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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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2
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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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3
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Zou Z, Ji Y, Schwaneberg U. Empowering Site-Specific Bioconjugations In Vitro and In Vivo: Advances in Sortase Engineering and Sortase-Mediated Ligation. Angew Chem Int Ed Engl 2024; 63:e202310910. [PMID: 38081121 DOI: 10.1002/anie.202310910] [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: 07/31/2023] [Indexed: 12/23/2023]
Abstract
Sortase-mediated ligation (SML) has emerged as a powerful and versatile methodology for site-specific protein conjugation, functionalization/labeling, immobilization, and design of biohybrid molecules and systems. However, the broader application of SML faces several challenges, such as limited activity and stability, dependence on calcium ions, and reversible reactions caused by nucleophilic side-products. Over the past decade, protein engineering campaigns and particularly directed evolution, have been extensively employed to overcome sortase limitations, thereby expanding the potential application of SML in multiple directions, including therapeutics, biorthogonal chemistry, biomaterials, and biosensors. This review provides an overview of achieved advancements in sortase engineering and highlights recent progress in utilizing SML in combination with other state-of-the-art chemical and biological methodologies. The aim is to encourage scientists to employ sortases in their conjugation experiments.
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Affiliation(s)
- Zhi Zou
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074, Aachen, Germany
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
| | - Yu Ji
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
| | - Ulrich Schwaneberg
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstraβe 50, 52074, Aachen, Germany
- RWTH Aachen University, Institute of Biotechnology, Worringerweg 3, 52074, Aachen, Germany
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4
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Ghosh S, Ahearn CP, Isabella CR, Marando VM, Dodge GJ, Bartlett H, McPherson RL, Dugan AE, Jain S, Neznanova L, Tettelin H, Putnik R, Grimes CL, Ruhl S, Kiessling LL, Imperiali B. Human oral lectin ZG16B acts as a cell wall polysaccharide probe to decode host-microbe interactions with oral commensals. Proc Natl Acad Sci U S A 2023; 120:e2216304120. [PMID: 37216558 PMCID: PMC10235990 DOI: 10.1073/pnas.2216304120] [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: 09/24/2022] [Accepted: 04/14/2023] [Indexed: 05/24/2023] Open
Abstract
The oral microbiome is critical to human health and disease, yet the role that host salivary proteins play in maintaining oral health is unclear. A highly expressed gene in human salivary glands encodes the lectin zymogen granule protein 16 homolog B (ZG16B). Despite the abundance of this protein, its interaction partners in the oral microbiome are unknown. ZG16B possesses a lectin fold, but whether it binds carbohydrates is unclear. We postulated that ZG16B would bind microbial glycans to mediate recognition of oral microbes. To this end, we developed a microbial glycan analysis probe (mGAP) strategy based on conjugating the recombinant protein to fluorescent or biotin reporter functionality. Applying the ZG16B-mGAP to dental plaque isolates revealed that ZG16B predominantly binds to a limited set of oral microbes, including Streptococcus mitis, Gemella haemolysans, and, most prominently, Streptococcus vestibularis. S. vestibularis is a commensal bacterium widely distributed in healthy individuals. ZG16B binds to S. vestibularis through the cell wall polysaccharides attached to the peptidoglycan, indicating that the protein is a lectin. ZG16B slows the growth of S. vestibularis with no cytotoxicity, suggesting that it regulates S. vestibularis abundance. The mGAP probes also revealed that ZG16B interacts with the salivary mucin MUC7. Analysis of S. vestibularis and MUC7 with ZG16B using super-resolution microscopy supports ternary complex formation that can promote microbe clustering. Together, our data suggest that ZG16B influences the compositional balance of the oral microbiome by capturing commensal microbes and regulating their growth using a mucin-assisted clearance mechanism.
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Affiliation(s)
- Soumi Ghosh
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Christian P. Ahearn
- Department of Oral Biology, University at Buffalo School of Dental Medicine, Buffalo, NY14214
| | | | - Victoria M. Marando
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Gregory J. Dodge
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Helen Bartlett
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Robert L. McPherson
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Amanda E. Dugan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Shikha Jain
- Department of Oral Biology, University at Buffalo School of Dental Medicine, Buffalo, NY14214
| | - Lubov Neznanova
- Department of Oral Biology, University at Buffalo School of Dental Medicine, Buffalo, NY14214
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD21201
| | - Rachel Putnik
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Catherine L. Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE19716
| | - Stefan Ruhl
- Department of Oral Biology, University at Buffalo School of Dental Medicine, Buffalo, NY14214
| | - Laura L. Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
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5
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Debon A, Siirola E, Snajdrova R. Enzymatic Bioconjugation: A Perspective from the Pharmaceutical Industry. JACS AU 2023; 3:1267-1283. [PMID: 37234110 PMCID: PMC10207132 DOI: 10.1021/jacsau.2c00617] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 05/27/2023]
Abstract
Enzymes have firmly established themselves as bespoke catalysts for small molecule transformations in the pharmaceutical industry, from early research and development stages to large-scale production. In principle, their exquisite selectivity and rate acceleration can also be leveraged for modifying macromolecules to form bioconjugates. However, available catalysts face stiff competition from other bioorthogonal chemistries. In this Perspective, we seek to illuminate applications of enzymatic bioconjugation in the face of an expanding palette of new drug modalities. With these applications, we wish to highlight some examples of current successes and pitfalls of using enzymes for bioconjugation along the pipeline and try to illustrate opportunities for further development.
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Affiliation(s)
- Aaron Debon
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
| | - Elina Siirola
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
| | - Radka Snajdrova
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
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6
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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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7
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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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8
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Negi S, Hamori M, Sato A, Shimizu K, Kawahara-Nakagawa Y, Manabe T, Shibata N, Kitagishi H, Mashimo M, Sugiura Y. Transpeptidation reaction mediated by ligand- and metal cofactor-substituted Sortase A from Staphylococcus aureus. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shigeru Negi
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
| | - Mami Hamori
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
| | - Ayaka Sato
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
| | - Kyoko Shimizu
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
| | - Yuka Kawahara-Nakagawa
- Graduate School of Faculty of Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, 678-1297
| | - Takayuki Manabe
- Clinical Research Support Center, Asahikawa Medical University Hospital, 2-1-1-1 Midorigaoka Higashi, Asahikawa 078-8510
| | - Nobuhito Shibata
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
| | - Hiroaki Kitagishi
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321
| | - Masato Mashimo
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
| | - Yukio Sugiura
- Faculty of Pharmaceutical Science, Doshisha Women's University, Koudo, Kyotanabe, Kyoto 610-0395
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9
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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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10
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Vogl DP, Conibear AC, Becker CFW. Segmental and site-specific isotope labelling strategies for structural analysis of posttranslationally modified proteins. RSC Chem Biol 2021; 2:1441-1461. [PMID: 34704048 PMCID: PMC8496066 DOI: 10.1039/d1cb00045d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
Posttranslational modifications can alter protein structures, functions and locations, and are important cellular regulatory and signalling mechanisms. Spectroscopic techniques such as nuclear magnetic resonance, infrared and Raman spectroscopy, as well as small-angle scattering, can provide insights into the structural and dynamic effects of protein posttranslational modifications and their impact on interactions with binding partners. However, heterogeneity of modified proteins from natural sources and spectral complexity often hinder analyses, especially for large proteins and macromolecular assemblies. Selective labelling of proteins with stable isotopes can greatly simplify spectra, as one can focus on labelled residues or segments of interest. Employing chemical biology tools for modifying and isotopically labelling proteins with atomic precision provides access to unique protein samples for structural biology and spectroscopy. Here, we review site-specific and segmental isotope labelling methods that are employed in combination with chemical and enzymatic tools to access posttranslationally modified proteins. We discuss illustrative examples in which these methods have been used to facilitate spectroscopic studies of posttranslationally modified proteins, providing new insights into biology.
