1
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Kapitonova AA, Perfilova KV, Cooley RB, Sluchanko NN. Phosphorylation Code of Human Nucleophosmin Includes Four Cryptic Sites for Hierarchical Binding of 14-3-3 Proteins. J Mol Biol 2024; 436:168592. [PMID: 38702038 DOI: 10.1016/j.jmb.2024.168592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/18/2024] [Accepted: 04/27/2024] [Indexed: 05/06/2024]
Abstract
Nucleophosmin (NPM1) is the 46th most abundant human protein with many functions whose dysregulation leads to various cancers. Pentameric NPM1 resides in the nucleolus but can also shuttle to the cytosol. NPM1 is regulated by multisite phosphorylation, yet molecular consequences of site-specific NPM1 phosphorylation remain elusive. Here we identify four 14-3-3 protein binding sites in NPM1 concealed within its oligomerization and α-helical C-terminal domains that are found phosphorylated in vivo. By combining mutagenesis, in-cell phosphorylation and PermaPhos technology for site-directed incorporation of a non-hydrolyzable phosphoserine mimic, we show how phosphorylation promotes NPM1 monomerization and partial unfolding, to recruit 14-3-3 dimers with low-micromolar affinity. Using fluorescence anisotropy we quantified pairwise interactions of all seven human 14-3-3 isoforms with four recombinant NPM1 phosphopeptides and assessed their druggability by fusicoccin. This revealed a complex hierarchy of 14-3-3 affinities toward the primary (S48, S293) and secondary (S106, S260) sites, differentially modulated by the small molecule. As three of these 14-3-3 binding phosphosites in NPM1 reside within signal sequences, this work suggests a mechanism of NPM1 regulation by which NPM1 phosphorylation can promote 14-3-3 binding to affect NPM1 shuttling between cell compartments. It also provides further evidence that phosphorylation-induced structural rearrangements of globular proteins serve to expose otherwise cryptic 14-3-3-binding sites that are important for cellular function.
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Affiliation(s)
- Anna A Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Kristina V Perfilova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Richard B Cooley
- GCE4All Center, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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2
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Allen MC, Karplus PA, Mehl RA, Cooley RB. Genetic Encoding of Phosphorylated Amino Acids into Proteins. Chem Rev 2024; 124:6592-6642. [PMID: 38691379 DOI: 10.1021/acs.chemrev.4c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Reversible phosphorylation is a fundamental mechanism for controlling protein function. Despite the critical roles phosphorylated proteins play in physiology and disease, our ability to study individual phospho-proteoforms has been hindered by a lack of versatile methods to efficiently generate homogeneous proteins with site-specific phosphoamino acids or with functional mimics that are resistant to phosphatases. Genetic code expansion (GCE) is emerging as a transformative approach to tackle this challenge, allowing direct incorporation of phosphoamino acids into proteins during translation in response to amber stop codons. This genetic programming of phospho-protein synthesis eliminates the reliance on kinase-based or chemical semisynthesis approaches, making it broadly applicable to diverse phospho-proteoforms. In this comprehensive review, we provide a brief introduction to GCE and trace the development of existing GCE technologies for installing phosphoserine, phosphothreonine, phosphotyrosine, and their mimics, discussing both their advantages as well as their limitations. While some of the technologies are still early in their development, others are already robust enough to greatly expand the range of biologically relevant questions that can be addressed. We highlight new discoveries enabled by these GCE approaches, provide practical considerations for the application of technologies by non-GCE experts, and also identify avenues ripe for further development.
