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Boliukh I, Rombel-Bryzek A, Bułdak RJ. Lectins in oncology and virology: Mechanisms of anticancer activity and SARS-CoV-2 inhibition. Int J Biol Macromol 2024:133664. [PMID: 38969035 DOI: 10.1016/j.ijbiomac.2024.133664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 06/10/2024] [Accepted: 07/02/2024] [Indexed: 07/07/2024]
Abstract
Lectins are proteins or glycoproteins of non-immune origin with carbohydrate-binding properties. They are found both prokaryotic and eukaryotic organisms. The most abundant source of the lectins are plants. Many lectins have anticancer effects by directly exerting cytotoxic effects on malignant cells or indirectly activating the immune system. Lectins also have antiviral activities. These proteins can recognise glycoproteins on the surface of enveloped viruses and bind to them. This creates a physical barrier between them and the corresponding receptors on the surface of the host cell, which prevents the virus from entering the cell and can thus effectively inhibit the replication of the virus. In this review, we focus on the anticancer activities of selected lectins and the underlying mechanisms. We also discuss different types of lectins with antiviral activity. We have paid special attention to lectins with inhibitory activity against SARS-CoV-2. Finally, we outline the challenges of using lectins in therapy and suggest future research directions.
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Affiliation(s)
- Iryna Boliukh
- Institute of Medical Sciences, University of Opole, Opole, Poland
| | | | - Rafał J Bułdak
- Institute of Medical Sciences, University of Opole, Opole, Poland
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2
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Das D, Ainavarapu SRK. Protein engineering using circular permutation - structure, function, stability, and applications. FEBS J 2024. [PMID: 38676939 DOI: 10.1111/febs.17146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/13/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024]
Abstract
Protein engineering is important for creating novel variants from natural proteins, enabling a wide range of applications. Approaches such as rational design and directed evolution are routinely used to make new protein variants. Computational tools like de novo design can introduce new protein folds. Expanding the amino acid repertoire to include unnatural amino acids with non-canonical side chains in vitro by native chemical ligation and in vivo via codon expansion methods broadens sequence and structural possibilities. Circular permutation (CP) is an invaluable approach to redesigning a protein by rearranging the amino acid sequence, where the connectivity of the secondary structural elements is altered without changing the overall structure of the protein. Artificial CP proteins (CPs) are employed in various applications such as biocatalysis, sensing of small molecules by fluorescence, genome editing, ligand-binding protein switches, and optogenetic engineering. Many studies have shown that CP can lead to either reduced or enhanced stability or catalytic efficiency. The effects of CP on a protein's energy landscape cannot be predicted a priori. Thus, it is important to understand how CP can affect the thermodynamic and kinetic stability of a protein. In this review, we discuss the discovery and advancement of techniques to create protein CP, and existing reviews on CP. We delve into the plethora of biological applications for designed CP proteins. We subsequently discuss the experimental and computational reports on the effects of CP on the thermodynamic and kinetic stabilities of proteins of various topologies. An understanding of the various aspects of CP will allow the reader to design robust CP proteins for their specific purposes.
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Affiliation(s)
- Debanjana Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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3
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Osterne VJ, Pinto-Junior VR, Oliveira MV, Nascimento KS, Van Damme EJ, Cavada BS. Computational insights into the circular permutation roles on ConA binding and structural stability. Curr Res Struct Biol 2024; 7:100140. [PMID: 38559841 PMCID: PMC10979261 DOI: 10.1016/j.crstbi.2024.100140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
The mechanisms behind Concanavalin A (ConA) circular permutation have been under investigation since 1985. Although a vast amount of information is available about this lectin and its applications, the exact purpose of its processing remains unclear. To shed light on this, this study employed computer simulations to compare the unprocessed ProConA with the mature ConA. This approach aimed to reveal the importance of the post-translational modifications, especially how they affect the lectin stability and carbohydrate-binding properties. To achieve these goals, we conducted 200 ns molecular dynamics simulations and trajectory analyses on the monomeric forms of ProConA and ConA (both unbound and in complex with D-mannose and the GlcNAc2Man9 N-glycan), as well as on their oligomeric forms. Our findings reveal significant stability differences between ProConA and ConA at both the monomeric and tetrameric levels, with ProConA exhibiting consistently lower stability parameters compared to ConA. In terms of carbohydrate binding properties, however, both lectins showed remarkable similarities in their interaction profiles, contact numbers, and binding free energies with D-mannose and the high-mannose N-glycan. Overall, our results suggest that the processing of ProConA significantly enhances the stability of the mature lectin, especially in maintaining the tetrameric oligomer, without substantially affecting its carbohydrate-binding properties.