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Affiliation(s)
- Dominik P Vogl
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry Währinger Straße 38 1090 Vienna Austria +43-1-4277-870510 +43-1-4277-70510
| | - Anne C Conibear
- The University of Queensland, School of Biomedical Sciences St Lucia Brisbane 4072 QLD Australia
| | - Christian F W Becker
- University of Vienna, Faculty of Chemistry, Institute of Biological Chemistry Währinger Straße 38 1090 Vienna Austria +43-1-4277-870510 +43-1-4277-70510
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11
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Bolzati C, Spolaore B. Enzymatic Methods for the Site-Specific Radiolabeling of Targeting Proteins. Molecules 2021; 26:3492. [PMID: 34201280 PMCID: PMC8229434 DOI: 10.3390/molecules26123492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/19/2022] Open
Abstract
Site-specific conjugation of proteins is currently required to produce homogenous derivatives for medicine applications. Proteins derivatized at specific positions of the polypeptide chain can actually show higher stability, superior pharmacokinetics, and activity in vivo, as compared with conjugates modified at heterogeneous sites. Moreover, they can be better characterized regarding the composition of the derivatization sites as well as the conformational and activity properties. To this aim, several site-specific derivatization approaches have been developed. Among these, enzymes are powerful tools that efficiently allow the generation of homogenous protein-drug conjugates under physiological conditions, thus preserving their native structure and activity. This review will summarize the progress made over the last decade on the use of enzymatic-based methodologies for the production of site-specific labeled immunoconjugates of interest for nuclear medicine. Enzymes used in this field, including microbial transglutaminase, sortase, galactosyltransferase, and lipoic acid ligase, will be overviewed and their recent applications in the radiopharmaceutical field will be described. Since nuclear medicine can benefit greatly from the production of homogenous derivatives, we hope that this review will aid the use of enzymes for the development of better radio-conjugates for diagnostic and therapeutic purposes.
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Affiliation(s)
- Cristina Bolzati
- Institute of Condensed Matter Chemistry and Technologies for Energy ICMATE-CNR, Corso Stati Uniti, 4, I-35127 Padova, Italy
| | - Barbara Spolaore
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via Marzolo, 5, I-35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padua, Viale G. Colombo, 3, I-35131 Padova, Italy
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12
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Hayes HC, Luk LYP, Tsai YH. Approaches for peptide and protein cyclisation. Org Biomol Chem 2021; 19:3983-4001. [PMID: 33978044 PMCID: PMC8114279 DOI: 10.1039/d1ob00411e] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/01/2021] [Indexed: 12/26/2022]
Abstract
The cyclisation of polypeptides can play a crucial role in exerting biological functions, maintaining stability under harsh conditions and conferring proteolytic resistance, as demonstrated both in nature and in the laboratory. To date, various approaches have been reported for polypeptide cyclisation. These approaches range from the direct linkage of N- and C- termini to the connection of amino acid side chains, which can be applied both in reaction vessels and in living systems. In this review, we categorise the cyclisation approaches into chemical methods (e.g. direct backbone cyclisation, native chemical ligation, aldehyde-based ligations, bioorthogonal reactions, disulphide formation), enzymatic methods (e.g. subtiligase variants, sortases, asparaginyl endopeptidases, transglutaminases, non-ribosomal peptide synthetases) and protein tags (e.g. inteins, engineered protein domains for isopeptide bond formation). The features of each approach and the considerations for selecting an appropriate method of cyclisation are discussed.
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Affiliation(s)
- Heather C Hayes
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Louis Y P Luk
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT.
| | - Yu-Hsuan Tsai
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK and Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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13
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Kuan SL, Raabe M. Solid-Phase Protein Modifications: Towards Precision Protein Hybrids for Biological Applications. ChemMedChem 2021; 16:94-104. [PMID: 32667697 PMCID: PMC7818443 DOI: 10.1002/cmdc.202000412] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Indexed: 12/13/2022]
Abstract
Proteins have attracted increasing attention as biopharmaceutics and diagnostics due to their high specificity, biocompatibility, and biodegradability. The biopharmaceutical sector in particular is experiencing rapid growth, which has led to an increase in the production and sale of protein drugs and diagnostics over the last two decades. Since the first-generation biopharmaceutics dominated by native proteins, both recombinant and chemical technologies have evolved and transformed the outlook of this rapidly developing field. This review article presents updates on the fabrication of covalent and supramolecular fusion hybrids, as well as protein-polymer hybrids using solid-phase approaches that hold great promise for preparing protein hybrids with precise control at the macromolecular level to incorporate additional features. In addition, the applications of the resultant protein hybrids in medicine and diagnostics are highlighted where possible.
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Affiliation(s)
- Seah Ling Kuan
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
| | - Marco Raabe
- Max Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
- Institute of Inorganic Chemistry IUlm UniversityAlbert-Einstein-Allee 1189081UlmGermany
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14
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Zou Z, Mate DM, Nöth M, Jakob F, Schwaneberg U. Enhancing Robustness of Sortase A by Loop Engineering and Backbone Cyclization. Chemistry 2020; 26:13568-13572. [PMID: 32649777 PMCID: PMC7693181 DOI: 10.1002/chem.202002740] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/08/2020] [Indexed: 12/13/2022]
Abstract
Staphylococcus aureus sortase A (SaSrtA) is widely used for site-specific protein modifications, but it lacks the robustness for performing bioconjugation reactions at elevated temperatures or in presence of denaturing agents. Loop engineering and subsequent head-to-tail backbone cyclization of SaSrtA yielded the cyclized variant CyM6 that has a 7.5 °C increased melting temperature and up to 4.6-fold increased resistance towards denaturants when compared to the parent rM4. CyM6 gained up to 2.6-fold (vs. parent rM4) yield of conjugate in ligation of peptide and primary amine under denaturing conditions.
