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Xiao Y, Wu M. Robust and Irreversible Sortase-Mediated Ligation by Empolyment of Sarkosyl. Chemistry 2024; 30:e202401961. [PMID: 39046730 DOI: 10.1002/chem.202401961] [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: 05/20/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 07/25/2024]
Abstract
Sortase-mediated ligation (SML) is a widely used method for peptide and protein ligation due to ease of substrate preparation and fast enzymatic kinetics. But there are drawbacks that limit broader applications. Sorting motif in substrates may not be exposed to sortase efficiently due to folding or aggregation. In addition, the ligation is reversible under transpeptidation equilibrium that restricts ligation yield. Here we report a simple but robust method to overcome such limitations. By employment of sarkosyl, the detergent alters substrate conformation to raise sorting motif accessibility for sortase catalysis. Moreover, transpeptidation becomes irreversible presumably by formation of micelle to shield ligation products from sortase. In consequence, excellent yields were achieved from sortase variants with different substrate specificity. Notably, this method is compatible with peptides or proteins capable of forming liquid-liquid phase separation (LLPS), presenting a powerful approach for the conjugation of aggregation-prone substrates. Therefore, we believe the sarkosyl-enhanced SML could be widely applied in peptide and protein chemistry and the unique irreversible transpeptidation mechanism offers an insight to detergent-driven equilibrium.
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Affiliation(s)
- Yihang Xiao
- Department of Chemistry, School of Science Westlake University, Hangzhou, 310030, Zhejiang Province, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, Zhejiang Province, China
| | - Mingxuan Wu
- Department of Chemistry, School of Science Westlake University, Hangzhou, 310030, Zhejiang Province, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang Province, China
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2
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Ai H, Pan M, Liu L. Chemical Synthesis of Human Proteoforms and Application in Biomedicine. ACS CENTRAL SCIENCE 2024; 10:1442-1459. [PMID: 39220697 PMCID: PMC11363345 DOI: 10.1021/acscentsci.4c00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 09/04/2024]
Abstract
Limited understanding of human proteoforms with complex posttranslational modifications and the underlying mechanisms poses a major obstacle to research on human health and disease. This Outlook discusses opportunities and challenges of de novo chemical protein synthesis in human proteoform studies. Our analysis suggests that to develop a comprehensive, robust, and cost-effective methodology for chemical synthesis of various human proteoforms, new chemistries of the following types need to be developed: (1) easy-to-use peptide ligation chemistries allowing more efficient de novo synthesis of protein structural domains, (2) robust temporary structural support strategies for ligation and folding of challenging targets, and (3) efficient transpeptidative protein domain-domain ligation methods for multidomain proteins. Our analysis also indicates that accurate chemical synthesis of human proteoforms can be applied to the following aspects of biomedical research: (1) dissection and reconstitution of the proteoform interaction networks, (2) structural mechanism elucidation and functional analysis of human proteoform complexes, and (3) development and evaluation of drugs targeting human proteoforms. Overall, we suggest that through integrating chemical protein synthesis with in vivo functional analysis, mechanistic biochemistry, and drug development, synthetic chemistry would play a pivotal role in human proteoform research and facilitate the development of precision diagnostics and therapeutics.
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Affiliation(s)
- Huasong Ai
- New
Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life
Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and
Chemical Biology, Center for Synthetic and Systems Biology, Department
of Chemistry, Tsinghua University, Beijing 100084, China
- Institute
of Translational Medicine, School of Pharmacy, School of Chemistry
and Chemical Engineering, National Center for Translational Medicine
(Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Man Pan
- Institute
of Translational Medicine, School of Pharmacy, School of Chemistry
and Chemical Engineering, National Center for Translational Medicine
(Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Liu
- New
Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life
Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and
Chemical Biology, Center for Synthetic and Systems Biology, Department
of Chemistry, Tsinghua University, Beijing 100084, China
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3
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Bondarchuk T, Vaskiv D, Zhuravel E, Shyshlyk O, Hrynyshyn Y, Nedialko O, Pokholenko O, Pohribna A, Kuchuk O, Brovarets V, Zozulya S. Synthetic Amine Linkers for Efficient Sortagging. Bioconjug Chem 2024; 35:1172-1181. [PMID: 38994647 DOI: 10.1021/acs.bioconjchem.4c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Enzymatic site-specific bioconjugation techniques, in particular sortase-mediated ligation, are increasingly used to generate conjugated proteins for a wide array of applications. Extension of the utility and practicality of sortagging for diverse purposes is critically dependent on further improvement of the efficiency of sortagging reactions with a wider structural variety of substrates. We present a comprehensive comparative mass spectrometry screening study of synthetic nonpeptidic incoming amine nucleophile substrates of Staphylococcus aureus Sortase A enzyme. We have identified the optimal structural motifs among the chemically diverse set of 452 model primary and secondary amine-containing sortagging substrates, and we demonstrate the utility of representative amine linkers for efficient C-terminal biotinylation of nanobodies.
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Affiliation(s)
- Tetiana Bondarchuk
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
| | - Diana Vaskiv
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
| | - Elena Zhuravel
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
| | - Oleh Shyshlyk
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, Academician Kukhar Street 1, Kyiv 02094, Ukraine
| | - Yevhenii Hrynyshyn
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
| | - Oleksandr Nedialko
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
- V. N. Karazin Kharkiv National University, 4 Svobody Square, Kharkiv 61022, Ukraine
| | - Oleksandr Pokholenko
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
- Department of Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska Street 64, Kyiv 01033, Ukraine
| | - Alla Pohribna
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
| | - Olga Kuchuk
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
| | - Volodymyr Brovarets
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, Academician Kukhar Street 1, Kyiv 02094, Ukraine
| | - Sergey Zozulya
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyiv 02094, Ukraine
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4
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Chatziargyri AG, Stasi EA, Tsirigos KI, Litou ZI, Iconomidou VA, Bagos PG. CW-PRED: Prediction of C-terminal surface anchoring sorting signals in bacteria and Archaea. J Bioinform Comput Biol 2024; 22:2450021. [PMID: 39215524 DOI: 10.1142/s0219720024500215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Sorting signals are crucial for the anchoring of proteins to the cell surface in archaea and bacteria. These proteins often feature distinct motifs at their C-terminus, cleaved by sortase or sortase-like enzymes. Gram-positive bacteria exhibit the LPXTGX consensus motif, cleaved by sortases, while Gram-negative bacteria employ exosortases recognizing motifs like PEP. Archaea utilize exosortase homologs known as archaeosortases for signal anchoring. Traditionally identification of such C-terminal sorting signals was performed with profile Hidden Markov Models (pHMMs). The Cell-Wall PREDiction (CW-PRED) method introduced for the first time a custom-made class HMM for proteins in Gram-positive bacteria that contain a cell wall sorting signal which begins with an LPXTG motif, followed by a hydrophobic domain and a tail of positively charged residues. Here we present a new and updated version of CW-PRED for predicting C-terminal sorting signals in Archaea, Gram-positive, and Gram-negative bacteria. We used a large training set and several model enhancements that improve motif identification in order to achieve better discrimination between C-terminal signals and other proteins. Cross-validation demonstrates CW-PRED's superiority in sensitivity and specificity compared to other methods. Application of the method in reference proteomes reveals a large number of potential surface proteins not previously identified. The method is available for academic use at http://195.251.108.230/apps.compgen.org/CW-PRED/ and as standalone software.
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Affiliation(s)
- Aikaterini G Chatziargyri
- Section of Cell Biology and Biophysics, Department of Biology, National and Kapodistrian University of Athens Athens 15701, Greece
| | - Evangelia A Stasi
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia 35100, Greece
| | - Konstantinos I Tsirigos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia 35100, Greece
| | - Zoi I Litou
- Section of Cell Biology and Biophysics, Department of Biology, National and Kapodistrian University of Athens Athens 15701, Greece
| | - Vassiliki A Iconomidou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia 35100, Greece
| | - Pantelis G Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia 35100, Greece
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5
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Tereshin MN, Melikhova TD, Eletskaya BZ, Ivanova EA, Onoprienko LV, Makarov DA, Razumikhin MV, Myagkikh IV, Fabrichniy IP, Stepanenko VN. Biocatalytic Method for Producing an Affinity Resin for the Isolation of Immunoglobulins. Biomolecules 2024; 14:849. [PMID: 39062563 PMCID: PMC11274487 DOI: 10.3390/biom14070849] [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: 06/12/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Affinity chromatography is a widely used technique for antibody isolation. This article presents the successful synthesis of a novel affinity resin with a mutant form of protein A (BsrtA) immobilized on it as a ligand. The key aspect of the described process is the biocatalytic immobilization of the ligand onto the matrix using the sortase A enzyme. Moreover, we used a matrix with primary amino groups without modification, which greatly simplifies the synthesis process. The resulting resin shows a high dynamic binding capacity (up to 50 mg IgG per 1 mL of sorbent). It also demonstrates high tolerance to 0.1 M NaOH treatment and maintains its effectiveness even after 100 binding, elution, and sanitization cycles.
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Affiliation(s)
- Mikhail N. Tereshin
- Lomonosov Institute of Fine Chemical Technologies, MIREA—Russian Technological University, Vernadskogo Pr. 86, 119571 Moscow, Russia; (M.N.T.); (V.N.S.)
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 8-2 Trubetskaya Str., 119991 Moscow, Russia;
| | - Tatiana D. Melikhova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117437 Moscow, Russia; (T.D.M.); (L.V.O.); (I.V.M.)
| | - Barbara Z. Eletskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117437 Moscow, Russia; (T.D.M.); (L.V.O.); (I.V.M.)
| | - Elena A. Ivanova
- International Biotechnology Center “Generium” LLC, Vladimirskaya st. 14, 601125 Volginsky, Russia; (E.A.I.); (I.P.F.)
| | - Lyudmila V. Onoprienko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117437 Moscow, Russia; (T.D.M.); (L.V.O.); (I.V.M.)
| | - Dmitry A. Makarov
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 8-2 Trubetskaya Str., 119991 Moscow, Russia;
| | | | - Igor V. Myagkikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117437 Moscow, Russia; (T.D.M.); (L.V.O.); (I.V.M.)
| | - Igor P. Fabrichniy
- International Biotechnology Center “Generium” LLC, Vladimirskaya st. 14, 601125 Volginsky, Russia; (E.A.I.); (I.P.F.)
| | - Vasiliy N. Stepanenko
- Lomonosov Institute of Fine Chemical Technologies, MIREA—Russian Technological University, Vernadskogo Pr. 86, 119571 Moscow, Russia; (M.N.T.); (V.N.S.)