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Affiliation(s)
- Michael C Allen
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, GCE4All Research Center, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331 United States
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3
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Kapitonova AA, Perfilova KV, Cooley RB, Sluchanko NN. Phosphorylation code of human nucleophosmin includes four cryptic sites for hierarchical binding of 14-3-3 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580064. [PMID: 38405961 PMCID: PMC10888825 DOI: 10.1101/2024.02.13.580064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Nucleophosmin (NPM1) is the 46th most abundant human protein with many functions whose dysregulation leads to various cancers. Pentameric NPM1 resides in the nucleolus but can also shuttle to the cytosol. NPM1 is regulated by multisite phosphorylation, yet molecular consequences of site-specific NPM1 phosphorylation remain elusive. Here we identify four 14-3-3 protein binding sites in NPM1 concealed within its oligomerization and α-helical C-terminal domains that are found phosphorylated in vivo. By combining mutagenesis, in-cell phosphorylation and PermaPhos technology for site-directed incorporation of a non-hydrolyzable phosphoserine mimic, we show how phosphorylation promotes NPM1 monomerization and partial unfolding, to recruit 14-3-3 dimers with low-micromolar affinity. Using fluorescence anisotropy we quantified pairwise interactions of all seven human 14-3-3 isoforms with four recombinant NPM1 phosphopeptides and assessed their druggability by fusicoccin. This revealed a complex hierarchy of 14-3-3 affinities toward the primary (S48, S293) and secondary (S106, S260) sites, differentially modulated by the small molecule. As three of these 14-3-3 binding phospho-sites in NPM1 reside within signal sequences, this work highlights a key mechanism of NPM1 regulation by which NPM1 phosphorylation promotes 14-3-3 binding to control nucleocytoplasmic shuttling. It also provides further evidence that phosphorylation-induced structural rearrangements of globular proteins serve to expose otherwise cryptic 14-3-3-binding sites that are important for cellular function.
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Affiliation(s)
- Anna A. Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Kristina V. Perfilova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Richard B. Cooley
- GCE4All Center, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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4
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Zhu P, Stanisheuski S, Franklin R, Vogel A, Vesely CH, Reardon P, Sluchanko NN, Beckman JS, Karplus PA, Mehl RA, Cooley RB. Autonomous Synthesis of Functional, Permanently Phosphorylated Proteins for Defining the Interactome of Monomeric 14-3-3ζ. ACS CENTRAL SCIENCE 2023; 9:816-835. [PMID: 37122473 PMCID: PMC10141581 DOI: 10.1021/acscentsci.3c00191] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Indexed: 05/03/2023]
Abstract
14-3-3 proteins are dimeric hubs that bind hundreds of phosphorylated "clients" to regulate their function. Installing stable, functional mimics of phosphorylated amino acids into proteins offers a powerful strategy to study 14-3-3 function in cellular-like environments, but a previous genetic code expansion (GCE) system to translationally install nonhydrolyzable phosphoserine (nhpSer), with the γ-oxygen replaced with CH2, site-specifically into proteins has seen limited usage. Here, we achieve a 40-fold improvement in this system by engineering into Escherichia coli a six-step biosynthetic pathway that produces nhpSer from phosphoenolpyruvate. Using this autonomous "PermaPhos" expression system, we produce three biologically relevant proteins with nhpSer and confirm that nhpSer mimics the effects of phosphoserine for activating GSK3β phosphorylation of the SARS-CoV-2 nucleocapsid protein, promoting 14-3-3/client complexation, and monomerizing 14-3-3 dimers. Then, to understand the biological function of these phosphorylated 14-3-3ζ monomers (containing nhpSer at Ser58), we isolate its interactome from HEK293T lysates and compare it with that of wild-type 14-3-3ζ. These data identify two new subsets of 14-3-3 client proteins: (i) those that selectively bind dimeric 14-3-3ζ and (ii) those that selectively bind monomeric 14-3-3ζ. We discover that monomeric-but not dimeric-14-3-3ζ interacts with cereblon, an E3 ubiquitin-ligase adaptor protein of pharmacological interest.
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Affiliation(s)
- Phillip Zhu
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Stanislau Stanisheuski
- Department
of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States
| | - Rachel Franklin
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Amber Vogel
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Cat Hoang Vesely
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Patrick Reardon
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Nikolai N. Sluchanko
- A.N.
Bach Institute of Biochemistry, Federal Research Center of Biotechnology
of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Joseph S. Beckman
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
- e-MSion
Inc., 2121 NE Jack London
St., Corvallis, Oregon 97330, United States
| | - P. Andrew Karplus
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Ryan A. Mehl
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
| | - Richard B. Cooley
- Department
of Biochemistry and Biophysics, Oregon State
University, 2011 Agricultural and Life Sciences, Corvallis, Oregon 97331, United States
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5
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Tugaeva KV, Sysoev AA, Kapitonova AA, Smith JLR, Zhu P, Cooley RB, Antson AA, Sluchanko NN. Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation. J Mol Biol 2023; 435:167891. [PMID: 36427566 PMCID: PMC9683861 DOI: 10.1016/j.jmb.2022.167891] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/06/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022]
Abstract
Phosphorylation of SARS-CoV-2 nucleoprotein recruits human cytosolic 14-3-3 proteins playing a well-recognized role in replication of many viruses. Here we use genetic code expansion to demonstrate that 14-3-3 binding is triggered by phosphorylation of SARS-CoV-2 nucleoprotein at either of two pseudo-repeats centered at Ser197 and Thr205. According to fluorescence anisotropy measurements, the pT205-motif,presentin SARS-CoV-2 but not in SARS-CoV, is preferred over the pS197-motif by all seven human 14-3-3 isoforms, which collectively display an unforeseen pT205/pS197 peptide binding selectivity hierarchy. Crystal structures demonstrate that pS197 and pT205 are mutually exclusive 14-3-3-binding sites, whereas SAXS and biochemical data obtained on the full protein-protein complex indicate that 14-3-3 binding occludes the Ser/Arg-rich region of the nucleoprotein, inhibiting its dephosphorylation. This Ser/Arg-rich region is highly prone to mutations, as exemplified by the Omicron and Delta variants, with our data suggesting that the strength of 14-3-3/nucleoprotein interaction can be linked with the replicative fitness of the virus.