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Affiliation(s)
- Zhi Zou
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
- DWI–Leibniz-Institute for Interactive MaterialsForckenbeckstraβe 5052074AachenGermany
| | - Diana M. Mate
- DWI–Leibniz-Institute for Interactive MaterialsForckenbeckstraβe 5052074AachenGermany
- Current address: Center of Molecular Biology “Severo Ochoa”Universidad Autónoma de MadridNicolás Cabrera 128049MadridSpain
| | - Maximilian Nöth
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
- DWI–Leibniz-Institute for Interactive MaterialsForckenbeckstraβe 5052074AachenGermany
| | - Felix Jakob
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
- DWI–Leibniz-Institute for Interactive MaterialsForckenbeckstraβe 5052074AachenGermany
| | - Ulrich Schwaneberg
- Institute of BiotechnologyRWTH Aachen UniversityWorringerweg 352074AachenGermany
- DWI–Leibniz-Institute for Interactive MaterialsForckenbeckstraβe 5052074AachenGermany
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15
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Flow chemistry as a tool to access novel chemical space for drug discovery. Future Med Chem 2020; 12:1547-1563. [DOI: 10.4155/fmc-2020-0075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
This perspective scrutinizes flow chemistry as a useful tool for medicinal chemists to expand the current chemical capabilities in drug discovery. This technology has demonstrated his value not only for the traditional reactions used in Pharma for the last 20 years, but also for bringing back to the lab underused chemistries to access novel chemical space. The combination with other technologies, such as photochemistry and electrochemistry, is opening new avenues for reactivity that will smoothen the access to complex molecules. The introduction of all these technologies in automated platforms will improve the productivity of medicinal chemistry labs reducing the cycle times to get novel and differentiated bioactive molecules, accelerating discovery cycle times.
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16
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Insights into the biochemical and functional characterization of sortase E transpeptidase of Corynebacterium glutamicum. Biochem J 2020; 476:3835-3847. [PMID: 31815278 DOI: 10.1042/bcj20190812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 12/30/2022]
Abstract
Most Gram-positive bacteria contain a membrane-bound transpeptidase known as sortase which covalently incorporates the surface proteins on to the cell wall. The sortase-displayed protein structures are involved in cell attachment, nutrient uptake and aerial hyphae formation. Among the six classes of sortase (A-F), sortase A of S. aureus is the well-characterized housekeeping enzyme considered as an ideal drug target and a valuable biochemical reagent for protein engineering. Similar to SrtA, class E sortase in GC rich bacteria plays a housekeeping role which is not studied extensively. However, C. glutamicum ATCC 13032, an industrially important organism known for amino acid production, carries a single putative sortase (NCgl2838) gene but neither in vitro peptide cleavage activity nor biochemical characterizations have been investigated. Here, we identified that the gene is having a sortase activity and analyzed its structural similarity with Cd-SrtF. The purified enzyme showed a greater affinity toward LAXTG substrate with a calculated KM of 12 ± 1 µM, one of the highest affinities reported for this class of enzyme. Moreover, site-directed mutation studies were carried to ascertain the structure functional relationship of Cg-SrtE and all these are new findings which will enable us to perceive exciting protein engineering applications with this class of enzyme from a non-pathogenic microbe.
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17
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Sue CK, McConnell SA, Ellis-Guardiola K, Muroski J, McAllister RA, Yu J, Alvarez AI, Chang C, Ogorzalek Loo RR, Loo JA, Ton-That H, Clubb RT. Kinetics and Optimization of the Lysine-Isopeptide Bond Forming Sortase Enzyme from Corynebacterium diphtheriae. Bioconjug Chem 2020; 31:1624-1634. [PMID: 32396336 PMCID: PMC8153732 DOI: 10.1021/acs.bioconjchem.0c00163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Site-specifically modified protein bioconjugates have important applications in biology, chemistry, and medicine. Functionalizing specific protein side chains with enzymes using mild reaction conditions is of significant interest, but remains challenging. Recently, the lysine-isopeptide bond forming activity of the sortase enzyme that builds surface pili in Corynebacterium diphtheriae (CdSrtA) has been reconstituted in vitro. A mutationally activated form of CdSrtA was shown to be a promising bioconjugating enzyme that can attach Leu-Pro-Leu-Thr-Gly peptide fluorophores to a specific lysine residue within the N-terminal domain of the SpaA protein (NSpaA), enabling the labeling of target proteins that are fused to NSpaA. Here we present a detailed analysis of the CdSrtA catalyzed protein labeling reaction. We show that the first step in catalysis is rate limiting, which is the formation of the CdSrtA-peptide thioacyl intermediate that subsequently reacts with a lysine ε-amine in NSpaA. This intermediate is surprisingly stable, limiting spurious proteolysis of the peptide substrate. We report the discovery of a new enzyme variant (CdSrtAΔ) that has significantly improved transpeptidation activity, because it completely lacks an inhibitory polypeptide appendage ("lid") that normally masks the active site. We show that the presence of the lid primarily impairs formation of the thioacyl intermediate and not the recognition of the NSpaA substrate. Quantitative measurements reveal that CdSrtAΔ generates its cross-linked product with a catalytic turnover number of 1.4 ± 0.004 h-1 and that it has apparent KM values of 0.16 ± 0.04 and 1.6 ± 0.3 mM for its NSpaA and peptide substrates, respectively. CdSrtAΔ is 7-fold more active than previously studied variants, labeling >90% of NSpaA with peptide within 6 h. The results of this study further improve the utility of CdSrtA as a protein labeling tool and provide insight into the enzyme catalyzed reaction that underpins protein labeling and pilus biogenesis.
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Affiliation(s)
- Christopher K. Sue
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Scott A. McConnell
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Ken Ellis-Guardiola
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - John Muroski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Rachel A. McAllister
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Justin Yu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Ana I. Alvarez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Chungyu Chang
- Molecular Biology Institute and the University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Rachel R. Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- Molecular Biology Institute and the University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Hung Ton-That
- Molecular Biology Institute and the University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- Molecular Biology Institute and the University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
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18
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Hartrampf N, Saebi A, Poskus M, Gates ZP, Callahan AJ, Cowfer AE, Hanna S, Antilla S, Schissel CK, Quartararo AJ, Ye X, Mijalis AJ, Simon MD, Loas A, Liu S, Jessen C, Nielsen TE, Pentelute BL. Synthesis of proteins by automated flow chemistry. Science 2020; 368:980-987. [PMID: 32467387 DOI: 10.1126/science.abb2491] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022]
Abstract
Ribosomes can produce proteins in minutes and are largely constrained to proteinogenic amino acids. Here, we report highly efficient chemistry matched with an automated fast-flow instrument for the direct manufacturing of peptide chains up to 164 amino acids long over 327 consecutive reactions. The machine is rapid: Peptide chain elongation is complete in hours. We demonstrate the utility of this approach by the chemical synthesis of nine different protein chains that represent enzymes, structural units, and regulatory factors. After purification and folding, the synthetic materials display biophysical and enzymatic properties comparable to the biologically expressed proteins. High-fidelity automated flow chemistry is an alternative for producing single-domain proteins without the ribosome.