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, 8-2 Trubetskaya Str., 119991 Moscow, Russia;
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6
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Yan W, Li Y, Xie S, Tao WA, Hu J, Liu H, Zhang G, Liu F, Nie Y, Chen X, Zhang X, Liu Y, Wei D, Ma C, Zhang H, Xu H, Wang S. Chondrocyte-Targeted Delivery System of Sortase A-Engineered Extracellular Vesicles Silencing MMP13 for Osteoarthritis Therapy. Adv Healthc Mater 2024; 13:e2303510. [PMID: 38545904 DOI: 10.1002/adhm.202303510] [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: 10/13/2023] [Revised: 03/21/2024] [Indexed: 04/09/2024]
Abstract
Targeted drug delivery and the reduction of off-target effects are crucial for the promising clinical application of nucleic acid drugs. To address this challenge, a new approach for treating osteoarthritis (OA) that accurately delivers antisense oligonucleotides (ASO) targeting matrix metalloproteinase-13 (ASO-MMP13) to chondrocytes, is developed. Small extracellular vesicles (exos) are ligated with chondrocyte affinity peptide (CAP) using Sortase A and subsequently incubated with cholesterol-modified ASO-MMP13 to construct a chondrocyte-targeted drug delivery exo (CAP-exoASO). Compared with exos without CAP (ExoASO), CAP-exoASOs attenuate IL-1β-induced chondrocyte damage and prolong the retention time of ASO-MMP13 in the joint without distribution in major organs following intra-articular injection. Notably, CAP-exoASOs decrease MMP13 expression (P < 0.001) and upregulate COL2A1 expression (P = 0.006), resulting in reorganization of the cartilage matrix and alleviation of progression in the OA model. Furthermore, the Osteoarthritis Research Society International (OARSI) score of articular cartilage tissues treated with CAP-exoASO is comparable with that of healthy rats (P = 0.148). A mechanistic study demonstrates that CAP-exoASO may reduce inflammation by suppressing the IL-17 and TNF signaling pathways. Based on the targeted delivery effect, CAP-exoASOs successfully accomplish cartilage repair and have considerable potential for development as a promising therapeutic modality for satisfactory OA therapy.
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Affiliation(s)
- Wenjing Yan
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210003, China
| | - Ying Li
- Center of Clinical Laboratory Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
- Department of Epidemiology, School of Public Health of Suzhou University, Suzhou, Jiangsu, 215127, China
| | - Shuqian Xie
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210003, China
| | - W Andy Tao
- Departments of Chemistry and Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jing Hu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210003, China
| | - Haohan Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210003, China
| | - Guiyuan Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Fengying Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210003, China
| | - Yamei Nie
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210003, China
| | - Xue Chen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210003, China
| | - Xing Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210003, China
| | - Yufeng Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Dong Wei
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Changyan Ma
- Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Hao Zhang
- EVLiXiR Biotech Inc., Nanjing, Jiangsu, 210032, China
| | - Hongtao Xu
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210003, China
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7
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Liu Y, Lu Z, Wu P, Liang Z, Yu Z, Ni K, Ma L. The Transpeptidase Sortase A Binds Nucleic Acids and Mediates Mammalian Cell Labeling. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305605. [PMID: 38581131 DOI: 10.1002/advs.202305605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 03/10/2024] [Indexed: 04/08/2024]
Abstract
Wild-type sortase A is an important virulence factor displaying a diverse array of proteins on the surface of bacteria. This protein display relies on the transpeptidase activity of sortase A, which is widely engineered to allow protein ligation and protein engineering based on the interaction between sortase A and peptides. Here an unknown interaction is found between sortase A from Staphylococcus aureus and nucleic acids, in which exogenously expressed engineered sortase A binds oligonucleotides in vitro and is independent of its canonical transpeptidase activity. When incubated with mammalian cells, engineered sortase A further mediates oligonucleotide labeling to the cell surface, where sortase A attaches itself and is part of the labeled moiety. The labeling reaction can also be mediated by many classes of wild-type sortases as well. Cell surface GAG appears involved in sortase-mediated oligonucleotide cell labeling, as demonstrated by CRISPR screening. This interaction property is utilized to develop a technique called CellID to facilitate sample multiplexing for scRNA-seq and shows the potential of using sortases to label cells with diverse oligonucleotides. Together, the binding between sortase A and nucleic acids opens a new avenue to understanding the virulence of wild-type sortases and exploring the application of sortases in biotechnology.
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Affiliation(s)
- Yingzheng Liu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou, 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Zhike Lu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou, 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Panfeng Wu
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou, 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Zhaohui Liang
- AIdit Therapeutics, 1 Yunmeng Road, Building 1, Hangzhou, 310024, China
| | - Zhenxing Yu
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou, 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, China
| | - Ke Ni
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou, 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, China
- AIdit Therapeutics, 1 Yunmeng Road, Building 1, Hangzhou, 310024, China
| | - Lijia Ma
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, 310024, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou, 310030, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, China
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8
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Tang J, Hao M, Liu J, Chen Y, Wufuer G, Zhu J, Zhang X, Zheng T, Fang M, Zhang S, Li T, Ge S, Zhang J, Xia N. Design of a recombinant asparaginyl ligase for site-specific modification using efficient recognition and nucleophile motifs. Commun Chem 2024; 7:87. [PMID: 38637620 PMCID: PMC11026461 DOI: 10.1038/s42004-024-01173-8] [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: 06/26/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Asparaginyl ligases have been extensively utilized as valuable tools for site-specific bioconjugation or surface-modification. However, the application is hindered by the laborious and poorly reproducible preparation processes, unstable activity and ambiguous substrate requirements. To address these limitations, this study employed a structure-based rational approach to obtain a high-yield and high-activity protein ligase called OaAEP1-C247A-aa55-351. It was observed that OaAEP1-C247A-aa55-351 exhibits appreciable catalytic activities across a wide pH range, and the addition of the Fe3+ metal ion effectively enhances the catalytic power. Importantly, this study provides insight into the recognition and nucleophile peptide profiles of OaAEP1-C247A-aa55-351. The ligase demonstrates a higher recognition ability for the "Asn-Ala-Leu" motif and an N-terminus "Arg-Leu" as nucleophiles, which significantly increases the reaction yield. Consequently, the catalytic activity of OaAEP1-C247A-aa55-351 with highly efficient recognition and nucleophile motif, "Asn-Ala-Leu" and "Arg-Leu" under the buffer containing Fe3+ is 70-fold and 2-fold higher than previously reported OaAEP1-C247A and the most efficient butelase-1, respectively. Thus, the designed OaAEP1-C247A-aa55-351, with its highly efficient recognition and alternative nucleophile options, holds promising potential for applications in protein engineering, chemo-enzymatic modification, and the development of drugs.
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Affiliation(s)
- Jiabao Tang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Mengling Hao
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Junxian Liu
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Yaling Chen
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Gulimire Wufuer
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Jie Zhu
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Petrochemical Engineering, Changzhou University, 213164, Changzhou, China
| | - Xuejie Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Tingquan Zheng
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Mujin Fang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Shiyin Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Tingdong Li
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China.
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China.
| | - Shengxiang Ge
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China.
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China.
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China.
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China.
| | - Jun Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, 361102, Xiamen, China
- National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, 361102, Xiamen, China
- NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, School of Public Health, Xiamen University, 361102, Xiamen, China
- Department of Laboratory Medicine, School of Public Health, Xiamen University, 361102, Xiamen, China
- Xiang An Biomedicine Laboratory, 361102, Xiamen, China
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9
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Machin DC, Williamson DJ, Fisher P, Miller VJ, Arnott ZLP, Stevenson CME, Wildsmith GC, Ross JF, Wasson CW, Macdonald A, Andrews BI, Ungar D, Turnbull WB, Webb ME. Sortase-Modified Cholera Toxoids Show Specific Golgi Localization. Toxins (Basel) 2024; 16:194. [PMID: 38668619 PMCID: PMC11054894 DOI: 10.3390/toxins16040194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/18/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
Cholera toxoid is an established tool for use in cellular tracing in neuroscience and cell biology. We use a sortase labeling approach to generate site-specific N-terminally modified variants of both the A2-B5 heterohexamer and B5 pentamer forms of the toxoid. Both forms of the toxoid are endocytosed by GM1-positive mammalian cells, and while the heterohexameric toxoid was principally localized in the ER, the B5 pentamer showed an unexpectedly specific localization in the medial/trans-Golgi. This study suggests a future role for specifically labeled cholera toxoids in live-cell imaging beyond their current applications in neuronal tracing and labeling of lipid rafts in fixed cells.
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Affiliation(s)
- Darren C. Machin
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - Daniel J. Williamson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - Peter Fisher
- Department of Biology, University of York, York YO10 5DD, UK
| | | | - Zoe L. P. Arnott
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - Charlotte M. E. Stevenson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - Gemma C. Wildsmith
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - James F. Ross
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - Christopher W. Wasson
- Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK (A.M.)
| | - Andrew Macdonald
- Faculty of Biological Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK (A.M.)
| | - Benjamin I. Andrews
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Daniel Ungar
- Department of Biology, University of York, York YO10 5DD, UK
| | - W. Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
| | - Michael E. Webb
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; (D.C.M.)
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10
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Raniszewski NR, Beyer JN, Noel MI, Burslem GM. Sortase mediated protein ubiquitination with defined chain length and topology. RSC Chem Biol 2024; 5:321-327. [PMID: 38576722 PMCID: PMC10989510 DOI: 10.1039/d3cb00229b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/01/2024] [Indexed: 04/06/2024] Open
Abstract
Ubiquitination is a key post-translational modification on protein lysine sidechains known to impact protein stability, signal transduction cascades, protein-protein interactions, and beyond. Great strides have been made towards developing new methods to generate discrete chains of polyubiquitin and conjugate them onto proteins site-specifically, with methods ranging from chemical synthetic approaches, to enzymatic approaches and many in between. Previous work has demonstrated the utility of engineered variants of the bacterial transpeptidase enzyme sortase (SrtA) for conjugation of ubiquitin site-specifically onto target proteins. In this manuscript, we've combined the classical E1/E2-mediated polyubiquitin chain extension approach with sortase-mediated ligation and click chemistry to enable the generation of mono, di, and triubiquitinated proteins sfGFP and PCNA. We demonstrate the utility of this strategy to generate both K48-linked and K63-linked polyubiquitins and attach them both N-terminally and site-specifically to the proteins of interest. Further, we highlight differential activity between two commonly employed sortase variants, SrtA 5M and 7M, and demonstrate that while SrtA 7M can be used to conjugate these ubiquitins to substrates, SrtA 5M can be employed to release the ubiquitin from the substrates as well as to cleave C-terminal tags from the ubiquitin variants used. Overall, we envision that this approach is broadly applicable to readily generate discrete polyubiquitin chains of any linkage type that is accessible via E1/E2 systems and conjugate site-specifically onto proteins of interest, thus granting access to bespoke ubiquitinated proteins that are not currently possible.