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Affiliation(s)
- Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Andrey A Sysoev
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anna A Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Phillip Zhu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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6
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Liu D, Liu Y, Duan HZ, Chen X, Wang Y, Wang T, Yu Q, Chen YX, Lu Y. Customized synthesis of phosphoprotein bearing phosphoserine or its nonhydrolyzable analog. Synth Syst Biotechnol 2022; 8:69-78. [PMID: 36514487 PMCID: PMC9719085 DOI: 10.1016/j.synbio.2022.11.004] [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: 07/29/2022] [Revised: 10/13/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
Studies on the mechanism of protein phosphorylation and therapeutic interventions of its related molecular processes are limited by the difficulty in the production of purpose-built phosphoproteins harboring site-specific phosphorylated amino acids or their nonhydrolyzable analogs. Here we address this limitation by customizing the cell-free protein synthesis (CFPS) machinery via chassis strain selection and orthogonal translation system (OTS) reconfiguration screening. The suited chassis strains and reconfigured OTS combinations with high orthogonality were consequently picked out for individualized phosphoprotein synthesis. Specifically, we synthesized the sfGFP protein and MEK1 protein with site-specific phosphoserine (O-pSer) or its nonhydrolyzable analog, 2-amino-4-phosphonobutyric acid (C-pSer). This study successfully realized building cell-free systems for site-specific incorporation of phosphonate mimics into the target protein. Our work lays the foundation for developing a highly expansible CFPS platform and the streamlined production of user-defined phosphoproteins, which can facilitate research on the physiological mechanism and potential interference tools toward protein phosphorylation.
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Affiliation(s)
- Dong Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yingying Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Hua-Zhen Duan
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Xinjie Chen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yanan Wang
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Ting Wang
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Qing Yu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yong-Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
- Corresponding author.
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
- Corresponding author.
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7
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Liang X, Deng H, Bai Y, Fan TP, Zheng X, Cai Y. Highly efficient biosynthesis of spermidine from L-homoserine and putrescine using an engineered Escherichia coli with NADPH self-sufficient system. Appl Microbiol Biotechnol 2022; 106:5479-5493. [PMID: 35931895 DOI: 10.1007/s00253-022-12110-x] [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: 06/02/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/30/2022]
Abstract
Spermidine is an important polyamine that can be used for the synthesis of various bioactive compounds in the food and pharmaceutical fields. In this study, a novel efficient whole-cell biocatalytic method with an NADPH self-sufficient cycle for spermidine biosynthesis was designed and constructed by co-expressing homoserine dehydrogenase (HSD), carboxyspermidine dehydrogenase (CASDH), and carboxyspermidine decarboxylase (CASDC). First, the enzyme-substrate coupled cofactor regeneration system from co-expression of NADP+-dependent ScHSD and NADPH-dependent AfCASDH exactly provides an efficient method for cofactor cycling. Second, we identified and characterized a putative CASDC with high decarboxylase activity from Butyrivibrio crossotus DSM 2876; it showed an optimum temperature of 35 °C and an optimum pH of 7.0, which make it better suited for the designed synthetic route. Subsequently, the protein expression level of each enzyme was optimized through the variation of the gene copy number, and a whole-cell catalyst with high catalytic efficiency was constructed successfully. Finally, a yield of 28.6 mM of spermidine was produced in a 1-L scale of E. coli whole-cell catalytic system with a 95.3% molar conversion rate after optimization of temperature, the ratio of catalyst-to-substrate, and the amount of NADP+, and a productivity of 0.17 g·L-1·h-1 was achieved. In summary, this novel pathway of constructing a whole-cell catalytic system from L-homoserine and putrescine could provide a green alternative method for the efficient synthesis of spermidine. KEY POINTS: • A novel pathway for spermidine biosynthesis was developed in Escherichia coli. • The enzyme-substrate coupled system provides an NADPH self-sufficient cycle. • Spermidine with 28.6 mM was obtained using an optimized whole-cell system.