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Affiliation(s)
- N Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A Saebi
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - M Poskus
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Z P Gates
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A J Callahan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A E Cowfer
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - S Hanna
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - S Antilla
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - C K Schissel
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A J Quartararo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - X Ye
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A J Mijalis
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - M D Simon
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - A Loas
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - S Liu
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - C Jessen
- Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - T E Nielsen
- Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark
| | - B L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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19
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Reed SA, Brzovic DA, Takasaki SS, Boyko KV, Antos JM. Efficient Sortase-Mediated Ligation Using a Common C-Terminal Fusion Tag. Bioconjug Chem 2020; 31:1463-1473. [PMID: 32324377 PMCID: PMC7357393 DOI: 10.1021/acs.bioconjchem.0c00156] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sortase-mediated ligation is a powerful method for generating site-specifically modified proteins. However, this process is limited by the inherent reversibility of the ligation reaction. To address this, here we report the continued development and optimization of an experimentally facile strategy for blocking reaction reversibility. This approach, which we have termed metal-assisted sortase-mediated ligation (MA-SML), relies on the use of a solution additive (Ni2+) and a C-terminal tag (LPXTGGHH5) that is widely used for converting protein targets into sortase substrates. In a series of model systems utilizing a 1:1 molar ratio of sortase substrate and glycine amine nucleophile, we find that MA-SML consistently improves the extent of ligation. This enables the modification of proteins with fluorophores, PEG, and a bioorthogonal cyclooctyne moiety without the need to use precious reagents in excess. Overall, these results demonstrate the potential of MA-SML as a general strategy for improving reaction efficiency in a broad range of sortase-based protein engineering applications.
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Affiliation(s)
- Sierra A. Reed
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, United States
| | - David A. Brzovic
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, United States
| | - Savanna S. Takasaki
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, United States
| | - Kristina V. Boyko
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, United States
| | - John M. Antos
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225, United States
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20
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Luo Y, Jiang C, Yu L, Yang A. Chemical Biology of Autophagy-Related Proteins With Posttranslational Modifications: From Chemical Synthesis to Biological Applications. Front Chem 2020; 8:233. [PMID: 32309274 PMCID: PMC7145982 DOI: 10.3389/fchem.2020.00233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/11/2020] [Indexed: 02/03/2023] Open
Abstract
Macroautophagy (hereafter referred to as autophagy) is an evolutionarily conserved lysosomal degradation pathway in all eukaryotic cells, which is critical for maintaining cell homeostasis. A series of autophagy-related (ATG) proteins are involved in the regulation of autophagy. The activities of ATG proteins are mainly modulated by posttranslational modifications (PTMs), such as phosphorylation, lipidation, acetylation, ubiquitination, and sumoylation. To tackle molecular mechanisms of autophagy, more and more researches are focusing on the roles of PTMs in regulation of the activity of ATG proteins and autophagy process. The protein ligation techniques have emerged as powerful tools for the chemical engineering of proteins with PTMs, and provided effective methods to elucidate the molecular mechanism and physiological significance of PTMs. Recently, several ATG proteins with PTM were prepared by protein ligation techniques such as native chemical ligation (NCL), expressed protein ligation (EPL), peptide hydrazide-based NCL, and Sortase A-mediated ligation (SML). More importantly, the synthesized ATG proteins are successfully used to probe the mechanism of autophagy. In this review, we summarize protein ligation techniques for the preparation of ATG proteins with PTMs. In addition, we highlight the biological applications of synthetic ATG proteins to probe the autophagy mechanism.
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Affiliation(s)
- Yu Luo
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Chen Jiang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lihua Yu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China
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21
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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22
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Peng Q, Zang B, Zhao W, Li D, Ren J, Ji F, Jia L. Efficient continuous-flow aldehyde tag conversion using immobilized formylglycine generating enzyme. Catal Sci Technol 2020. [DOI: 10.1039/c9cy01856e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Immobilized formylglycine generating enzyme for efficient aldehyde tag conversion under continuous flow conditions.
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Affiliation(s)
- Qiang Peng
- Liaoning Key Laboratory of Molecular Recognition and Imaging
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian
- P. R. China
| | - Berlin Zang
- Liaoning Key Laboratory of Molecular Recognition and Imaging
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian
- P. R. China
| | - Wei Zhao
- Liaoning Key Laboratory of Molecular Recognition and Imaging
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian
- P. R. China
| | - Da Li
- Liaoning Key Laboratory of Molecular Recognition and Imaging
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian
- P. R. China
| | - Jun Ren
- Liaoning Key Laboratory of Molecular Recognition and Imaging
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian
- P. R. China
| | - Fangling Ji
- Liaoning Key Laboratory of Molecular Recognition and Imaging
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian
- P. R. China
| | - Lingyun Jia
- Liaoning Key Laboratory of Molecular Recognition and Imaging
- School of Life Science and Biotechnology
- Dalian University of Technology
- Dalian
- P. R. China
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23
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Kim HW, Byun S, Kim SM, Kim HJ, Lei C, Kang DY, Cho A, Kim BM, Park JK. Simple reversible fixation of a magnetic catalyst in a continuous flow system: ultrafast reduction of nitroarenes and subsequent reductive amination using ammonia borane. Catal Sci Technol 2020. [DOI: 10.1039/c9cy02021g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Continuous reductive amination was performed using NH3BH3 through reversible magnetic bimetallic fixation at room temperature.
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Affiliation(s)
- Hong Won Kim
- Department of Chemistry and Chemistry Institute of Functional Materials
- Pusan National University
- Busan 46241
- Korea
| | - Sangmoon Byun
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Korea
| | - Seong Min Kim
- Department of Chemistry and Chemistry Institute of Functional Materials
- Pusan National University
- Busan 46241
- Korea
| | - Ha Joon Kim
- Department of Chemistry and Chemistry Institute of Functional Materials
- Pusan National University
- Busan 46241
- Korea
| | - Cao Lei
- Department of Chemistry and Chemistry Institute of Functional Materials
- Pusan National University
- Busan 46241
- Korea
| | - Dong Yun Kang
- Department of Chemistry and Chemistry Institute of Functional Materials
- Pusan National University
- Busan 46241
- Korea
| | - Ahra Cho
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Korea
| | - B. Moon Kim
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Korea
| | - Jin Kyoon Park
- Department of Chemistry and Chemistry Institute of Functional Materials
- Pusan National University
- Busan 46241
- Korea
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24
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Nuijens T, Toplak A, Schmidt M, Ricci A, Cabri W. Natural Occurring and Engineered Enzymes for Peptide Ligation and Cyclization. Front Chem 2019; 7:829. [PMID: 31850317 PMCID: PMC6895249 DOI: 10.3389/fchem.2019.00829] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022] Open
Abstract
The renaissance of peptides as prospective therapeutics has fostered the development of novel strategies for their synthesis and modification. In this context, besides the development of new chemical peptide ligation approaches, especially the use of enzymes as a versatile tool has gained increased attention. Nowadays, due to their inherent properties such as excellent regio- and chemoselectivity, enzymes represent invaluable instruments in both academic and industrial laboratories. This mini-review focuses on natural- and engineered peptide ligases that can form a new peptide (amide) bond between the C-terminal carboxy and N-terminal amino group of a peptide and/or protein. The pro's and cons of several enzyme classes such as Sortases, Asparaginyl Endoproteases, Trypsin related enzymes and as a central focus subtilisin-derived variants are summarized. Most recent developments with regards to ligation and cyclization are highlighted.