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Affiliation(s)
- Vinicius J.S. Osterne
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Vanir R. Pinto-Junior
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
- Department of Physics, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
| | - Messias V. Oliveira
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
| | - Kyria S. Nascimento
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
| | - Els J.M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Benildo S. Cavada
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
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4
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Lossio CF, Osterne VJS, Pinto-Junior VR, Chen S, Oliveira MV, Verduijn J, Verbeke I, Serna S, Reichardt NC, Skirtach A, Cavada BS, Van Damme EJM, Nascimento KS. Structural Analysis and Characterization of an Antiproliferative Lectin from Canavalia villosa Seeds. Int J Mol Sci 2023; 24:15966. [PMID: 37958949 PMCID: PMC10649158 DOI: 10.3390/ijms242115966] [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: 09/14/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Cells use glycans to encode information that modulates processes ranging from cell-cell recognition to programmed cell death. This information is encoded within a glycocode, and its decoding is performed by carbohydrate-binding proteins. Among these, lectins stand out due to their specific and reversible interaction with carbohydrates. Changes in glycosylation patterns are observed in several pathologies, including cancer, where abnormal glycans are found on the surfaces of affected tissues. Given the importance of the bioprospection of promising biomolecules, the current work aimed to determine the structural properties and anticancer potential of the mannose-specific lectin from seeds of Canavalia villosa (Cvill). Experimental elucidation of the primary and 3D structures of the lectin, along with glycan array and molecular docking, facilitated the determination of its fine carbohydrate-binding specificity. These structural insights, coupled with the lectin's specificity, have been combined to explain the antiproliferative effect of Cvill against cancer cell lines. This effect is dependent on the carbohydrate-binding activity of Cvill and its uptake in the cells, with concomitant activation of autophagic and apoptotic pathways.
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Affiliation(s)
- Claudia F. Lossio
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
| | - Vinicius J. S. Osterne
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Vanir R. Pinto-Junior
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
- Department of Physics, Federal University of Ceara, Fortaleza 60440-970, Brazil
| | - Simin Chen
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Messias V. Oliveira
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
| | - Joost Verduijn
- Nano-Biotechnology Group, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Isabel Verbeke
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Sonia Serna
- Glycotechnology Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
| | - Niels C. Reichardt
- Glycotechnology Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
- Centro de Investigación Biomédica en Red (CIBER-BBN), Paseo de Miramon 194, 20014 Donostia-San Sebastián, Spain
| | - Andre Skirtach
- Nano-Biotechnology Group, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Benildo S. Cavada
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
| | - Els J. M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Kyria S. Nascimento
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza 60440-970, Brazil (B.S.C.)
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Hemu X, Chan NY, Liew HT, Hu S, Zhang X, Serra A, Lescar J, Liu CF, Tam JP. Substrate-binding glycine residues are major determinants for hydrolase and ligase activity of plant legumains. THE NEW PHYTOLOGIST 2023; 238:1534-1545. [PMID: 36843268 DOI: 10.1111/nph.18841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Peptide asparaginyl ligases (PALs) are useful tools for precision modifications of proteins and live-cell surfaces by ligating peptides after Asn/Asp (Asx). They share high sequence and structural similarity to plant legumains that are generally known as asparaginyl endopeptidases (AEPs), thus making it challenging to identify PALs from AEPs. In this study, we investigate 875 plant species from algae to seed plants with available sequence data in public databases to identify new PALs. We conducted evolutionary trace analysis on 1500 plant legumains, including eight known PALs, to identify key residues that could differentiate ligases and proteases, followed by recombinant expression and functional validation of 16 novel legumains. Previously, we showed that the substrate-binding sequences flanking the catalytic site can strongly influence the enzymatic direction of a legumain and which we named as ligase-activity determinants (LADs). Here, we show that two conserved substrate-binding Gly residues of LADs are critical, but negative determinants for ligase activity. Our results suggest that specific glycine residues are molecular determinants to identify PALs and AEPs as two different legumain subfamilies, accounting for c. 1% and 88%, respectively.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Ning-Yu Chan