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Affiliation(s)
- Xinxin Liang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Huaxiang Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, CB2 1T, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China.
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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8
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Liang X, Deng H, Xiong T, Bai Y, Fan TP, Zheng X, Cai Y. Overexpression and biochemical characterization of a carboxyspermidine dehydrogenase from Agrobacterium fabrum str. C58 and its application to carboxyspermidine production. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:3858-3868. [PMID: 34932223 DOI: 10.1002/jsfa.11735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/18/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Carboxyspermidine (C-Spd) is a potentially valuable polyamine carboxylate compound and an excellent building block for spermidine synthesis, which is a critical polyamine with significant implications for human health and longevity. C-Spd can also be used to prepare multivalent cationic lipids and modify nucleoside probes. Because of these positive effects on human health, C-Spd is of considerable interest as a food additive and pharmaceutical target. RESULTS A putative gene afcasdh from Agrobacterium fabrum str. C58, encoding carboxyspermidine dehydrogenase with C-Spd biosynthesis activity, was synthesized and transformed into Escherichia coli BL21 (DE3) for overexpression. The recombinant AfCASDH was purified and fully characterized. The optimum temperature and pH for the recombinant enzyme were 30 °C and 7.5, respectively. The coupled catalytic strategy of AfCASDH and various NADPH regeneration systems were developed to enhance the efficient production of C-Spd compound. Finally, the maximum titer of C-Spd production successfully achieved 1.82 mmol L-1 with a yield of 91% by optimizing the catalytic conditions. CONCLUSION A novel AfCASDH from A. fabrum str. C58 was characterized that could catalyze the formation of C-Spd from putrescine and l-aspartate-β-semialdehyde (L-Asa). A whole-cell catalytic strategy coupled with NADPH regeneration was established successfully for C-Spd biosynthesis for the first time. The coupled system indicated that AfCASDH might provide a feasible method for the industrial production of C-Spd. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Xinxin Liang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Huaxiang Deng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Tianzhen Xiong
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, China
| | - Yujie Cai
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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9
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Chang R, Liu Y, Zhang Y, Zhang S, Han B, Chen F, Chen Y. Phosphorylated and Phosphonated Low-Complexity Protein Segments for Biomimetic Mineralization and Repair of Tooth Enamel. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103829. [PMID: 34978158 PMCID: PMC8867149 DOI: 10.1002/advs.202103829] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/18/2021] [Indexed: 05/03/2023]
Abstract
Biomimetic mineralization based on self-assembly has made great progress, providing bottom-up strategies for the construction of new organic-inorganic hybrid materials applied in the treatment of hard tissue defects. Herein, inspired by the cooperative effects of key components in biomineralization microenvironments, a new type of biocompatible peptide scaffold based on flexibly self-assembling low-complexity protein segments (LCPSs) containing phosphate or phosphonate groups is developed. These LCPSs can retard the transformation of amorphous calcium phosphate into hydroxyapatite (HAP), leading to merged mineralization structures. Moreover, the application of phosphonated LCPS over phosphorylated LCPS can prevent hydrolysis by phosphatases that are enriched in extracellular mineralization microenvironments. After being coated on the etched tooth enamel, these LCPSs facilitate the growth of HAP to generate new enamel layers comparable to the natural layers and mitigate the adhesion of Streptococcus mutans. In addition, they can effectively stimulate the differentiation pathways of osteoblasts. These results shed light on the potential biomedical applications of two LCPSs in hard tissue repair.