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Affiliation(s)
- Timo Nuijens
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
| | - Ana Toplak
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
| | - Marcel Schmidt
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
| | | | - Walter Cabri
- Fresenius Kabi iPSUM, I&D Center EnzyPep B.V., Geleen, Netherlands
- Fresenius Kabi iPSUM Srl, Villadose, Italy
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25
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Dai X, Böker A, Glebe U. Broadening the scope of sortagging. RSC Adv 2019; 9:4700-4721. [PMID: 35514663 PMCID: PMC9060782 DOI: 10.1039/c8ra06705h] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 01/31/2019] [Indexed: 01/20/2023] Open
Abstract
Sortases are enzymes occurring in the cell wall of Gram-positive bacteria. Sortase A (SrtA), the best studied sortase class, plays a key role in anchoring surface proteins with the recognition sequence LPXTG covalently to oligoglycine units of the bacterial cell wall. This unique transpeptidase activity renders SrtA attractive for various purposes and motivated researchers to study multiple in vivo and in vitro ligations in the last decades. This ligation technique is known as sortase-mediated ligation (SML) or sortagging and developed to a frequently used method in basic research. The advantages are manifold: extremely high substrate specificity, simple access to substrates and enzyme, robust nature and easy handling of sortase A. In addition to the ligation of two proteins or peptides, early studies already included at least one artificial (peptide equipped) substrate into sortagging reactions - which demonstrates the versatility and broad applicability of SML. Thus, SML is not only a biology-related technique, but has found prominence as a major interdisciplinary research tool. In this review, we provide an overview about the use of sortase A in interdisciplinary research, mainly for protein modification, synthesis of protein-polymer conjugates and immobilization of proteins on surfaces.
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Affiliation(s)
- Xiaolin Dai
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam-Golm Germany
- Lehrstuhl für Polymermaterialien und Polymertechnologie, Universität Potsdam 14476 Potsdam-Golm Germany
| | - Alexander Böker
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam-Golm Germany
- Lehrstuhl für Polymermaterialien und Polymertechnologie, Universität Potsdam 14476 Potsdam-Golm Germany
| | - Ulrich Glebe
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam-Golm Germany
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Wang HH, Tsourkas A. Site-Specific C-Terminal Labeling of Recombinant Proteins with Proximity-Based Sortase-Mediated Ligation (PBSL). Methods Mol Biol 2019; 2012:15-28. [PMID: 31161501 DOI: 10.1007/978-1-4939-9546-2_2] [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: 12/31/2022]
Abstract
S. aureus sortase A (SrtA), a calcium-dependent transpeptidase, is frequently employed to site-specifically label the C-terminus of recombinant proteins bearing an LPXTG SrtA recognition motif. Unfortunately, SrtA suffers from low turnover rates, resulting in poor ligation efficiencies even with optimized reaction conditions. In this chapter, we describe proximity-based sortase-mediated ligation (PBSL), which uses the SpyTag-SpyCatcher peptide-protein pair to link SrtA to target proteins and dramatically improves reaction rate and ligation efficiency.
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Affiliation(s)
- Hejia Henry Wang
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Tsourkas
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
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Wang HH, Tsourkas A. Overcoming the Limitations of Sortase with Proximity-Based Sortase-Mediated Ligation (PBSL). Methods Mol Biol 2019; 2008:165-177. [PMID: 31124096 DOI: 10.1007/978-1-4939-9537-0_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
S. aureus sortase A (SrtA), a calcium-dependent bacterial transpeptidase, is commonly used to site-specifically label proteins containing a LPXTG SrtA recognition motif with a wide array of chemical moieties. A major limitation of sortase-mediated labeling, however, is SrtA's poor binding affinity to its recognition motif, resulting in long reaction times and poor ligation efficiencies. Here we describe proximity-based sortase-mediated ligation (PBSL), which utilizes the SpyTag-SpyCatcher peptide-protein pair to tether target proteins with a SrtA recognition motif to SrtA, dramatically increasing their local concentrations and overcoming this limitation.
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Affiliation(s)
- Hejia Henry Wang
- Graduate group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
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Zhang Y, Park KY, Suazo KF, Distefano MD. Recent progress in enzymatic protein labelling techniques and their applications. Chem Soc Rev 2018; 47:9106-9136. [PMID: 30259933 PMCID: PMC6289631 DOI: 10.1039/c8cs00537k] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein-based conjugates are valuable constructs for a variety of applications. Conjugation of proteins to fluorophores is commonly used to study their cellular localization and the protein-protein interactions. Modification of therapeutic proteins with either polymers or cytotoxic moieties greatly enhances their pharmacokinetics or potency. To label a protein of interest, conventional direct chemical reaction with the side-chains of native amino acids often yields heterogeneously modified products. This renders their characterization complicated, requires difficult separation steps and may impact protein function. Although modification can also be achieved via the insertion of unnatural amino acids bearing bioorthogonal functional groups, these methods can have lower protein expression yields, limiting large scale production. As a site-specific modification method, enzymatic protein labelling is highly efficient and robust under mild reaction conditions. Significant progress has been made over the last five years in modifying proteins using enzymatic methods for numerous applications, including the creation of clinically relevant conjugates with polymers, cytotoxins or imaging agents, fluorescent or affinity probes to study complex protein interaction networks, and protein-linked materials for biosensing. This review summarizes developments in enzymatic protein labelling over the last five years for a panel of ten enzymes, including sortase A, subtiligase, microbial transglutaminase, farnesyltransferase, N-myristoyltransferase, phosphopantetheinyl transferases, tubulin tyrosin ligase, lipoic acid ligase, biotin ligase and formylglycine generating enzyme.