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Affiliation(s)
- Nicole R Raniszewski
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
| | - Jenna N Beyer
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
| | - Myles I Noel
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
| | - George M Burslem
- Department of Biochemistry and Biophysics, Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania PA 19104 USA
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11
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Zhou Y, Durek T, Craik DJ, Rehm FBH. Sortase-Catalyzed Protein Domain Inversion. Angew Chem Int Ed Engl 2024; 63:e202316777. [PMID: 38366985 DOI: 10.1002/anie.202316777] [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: 11/05/2023] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Topological transformations and permutations of proteins have attracted significant interest as strategies to generate new protein functionalities or stability. These efforts have mainly been inspired by naturally occurring post-translational modifications, such as head-to-tail cyclization, circular permutation, or lasso-like entanglement. Such approaches can be realized experimentally via genetic encoding, in the case of circular permutation, or via enzymatic processing, in the case of cyclization. Notably, these previously described strategies leave the polypeptide backbone orientation unaltered. Here we describe an unnatural protein permutation, the protein domain inversion, whereby a C-terminal portion of a protein is enzymatically inverted from the canonical N-to-C to a C-to-C configuration with respect to the N-terminal part of the protein. The closest conceptually analogous biological process is perhaps the inversion of DNA segments as catalyzed by recombinases. We achieve these inversions using an engineered sortase A, a widely used transpeptidase. Our reactions proceed efficiently under mild conditions at 4-25 °C and are compatible with entirely heterologously-produced protein substrates.
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Affiliation(s)
- Yan Zhou
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Thomas Durek
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Craik
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Fabian B H Rehm
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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12
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Martinusen SG, Denard CA. Leveraging yeast sequestration to study and engineer posttranslational modification enzymes. Biotechnol Bioeng 2024; 121:903-914. [PMID: 38079116 PMCID: PMC11229454 DOI: 10.1002/bit.28621] [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: 05/17/2023] [Revised: 11/04/2023] [Accepted: 11/27/2023] [Indexed: 02/20/2024]
Abstract
Enzymes that catalyze posttranslational modifications (PTMs) of peptides and proteins (PTM-enzymes)-proteases, protein ligases, oxidoreductases, kinases, and other transferases-are foundational to our understanding of health and disease and empower applications in chemical biology, synthetic biology, and biomedicine. To fully harness the potential of PTM-enzymes, there is a critical need to decipher their enzymatic and biological mechanisms, develop molecules that can probe and modulate them, and endow them with improved and novel functions. These objectives are contingent upon implementation of high-throughput functional screens and selections that interrogate large sequence libraries to isolate desired PTM-enzyme properties. This review discusses the principles of Saccharomyces cerevisiae organelle sequestration to study and engineer PTM-enzymes. These include outer membrane sequestration, specifically methods that modify yeast surface display, and cytoplasmic sequestration based on enzyme-mediated transcription activation. Furthermore, we present a detailed discussion of yeast endoplasmic reticulum sequestration for the first time. Where appropriate, we highlight the major features and limitations of different systems, specifically how they can measure and control enzyme catalytic efficiencies. Taken together, yeast-based high-throughput sequestration approaches significantly lower the barrier to understanding how PTM-enzymes function and how to reprogram them.
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Affiliation(s)
- Samantha G Martinusen
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
| | - Carl A Denard
- Department of Chemical Engineering, University of Florida, Gainesville, Florida, USA
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13
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Tereshin MN, Melikhova TD, Eletskaya BZ, Ksenofontova OB, Pantyushenko PV, Berzina MY, Ivanov I, Myagkikh IV, Stepanenko VN. Affinity Resins for the Isolation of Immunoglobulins G Obtained Using Biocatalytic Technology. Int J Mol Sci 2024; 25:1367. [PMID: 38338645 PMCID: PMC10855859 DOI: 10.3390/ijms25031367] [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: 12/12/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Affinity chromatography resins that are obtained by conjugation of matrices with proteins of bacterial origin, like protein A, are frequently used for the purification of numerous therapeutic monoclonal antibodies. This article presents the development of a biocatalytic method for the production of novel affinity resins with an immobilized mutant form of protein A via sortase A mediated reaction. The conditions for activation of the agarose Seplife 6FF matrix, selection of different types of linkers with free amino groups and conditions for immobilization of recombinant protein A on the surface of the activated matrix were studied. Finally, the basic operational properties, like dynamic binding capacity (DBC), temperature dependance of DBC and stability during the cleaning-in-place process of the affinity resin with the Gly-Gly-EDA-Gly-Gly linker, were assessed using recombinant hyperchimeric monoclonal antibodies. The main characteristics show comparable results with the widely used commercial samples.
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Affiliation(s)
- Mikhail N. Tereshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117437 Moscow, Russia; (M.N.T.); (T.D.M.); (B.Z.E.); (O.B.K.); (P.V.P.); (I.V.M.); (V.N.S.)
- Lomonosov Institute of Fine Chemical Technologies, MIREA—Russian Technological University, Vernadskogo pr. 86, 119571 Moscow, Russia;
| | - Tatiana D. Melikhova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117437 Moscow, Russia; (M.N.T.); (T.D.M.); (B.Z.E.); (O.B.K.); (P.V.P.); (I.V.M.); (V.N.S.)
| | - Barbara Z. Eletskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117437 Moscow, Russia; (M.N.T.); (T.D.M.); (B.Z.E.); (O.B.K.); (P.V.P.); (I.V.M.); (V.N.S.)
| | - Olga B. Ksenofontova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117437 Moscow, Russia; (M.N.T.); (T.D.M.); (B.Z.E.); (O.B.K.); (P.V.P.); (I.V.M.); (V.N.S.)
| | - Pavel V. Pantyushenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117437 Moscow, Russia; (M.N.T.); (T.D.M.); (B.Z.E.); (O.B.K.); (P.V.P.); (I.V.M.); (V.N.S.)
| | - Maria Ya. Berzina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117437 Moscow, Russia; (M.N.T.); (T.D.M.); (B.Z.E.); (O.B.K.); (P.V.P.); (I.V.M.); (V.N.S.)
| | - Igor Ivanov
- Lomonosov Institute of Fine Chemical Technologies, MIREA—Russian Technological University, Vernadskogo pr. 86, 119571 Moscow, Russia;
| | - Igor V. Myagkikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117437 Moscow, Russia; (M.N.T.); (T.D.M.); (B.Z.E.); (O.B.K.); (P.V.P.); (I.V.M.); (V.N.S.)
| | - Vasiliy N. Stepanenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117437 Moscow, Russia; (M.N.T.); (T.D.M.); (B.Z.E.); (O.B.K.); (P.V.P.); (I.V.M.); (V.N.S.)
- Lomonosov Institute of Fine Chemical Technologies, MIREA—Russian Technological University, Vernadskogo pr. 86, 119571 Moscow, Russia;
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14
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Wu J, Chu T, Hao J, Lin L. SpSrtA-Catalyzed Isopeptide Ligation on Lysine Residues. Microorganisms 2024; 12:179. [PMID: 38258005 PMCID: PMC10818881 DOI: 10.3390/microorganisms12010179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Sortase-mediated ligation (SML) is widely used for protein bioconjugation. However, the sortase used in this strategy typically recognizes only the N-terminal oligoglycine, which is absent in most natural proteins. To broaden the spectrum of substrates compatible with SML, we focus on a novel sortase, sortase A from Streptococcus pneumoniae (SpSrtA), known for its expanded substrate specificity (N-terminal glycine, alanine, and serine). We present the first evidence showing that the reported SpSrtA mutant (SpSrtA*) can modify lysine residues in itself and other proteins. The modification sites of SpSrtA* were identified through LC-MS/MS analysis. Moreover, we discovered an optimal lysine-containing peptide tag by fusing it onto sfGFP, resulting in a labeling efficiency of 57%. Inspired by this, we applied the method to modify proteins on microorganism surfaces up to 13.5-fold. To enhance labeling efficiency, we fused the SpSrtA* onto a surface protein and achieved a 2.64-fold improvement. We further developed a high-throughput yeast display screening method for the directed evolution of SpSrtA*, achieving a 10-fold improvement in the labeling efficiency of this surface protein. Our study provides a novel strategy for modifying the lysine residues that will be a powerful addition to the protein bioconjugation toolbox.
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Affiliation(s)
- Jiajia Wu
- Department of Chemistry, Shanghai University, Shanghai 200444, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tianyu Chu
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jian Hao
- Department of Chemistry, Shanghai University, Shanghai 200444, China
| | - Liang Lin
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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15
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Liu K, Tong J, Liu X, Liang D, Ren F, Jiang N, Hao Z, Li S, Wang Q. The Discovery of Novel Agents against Staphylococcus aureus by Targeting Sortase A: A Combination of Virtual Screening and Experimental Validation. Pharmaceuticals (Basel) 2023; 17:58. [PMID: 38256891 PMCID: PMC11100315 DOI: 10.3390/ph17010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 01/24/2024] Open
Abstract
Staphylococcus aureus (S. aureus), commonly known as "superbugs", is a highly pathogenic bacterium that poses a serious threat to human health. There is an urgent need to replace traditional antibiotics with novel drugs to combat S. aureus. Sortase A (SrtA) is a crucial transpeptidase involved in the adhesion process of S. aureus. The reduction in virulence and prevention of S. aureus infections have made it a significant target for antimicrobial drugs. In this study, we combined virtual screening with experimental validation to identify potential drug candidates from a drug library. Three hits, referred to as Naldemedine, Telmisartan, and Azilsartan, were identified based on docking binding energy and the ratio of occupied functional sites of SrtA. The stability analysis manifests that Naldemedine and Telmisartan have a higher binding affinity to the hydrophobic pockets. Specifically, Telmisartan forms stable hydrogen bonds with SrtA, resulting in the highest binding energy. Our experiments prove that the efficiency of adhesion and invasion by S. aureus can be decreased without significantly affecting bacterial growth. Our work identifies Telmisartan as the most promising candidate for inhibiting SrtA, which can help combat S. aureus infection.
