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Guo Q, Yang YX, Li DX, Ji XJ, Wu N, Wang YT, Ye C, Shi TQ. Advances in multi-enzyme co-localization strategies for the construction of microbial cell factory. Biotechnol Adv 2024; 77:108453. [PMID: 39278372 DOI: 10.1016/j.biotechadv.2024.108453] [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: 07/03/2024] [Revised: 09/05/2024] [Accepted: 09/10/2024] [Indexed: 09/18/2024]
Abstract
Biomanufacturing, driven by technologies such as synthetic biology, offers significant potential to advance the bioeconomy and promote sustainable development. It is anticipated to transform traditional manufacturing and become a key industry in future strategies. Cell factories are the core of biomanufacturing. The advancement of synthetic biology and growing market demand have led to the production of a greater variety of natural products and increasingly complex metabolic pathways. However, this progress also presents challenges, notably the conflict between natural product production and chassis cell growth. This conflict results in low productivity and yield, adverse side effects, metabolic imbalances, and growth retardation. Enzyme co-localization strategies have emerged as a promising solution. This article reviews recent progress and applications of these strategies in constructing cell factories for efficient natural product production. It comprehensively describes the applications of enzyme-based compartmentalization, metabolic pathway-based compartmentalization, and synthetic organelle-based compartmentalization in improving product titers. The article also explores future research directions and the prospects of combining multiple strategies with advanced technologies.
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Affiliation(s)
- Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Yu-Xin Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Dong-Xun Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Na Wu
- College of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China.
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China.
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2
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Levillayer L, Brighelli C, Demeret C, Sakuntabhai A, Bureau JF. Role of two modules controlling the interaction between SKAP1 and SRC kinases comparison with SKAP2 architecture and consequences for evolution. PLoS One 2024; 19:e0296230. [PMID: 38483858 PMCID: PMC10939263 DOI: 10.1371/journal.pone.0296230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
SRC kinase associated phosphoprotein 1 (SKAP1), an adaptor for protein assembly, plays an important role in the immune system such as stabilizing immune synapses. Understanding how these functions are controlled at the level of the protein-protein interactions is necessary to describe these processes and to develop therapeutics. Here, we dissected the SKAP1 modular organization to recognize SRC kinases and compared it to that of its paralog SRC kinase associated phosphoprotein 2 (SKAP2). Different conserved motifs common to either both proteins or specific to SKAP2 were found using this comparison. Two modules harboring different binding properties between SKAP1 and SKAP2 were identified: one composed of two conserved motifs located in the second interdomain interacting at least with the SH2 domain of SRC kinases and a second one composed of the DIM domain modulated by the SH3 domain and the activation of SRC kinases. This work suggests a convergent evolution of the binding properties of some SRC kinases interacting specifically with either SKAP1 or SKAP2.
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Affiliation(s)
- Laurine Levillayer
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
| | - Camille Brighelli
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
| | - Caroline Demeret
- Institut Pasteur, Université de Paris-Cité, Laboratoire Interactomique, ARN et Immunité ‐ Interactomics, RNA and Immunity, Paris, France
| | - Anavaj Sakuntabhai
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
| | - Jean-François Bureau
- Institut Pasteur, Institut National de Recherche pour l’Agriculture, Université de Paris-Cité, CNRS UMR 2000, l’Alimentation et l’Environnement (INRAE) USC 1510, Unité Écologie et Émergence des Pathogènes Transmis par les Arthropodes (EEPTA), Paris, France
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3
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Bashyal A, Brodbelt JS. Uncommon posttranslational modifications in proteomics: ADP-ribosylation, tyrosine nitration, and tyrosine sulfation. MASS SPECTROMETRY REVIEWS 2024; 43:289-326. [PMID: 36165040 PMCID: PMC10040477 DOI: 10.1002/mas.21811] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Posttranslational modifications (PTMs) are covalent modifications of proteins that modulate the structure and functions of proteins and regulate biological processes. The development of various mass spectrometry-based proteomics workflows has facilitated the identification of hundreds of PTMs and aided the understanding of biological significance in a high throughput manner. Improvements in sample preparation and PTM enrichment techniques, instrumentation for liquid chromatography-tandem mass spectrometry (LC-MS/MS), and advanced data analysis tools enhance the specificity and sensitivity of PTM identification. Highly prevalent PTMs like phosphorylation, glycosylation, acetylation, ubiquitinylation, and methylation are extensively studied. However, the functions and impact of less abundant PTMs are not as well understood and underscore the need for analytical methods that aim to characterize these PTMs. This review focuses on the advancement and analytical challenges associated with the characterization of three less common but biologically relevant PTMs, specifically, adenosine diphosphate-ribosylation, tyrosine sulfation, and tyrosine nitration. The advantages and disadvantages of various enrichment, separation, and MS/MS techniques utilized to identify and localize these PTMs are described.