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Affiliation(s)
- Yi Zhang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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Wang X, Chen JL, Otting G, Su XC. Conversion of an amide to a high-energy thioester by Staphylococcus aureus sortase A is powered by variable binding affinity for calcium. Sci Rep 2018; 8:16371. [PMID: 30401805 PMCID: PMC6219580 DOI: 10.1038/s41598-018-34752-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/25/2018] [Indexed: 12/21/2022] Open
Abstract
Thioesters are key intermediates in biology, which often are generated from less energy-rich amide precursors. Staphylococcus aureus sortase A (SrtA) is an enzyme widely used in biotechnology for peptide ligation. The reaction proceeds in two steps, where the first step involves the conversion of an amide bond of substrate peptide into a thioester intermediate with the enzyme. Here we show that the free energy required for this step is matched by an about 30-fold increase in binding affinity of a calcium ion at the calcium binding site of SrtA, which is remote from the thioester bond. The magnitude of this allosteric effect highlights the importance of calcium for the activity of SrtA. The increase in calcium binding affinity upon binding of substrate not only achieves catalytic formation of an energy-rich intermediate in the absence of nucleotide triphosphates or any tight non-covalent enzyme-substrate interactions, but is also accompanied by accumulation of the labile thioester intermediate, which makes it directly observable in nuclear magnetic resonance (NMR) spectra.
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Affiliation(s)
- Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, College of Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, College of Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemical Biology, College of Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China.
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Abstract
Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.
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32
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Sortase-Mediated Ligation of Purely Artificial Building Blocks. Polymers (Basel) 2018; 10:polym10020151. [PMID: 30966187 PMCID: PMC6414994 DOI: 10.3390/polym10020151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/19/2018] [Accepted: 02/02/2018] [Indexed: 01/16/2023] Open
Abstract
Sortase A (SrtA) from Staphylococcus aureus has been often used for ligating a protein with other natural or synthetic compounds in recent years. Here we show that SrtA-mediated ligation (SML) is universally applicable for the linkage of two purely artificial building blocks. Silica nanoparticles (NPs), poly(ethylene glycol) and poly(N-isopropyl acrylamide) are chosen as synthetic building blocks. As a proof of concept, NP–polymer, NP–NP, and polymer–polymer structures are formed by SrtA catalysis. Therefore, the building blocks are equipped with the recognition sequence needed for SrtA reaction—the conserved peptide LPETG—and a pentaglycine motif. The successful formation of the reaction products is shown by means of transmission electron microscopy (TEM), matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-ToF MS), and dynamic light scattering (DLS). The sortase catalyzed linkage of artificial building blocks sets the stage for the development of a new approach to link synthetic structures in cases where their synthesis by established chemical methods is complicated.
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Yang M, Hong H, Liu S, Zhao X, Wu Z. Immobilization of Staphylococcus aureus Sortase A on Chitosan Particles and Its Applications in Peptide-to-Peptide Ligation and Peptide Cyclization. Molecules 2018; 23:molecules23010192. [PMID: 29351256 PMCID: PMC6017383 DOI: 10.3390/molecules23010192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/11/2018] [Accepted: 01/14/2018] [Indexed: 11/16/2022] Open
Abstract
Chitosan macro-particles prepared by the neutralization method were applied to Sortase A (SrtA) immobilization using glutaraldehyde as a crosslinking agent. The particles were characterized by Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). Response surface methodology (RSM) was employed to optimize the immobilization process. An average specific activity of 3142 U (mg protein)-1 was obtained under optimized immobilization conditions (chitosan concentration 3%, SrtA concentration 0.5 mg·mL-1, glutaraldehyde concentration 0.5%, crosslinking and immobilization at 20 °C, crosslinking for 3 h, and an immobilization time of 8 h). The transpeptidase activity of immobilized SrtA was proved by a peptide-to-peptide ligation with a conversion yield approximately at 80%, and the immobilized catalyst was successfully reused for five cycles without obvious activity loss. Moreover, the scale-up capability of using immobilized SrtA to catalyze a head-to-tail peptide cyclization was investigated in a batch reaction and the conversion yield was more than 95% when using 20 mg of peptide as a substrate.
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Affiliation(s)
- Min Yang
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Haofei Hong
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Shaozhong Liu
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Xinrui Zhao
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
| | - Zhimeng Wu
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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Li Y, Sun S, Fan L, Hu S, Huang Y, Zhang K, Nie Z, Yao S. Peptide Logic Circuits Based on Chemoenzymatic Ligation for Programmable Cell Apoptosis. Angew Chem Int Ed Engl 2017; 56:14888-14892. [DOI: 10.1002/anie.201708327] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Yong Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Sujuan Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Lin Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Shanfang Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Ke Zhang
- Department of Chemistry and Chemical Biology; Northeastern University; Boston MA 02115 USA
- Institute of Chemical Biology and Nanomedicine; Hunan University; Changsha 410081 P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Shouzhou Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
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35
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Li Y, Sun S, Fan L, Hu S, Huang Y, Zhang K, Nie Z, Yao S. Peptide Logic Circuits Based on Chemoenzymatic Ligation for Programmable Cell Apoptosis. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yong Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Sujuan Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Lin Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Shanfang Hu
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Ke Zhang
- Department of Chemistry and Chemical Biology; Northeastern University; Boston MA 02115 USA
- Institute of Chemical Biology and Nanomedicine; Hunan University; Changsha 410081 P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
| | - Shouzhou Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics; College of Chemistry and Chemical Engineering; Hunan University; Changsha 410082 P. R. China
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Spycher PR, Amann CA, Wehrmüller JE, Hurwitz DR, Kreis O, Messmer D, Ritler A, Küchler A, Blanc A, Béhé M, Walde P, Schibli R. Dual, Site-Specific Modification of Antibodies by Using Solid-Phase Immobilized Microbial Transglutaminase. Chembiochem 2017; 18:1923-1927. [PMID: 28771896 DOI: 10.1002/cbic.201700188] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Indexed: 12/11/2022]
Abstract
Microbial transglutaminase (MTG) was stably solid-phase immobilized on glass microbeads by using a second-generation dendronized polymer. Immobilized MTG enabled the efficient generation of site-specifically conjugated proteins, including antibody fragments, as well as whole antibodies through distinct glutamines and, unprecedentedly, also through lysines with various bifunctional substrates with defined stoichiometries. With this method, we generated dual, site-specifically modified antibodies comprising a fluorescent probe and a metal chelator for radiolabeling-a strategy anticipated to design antibodies for imaging and simultaneous therapy. Furthermore, we provide evidence that immobilized MTG features higher siteselectivity than soluble MTG.