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Heng Tai Liew
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Side Hu
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 637921, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Aida Serra
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- Neuroscience Area, +Pec Proteomics Research Group (+PPRG), Faculty of Medicine, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRB Lleida), University of Lleida, Av. Rovira Roure, 80, Lleida, 25198, Spain
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 637921, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 637921, Singapore
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Hemu X, Zhang X, Chang HY, Poh JE, Tam JP. Consensus design and engineering of an efficient and high-yield peptide asparaginyl ligase for protein cyclization and ligation. J Biol Chem 2023; 299:102997. [PMID: 36764523 PMCID: PMC10017362 DOI: 10.1016/j.jbc.2023.102997] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Plant legumains are Asn/Asp-specific endopeptidases that have diverse functions in plants. Peptide asparaginyl ligases (PALs) are a special legumain subtype that primarily catalyze peptide bond formation rather than hydrolysis. PALs are versatile protein engineering tools but are rarely found in nature. To overcome this limitation, here we describe a two-step method to design and engineer a high-yield and efficient recombinant PAL based on commonly found asparaginyl endopeptidases. We first constructed a consensus sequence derived from 1500 plant legumains to design the evolutionarily stable legumain conLEG that could be produced in E. coli with 20-fold higher yield relative to that for natural legumains. We then applied the ligase-activity determinant hypothesis to exploit conserved residues in PAL substrate-binding pockets and convert conLEG into conPAL1-3. Functional studies showed that conLEG is primarily a hydrolase, whereas conPALs are ligases. Importantly, conPAL3 is a superefficient and broadly active PAL for protein cyclization and ligation.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hong Yi Chang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore; Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Jin En Poh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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7
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Huldani H, Rashid AI, Turaev KN, Opulencia MJC, Abdelbasset WK, Bokov DO, Mustafa YF, Al-Gazally ME, Hammid AT, Kadhim MM, Ahmadi SH. Concanavalin A as a promising lectin-based anti-cancer agent: the molecular mechanisms and therapeutic potential. Cell Commun Signal 2022; 20:167. [PMID: 36289525 PMCID: PMC9597983 DOI: 10.1186/s12964-022-00972-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/17/2022] [Indexed: 11/29/2022] Open
Abstract
Concanavalin A (ConA), the most studied plant lectin, has been known as a potent anti-neoplastic agent for a long time. Since initial reports on its capacity to kill cancer cells, much attention has been devoted to unveiling the lectin's exact molecular mechanism. It has been revealed that ConA can bind to several receptors on cancerous and normal cells and modulate the related signaling cascades. The most studied host receptor for ConA is MT1-MMP, responsible for most of the lectin's modulations, ranging from activating immune cells to killing tumor cells. In this study, in addition to studying the effect of ConA on signaling and immune cell function, we will focus on the most up-to-date advancements that unraveled the molecular mechanisms by which ConA can induce autophagy and apoptosis in various cancer cell types, where it has been found that P73 and JAK/STAT3 are the leading players. Moreover, we further discuss the main signaling molecules causing liver injury as the most significant side effect of the lectin injection. Altogether, these findings may shed light on the complex signaling pathways controlling the diverse responses created via ConA treatment, thereby modulating these complex networks to create more potent lectin-based cancer therapy. Video Abstract
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Affiliation(s)
- Huldani Huldani
- grid.443126.60000 0001 2193 0299Department of Physiology, Faculty of Medicine, Lambung Mangkurat University, Banjarmasin, South Kalimantan Indonesia
| | - Ahmed Ibraheem Rashid
- grid.427646.50000 0004 0417 7786Department of Pharmacology, Collage of Medicine, University of Babylon, Hilla, Iraq
| | - Khikmatulla Negmatovich Turaev