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Affiliation(s)
- Kang Liu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Jiangbo Tong
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Xu Liu
- College of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou 225009, China;
| | - Dan Liang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Fangzhe Ren
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Nan Jiang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Zhenyu Hao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Shixin Li
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (K.L.); (J.T.); (D.L.); (F.R.); (N.J.); (Z.H.)
| | - Qiang Wang
- Department of the Heart and Great Vessels, Affiliated Hospital of Yangzhou University, Yangzhou 225009, China
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16
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Mohammad Faizal NDF, Ramli NA, Mat Rani NNI, Shaibie NA, Aarti, Poonsawas P, Sharma SK, Mohd Amin MCI. Leveraging immunoliposomes as nanocarriers against SARS-CoV-2 and its emerging variants. Asian J Pharm Sci 2023; 18:100855. [PMID: 38125653 PMCID: PMC10730353 DOI: 10.1016/j.ajps.2023.100855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 12/23/2023] Open
Abstract
The global COVID-19 pandemic arising from SARS-CoV-2 has impacted many lives, gaining interest worldwide ever since it was first identified in December 2019. Till 2023, 752 million cumulative cases and 6.8 million deaths were documented globally. COVID-19 has been rapidly evolving, affecting virus transmissibility and properties and contributing to increased disease severity. The Omicron is the most circulating variant of concern. Although success in its treatment has indicated progress in tackling the virus, limitations in delivering the current antiviral agents in battling emerging variants remain remarkable. With the latest advancements in nanotechnology for controlling infectious diseases, liposomes have the potential to counteract SARS-CoV-2 because of their ability to employ different targeting strategies, incorporating monoclonal antibodies for the active and passive targeting of infected patients. This review will present a concise summary of the possible strategies for utilizing immunoliposomes to improve current treatment against the occurrence of SARS-CoV-2 and its variants.
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Affiliation(s)
- Nur Dini Fatini Mohammad Faizal
- Centre for Drug Delivery Technology and Vaccine (CENTRIC), Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| | - Nurul Afina Ramli
- Centre for Drug Delivery Technology and Vaccine (CENTRIC), Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| | - Nur Najihah Izzati Mat Rani
- Faculty of Pharmacy, University Royal College of Medicine Perak (UniKL RCMP) No.3, Jalan Greentown, Ipoh 30450, Perak, Malaysia
| | - Nur Adania Shaibie
- Centre for Drug Delivery Technology and Vaccine (CENTRIC), Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| | - Aarti
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | | | - Sunil K. Sharma
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Mohd Cairul Iqbal Mohd Amin
- Centre for Drug Delivery Technology and Vaccine (CENTRIC), Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
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17
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Liu L, Gray JL, Tate EW, Yang A. Bacterial enzymes: powerful tools for protein labeling, cell signaling, and therapeutic discovery. Trends Biotechnol 2023; 41:1385-1399. [PMID: 37328400 DOI: 10.1016/j.tibtech.2023.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/01/2023] [Accepted: 05/16/2023] [Indexed: 06/18/2023]
Abstract
Bacteria have evolved a diverse set of enzymes that enable them to subvert host defense mechanisms as well as to form part of the prokaryotic immune system. Due to their unique and varied biochemical activities, these bacterial enzymes have emerged as key tools for understanding and investigating biological systems. In this review, we summarize and discuss some of the most prominent bacterial enzymes used for the site-specific modification of proteins, in vivo protein labeling, proximity labeling, interactome mapping, signaling pathway manipulation, and therapeutic discovery. Finally, we provide a perspective on the complementary advantages and limitations of using bacterial enzymes compared with chemical probes for exploring biological systems.
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Affiliation(s)
- Lu Liu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Janine L Gray
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK.
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
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18
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de Sandozequi A, Martínez‐Anaya C. Bacterial surface-exposed lipoproteins and sortase-mediated anchored cell surface proteins in plant infection. Microbiologyopen 2023; 12:e1382. [PMID: 37877658 PMCID: PMC10501053 DOI: 10.1002/mbo3.1382] [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: 04/07/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 10/26/2023] Open
Abstract
The bacterial cell envelope is involved in all stages of infection and the study of its components and structures is important to understand how bacteria interact with the extracellular milieu. Thanks to new techniques that focus on identifying bacterial surface proteins, we now better understand the specific components involved in host-pathogen interactions. In the fight against the deleterious effects of pathogenic bacteria, bacterial surface proteins (at the cell envelope) are important targets as they play crucial roles in the colonization and infection of host tissues. These surface proteins serve functions such as protection, secretion, biofilm formation, nutrient intake, metabolism, and virulence. Bacteria use different mechanisms to associate proteins to the cell surface via posttranslational modification, such as the addition of a lipid moiety to create lipoproteins and attachment to the peptidoglycan layer by sortases. In this review, we focus on these types of proteins (and provide examples of others) that are associated with the bacterial cell envelope by posttranslational modifications and their roles in plant infection.
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Affiliation(s)
- Andrés de Sandozequi
- Departamento de Ingeniería Celular y BiocatálisisInstituto de BiotecnologíaCuernavacaMéxico
| | - Claudia Martínez‐Anaya
- Departamento de Ingeniería Celular y BiocatálisisInstituto de BiotecnologíaCuernavacaMéxico
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19
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Pakula RJ, Scott PJH. Applications of radiolabeled antibodies in neuroscience and neuro-oncology. J Labelled Comp Radiopharm 2023; 66:269-285. [PMID: 37322805 DOI: 10.1002/jlcr.4049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023]
Abstract
Positron emission tomography (PET) is a powerful tool in medicine and drug development, allowing for non-invasive imaging and quantitation of biological processes in live organisms. Targets are often probed with small molecules, but antibody-based PET is expanding because of many benefits, including ease of design of new antibodies toward targets, as well as the very strong affinities that can be expected. Application of antibodies to PET imaging of targets in the central nervous system (CNS) is a particularly nascent field, but one with tremendous potential. In this review, we discuss the growth of PET in imaging of CNS targets, present the promises and progress in antibody-based CNS PET, explore challenges faced by the field, and discuss questions that this promising approach will need to answer moving forward for imaging and perhaps even radiotherapy.
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Affiliation(s)
- Ryan J Pakula
- Department of Radiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter J H Scott
- Department of Radiology, University of Michigan, Ann Arbor, Michigan, USA
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20
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Nawrocka D, Krzyscik MA, Sluzalska KD, Otlewski J. Dual-Warhead Conjugate Based on Fibroblast Growth Factor 2 Dimer Loaded with α-Amanitin and Monomethyl Auristatin E Exhibits Superior Cytotoxicity towards Cancer Cells Overproducing Fibroblast Growth Factor Receptor 1. Int J Mol Sci 2023; 24:10143. [PMID: 37373291 DOI: 10.3390/ijms241210143] [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: 05/12/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Targeting fibroblast growth factor receptor 1 (FGFR1) is a promising therapeutic strategy for various cancers associated with alterations in the FGFR1 gene. In this study, we developed a highly cytotoxic bioconjugate based on fibroblast growth factor 2 (FGF2), which is a natural ligand of this receptor, and two potent cytotoxic drugs-α-amanitin and monomethyl auristatin E-with completely independent mechanistic modes of action. Utilizing recombinant DNA technology, we produced an FGF2 N- to C-end dimer that exhibited superior internalization capacity in FGFR1-positive cells. The drugs were site-specifically attached to the targeting protein using SnoopLigase- and evolved sortase A-mediated ligations. The resulting dimeric dual-warhead conjugate selectively binds to the FGFR1 and utilizes receptor-mediated endocytosis to enter the cells. Moreover, our results demonstrate that the developed conjugate exhibits about 10-fold higher cytotoxic potency against FGFR1-positive cell lines than an equimolar mixture of single-warhead conjugates. The diversified mode of action of the dual-warhead conjugate may help to overcome the potential acquired resistance of FGFR1-overproducing cancer cells to single cytotoxic drugs.
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Affiliation(s)
- Daria Nawrocka
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Mateusz Adam Krzyscik
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Katarzyna Dominika Sluzalska
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Jacek Otlewski
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland
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21
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Obeng EM, Fulcher AJ, Wagstaff KM. Harnessing sortase A transpeptidation for advanced targeted therapeutics and vaccine engineering. Biotechnol Adv 2023; 64:108108. [PMID: 36740026 DOI: 10.1016/j.biotechadv.2023.108108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
The engineering of potent prophylactic and therapeutic complexes has always required careful protein modification techniques with seamless capabilities. In this light, methods that favor unobstructed multivalent targeting and correct antigen presentations remain essential and very demanding. Sortase A (SrtA) transpeptidation has exhibited these attributes in various settings over the years. However, its applications for engineering avidity-inspired therapeutics and potent vaccines have yet to be significantly noticed, especially in this era where active targeting and multivalent nanomedications are in great demand. This review briefly presents the SrtA enzyme and its associated transpeptidation activity and describes interesting sortase-mediated protein engineering and chemistry approaches for achieving multivalent therapeutic and antigenic responses. The review further highlights advanced applications in targeted delivery systems, multivalent therapeutics, adoptive cellular therapy, and vaccine engineering. These innovations show the potential of sortase-mediated techniques in facilitating the development of simple plug-and-play nanomedicine technologies against recalcitrant diseases and pandemics such as cancer and viral infections.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
| | - Alex J Fulcher
- Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Kylie M Wagstaff
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
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22
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Abstract
The ability to manipulate the chemical composition of proteins and peptides has been central to the development of improved polypeptide-based therapeutics and has enabled researchers to address fundamental biological questions that would otherwise be out of reach. Protein ligation, in which two or more polypeptides are covalently linked, is a powerful strategy for generating semisynthetic products and for controlling polypeptide topology. However, specialized tools are required to efficiently forge a peptide bond in a chemoselective manner with fast kinetics and high yield. Fortunately, nature has addressed this challenge by evolving enzymatic mechanisms that can join polypeptides using a diverse set of chemical reactions. Here, we summarize how such nature-inspired protein ligation strategies have been repurposed as chemical biology tools that afford enhanced control over polypeptide composition.
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Affiliation(s)
- Rasmus Pihl
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, OH, USA.