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Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
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4
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Martyn GD, Veggiani G, Sidhu SS. Engineering SH2 Domains with Tailored Specificities and Affinities. Methods Mol Biol 2023; 2705:307-348. [PMID: 37668982 DOI: 10.1007/978-1-0716-3393-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The Src Homology 2 (SH2) domain is an emerging biotechnology with applications in basic science, drug discovery, and even diagnostics. The SH2 domains rapid uptake into different areas of research is a direct result of the wealth of information generated on its biochemical, biological, and biophysical role in mammalian cell biology. Functionally, the SH2 domain binds and recognizes specific phosphotyrosine (pTyr) residues in the cell to mediate protein-protein interactions (PPIs) that govern signal transduction networks. These signal transduction networks are responsible for relaying growth and stress state signals to the cell's nucleus, ultimately effecting a change in cell biology. Protein engineers have been able to increase the affinity of SH2 domains for pTyr while also tailoring the domains' specificity to unique amino acid sequences flanking the pTyr residue. In this way, it has been possible to develop unique SH2 variants for use in affinity-purification coupled to mass spectrometry (AP-MS) experiments, microscopy, or even synthetic biology. This chapter outlines methods to tailor the affinity and specificity of virtually any human SH2 domain using a combination of rational engineering and phage-display approaches.
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Affiliation(s)
- Gregory D Martyn
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Gianluca Veggiani
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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5
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Waldrop SP, Niu W, Guo J. Engineering of SH2 Domains for the Recognition of Protein Tyrosine O-Sulfation Sites. Methods Mol Biol 2023; 2705:293-305. [PMID: 37668981 DOI: 10.1007/978-1-0716-3393-9_16] [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] [Indexed: 09/06/2023]
Abstract
Protein engineering has brought advances to industrial processes, biomaterials, nanotechnology, biosensors, and biomedical applications. This chapter will focus on the engineering of Src Homology 2 domains (SH2) to act as an antibody mimetic for the recognition of sulfotyrosine-containing peptides or proteins. In comparison to anti-sulfotyrosine antibodies, SH2 mutants have much smaller size and can be heterologously expressed and purified in large quantity at low cost. This chapter will describe the use of phage display to identify a sulfotyrosine-binding SH2 mutant and the subsequent enrichment of sulfotyrosine-containing peptides in complex biological samples.
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Affiliation(s)
- Sean Paul Waldrop
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA.
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6
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Stewart V, Ronald PC. Sulfotyrosine residues: interaction specificity determinants for extracellular protein-protein interactions. J Biol Chem 2022; 298:102232. [PMID: 35798140 PMCID: PMC9372746 DOI: 10.1016/j.jbc.2022.102232] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
Tyrosine sulfation, a post-translational modification, can determine and often enhance protein–protein interaction specificity. Sulfotyrosyl residues (sTyrs) are formed by the enzyme tyrosyl-protein sulfotransferase during protein maturation in the Golgi apparatus and most often occur singly or as a cluster within a six-residue span. With both negative charge and aromatic character, sTyr facilitates numerous atomic contacts as visualized in binding interface structural models, thus there is no discernible binding site consensus. Found exclusively in secreted proteins, in this review, we discuss the four broad sequence contexts in which sTyr has been observed: first, a solitary sTyr has been shown to be critical for diverse high-affinity interactions, such as between peptide hormones and their receptors, in both plants and animals. Second, sTyr clusters within structurally flexible anionic segments are essential for a variety of cellular processes, including coreceptor binding to the HIV-1 envelope spike protein during virus entry, chemokine interactions with receptors, and leukocyte rolling cell adhesion. Third, a subcategory of sTyr clusters is found in conserved acidic sequences termed hirudin-like motifs that enable proteins to interact with thrombin; consequently, many proven and potential therapeutic proteins derived from blood-consuming invertebrates depend on sTyrs for their activity. Finally, several proteins that interact with collagen or similar proteins contain one or more sTyrs within an acidic residue array. Refined methods to direct sTyr incorporation in peptides synthesized both in vitro and in vivo, together with continued advances in mass spectrometry and affinity detection, promise to accelerate discoveries of sTyr occurrence and function.
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Affiliation(s)
- Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, USA.
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, USA; Genome Center, University of California, Davis, USA.