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Affiliation(s)
- Philipp R Spycher
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Christian A Amann
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Jöri E Wehrmüller
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - David R Hurwitz
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Olivier Kreis
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Daniel Messmer
- Laboratory of Polymer Chemistry, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093, Zürich, Switzerland
| | - Andreas Ritler
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland.,Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Andreas Küchler
- Laboratory of Polymer Chemistry, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093, Zürich, Switzerland
| | - Alain Blanc
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Martin Béhé
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Peter Walde
- Laboratory of Polymer Chemistry, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093, Zürich, Switzerland
| | - Roger Schibli
- Center for Radiopharmaceutical Sciences ETH-PSI-USZ, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland.,Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
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Tan XL, Pan M, Zheng Y, Gao S, Liang LJ, Li YM. Sortase-mediated chemical protein synthesis reveals the bidentate binding of bisphosphorylated p62 with K63 diubiquitin. Chem Sci 2017; 8:6881-6887. [PMID: 29147513 PMCID: PMC5636944 DOI: 10.1039/c7sc02937c] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 08/03/2017] [Indexed: 12/21/2022] Open
Abstract
Phosphorylation of S403 or S407 of the autophagic receptor protein p62 has recently been discovered to enhance the binding of p62 with ubiquitinated protein substrates to upregulate selective autophagy. To elucidate the molecular mechanism of how phosphorylation regulates the recruitment of ubiquitinated proteins, we report the first chemical synthesis of homogeneously phosphorylated p62, which enables the setting up of accurate in vitro systems for biochemical studies. Our synthesis employs the technology of sortase A-mediated protein hydrazide ligation, which successfully affords three types of phosphorylated p62 at the multi-milligram scale. Quantitative biochemical measurements show that the binding affinity of S403/S407-bisphosphorylated p62 to K63 diubiquitin is significantly higher than that of mono-phosphorylated p62. This finding suggests that phosphorylated S403 and S407 sites should bind to different epitopes on the ubiquitin chain. Furthermore, glutamate mutation is found to give a significantly impaired binding affinity, implying the necessity of using chemically synthesized phosphorylated p62 for the biochemical study of selective autophagy.
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Affiliation(s)
- Xiang-Long Tan
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Biological and Medical Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China .
| | - Man Pan
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Yong Zheng
- School of Biological and Medical Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China . .,High Magnetic Field Laboratory , Chinese Academy of Sciences , Hefei 230031 , China
| | - Shuai Gao
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , 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 , Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Yi-Ming Li
- School of Biological and Medical Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China .
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Antos JM, Ingram J, Fang T, Pishesha N, Truttmann MC, Ploegh HL. Site-Specific Protein Labeling via Sortase-Mediated Transpeptidation. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2017; 89:15.3.1-15.3.19. [PMID: 28762490 PMCID: PMC5810355 DOI: 10.1002/cpps.38] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Strategies for site-specific protein modification are highly desirable for the construction of conjugates containing non-genetically-encoded functional groups. Ideally, these strategies should proceed under mild conditions, and be compatible with a wide range of protein targets and non-natural moieties. The transpeptidation reaction catalyzed by bacterial sortases is a prominent strategy for protein derivatization that possesses these features. Naturally occurring or engineered variants of sortase A from Staphylococcus aureus catalyze a ligation reaction between a five-amino-acid substrate motif (LPXTG) and oligoglycine nucleophiles. By pairing proteins and synthetic peptides that possess these ligation handles, it is possible to install modifications onto the protein N- or C-terminus in site-specific fashion. As described in this unit, the successful implementation of sortase-mediated labeling involves straightforward solid-phase synthesis and molecular biology techniques, and this method is compatible with proteins in solution or on the surface of live cells. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- John M Antos
- Department of Chemistry, Western Washington University, Bellingham, Washington
| | - Jessica Ingram
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Tao Fang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Matthias C Truttmann
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
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Zhao X, Hong H, Cheng X, Liu S, Deng T, Guo Z, Wu Z. One-step purification and immobilization of extracellularly expressed sortase A by magnetic particles to develop a robust and recyclable biocatalyst. Sci Rep 2017; 7:6561. [PMID: 28747746 PMCID: PMC5529518 DOI: 10.1038/s41598-017-06856-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/19/2017] [Indexed: 12/21/2022] Open
Abstract
Sortase A (SrtA) is a transpeptidase widely used to site-specifically modify peptides and proteins and shows promise for industrial applications. In this study, a novel strategy was developed for constructing immobilized-SrtA as a robust and recyclable enzyme via direct immobilization of extracellularly expressed SrtA in the fermentation supernatant using magnetic particles. Efficient extracellular SrtA expression was achieved in Escherichia coli through molecular engineering, including manipulation of the protein transport pathway, codon optimization, and co-expression of molecular chaperones to promote expressed SrtA secretion into the medium at high levels. Subsequently, a simple one-step protocol was established for the purification and immobilization of SrtA containing a His-tag from the fermentation supernatant onto a nickel-modified magnetic particle. The immobilized SrtA was proved to retain full enzymatic activity for peptide-to-peptide ligation and protein modification, and was successfully reused for five cycles without obvious activity loss.
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Affiliation(s)
- Xinrui Zhao
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Haofei Hong
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiaozhong Cheng
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shaozhong Liu
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Tao Deng
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, Florida, 32611, United States of America
| | - Zhimeng Wu
- Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.
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Milczek EM. Commercial Applications for Enzyme-Mediated Protein Conjugation: New Developments in Enzymatic Processes to Deliver Functionalized Proteins on the Commercial Scale. Chem Rev 2017. [DOI: 10.1021/acs.chemrev.6b00832] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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41
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Enzyme-mediated ligation technologies for peptides and proteins. Curr Opin Chem Biol 2017; 38:1-7. [PMID: 28229906 DOI: 10.1016/j.cbpa.2017.01.017] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/12/2017] [Accepted: 01/25/2017] [Indexed: 11/21/2022]
Abstract
With the steadily increasing complexity and quantity requirements for peptides in industry and academia, the efficient and site-selective ligation of peptides and proteins represents a highly desirable goal. Within this context, enzyme-mediated ligation technologies for peptides and proteins have attracted great interest in recent years as they represent an extremely powerful extension to the scope of chemical methodologies (e.g. native chemical ligation) in basic and applied research. Compared to chemical ligation methods, enzymatic strategies using ligases such as sortase, butelase, peptiligase or omniligase generally feature excellent chemoselectivity, therefore making them valuable tools for protein and peptide chemists.
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42
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Wang HH, Altun B, Nwe K, Tsourkas A. Proximity-Based Sortase-Mediated Ligation. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hejia Henry Wang
- Department of Biochemistry and Biophysics; Perelman School of Medicine; University of Pennsylvania; Philadelphia PA 19104 USA
| | - Burcin Altun
- Department of Bioengineering; University of Pennsylvania; 210 S. 33rd Street, 240 Skirkanich Hall Philadelphia PA 19104 USA
| | - Kido Nwe
- Department of Bioengineering; University of Pennsylvania; 210 S. 33rd Street, 240 Skirkanich Hall Philadelphia PA 19104 USA
| | - Andrew Tsourkas
- Department of Bioengineering; University of Pennsylvania; 210 S. 33rd Street, 240 Skirkanich Hall Philadelphia PA 19104 USA
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43
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Wang HH, Altun B, Nwe K, Tsourkas A. Proximity-Based Sortase-Mediated Ligation. Angew Chem Int Ed Engl 2017; 56:5349-5352. [PMID: 28374553 DOI: 10.1002/anie.201701419] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/10/2017] [Indexed: 01/31/2023]
Abstract
Protein bioconjugation has been a crucial tool for studying biological processes and developing therapeutics. Sortase A (SrtA), a bacterial transpeptidase, has become widely used for its ability to site-specifically label proteins with diverse functional moieties, but a significant limitation is its poor reaction kinetics. In this work, we address this by developing proximity-based sortase-mediated ligation (PBSL), which improves the ligation efficiency to over 95 % by linking the target protein to SrtA using the SpyTag-SpyCatcher peptide-protein pair. By expressing the target protein with SpyTag C-terminal to the SrtA recognition motif, it can be covalently captured by an immobilized SpyCatcher-SrtA fusion protein during purification. Following the ligation reaction, SpyTag is cleaved off, rendering PBSL traceless, and only the labeled protein is released, simplifying target protein purification and labeling to a single step.