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA.
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23
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Jeon J, Subramani SV, Lee KZ, Jiang B, Zhang F. Microbial Synthesis of High-Molecular-Weight, Highly Repetitive Protein Polymers. Int J Mol Sci 2023; 24:6416. [PMID: 37047388 PMCID: PMC10094428 DOI: 10.3390/ijms24076416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 03/30/2023] Open
Abstract
High molecular weight (MW), highly repetitive protein polymers are attractive candidates to replace petroleum-derived materials as these protein-based materials (PBMs) are renewable, biodegradable, and have outstanding mechanical properties. However, their high MW and highly repetitive sequence features make them difficult to synthesize in fast-growing microbial cells in sufficient amounts for real applications. To overcome this challenge, various methods were developed to synthesize repetitive PBMs. Here, we review recent strategies in the construction of repetitive genes, expression of repetitive proteins from circular mRNAs, and synthesis of repetitive proteins by ligation and protein polymerization. We discuss the advantages and limitations of each method and highlight future directions that will lead to scalable production of highly repetitive PBMs for a wide range of applications.
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Affiliation(s)
- Juya Jeon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.J.); (S.V.S.); (K.Z.L.); (B.J.)
| | - Shri Venkatesh Subramani
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.J.); (S.V.S.); (K.Z.L.); (B.J.)
| | - Kok Zhi Lee
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.J.); (S.V.S.); (K.Z.L.); (B.J.)
| | - Bojing Jiang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.J.); (S.V.S.); (K.Z.L.); (B.J.)
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.J.); (S.V.S.); (K.Z.L.); (B.J.)
- Institute of Materials Science and Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO 63130, USA
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24
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Xia Y, Li F, Zhang X, Balamkundu S, Tang F, Hu S, Lescar J, Tam JP, Liu CF. A Cascade Enzymatic Reaction Scheme for Irreversible Transpeptidative Protein Ligation. J Am Chem Soc 2023; 145:6838-6844. [PMID: 36924109 DOI: 10.1021/jacs.2c13628] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Enzymatic peptide ligation holds great promise in the study of protein functions and development of protein therapeutics. Owing to their high catalytic efficiency and a minimal tripeptide recognition motif, peptidyl asparaginyl ligases (PALs) are particularly useful tools for bioconjugation. However, as an inherent limitation of transpeptidases, PAL-mediated ligation is reversible, requiring a large excess of one of the ligation partners to shift the reaction equilibrium in the forward direction. Herein, we report a method to make PAL-mediated intermolecular ligation irreversible by coupling it to glutaminyl cyclase (QC)-catalyzed pyroglutamyl formation. In this method, the acyl donor substrate of PALs is designed to have glutamine at the P1' position of the Asn-P1'-P2' tripeptide PAL recognition motif. Upon ligation with an acyl acceptor substrate, the acyl donor substrate releases a leaving group in which the exposed N-terminal glutamine is cyclized by QC, quenching the Gln Nα-amine in a lactam. Using this method, PAL-mediated ligation can achieve near-quantitative yields even at an equal molar ratio between the two ligation partners. We have demonstrated this method for a wide range of applications, including protein-to-protein ligations. We anticipate that this cascade enzymatic reaction scheme will make PAL enzymes well suited for numerous new uses in biotechnology.
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Affiliation(s)
- Yiyin Xia
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Fupeng Li
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | | | - Fan Tang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Side Hu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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25
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Dunleavy R, Chandrasekaran S, Crane BR. Enzymatic Spin-Labeling of Protein N- and C-Termini for Electron Paramagnetic Resonance Spectroscopy. Bioconjug Chem 2023:10.1021/acs.bioconjchem.3c00029. [PMID: 36921260 PMCID: PMC10502183 DOI: 10.1021/acs.bioconjchem.3c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for investigating the structure and dynamics of proteins. The introduction of paramagnetic moieties at specific positions in a protein enables precise measurement of local structure and dynamics. This technique, termed site-directed spin-labeling, has traditionally been performed using cysteine-reactive radical-containing probes. However, large proteins are more likely to contain multiple cysteine residues and cysteine labeling at specific sites may be infeasible or impede function. To address this concern, we applied three peptide-ligating enzymes (sortase, asparaginyl endopeptidase, and inteins) for nitroxide labeling of N- and C-termini of select monomeric and dimeric proteins. Continuous wave and pulsed EPR (double electron electron resonance) experiments reveal specific attachment of nitroxide probes to ether N-termini (OaAEP1) or C-termini (sortase and intein) across three test proteins (CheY, CheA, and iLOV), thereby enabling a straightforward, highly specific, and general method for protein labeling. Importantly, the linker length (3, 5, and 9 residues for OaAEP1, intein, and sortase reactions, respectively) between the probe and the target protein has a large impact on the utility of distance measurements by pulsed EPR, with longer linkers leading to broader distributions. As these methods are only dependent on accessible N- and C-termini, we anticipate application to a wide range of protein targets for biomolecular EPR spectroscopy.
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Affiliation(s)
- Robert Dunleavy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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26
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Fan L, Du M, Kong L, Cai Y, Hu X. Recognition Site Modifiable Macrocycle: Synthesis, Functional Group Variation and Structural Inspection. Molecules 2023; 28:molecules28031338. [PMID: 36771008 PMCID: PMC9921963 DOI: 10.3390/molecules28031338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Traditional macrocyclic molecules encode recognition sites in their structural backbones, which limits the variation of the recognition sites and thus, would restrict the adjustment of recognition properties. Here, we report a new oligoamide-based macrocycle capable of varying the recognition functional groups by post-synthesis modification on its structural backbone. Through six steps of common reactions, the parent macrocycle (9) can be produced in gram scale with an overall yield of 31%. The post-synthesis modification of 9 to vary the recognition sites are demonstrated by producing four different macrocycles (10-13) with distinct functional groups, 2-methoxyethoxyl (10), hydroxyl (11), carboxyl (12) and amide (13), respectively. The 1H NMR study suggests that the structure of these macrocycles is consistent with our design, i.e., forming hydrogen bonding network at both rims of the macrocyclic backbone. The 1H-1H NOESY NMR study indicates the recognition functional groups are located inside the cavity of macrocycles. At last, a preliminary molecular recognition study shows 10 can recognize n-octyl-β-D-glucopyranoside (14) in chloroform.
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27
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Fang Y, Chang AY, Verma D, Miyashita SI, Eszterhas S, Lee PG, Shen Y, Davis LR, Dong M, Bailey-Kellogg C, Griswold KE. Functional Deimmunization of Botulinum Neurotoxin Protease Domain via Computationally Driven Library Design and Ultrahigh-Throughput Screening. ACS Synth Biol 2023; 12:153-163. [PMID: 36623275 PMCID: PMC9872818 DOI: 10.1021/acssynbio.2c00426] [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: 08/05/2022] [Indexed: 01/11/2023]
Abstract
Botulinum neurotoxin serotype A (BoNT/A) is a widely used cosmetic agent that also has diverse therapeutic applications; however, adverse antidrug immune responses and associated loss of efficacy have been reported in clinical uses. Here, we describe computational design and ultrahigh-throughput screening of a massive BoNT/A light-chain (BoNT/A-LC) library optimized for reduced T cell epitope content and thereby dampened immunogenicity. We developed a functional assay based on bacterial co-expression of BoNT/A-LC library members with a Förster resonance energy transfer (FRET) sensor for BoNT/A-LC enzymatic activity, and we employed high-speed fluorescence-activated cell sorting (FACS) to identify numerous computationally designed variants having wild-type-like enzyme kinetics. Many of these variants exhibited decreased immunogenicity in humanized HLA transgenic mice and manifested in vivo paralytic activity when incorporated into full-length toxin. One variant achieved near-wild-type paralytic potency and a 300% reduction in antidrug antibody response in vivo. Thus, we have achieved a striking level of BoNT/A-LC functional deimmunization by combining computational library design and ultrahigh-throughput screening. This strategy holds promise for deimmunizing other biologics with complex superstructures and mechanisms of action.
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Affiliation(s)
- Yongliang Fang
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Andrew Y. Chang
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Deeptak Verma
- Department
of Computer Science, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Shin-Ichiro Miyashita
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Food, Aroma and Cosmetic Chemistry, Tokyo
University of Agriculture, 196 Yasaka, Abashiri 099-2493, Japan
| | - Susan Eszterhas
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Pyung-Gang Lee
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yi Shen
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Lydia R. Davis
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Min Dong
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Chris Bailey-Kellogg
- Department
of Computer Science, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Karl E. Griswold
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
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28
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Yang Q, Gao Y, Liu X, Xiao Y, Wu M. A General Method to Edit Histone H3 Modifications on Chromatin Via Sortase-Mediated Metathesis. Angew Chem Int Ed Engl 2022; 61:e202209945. [PMID: 36305862 DOI: 10.1002/anie.202209945] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Indexed: 11/07/2022]
Abstract
The post-translational modifications (PTMs) on the tail of histone H3 control chromatin structure and influence epigenetics and gene expression. The current chemical methods including unnatural amino acid incorporation and protein splicing enable preparations of the histone with diverse PTMs in cellular contexts, but they are not applicable to edit native chromatin. The manipulation of histone-modifying enzymes alter the endogenous histone PTMs but the lack of specificity of most histone-modifying enzymes prevents precise control of specific H3 tail PTM patterns. Here we report a new method to edit the N-tail of histone H3 via sortase mediated metathesis (SMM). The sortase can install desired PTM patterns into histone H3 on nucleosomes in vitro and in cellulo. This study expands the application scope of sortase from ligation to metathesis in live cells using cell-penetrating peptides (CPPs). In addition, it offers a strategy to edit PTMs of cellular histone H3 with potential for the development of precise epigenome editing.