- grid.444694.f0000 0004 0403 0119Department of Clinical Pharmacology, Samarkand State Medical Institute, Samarkand, Uzbekistan ,grid.513581.b0000 0004 6356 9173Department of Scientific Affairs, Tashkent State Dental Institute, Makhtumkuli Street 103, Tashkent, Uzbekistan 100047
| | | | - Walid Kamal Abdelbasset
- grid.449553.a0000 0004 0441 5588Department of Health and Rehabilitation Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia ,grid.7776.10000 0004 0639 9286Department of Physical Therapy, Kasr Al-Aini Hospital, Cairo University, Giza, Egypt
| | - Dmitry Olegovich Bokov
- grid.448878.f0000 0001 2288 8774Institute of Pharmacy, Sechenov First Moscow State Medical University, 8 Trubetskaya St., Bldg. 2, Moscow, 119991 Russian Federation ,grid.466474.3Laboratory of Food Chemistry, Federal Research Center of Nutrition, Biotechnology and Food Safety, 2/14 Ustyinsky Pr, Moscow, 109240 Russian Federation
| | - Yasser Fakri Mustafa
- grid.411848.00000 0000 8794 8152Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul-41001, Iraq
| | | | - Ali Thaeer Hammid
- grid.513683.a0000 0004 8495 7394Computer Engineering Techniques Department, Faculty of Information Technology, Imam Ja’afar Al-Sadiq University, Baghdad, Iraq
| | - Mustafa M. Kadhim
- Department of Dentistry, Kut University College, Kut, Wasit 52001 Iraq ,grid.444971.b0000 0004 6023 831XCollege of Technical Engineering, The Islamic University, Najaf, Iraq ,Department of Pharmacy, Osol Aldeen University College, Baghdad, Iraq
| | - Seyed Hossein Ahmadi
- grid.411705.60000 0001 0166 0922Research Center for Cell and Molecular Sciences, School of Medicine, Tehran University of Medical Sciences, PO Box 1417613151, Tehran, Iran
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Xu Y, Jia G, Li T, Zhou Z, Luo Y, Chao Y, Bao J, Su Z, Qu Q, Li D. Molecular insights into biogenesis of glycosylphosphatidylinositol anchor proteins. Nat Commun 2022; 13:2617. [PMID: 35551457 PMCID: PMC9098846 DOI: 10.1038/s41467-022-30250-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/22/2022] [Indexed: 02/08/2023] Open
Abstract
Eukaryotic cells are coated with an abundance of glycosylphosphatidylinositol anchor proteins (GPI-APs) that play crucial roles in fertilization, neurogenesis, and immunity. The removal of a hydrophobic signal peptide and covalent attachment of GPI at the new carboxyl terminus are catalyzed by an endoplasmic reticulum membrane GPI transamidase complex (GPI-T) conserved among all eukaryotes. Here, we report the cryo-electron microscopy (cryo-EM) structure of the human GPI-T at a global 2.53-Å resolution, revealing an equimolar heteropentameric assembly. Structure-based mutagenesis suggests a legumain-like mechanism for the recognition and cleavage of proprotein substrates, and an endogenous GPI in the structure defines a composite cavity for the lipid substrate. This elongated active site, stemming from the membrane and spanning an additional ~22-Å space toward the catalytic dyad, is structurally suited for both substrates which feature an amphipathic pattern that matches this geometry. Our work presents an important step towards the mechanistic understanding of GPI-AP biosynthesis. GPI-T catalyzes the committed step in GPI anchor protein biogenesis. Here, Xu et al. report the cryo-EM structure of the human GPI-T, revealing critical elements within an elongated, shared active site which is topologically arranged for substrate specificity.
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Affiliation(s)
- Yidan Xu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of CAS, Chinese Academy of Sciences (CAS), 320 Yueyang Road, 200030, Shanghai, China
| | - Guowen Jia
- State Key Laboratory of Biotherapy and Cancer Center, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, 610044, Chengdu, China
| | - Tingting Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of CAS, Chinese Academy of Sciences (CAS), 320 Yueyang Road, 200030, Shanghai, China
| | - Zixuan Zhou
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, 200032, Shanghai, China
| | - Yitian Luo
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of CAS, Chinese Academy of Sciences (CAS), 320 Yueyang Road, 200030, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China
| | - Yulin Chao
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, 200032, Shanghai, China
| | - Juan Bao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of CAS, Chinese Academy of Sciences (CAS), 320 Yueyang Road, 200030, Shanghai, China
| | - Zhaoming Su
- State Key Laboratory of Biotherapy and Cancer Center, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, 610044, Chengdu, China.
| | - Qianhui Qu
- Shanghai Stomatological Hospital, School of Stomatology, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Department of Systems Biology for Medicine, Fudan University, 200032, Shanghai, China.
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of CAS, Chinese Academy of Sciences (CAS), 320 Yueyang Road, 200030, Shanghai, China.