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Affiliation(s)
- Hejia Henry Wang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Burcin Altun
- Department of Bioengineering, University of Pennsylvania, 210 S. 33rd Street, 240 Skirkanich Hall, Philadelphia, PA, 19104, USA
| | - Kido Nwe
- Department of Bioengineering, University of Pennsylvania, 210 S. 33rd Street, 240 Skirkanich Hall, Philadelphia, PA, 19104, USA
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, 210 S. 33rd Street, 240 Skirkanich Hall, Philadelphia, PA, 19104, USA
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44
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Chen GY, Li Z, Duarte JN, Esteban A, Cheloha RW, Theile CS, Fink GR, Ploegh HL. Rapid capture and labeling of cells on single domain antibodies-functionalized flow cell. Biosens Bioelectron 2016; 89:789-794. [PMID: 27816596 DOI: 10.1016/j.bios.2016.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/01/2016] [Accepted: 10/05/2016] [Indexed: 01/13/2023]
Abstract
Current techniques to characterize leukocyte subgroups in blood require long sample preparation times and sizable sample volumes. A simplified method for leukocyte characterization using smaller blood volumes would thus be useful in diagnostic settings. Here we describe a flow system comprised of two functionalized graphene oxide (GO) surfaces that allow the capture of distinct leukocyte populations from small volumes blood using camelid single-domain antibodyfragments (VHHs) as capture agents. We used site-specifically labeled leukocytes to detect and identify cells exposed to fungal challenge. Combining the chemical and optical properties of GO with the versatility of the VHH scaffold in the context of a flow system provides a quick and efficient method for the capture and characterization of functional leukocytes.
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Affiliation(s)
- Guan-Yu Chen
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Institute of Biomedical Engineering, National Chiao Tung University, Hsinchu 30010, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Zeyang Li
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Joao N Duarte
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | - Ross W Cheloha
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | - Gerald R Fink
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hidde L Ploegh
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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45
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Antos JM, Truttmann MC, Ploegh HL. Recent advances in sortase-catalyzed ligation methodology. Curr Opin Struct Biol 2016; 38:111-8. [PMID: 27318815 DOI: 10.1016/j.sbi.2016.05.021] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 11/25/2022]
Abstract
The transpeptidation reaction catalyzed by bacterial sortases continues to see increasing use in the construction of novel protein derivatives. In addition to growth in the number of applications that rely on sortase, this field has also seen methodology improvements that enhance reaction performance and scope. In this opinion, we present an overview of key developments in the practice and implementation of sortase-based strategies, including applications relevant to structural biology. Topics include the use of engineered sortases to increase reaction rates, the use of redesigned acyl donors and acceptors to mitigate reaction reversibility, and strategies for expanding the range of substrates that are compatible with a sortase-based approach.
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Affiliation(s)
- John M Antos
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA 98229, USA.
| | - Matthias C Truttmann
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Hidde L Ploegh
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.
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46
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David Row R, Roark TJ, Philip MC, Perkins LL, Antos JM. Enhancing the efficiency of sortase-mediated ligations through nickel-peptide complex formation. Chem Commun (Camb) 2016; 51:12548-51. [PMID: 26152789 DOI: 10.1039/c5cc04657b] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A modified sortase A recognition motif containing a masked Ni(2+)-binding peptide was employed to boost the efficiency of sortase-catalyzed ligation reactions. Deactivation of the Ni(2+)-binding peptide using a Ni(2+) additive improved reaction performance at low to equimolar ratios of the glycine amine nucleophile and sortase substrate. The success of this approach was demonstrated with both peptide and protein substrates.
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Affiliation(s)
- R David Row
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA 98229, USA.
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47
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Cistrone PA, Dawson PE. Click-Based Libraries of SFTI-1 Peptides: New Methods Using Reversed-Phase Silica. ACS COMBINATORIAL SCIENCE 2016; 18:139-43. [PMID: 26914614 DOI: 10.1021/acscombsci.5b00195] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Performing sequential reactions for the orthogonal derivatization of peptides in solution often requires intermediate handling and purification steps. To solve these problems, we have exploited the distinct adsorption kinetics of peptides toward particulate reversed-phase (RP) C18 silica material, enabling consecutive reactions to be performed without intermediate elution. To illustrate this approach, sequential CuAAC/click reactions were used to modify an analog of the bicyclic peptide sunflower trypsin inhibitor 1 (SFTI-1), a potent scaffold for trypsin and chymotrypsin-like enzyme inhibitors. The SFTI-1 scaffold was synthesized containing both β-azido alanine and propargyl glycine residues. Despite the mutual reactivity of these groups, site isolation on RP silica enabled consecutive click reactions and associated washing steps to be performed while the peptide remained immobilized. Importantly, this approach eliminated side products that could form between two peptides or within a single peptide. These studies suggest a broad utility for RP silica in solving both peptide handling problems and in improving synthetic workflows.
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Affiliation(s)
- Philip A. Cistrone
- Department
of Chemistry, The Scripps Research Institute (TSRI), 10550 North Torrey
Pines Road, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Department
of Chemistry, The Scripps Research Institute (TSRI), 10550 North Torrey
Pines Road, La Jolla, California 92037, United States
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48
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Novartis Early Career Award: B. L. Pentelute and J. A. Prescher / Biotrans Award: W. Kroutil / Carus Medal: H. J. Wörner. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201509775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Novartis Early Career Award: B. L. Pentelute und J. A. Prescher / Biotrans-Preis: W. Kroutil / Carus-Medaille: H. J. Wörner. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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50
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Abstract
Directed evolution has proved to be an effective strategy for improving or altering the activity of biomolecules for industrial, research and therapeutic applications. The evolution of proteins in the laboratory requires methods for generating genetic diversity and for identifying protein variants with desired properties. This Review describes some of the tools used to diversify genes, as well as informative examples of screening and selection methods that identify or isolate evolved proteins. We highlight recent cases in which directed evolution generated enzymatic activities and substrate specificities not known to exist in nature.
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Affiliation(s)
- Michael S Packer
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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