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Zhao D, Li C, Jiang H, Yin Y, Zhou C, Huang H, Qi Y, Li L. Engineering of Src Homology 2 Domain Leading to Sulfotyrosine Recognition With a High Affinity by Integrating a Distinctive Selection Theme and Next-Generation Sequencing. Front Microbiol 2022; 13:901558. [PMID: 35722314 PMCID: PMC9204161 DOI: 10.3389/fmicb.2022.901558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Tyrosine sulfation plays a vital role in various biochemical reactions. Although sulfated tyrosine (sTyr) has a similar structure to phosphotyrosine (pTyr), the number of available sTyr sites is significantly less than that of pTyr sites, mainly because of the lack of effective sTyr probes. A few sTyr binders were identified on the basis of structural similarity by engineering the pTyr-binding pocket of an Src Homology 2 (SH2) domain through phage selections against sTyr peptides. Nevertheless, they still interact with pTyr peptides with comparable affinity. This study aims to identify sTyr superbinders using the SH2 domain as a template. We created a distinctive phage selection scheme that separately covered selections against sTyr and pTyr peptides, followed by next-generation sequencing (NGS). After selections, phage pools showed strong enzyme-linked immunosorbent assay (ELISA) signal intensities for both modified peptides, indicating that the variants evolved with a high affinity for these peptides, which causes difficulty in identifying sTyr-specific binders. In contrast, NGS data from selected pools showed significant differences, suggesting the enrichment of sTyr-specific variants during selections. Accordingly, we obtained the sTyr features based on NGS data analysis and prioritized a few potential sTyr binders. The variant SH2-4 showed a stronger affinity for sTyr than pTyr and was superior to previous sTyr binders as measured by the Biolayer Interferometry assay. In summary, we described the strategy of integrating NGS data mining with a novel selection scheme to identify sTyr superbinders.
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Affiliation(s)
- Dongping Zhao
- School of Basic Medicine, Qingdao University, Qingdao, China
- Department of Drug Discovery, Noventi Biopharmaceuticals Co., Ltd., Shanghai, China
| | - Chan Li
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Haoqiang Jiang
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Yuqing Yin
- Department of Drug Discovery, Noventi Biopharmaceuticals Co., Ltd., Shanghai, China
| | | | - Haiming Huang
- Department of Drug Discovery, Noventi Biopharmaceuticals Co., Ltd., Shanghai, China
| | - Yunkun Qi
- School of Pharmacy, Qingdao University, Qingdao, China
- *Correspondence: Yunkun Qi,
| | - Lei Li
- School of Basic Medicine, Qingdao University, Qingdao, China
- Lei Li,
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8
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Lawrie J, Waldrop S, Morozov A, Niu W, Guo J. Engineering of a Small Protein Scaffold To Recognize Sulfotyrosine with High Specificity. ACS Chem Biol 2021; 16:1508-1517. [PMID: 34251168 DOI: 10.1021/acschembio.1c00382] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein tyrosine O-sulfation is an essential post-translational modification required for effective biological processes such as hemostasis, inflammatory response, and visual phototransduction. Because of its unstable nature under mass spectrometry conditions and residing on low-abundance cell surface proteins, sulfated tyrosine (sulfotyrosine) residues are difficult to detect or analyze. Enrichment of sulfotyrosine-containing proteins (sulfoproteins) from complex biological samples are typically required before analysis. In this work, we seek to engineer the phosphotyrosine binding pocket of a Src Homology 2 (SH2) domain to act as an antisulfotyrosine antibody mimic. Using tailored selection schemes, several SH2 mutants are identified with high affinity and specificity to sulfotyrosine. Further molecular docking simulations highlight potential mechanisms supporting observed characteristics of these SH2 mutants. Utilities of the evolved SH2 mutants were demonstrated by the detection and enrichment of sulfoproteins.
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Affiliation(s)
- Justin Lawrie
- Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Sean Waldrop
- Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Anya Morozov
- Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska−Lincoln, Lincoln, Nebraska 68588, United States
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9
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Zhou XX, Bracken CJ, Zhang K, Zhou J, Mou Y, Wang L, Cheng Y, Leung KK, Wells JA. Targeting Phosphotyrosine in Native Proteins with Conditional, Bispecific Antibody Traps. J Am Chem Soc 2020; 142:17703-17713. [PMID: 32924468 DOI: 10.1021/jacs.0c08458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Engineering sequence-specific antibodies (Abs) against phosphotyrosine (pY) motifs embedded in folded polypeptides remains highly challenging because of the stringent requirement for simultaneous recognition of the pY motif and the surrounding folded protein epitope. Here, we present a method named phosphotyrosine Targeting by Recombinant Ab Pair, or pY-TRAP, for in vitro engineering of binders for native pY proteins. Specifically, we create the pY protein by unnatural amino acid misincorporation, mutagenize a universal pY-binding Ab to create a first binder B1 for the pY motif on the pY protein, and then select against the B1-pY protein complex for a second binder B2 that recognizes the composite epitope of B1 and the pY-containing protein complex. We applied pY-TRAP to create highly specific binders to folded Ub-pY59, a rarely studied Ub phosphoform exclusively observed in cancerous tissues, and ZAP70-pY248, a kinase phosphoform regulated in feedback signaling pathways in T cells. The pY-TRAPs do not have detectable binding to wild-type proteins or to other pY peptides or proteins tested. This pY-TRAP approach serves as a generalizable method for engineering sequence-specific Ab binders to native pY proteins.