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9
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Loo S, Tay SV, Kam A, Lee W, Tam JP. Hololectin Interdomain Linker Determines Asparaginyl Endopeptidase-Mediated Maturation of Antifungal Hevein-Like Peptides in Oats. FRONTIERS IN PLANT SCIENCE 2022; 13:899740. [PMID: 35620686 PMCID: PMC9127739 DOI: 10.3389/fpls.2022.899740] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/20/2022] [Indexed: 05/28/2023]
Abstract
Heveins and hevein-containing (hev-) lectins play important roles in stress and pathogenic responses in plants but cause health concerns in humans. Hev-hololectins contain multiple modular hev-peptide domains and are abundantly present in cereals and pseudocereals. However, it is unclear why some cereal hev-hololectins are presented as different forms of proteolytically processed proteoforms. Here we show the precursor architectures of hev-hololectins lead to different processing mechanisms to give either hololectins or hevein-like peptides. We used mass spectrometry and datamining to screen hev-peptides from common cereals, and identified from the oat plant Avena sativa nine novel hevein-like peptides, avenatide aV1-aV9. Bioinformatic analysis revealed that asparaginyl endopeptidase (AEP) can be responsible for the maturation of the highly homologous avenatides from five oat hev-hololectin precursors, each containing four tandemly repeating, hev-like avenatide domains connected by AEP-susceptible linkers with 13-16 residues in length. Further analysis of cereal hev-hololectins showed that the linker lengths provide a distinguishing feature between their cleavable and non-cleavable precursors, with the cleavables having considerably longer linkers (>13 amino acids) than the non-cleavables (<6 amino acids). A detailed study of avenatide aV1 revealed that it contains eight cysteine residues which form a structurally compact, metabolic-resistant cystine-knotted framework with a well-defined chitin-binding site. Antimicrobial assays showed that avenatide aV1 is anti-fungal and inhibits the growth of phyto-pathogenic fungi. Together, our findings of cleavable and non-cleavable hololectins found in cereals expand our knowledge to their biosynthesis and provide insights for hololectin-related health concerns in human.
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10
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Chen Y, Zhang D, Zhang X, Wang Z, Liu CF, Tam JP. Site-Specific Protein Modifications by an Engineered Asparaginyl Endopeptidase from Viola canadensis. Front Chem 2021; 9:768854. [PMID: 34746098 PMCID: PMC8568951 DOI: 10.3389/fchem.2021.768854] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/06/2021] [Indexed: 12/04/2022] Open
Abstract
Asparaginyl endopeptidases (AEPs) or legumains are Asn/Asp (Asx)-specific proteases that break peptide bonds, but also function as peptide asparaginyl ligases (PALs) that make peptide bonds. This ligase activity can be used for site-specific protein modifications in biochemical and biotechnological applications. Although AEPs are common, PALs are rare. We previously proposed ligase activity determinants (LADs) of these enzymes that could determine whether they catalyze formation or breakage of peptide bonds. LADs are key residues forming the S2 and S1' substrate-binding pockets flanking the S1 active site. Here, we build on the LAD hypothesis with the engineering of ligases from proteases by mutating the S2 and S1' pockets of VcAEP, an AEP from Viola canadensis. Wild type VcAEP yields <5% cyclic product from a linear substrate at pH 6.5, whereas the single mutants VcAEP-V238A (Vc1a) and VcAEP-Y168A (Vc1b) targeting the S2 and S1' substrate-binding pockets yielded 34 and 61% cyclic products, respectively. The double mutant VcAEP-V238A/Y168A (Vc1c) targeting both the S2 and S1' substrate-binding pockets yielded >90% cyclic products. Vc1c had cyclization efficiency of 917,759 M-1s-1, which is one of the fastest rates for ligases yet reported. Vc1c is useful for protein engineering applications, including labeling of DARPins and cell surface MCF-7, as well as producing cyclic protein sfGFP. Together, our work validates the importance of LADs for AEP ligase activity and provides valuable tools for site-specific modification of proteins and biologics.
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Affiliation(s)
- Yu Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
| | - Dingpeng Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
| | - Zhen Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
- Nanyang Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - James P. Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Synzymes and Natural Products Center, Nanyang Technological University, Singapore, Singapore
- Nanyang Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
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O’Leary BM. Circular permutation of concanavalin A: why the rarest protein modification in nature came to be. THE PLANT CELL 2021; 33:2521-2522. [PMID: 35233625 PMCID: PMC8408451 DOI: 10.1093/plcell/koab143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Brendan M. O’Leary
- Saskatoon Research Development Centre, Agriculture and Agri-food Canada, Saskatoon, Saskatchewan, Canada
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