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Affiliation(s)
- Rong Chang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua UniversityBeijing100084China
| | - Yang‐Jia Liu
- Central LaboratoryPeking University Hospital of StomatologyBeijing100081China
| | - Yun‐Lai Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua UniversityBeijing100084China
| | - Shi‐Ying Zhang
- Central LaboratoryPeking University Hospital of StomatologyBeijing100081China
| | - Bei‐Bei Han
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua UniversityBeijing100084China
| | - Feng Chen
- Central LaboratoryPeking University Hospital of StomatologyBeijing100081China
| | - Yong‐Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua UniversityBeijing100084China
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10
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Zhu P, Franklin R, Vogel A, Stanisheuski S, Reardon P, Sluchanko NN, Beckman JS, Karplus PA, Mehl RA, Cooley RB. PermaPhos Ser : autonomous synthesis of functional, permanently phosphorylated proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.10.22.465468. [PMID: 34931187 PMCID: PMC8687462 DOI: 10.1101/2021.10.22.465468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Installing stable, functional mimics of phosphorylated amino acids into proteins offers a powerful strategy to study protein regulation. Previously, a genetic code expansion (GCE) system was developed to translationally install non-hydrolyzable phosphoserine (nhpSer), with the γ-oxygen replaced with carbon, but it has seen limited usage. Here, we achieve a 40-fold improvement in this system by engineering into Escherichia coli a biosynthetic pathway that produces nhpSer from the central metabolite phosphoenolpyruvate. Using this "PermaPhos Ser " system - an autonomous 21-amino acid E. coli expression system for incorporating nhpSer into target proteins - we show that nhpSer faithfully mimics the effects of phosphoserine in three stringent test cases: promoting 14-3-3/client complexation, disrupting 14-3-3 dimers, and activating GSK3β phosphorylation of the SARS-CoV-2 nucleocapsid protein. This facile access to nhpSer containing proteins should allow nhpSer to replace Asp and Glu as the go-to pSer phosphomimetic for proteins produced in E. coli .
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Affiliation(s)
- Phillip Zhu
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Rachel Franklin
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Amber Vogel
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Stanislau Stanisheuski
- Oregon State University, Department of Chemistry, 153 Gilbert Hall, Oregon State University, Corvallis, Oregon 97331
| | - Patrick Reardon
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Joseph S. Beckman
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
- e-MSion Inc., 2121 NE Jack London St, Corvallis, Oregon 97330
| | - P. Andrew Karplus
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Ryan A. Mehl
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
| | - Richard B. Cooley
- Oregon State University, Department of Biochemistry and Biophysics, 2011 Agricultural and Life Sciences, Corvallis, OR 97331
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11
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Mann G, Satish G, Sulkshane P, Mandal S, Glickman MH, Brik A. Synthesis and delivery of a stable phosphorylated ubiquitin probe to study ubiquitin conjugation in mitophagy. Chem Commun (Camb) 2021; 57:9438-9441. [PMID: 34528945 PMCID: PMC8445162 DOI: 10.1039/d1cc04045f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/10/2021] [Indexed: 12/13/2022]
Abstract
Protein post-translational modifications are involved in essentially all aspects of cellular signaling. Their dynamic nature and the difficulties in installing them using enzymatic approaches limits their direct study in human cells. Reported herein is the first synthesis, delivery and cellular study of a stable phosphoubiquitin probe. Our results compare Parkin's substrate preference during mitophagy via direct visualization of a phosphorylated ubiquitin probe in the cellular environment.
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Affiliation(s)
- Guy Mann
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Gandhesiri Satish
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Prasad Sulkshane
- Faculty of Biology, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Shaswati Mandal
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Michael H Glickman
- Faculty of Biology, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Haifa, 3200008, Israel.
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12
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Unremitting progresses for phosphoprotein synthesis. Curr Opin Chem Biol 2020; 58:96-111. [PMID: 32889414 DOI: 10.1016/j.cbpa.2020.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 02/03/2023]
Abstract
Phosphorylation, one of the important protein post-translational modifications, is involved in many essential cellular processes. Site-specifical and homogeneous phosphoproteins can be used as probes for elucidating the protein phosphorylation network and as potential therapeutics for interfering their involved biological events. However, the generation of phosphoproteins has been challenging owing to the limitation of chemical synthesis and protein expression systems. Despite the pioneering discoveries in phosphoprotein synthesis, over the past decade, great progresses in this field have also been made to promote the biofunctional exploration of protein phosphorylation largely. Therefore, in this review, we mainly summarize recent advances in phosphoprotein synthesis, which includes five sections: 1) synthesis of the nonhydrolyzable phosphorylated amino acid mimetic building blocks, 2) chemical total and semisynthesis strategy, 3) in-cell and in vitro genetic code expansion strategy, 4) the late-stage modification strategy, 5) nonoxygen phosphoprotein synthesis.
