
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Nilüfer Baldir
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Nurettin Tokay
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Zeliş Nergiz
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Koç University Isbank Center for Infectious Diseases (KUISCID), Koç University, Istanbul, Türkiye
| | - Gözde Karakadioğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Seyide Seda Paydos
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Cahine Kulakman
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Cengiz Kaan Ferah
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Ömür Güven
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Necati Atalay
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Science, Gebze Technical University, Kocaeli, Türkiye
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Enver Kamil Akcan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Technical University, Istanbul, Türkiye
| | - Haluk Cetinok
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Nazlı Eylül Arslan
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Arel University, Istanbul, Türkiye
| | - Kardelen Şabanoğlu
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yıldız Technical University, Istanbul, Türkiye
| | - Bengisu Aşci
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Serra Tavli
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Helin Gümüsboğa
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
| | - Sevde Altuntaş
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
- Department of Tissue Engineering, Hamidiye Institute of Health Sciences, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
- Department of Drug Discovery, Science Farm Ltd., Kumamoto, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Şaban Teki N
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
- The Scientific and Technological Research Council of Türkiye (TÜBİTAK) Marmara Research Center (MAM), Life Sciences, Kocaeli, Türkiye
- Department of Basic Medical Sciences, Division of Medical Biology, Faculty of Medicine, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Halilibrahim Çi Ftçi
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
- Department of Drug Discovery, Science Farm Ltd., Kumamoto, Japan
| | - Serdar Durdaği
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Türkiye
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir, Türkiye
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir, Türkiye
| | - Burcu Kaplan Türköz
- Department of Food Engineering, Faculty of Engineering, Ege University, Izmir, Türkiye
| | - Burak Veli Kabasakal
- Turkish Accelerator and Radiation Laboratory (TARLA), Ankara University, Ankara, Türkiye
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Ahmet Kati
- Experimental Medicine Application & Research Center, University of Health Sciences Türkiye, Istanbul, Türkiye
- Department of Biotechnology, Hamidiye Institute of Health Sciences, University of Health Sciences Türkiye, Istanbul, Türkiye
| | - Hasan DeMi Rci
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul, Türkiye.
- Koç University Isbank Center for Infectious Diseases (KUISCID), Koç University, Istanbul, Türkiye.
- SLAC National Laboratory, Stanford PULSE Institute, Menlo Park, CA, USA.
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6
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Mazzei L, Greene-Cramer R, Bafna K, Jovanovic A, De Falco A, Acton TB, Royer CA, Ciurli S, Montelione GT. Protocol for production and purification of SARS-CoV-2 3CL pro. STAR Protoc 2023; 4:102326. [PMID: 37235475 DOI: 10.1016/j.xpro.2023.102326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/04/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023] Open
Abstract
3CLpro protease from SARS-CoV-2 is a primary target for COVID-19 antiviral drug development. Here, we present a protocol for 3CLpro production in Escherichia coli. We describe steps to purify 3CLpro, expressed as a fusion with the Saccharomyces cerevisiae SUMO protein, with yields up to 120 mg L-1 following cleavage. The protocol also provides isotope-enriched samples suitable for nuclear magnetic resonance (NMR) studies. We also present methods to characterize 3CLpro by mass spectrometry, X-ray crystallography, heteronuclear NMR, and a Förster-resonance-energy-transfer-based enzyme assay. For complete details on the use and execution of this protocol, please refer to Bafna et al.1.
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Affiliation(s)
- Luca Mazzei
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
| | - Rebecca Greene-Cramer
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Khushboo Bafna
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Aleksandar Jovanovic
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
| | - Anna De Falco
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Thomas B Acton
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Catherine Ann Royer
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Stefano Ciurli
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy.
| | - Gaetano T Montelione
- Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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