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Affiliation(s)
- Qingyun Yang
- Department of Chemistry, Zhejiang University, 310027, Hangzhou, Zhejiang Province, China.,Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, 310030, Hangzhou, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024, Hangzhou, Zhejiang Province, China
| | - Yingxiao Gao
- Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, 310030, Hangzhou, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024, Hangzhou, Zhejiang Province, China.,Department of Chemistry, Fudan University, 200438, Shanghai, China
| | - Xia Liu
- Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, 310030, Hangzhou, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024, Hangzhou, Zhejiang Province, China
| | - Yihang Xiao
- Department of Chemistry, Zhejiang University, 310027, Hangzhou, Zhejiang Province, China.,Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, 310030, Hangzhou, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024, Hangzhou, Zhejiang Province, China
| | - Mingxuan Wu
- Department of Chemistry, School of Science, Westlake University, 600 Dunyu Road, 310030, Hangzhou, Zhejiang Province, China.,Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, 310024, Hangzhou, Zhejiang Province, China.,Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang Province, China
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29
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Morgan H, Arnott ZLP, Kamiński TP, Turnbull WB, Webb ME. Combined Application of Orthogonal Sortases and Depsipeptide Substrates for Dual Protein Labeling. Bioconjug Chem 2022; 33:2341-2347. [PMID: 36356167 PMCID: PMC9782347 DOI: 10.1021/acs.bioconjchem.2c00411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Staphylococcus aureus sortase A is a transpeptidase that has been extensively exploited for site-specific modification of proteins and was originally used to attach a labeling reagent containing an LPXTG recognition sequence to a protein or peptide with an N-terminal glycine. Sortase mutants with other recognition sequences have also been reported, but in all cases, the reversibility of the transpeptidation reaction limits the efficiency of sortase-mediated labeling reactions. For the wildtype sortase, depsipeptide substrates, in which the scissile peptide bond is replaced with an ester, allow effectively irreversible sortase-mediated labeling as the alcohol byproduct is a poor competing nucleophile. In this paper, the use of depsipeptide substrates for evolved sortase variants is reported. Substrate specificities of three sortases have been investigated allowing identification of an orthogonal pair of enzymes accepting LPEToG and LPESoG depsipeptides, which have been applied to dual N-terminal labeling of a model protein mutant containing a second, latent N-terminal glycine residue. The method provides an efficient orthogonal site-specific labeling technique that further expands the biochemical protein labeling toolkit.
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30
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Scinto SL, Reagle TR, Fox JM. Affinity Bioorthogonal Chemistry (ABC) Tags for Site-Selective Conjugation, On-Resin Protein-Protein Coupling, and Purification of Protein Conjugates. Angew Chem Int Ed Engl 2022; 61:e202207661. [PMID: 36058881 PMCID: PMC10029600 DOI: 10.1002/anie.202207661] [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: 05/25/2022] [Indexed: 11/12/2022]
Abstract
The site-selective functionalization of proteins has broad application in chemical biology, but can be limited when mixtures result from incomplete conversion or the formation of protein containing side products. It is shown here that when proteins are covalently tagged with pyridyl-tetrazines, the nickel-iminodiacetate (Ni-IDA) resins commonly used for His-tags can be directly used for protein affinity purification. These Affinity Bioorthogonal Chemistry (ABC) tags serve a dual role by enabling affinity-based protein purification while maintaining rapid kinetics in bioorthogonal reactions. ABC-tagging works with a range of site-selective bioconjugation methods with proteins tagged at the C-terminus, N-terminus or at internal positions. ABC-tagged proteins can also be purified from complex mixtures including cell lysate. The combination of site-selective conjugation and clean-up with ABC-tagged proteins also allows for facile on-resin reactions to provide protein-protein conjugates.
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Affiliation(s)
- Samuel L Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
| | - Tyler R Reagle
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
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31
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Atypical nuclear envelope condensates linked to neurological disorders reveal nucleoporin-directed chaperone activities. Nat Cell Biol 2022; 24:1630-1641. [PMID: 36302970 PMCID: PMC10041656 DOI: 10.1038/s41556-022-01001-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 08/26/2022] [Indexed: 01/18/2023]
Abstract
DYT1 dystonia is a debilitating neurological movement disorder arising from mutation in the AAA+ ATPase TorsinA. The hallmark of Torsin dysfunction is nuclear envelope blebbing resulting from defects in nuclear pore complex biogenesis. Whether blebs actively contribute to disease manifestation is unknown. We report that FG-nucleoporins in the bleb lumen form aberrant condensates and contribute to DYT1 dystonia by provoking two proteotoxic insults. Short-lived ubiquitylated proteins that are normally rapidly degraded partition into the bleb lumen and become stabilized. In addition, blebs selectively sequester a specific HSP40-HSP70 chaperone network that is modulated by the bleb component MLF2. MLF2 suppresses the ectopic accumulation of FG-nucleoporins and modulates the selective properties and size of condensates in vitro. Our study identifies dual mechanisms of proteotoxicity in the context of condensate formation and establishes FG-nucleoporin-directed activities for a nuclear chaperone network.
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32
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Lee CH, Lee JH, Lee JY, Cui CH, Cho BK, Kim SC. Novel Split Intein-Mediated Enzymatic Channeling Accelerates the Multimeric Bioconversion Pathway of Ginsenoside. ACS Synth Biol 2022; 11:3296-3304. [PMID: 36150110 DOI: 10.1021/acssynbio.2c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Cascade reaction systems, such as protein fusion and synthetic protein scaffold systems, can both spatially control the metabolic flux and boost the productivity of multistep enzymatic reactions. Despite many efforts to generate fusion proteins, this task remains challenging due to the limited expression of complex enzymes. Therefore, we developed a novel fusion system that bypasses the limited expression of complex enzymes via a post-translational linkage. Here, we report a split intein-mediated cascade system wherein orthogonal split inteins serve as adapters for protein ligation. A genetically programmable, self-assembled, and traceless split intein was utilized to generate a biocatalytic cascade to produce the ginsenoside compound K (CK) with various pharmacological activities, including anticarcinogenic, anti-inflammatory, and antidiabetic effects. We used two types of split inteins, consensus atypical (Cat) and Rma DnaB, to form a covalent scaffold with the three enzymes involved in the CK conversion pathway. The multienzymatic complex with a size greater than 240 kDa was successfully assembled in a soluble form and exhibited specific activity toward ginsenoside conversion. Furthermore, our split intein cascade system significantly increased the CK conversion rate and reduced the production time by more than 2-fold. Our multienzymatic cascade system that uses split inteins can be utilized as a platform for regulating multimeric bioconversion pathways and boosting the production of various high-value substances.
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Affiliation(s)
- Cho-Heun Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Jun-Hyoung Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Ju Young Lee
- Research Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Korea
| | - Chang-Hao Cui
- Intelligent Synthetic Biology Center, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Sun-Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea.,Intelligent Synthetic Biology Center, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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33
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Apostolos AJ, Kelly JJ, Ongwae GM, Pires MM. Structure Activity Relationship of the Stem Peptide in Sortase A Mediated Ligation from Staphylococcus aureus. Chembiochem 2022; 23:e202200412. [PMID: 36018606 PMCID: PMC9632411 DOI: 10.1002/cbic.202200412] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/24/2022] [Indexed: 01/11/2023]
Abstract
The surfaces of most Gram-positive bacterial cells, including that of Staphylococcus aureus (S. aureus), are heavily decorated with proteins that coordinate cellular interactions with the extracellular space. In S. aureus, sortase A is the principal enzyme responsible for covalently anchoring proteins, which display the sorting signal LPXTG, onto the peptidoglycan (PG) matrix. Considerable efforts have been made to understand the role of this signal peptide in the sortase-mediated reaction. In contrast, much less is known about how the primary structure of the other substrate involved in the reaction (PG stem peptide) could impact sortase activity. To assess the sortase activity, a library of synthetic analogs of the stem peptide that mimic naturally existing variations found in the S. aureus PG primary sequence were evaluated. Using a combination of two unique assays, we showed that there is broad tolerability of substrate variations that are effectively processed by sortase A. While some of these stem peptide derivatives are naturally found in mature PG, they are not known to be present in the PG precursor, lipid II. These results suggest that sortase A could process both lipid II and mature PG as acyl-acceptor strands that might reside near the membrane, which has not been previously described.
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Affiliation(s)
| | - Joey J. Kelly
- Department of ChemistryUniversity of VirginiaCharlottesville, VA22904USA
| | - George M. Ongwae
- Department of ChemistryUniversity of VirginiaCharlottesville, VA22904USA
| | - Marcos M. Pires
- Department of ChemistryUniversity of VirginiaCharlottesville, VA22904USA
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34
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Wei W, Jiang D, Evangelista L, Cai W. Antibody-Based Imaging and Therapy for Precision Medicine. Mol Pharm 2022; 19:3453-3455. [PMID: 36184938 DOI: 10.1021/acs.molpharmaceut.2c00606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Weijun Wei
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Dawei Jiang
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei, China.,Hubei Key Laboratory of Molecular Imaging, Wuhan 430022, Hubei, China.,Key Laboratory of Biological Targeted Therapy, Ministry of Education, Wuhan 430022, China
| | - Laura Evangelista
- Nuclear Medicine Unit, Department of Medicine - DIMED, University of Padua, Padua 35122, Italy
| | - Weibo Cai
- Departments of Radiology and Medical Physics, University of Wisconsin-Madison Madison, Wisconsin 53705, United States
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35
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Obeng EM, Fianu I, Danquah MK. Multivalent ACE2 engineering-A promising pathway for advanced coronavirus nanomedicine development. NANO TODAY 2022; 46:101580. [PMID: 35942040 PMCID: PMC9350675 DOI: 10.1016/j.nantod.2022.101580] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/26/2022] [Accepted: 07/30/2022] [Indexed: 05/06/2023]
Abstract
The spread of coronavirus diseases has resulted in a clarion call to develop potent drugs and vaccines even as different strains appear beyond human prediction. An initial step that is integral to the viral entry into host cells results from an active-targeted interaction of the viral spike (S) proteins and the cell surface receptor, called angiotensin-converting enzyme 2 (ACE2). Thus, engineered ACE2 has been an interesting decoy inhibitor against emerging coronavirus infestation. This article discusses promising innovative ACE2 engineering pathways for current and emerging coronavirus therapeutic development. First, we provide a brief discussion of some ACE2-associated human coronaviruses and their cell invasion mechanism. Then, we describe and contrast the individual spike proteins and ACE2 receptor interactions, highlighting crucial hotspots across the ACE2-associated coronaviruses. Lastly, we address the importance of multivalency in ACE2 nanomedicine engineering and discuss novel approaches to develop and achieve multivalent therapeutic outcomes. Beyond coronaviruses, these approaches will serve as a paradigm to develop new and improved treatment technologies against pathogens that use ACE2 receptor for invasion.