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Affiliation(s)
- Xin X Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Colton J Bracken
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Kaihua Zhang
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States
| | - Jie Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Yun Mou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States.,Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
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10
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Lawrie J, Niu W, Guo J. Engineering of a sulfotyrosine-recognizing small protein scaffold for the study of protein tyrosine O-sulfation. Methods Enzymol 2019; 622:67-89. [PMID: 31155066 DOI: 10.1016/bs.mie.2019.02.004] [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: 12/21/2022]
Abstract
Protein tyrosine O-sulfation is considered as one of the most common types of posttranslational modification of tyrosine in nature. The introduction of a negatively charged sulfate group plays crucial roles in extracellular biomolecular interactions that dictate various cellular processes, including cell adhesion, leukocyte trafficking, hormone activities, and immune responses. Despite substantial advances in our knowledge about protein tyrosine O-sulfation in recent years, our understanding of its biological significance is still in its infancy. This is largely hindered by a chronic lack of suitable biochemical tools. We seek to meet this challenge by engineering a small protein scaffold that can recognize sulfated tyrosine (sulfotyrosine) residues with high affinity. In this chapter, we describe the directed evolution of a Src Homology 2 (SH2) domain to recognize sulfotyrosine. In the first part, the design strategy for the phage display of SH2 variants is discussed. In the second part, the techniques required for phage propagation and selection are described. The evolved SH2 variants are characterized and validated in vitro through fluorescence polarization assays. Finally, the evolved SH2 domain mutants are applied to the visualization of sulfated proteins on the cell surface.
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Affiliation(s)
- Justin Lawrie
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States.
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States.
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11
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CCR7 Sulfotyrosine Enhances CCL21 Binding. Int J Mol Sci 2017; 18:ijms18091857. [PMID: 28841151 PMCID: PMC5618506 DOI: 10.3390/ijms18091857] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 01/05/2023] Open
Abstract
Chemokines are secreted proteins that direct the migration of immune cells and are involved in numerous disease states. For example, CCL21 (CC chemokine ligand 21) and CCL19 (CC chemokine ligand 19) recruit antigen-presenting dendritic cells and naïve T-cells to the lymph nodes and are thought to play a role in lymph node metastasis of CCR7 (CC chemokine receptor 7)-expressing cancer cells. For many chemokine receptors, N-terminal posttranslational modifications, particularly the sulfation of tyrosine residues, increases the affinity for chemokine ligands and may contribute to receptor ligand bias. Chemokine sulfotyrosine (sY) binding sites are also potential targets for drug development. In light of the structural similarity between sulfotyrosine and phosphotyrosine (pY), the interactions of CCL21 with peptide fragments of CCR7 containing tyrosine, pY, or sY were compared using protein NMR (nuclear magnetic resonance) spectroscopy in this study. Various N-terminal CCR7 peptides maintain binding site specificity with Y8-, pY8-, or sY8-containing peptides binding near the α-helix, while Y17-, pY17-, and sY17-containing peptides bind near the N-loop and β3-stand of CCL21. All modified CCR7 peptides showed enhanced binding affinity to CCL21, with sY having the largest effect.
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12
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Abstract
Fluorescent proteins of different colors are useful probes to study protein structure and function, and to investigate cellular events and conditions. Large efforts have focused on engineering new properties into fluorescent proteins via rational design and directed evolution. In addition to applications in imaging of protein expression level and subcellular localization, fluorescent proteins have been increasingly engineered to act as biosensors to track concentrations of small-molecule metabolites, enzyme activities, and protein conformational changes in living cells. Unlike small-molecule fluorescence biosensors, fluorescent proteins are genetically encodable, and thus can be expressed inside living cells. Attachment of organelle-specific signals to the proteins allows their localization to be specified. Recently, a new class of fluorescent protein biosensors has been developed to include unnatural amino acids as the sensing element. The unique chemical and physical properties of the unnatural amino acids enable sensor designs that cannot be realized by using the standard genetic code with the 20 canonical amino acids. In this chapter, we detail the general procedure for the genetic incorporation of unnatural amino acids. We further present two protocols for the in vitro and in vivo detection of hydrogen peroxide (H2O2) using a fluorescent protein biosensor that contains an unnatural amino acid, p-boronophenylalanine.
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Affiliation(s)
- Wei Niu
- University of Nebraska-Lincoln, Lincoln, NE, United States.
| | - Jiantao Guo
- University of Nebraska-Lincoln, Lincoln, NE, United States.
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