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13
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Kafarski P. Phosphonopeptides containing free phosphonic groups: recent advances. RSC Adv 2020; 10:25898-25910. [PMID: 35518575 PMCID: PMC9055344 DOI: 10.1039/d0ra04655h] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/02/2020] [Indexed: 11/21/2022] Open
Abstract
Phosphonopeptides are mimetics of peptides in which phosphonic acid or related (phosphinic, phosphonous etc.) group replaces either carboxylic acid group present at C-terminus, is located in the peptidyl side chain, or phosphonamidate or phosphinic acid mimics peptide bond. Acting as inhibitors of key enzymes related to variable pathological states they display interesting and useful physiologic activities with potential applications in medicine and agriculture. Since the synthesis and biological properties of peptides containing C-terminal diaryl phosphonates and those with phosphonic fragment replacing peptide bond were comprehensively reviewed, this review concentrate on peptides holding free, unsubstituted phosphonic acid moiety. There are two groups of such mimetics: (i) peptides in which aminophosphonic acid is located at C-terminus of the peptide chain with most of them (including antibiotics isolated from bacteria and fungi) exhibiting antimicrobial activity; (ii) non-hydrolysable analogues of phosphonoamino acids, which are useful tools to study physiologic effects of phosphorylations.
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Affiliation(s)
- Paweł Kafarski
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 50-305 Wrocław Poland
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14
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Steigenberger B, Pieters RJ, Heck AJR, Scheltema RA. PhoX: An IMAC-Enrichable Cross-Linking Reagent. ACS CENTRAL SCIENCE 2019; 5:1514-1522. [PMID: 31572778 PMCID: PMC6764163 DOI: 10.1021/acscentsci.9b00416] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Indexed: 05/02/2023]
Abstract
Chemical cross-linking mass spectrometry is rapidly emerging as a prominent technique to study protein structures. Structural information is obtained by covalently connecting peptides in close proximity by small reagents and identifying the resulting peptide pairs by mass spectrometry. However, substoichiometric reaction efficiencies render routine detection of cross-linked peptides problematic. Here, we present a new trifunctional cross-linking reagent, termed PhoX, which is decorated with a stable phosphonic acid handle. This makes the cross-linked peptides amenable to the well-established immobilized metal affinity chromatography (IMAC) enrichment. The handle allows for 300× enrichment efficiency and 97% specificity. We exemplify the approach on various model proteins and protein complexes, e.g., resulting in a structural model of the LRP1/RAP complex. Almost completely removing linear peptides allows PhoX, although noncleavable, to be applied to complex lysates. Focusing the database search to the 1400 most abundant proteins, we were able to identify 1156 cross-links in a single 3 h measurement.
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Affiliation(s)
- Barbara Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,
Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Department of Chemical Biology & Drug Discovery,
Utrecht Institute for Pharmaceutical Sciences, Utrecht
University, P.O. Box 80082, 3508 TB Utrecht, The
Netherlands
| | - Roland J. Pieters
- Department of Chemical Biology & Drug Discovery,
Utrecht Institute for Pharmaceutical Sciences, Utrecht
University, P.O. Box 80082, 3508 TB Utrecht, The
Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,
Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Phone: +31 30 253 6797. Fax: +31 30
253 69 18. E-mail:
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,
Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Phone: +31 30 253 45 64. Fax: +31 30
253 69 18. E-mail:
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15
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Duan HZ, Chen HX, Yu Q, Hu J, Li YM, Chen YX. Stereoselective synthesis of a phosphonate pThr mimetic via palladium-catalyzed γ-C(sp3)–H activation for peptide preparation. Org Biomol Chem 2019; 17:2099-2102. [DOI: 10.1039/c8ob02999g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a facile and efficient synthetic strategy toward a CH2-substituted phosphonate pThr mimetic and its application in phosphopeptide inhibitor synthesis.
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Affiliation(s)
- Hua-Zhen Duan
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Hong-Xue Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Qing Yu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Jun Hu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Yan-Mei Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Yong-Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
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16
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Chen HX, Kang J, Chang R, Zhang YL, Duan HZ, Li YM, Chen YX. Synthesis of α,α-Difluorinated Phosphonate pSer/pThr Mimetics via Rhodium-Catalyzed Asymmetric Hydrogenation of β-Difluorophosphonomethyl α-(Acylamino)acrylates. Org Lett 2018; 20:3278-3281. [DOI: 10.1021/acs.orglett.8b01151] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Hong-Xue Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jie Kang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Rong Chang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yun-Lai Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Hua-Zhen Duan
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yan-Mei Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yong-Xiang Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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