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Affiliation(s)
- Eugene M Obeng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Isaac Fianu
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, 615 McCallie Ave, Chattanooga, TN 37403, United States
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36
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Volarić J, Thallmair S, Feringa BL, Szymanski W. Photoswitchable, Water‐soluble Bis‐azobenzene Cross‐linkers with Enhanced Properties for Biological Applications. CHEMPHOTOCHEM 2022. [DOI: 10.1002/cptc.202200170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jana Volarić
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Sebastian Thallmair
- Frankfurt Institute for Advanced Studies Frankfurt Institute for Advanced Studies GERMANY
| | - Ben L. Feringa
- University of Groningen: Rijksuniversiteit Groningen Stratingh Institute for Chemistry NETHERLANDS
| | - Wiktor Szymanski
- University Medical Center Groningen Department of Radiology Hanzeplein 1 9747AG Groningen NETHERLANDS
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37
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Cabalteja CC, Sachdev S, Cheloha RW. Characterization of a Nanobody-Epitope Tag Interaction and Its Application for Receptor Engineering. ACS Chem Biol 2022; 17:2296-2303. [PMID: 35930411 PMCID: PMC10200313 DOI: 10.1021/acschembio.2c00407] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Peptide epitope tags offer a valuable means for detection and manipulation of protein targets for which high quality detection reagents are not available. Most commonly used epitope tags are bound by conventional, full-size antibodies (Abs). The complex architecture of Abs complicates their application in protein engineering and intracellular applications. To address these shortcomings, single domain antibodies (nanobodies, Nbs) that recognize short peptide epitopes have become increasingly prized. Here, we characterize the interaction between a Nb (Nb6E) and a 14-mer peptide epitope. We identify residues in the peptide epitope essential for high affinity binding. Using this information in combination with computational modeling we propose a mode of interaction between Nb6E and this epitope. We apply this nanobody-epitope pair to augment the potency of a ligand at an engineered adenosine A2A receptor. This characterization of the nanobody-epitope pair opens the door to diverse applications including mechanistic studies of the G protein-coupled receptor function.
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Affiliation(s)
- Chino C. Cabalteja
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes, Digestive, and Kidney Diseases; National Institutes of Health. Bethesda, MD 20892, USA
| | - Shivani Sachdev
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes, Digestive, and Kidney Diseases; National Institutes of Health. Bethesda, MD 20892, USA
| | - Ross W. Cheloha
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes, Digestive, and Kidney Diseases; National Institutes of Health. Bethesda, MD 20892, USA
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38
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Zuo C, Ding R, Wu X, Wang Y, Chu GC, Liang LJ, Ai H, Tong ZB, Mao J, Zheng Q, Wang T, Li Z, Liu L, Sun D. Thioester-Assisted Sortase-A-Mediated Ligation. Angew Chem Int Ed Engl 2022; 61:e202201887. [PMID: 35514243 DOI: 10.1002/anie.202201887] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Indexed: 11/12/2022]
Abstract
Sortase A (SrtA)-mediated ligation, a popular method for protein labeling and semi-synthesis, is limited by its reversibility and dependence on the LPxTG motif, where "x" is any amino acid. Here, we report that SrtA can mediate the efficient and irreversible ligation of a protein/peptide containing a C-terminal thioester with another protein/peptide bearing an N-terminal Gly, with broad tolerance for a wide variety of LPxT-derived sequences. This strategy, the thioester-assisted SrtA-mediated ligation, enabled the expedient preparation of proteins bearing various N- or C-terminal labels, including post-translationally modified proteins such as the Ser139-phosphorylated histone H2AX and Lys9-methylated histone H3, with less dependence on the LPxTG motif. Our study validates the chemical modification of substrates as an effective means of augmenting the synthetic capability of existing enzymatic methods.
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Affiliation(s)
- Chong Zuo
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Ruichao Ding
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Xiangwei Wu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yuanxia Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Guo-Chao Chu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Huasong Ai
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Ze-Bin Tong
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Junxiong Mao
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Tian Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Zichen Li
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, State Key Laboratory of Chemical Oncogenomics (Shenzhen), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Demeng Sun
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230001, China
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Caers J, Duray E, Vrancken L, Marcion G, Bocuzzi V, De Veirman K, Krasniqi A, Lejeune M, Withofs N, Devoogdt N, Dumoulin M, Karlström AE, D’Huyvetter M. Radiotheranostic Agents in Hematological Malignancies. Front Immunol 2022; 13:911080. [PMID: 35865548 PMCID: PMC9294596 DOI: 10.3389/fimmu.2022.911080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/06/2022] [Indexed: 12/23/2022] Open
Abstract
Radioimmunotherapy (RIT) is a cancer treatment that combines radiation therapy with tumor-directed monoclonal antibodies (Abs). Although RIT had been introduced for the treatment of CD20 positive non-Hodgkin lymphoma decades ago, it never found a broad clinical application. In recent years, researchers have developed theranostic agents based on Ab fragments or small Ab mimetics such as peptides, affibodies or single-chain Abs with improved tumor-targeting capacities. Theranostics combine diagnostic and therapeutic capabilities into a single pharmaceutical agent; this dual application can be easily achieved after conjugation to radionuclides. The past decade has seen a trend to increased specificity, fastened pharmacokinetics, and personalized medicine. In this review, we discuss the different strategies introduced for the noninvasive detection and treatment of hematological malignancies by radiopharmaceuticals. We also discuss the future applications of these radiotheranostic agents.
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Affiliation(s)
- Jo Caers
- Laboratory of Hematology, GIGA I³, University of Liège, Liège, Belgium
- Department of Hematology, CHU de Liège, Liège, Belgium
- *Correspondence: Jo Caers,
| | - Elodie Duray
- Laboratory of Hematology, GIGA I³, University of Liège, Liège, Belgium
- Centre for Protein Engineering, Inbios, University of Liège, Liège, Belgium
| | - Louise Vrancken
- Laboratory of Hematology, GIGA I³, University of Liège, Liège, Belgium
- Department of Hematology, CHU de Liège, Liège, Belgium
| | - Guillaume Marcion
- Laboratory of Hematology, GIGA I³, University of Liège, Liège, Belgium
| | - Valentina Bocuzzi
- Laboratory of Hematology, GIGA I³, University of Liège, Liège, Belgium
| | - Kim De Veirman
- Department of Hematology and Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ahmet Krasniqi
- Laboratory of In Vivo Cellular and Molecular Imaging Laboratory (ICMI), Vrije Universiteit Brussel, Brussels, Belgium
| | - Margaux Lejeune
- Laboratory of Hematology, GIGA I³, University of Liège, Liège, Belgium
| | - Nadia Withofs
- Department of Nuclear Medicine, CHU de Liège, Liège, Belgium
| | - Nick Devoogdt
- Laboratory of In Vivo Cellular and Molecular Imaging Laboratory (ICMI), Vrije Universiteit Brussel, Brussels, Belgium
| | - Mireille Dumoulin
- Centre for Protein Engineering, Inbios, University of Liège, Liège, Belgium
| | - Amelie Eriksson Karlström
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Matthias D’Huyvetter
- Laboratory of In Vivo Cellular and Molecular Imaging Laboratory (ICMI), Vrije Universiteit Brussel, Brussels, Belgium
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40
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Li Q, Yin G, Wang J, Li L, Liang Q, Zhao X, Chen Y, Zheng X, Zhao X. An emerging paradigm to develop analytical methods based on immobilized transmembrane proteins and its applications in drug discovery. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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41
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Kumar V, Murmu S, Krishnan V. Deciphering the substrate specificity of housekeeping sortase A and pilus-specific sortase C of probiotic bacterium Lactococcus lactis. Biochimie 2022; 200:140-152. [PMID: 35654243 DOI: 10.1016/j.biochi.2022.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022]
Abstract
Several strains and species of lactic acid bacteria (LAB) are widely used in fermented foods, including dairy products and also as probiotics, because of their contribution to various health benefits in humans. Sortase enzymes decorate the bacterial cell wall with different surface proteins and pili for facilitating the interactions with host and environment for the colonization and beneficial effects. While the sortases and sortase anchored proteins from pathogens have been the prime focus of the research in the past, sortases from many non-pathogenic bacteria, including LAB strains, have attracted attention for their potential applications in vaccine delivery and other clinical interventions. Here, we report the purification and functional characterization of two sortases (housekeeping SrtA and pilus-specific SrtC) from a probiotic Lactococcus lactis. The purified sortases were found to be active against the putative LPXTG motif-based peptide substrates, albeit with differences. The in-silico analysis provides insights into the residues involved in substrate binding and specificity. Overall, this study sheds new light on the aspects of structure, substrate specificity, and function of sortases from non-pathogenic bacteria, which may have physiological ramifications as well as their applications in sortase-mediated protein bioconjugation.
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Affiliation(s)
- Vijay Kumar
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, Haryana (NCR Delhi), India
| | - Sumit Murmu
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, Haryana (NCR Delhi), India
| | - Vengadesan Krishnan
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, Haryana (NCR Delhi), India.
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42
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Zuo C, Ding R, Wu X, Wang Y, Chu GC, Liang LJ, Ai H, Tong ZB, Mao J, Zheng Q, Wang T, Li Z, Liu L, Sun D. Thioester‐Assisted Sortase‐A ‐ Mediated Ligation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Chong Zuo
- Tsinghua University Tsinghua-Peking Center for Life Sciences CHINA
| | - Ruichao Ding
- Tsinghua University Tsinghua-Peking Center for Life Sciences CHINA
| | - Xiangwei Wu
- Tsinghua University Tsinghua-Peking Center for Life Sciences CHINA
| | - Yuanxia Wang
- University of Science and Technology of China School of Life Sciences CHINA
| | - Guo-Chao Chu
- Tsinghua University Department of Chemistry CHINA
| | - Lu-Jun Liang
- Tsinghua University Department of Chemistry CHINA
| | - Huasong Ai
- Tsinghua University Department of Chemistry CHINA
| | - Ze-Bin Tong
- Tsinghua University Department of Chemistry CHINA
| | - Junxiong Mao
- Tsinghua University Department of Chemistry CHINA
| | | | - Tian Wang
- Tsinghua University Tsinghua-Peking Center for Life Sciences CHINA
| | - Zichen Li
- Tsinghua University Department of Chemistry CHINA
| | - Lei Liu
- Tsinghua University Department of Chemistry CHINA
| | - Demeng Sun
- University of Science and Technology of China School of Life Sciences 96 Jinzhai Road 230026 Hefei CHINA
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43
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Li R, Schmidt M, Zhu T, Yang X, Feng J, Tian Y, Cui Y, Nuijens T, Wu B. Traceless enzymatic protein synthesis without ligation sites constraint. Natl Sci Rev 2022; 9:nwab158. [PMID: 35663243 PMCID: PMC9155641 DOI: 10.1093/nsr/nwab158] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
Protein synthesis and semisynthesis offer immense promise for life sciences and have impacted pharmaceutical innovation. The absence of a generally applicable method for traceless peptide conjugation with a flexible choice of junction sites remains a bottleneck for accessing many important synthetic targets, however. Here we introduce the PALME (protein activation and ligation with multiple enzymes) platform designed for sequence-unconstrained synthesis and modification of biomacromolecules. The upstream activating modules accept and process easily accessible synthetic peptides and recombinant proteins, avoiding the challenges associated with preparation and manipulation of activated peptide substrates. Cooperatively, the downstream coupling module provides comprehensive solutions for sequential peptide condensation, cyclization and protein N/C-terminal or internal functionalization. The practical utility of this methodology is demonstrated by synthesizing a series of bioactive targets ranging from pharmaceutical ingredients to synthetically challenging proteins. The modular PALME platform exhibits unprecedentedly broad accessibility for traceless protein synthesis and functionalization, and holds enormous potential to extend the scope of protein chemistry and synthetic biology.
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Affiliation(s)
- Ruifeng Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Marcel Schmidt
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen 6167 RD, the Netherlands
| | - Tong Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xinyu Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Feng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu'e Tian
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yinglu Cui
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Timo Nuijens
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen 6167 RD, the Netherlands
| | - Bian Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Fay R, Törő I, Schinke AL, Simic B, Schaefer JV, Dreier B, Plückthun A, Holland JP. Sortase-Mediated Site-Specific Conjugation and 89Zr-Radiolabeling of Designed Ankyrin Repeat Proteins for PET. Mol Pharm 2022; 19:3576-3585. [DOI: 10.1021/acs.molpharmaceut.2c00136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rachael Fay
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Imre Törő
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anna-Lena Schinke
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Branko Simic
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jonas V. Schaefer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jason P. Holland
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Yang E, Liu Q, Huang G, Liu J, Wei W. Engineering nanobodies for next-generation molecular imaging. Drug Discov Today 2022; 27:1622-1638. [PMID: 35331925 DOI: 10.1016/j.drudis.2022.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/04/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022]
Abstract
In recent years, nanobodies have emerged as ideal imaging agents for molecular imaging. Molecular nanobody imaging combines the specificity of nanobodies with the sensitivity of state-of-the-art molecular imaging modalities, such as positron emission tomography (PET). Given that modifications of nanobodies alter their pharmacokinetics (PK), the engineering strategies that combine nanobodies with radionuclides determine the effectiveness, reliability, and safety of the molecular imaging probes. In this review, we introduce conjugation strategies that have been applied to nanobodies, including random conjugation, 99mTc tricarbonyl chemistry, sortase A-mediated site-specific conjugation, maleimide-cysteine chemistry, and click chemistries. We also summarize the latest advances in nanobody tracers, emphasizing their preclinical and clinical use. In addition, we elaborate on nanobody-based near-infrared fluorescence (NIRF) imaging and image-guided surgery.
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Affiliation(s)
- Erpeng Yang
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, China
| | - Qiufang Liu
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Gang Huang
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, China
| | - Jianjun Liu
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, China.
| | - Weijun Wei
- Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200217, China.
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Zhang CH, Shao XX, Wang XB, Shou LL, Liu YL, Xu ZG, Guo ZY. Development of a general bioluminescent activity assay for peptide ligases. FEBS J 2022; 289:5241-5258. [PMID: 35239242 DOI: 10.1111/febs.16416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/13/2022] [Accepted: 02/28/2022] [Indexed: 11/28/2022]
Abstract
In recent years, some peptide ligases have been identified, such as bacterial sortases and certain plant asparaginyl or prolyl endopeptidases. Peptide ligases have wide applications in protein labelling and cyclic peptide synthesis. To characterize various known peptide ligases or identify new ones, we propose a general bioluminescent activity assay via the genetic fusion of a recognition motif of peptide ligase(s) to the C-terminus of an inactive large NanoLuc fragment (LgBiT) and the chemical introduction of a nucleophilic motif preferred by the peptide ligase(s) to the N-terminus of the low-affinity SmBiT complementation tag. After the inactive ligation version LgBiT protein was ligated with the low-affinity ligation version SmBiT tag by the expected peptide ligase(s), its luciferase activity would be restored and could be quantified sensitively according to the measured bioluminescence. In the present study, we first validated the bioluminescent activity assay using bacterial sortase A and plant-derived butelase-1. Subsequently, we screened novel peptide ligases from crude extracts of selected plants using two LgBiT-SmBiT ligation pairs. Among 80 common higher plants, we identified that five of them likely express asparaginyl endopeptidase-type peptide ligase and four of them likely express prolyl endopeptidase-type peptide ligase, suggesting that peptide ligases are not so rare in higher plants and more of them await discovery. The present bioluminescent activity assay is ultrasensitive, convenient for use, and resistant to protease interference, and thus would have wide applications for characterizing known peptide ligases or screening new ones from various sources in future studies.
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Affiliation(s)
- Cong-Hui Zhang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiao-Xia Shao
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xin-Bo Wang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Li-Li Shou
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ya-Li Liu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zeng-Guang Xu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhan-Yun Guo
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
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47
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Rocha RA, Speight RE, Scott C. Engineering Enzyme Properties for Improved Biocatalytic Processes in Batch and Continuous Flow. Org Process Res Dev 2022. [DOI: 10.1021/acs.oprd.1c00424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Raquel A. Rocha
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
| | - Robert E. Speight
- School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Queensland 4000, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, Queensland 4000, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, Black Mountain Science and Innovation Park, Canberra, ACT 2601, Australia
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Obeng EM, Dzuvor CKO, Danquah MK. Anti-SARS-CoV-1 and -2 nanobody engineering towards avidity-inspired therapeutics. NANO TODAY 2022; 42:101350. [PMID: 34840592 PMCID: PMC8608585 DOI: 10.1016/j.nantod.2021.101350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/22/2021] [Accepted: 11/18/2021] [Indexed: 05/15/2023]
Abstract
In the past two decades, the emergence of coronavirus diseases has been dire distress on both continental and global fronts and has resulted in the search for potent treatment strategies. One crucial challenge in this search is the recurrent mutations in the causative virus spike protein, which lead to viral escape issues. Among the current promising therapeutic discoveries is the use of nanobodies and nanobody-like molecules. While these nanobodies have demonstrated high-affinity interaction with the virus, the unpredictable spike mutations have warranted the need for avidity-inspired therapeutics of potent inhibitors such as nanobodies. This article discusses novel approaches for the design of anti-SARS-CoV-1 and -2 nanobodies to facilitate advanced innovations in treatment technologies. It further discusses molecular interactions and suggests multivalent protein nanotechnology and chemistry approaches to translate mere molecular affinity into avidity.
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Affiliation(s)
- Eugene M Obeng
- Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Christian K O Dzuvor
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, United States
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Berguer PM, Blaustein M, Bredeston LM, Craig PO, D’Alessio C, Elias F, Farré PC, Fernández NB, Gentili HG, Gándola YB, Gasulla J, Gudesblat GE, Herrera MG, Ibañez LI, Idrovo-Hidalgo T, Nadra AD, Noseda DG, Paván CH, Pavan MF, Pignataro MF, Roman EA, Ruberto LAM, Rubinstein N, Sanchez MV, Santos J, Wetzler DE, Zelada AM. Covalent coupling of Spike's receptor binding domain to a multimeric carrier produces a high immune response against SARS-CoV-2. Sci Rep 2022; 12:692. [PMID: 35027583 PMCID: PMC8758758 DOI: 10.1038/s41598-021-03675-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/01/2021] [Indexed: 11/26/2022] Open
Abstract
The receptor binding domain (RBD) of the Spike protein from SARS-CoV-2 is a promising candidate to develop effective COVID-19 vaccines since it can induce potent neutralizing antibodies. We have previously reported the highly efficient production of RBD in Pichia pastoris, which is structurally similar to the same protein produced in mammalian HEK-293T cells. In this work we designed an RBD multimer with the purpose of increasing its immunogenicity. We produced multimeric particles by a transpeptidation reaction between RBD expressed in P. pastoris and Lumazine Synthase from Brucella abortus (BLS), which is a highly immunogenic and very stable decameric 170 kDa protein. Such particles were used to vaccinate mice with two doses 30 days apart. When the particles ratio of RBD to BLS units was high (6-7 RBD molecules per BLS decamer in average), the humoral immune response was significantly higher than that elicited by RBD alone or by RBD-BLS particles with a lower RBD to BLS ratio (1-2 RBD molecules per BLS decamer). Remarkably, multimeric particles with a high number of RBD copies elicited a high titer of neutralizing IgGs. These results indicate that multimeric particles composed of RBD covalent coupled to BLS possess an advantageous architecture for antigen presentation to the immune system, and therefore enhancing RBD immunogenicity. Thus, multimeric RBD-BLS particles are promising candidates for a protein-based vaccine.
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Zhang D, Wang Z, Hu S, Lescar J, Tam JP, Liu CF. Vypal2: A Versatile Peptide Ligase for Precision Tailoring of Proteins. Int J Mol Sci 2021; 23:ijms23010458. [PMID: 35008882 PMCID: PMC8745061 DOI: 10.3390/ijms23010458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 12/19/2022] Open
Abstract
The last two decades have seen an increasing demand for new protein-modification methods from the biotech industry and biomedical research communities. Owing to their mild aqueous reaction conditions, enzymatic methods based on the use of peptide ligases are particularly desirable. In this regard, the recently discovered peptidyl Asx-specific ligases (PALs) have emerged as powerful biotechnological tools in recent years. However, as a new class of peptide ligases, their scope and application remain underexplored. Herein, we report the use of a new PAL, VyPAL2, for a diverse range of protein modifications. We successfully showed that VyPAL2 was an efficient biocatalyst for protein labelling, inter-protein ligation, and protein cyclization. The labelled or cyclized protein ligands remained functionally active in binding to their target receptors. We also demonstrated on-cell labelling of protein ligands pre-bound to cellular receptors and cell-surface engineering via modifying a covalently anchored peptide substrate pre-installed on cell-surface glycans. Together, these examples firmly establish Asx-specific ligases, such as VyPAL2, as the biocatalysts of the future for site-specific protein modification, with a myriad of applications in basic research and drug discovery.
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