1
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A chemogenetic platform for controlling plasma membrane signaling and synthetic signal oscillation. Cell Chem Biol 2022; 29:1446-1464.e10. [PMID: 35835118 DOI: 10.1016/j.chembiol.2022.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/22/2022] [Accepted: 06/20/2022] [Indexed: 12/31/2022]
Abstract
Chemogenetic methods enabling the rapid translocation of specific proteins to the plasma membrane (PM) in a single protein-single ligand manner are useful tools in cell biology. We recently developed a technique, in which proteins fused to an Escherichia coli dihydrofolate reductase (eDHFR) variant carrying N-terminal hexalysine residues are recruited from the cytoplasm to the PM using the synthetic myristoyl-d-Cys-tethered trimethoprim (mDcTMP) ligand. However, this system achieved PM-specific translocation only when the eDHFR tag was fused to the N terminus of proteins, thereby limiting its application. In this report, we engineered a universal PM-targeting tag for mDcTMP-induced protein translocation by grafting the hexalysine motif into an intra-loop region of eDHFR. We demonstrate the broad applicability of the new loop-engineered eDHFR tag and mDcTMP pair for conditional PM recruitment and activation of various tag-fused signaling proteins with different fusion configurations and for reversibly and repeatedly controlling protein localization to generate synthetic signal oscillations.
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2
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Ma C, Jiang C, Zhao D, Li S, Li R, Li L. Development in Detection Methods for the Expression of Surface-Displayed Proteins. Front Microbiol 2022; 13:899578. [PMID: 35558116 PMCID: PMC9085562 DOI: 10.3389/fmicb.2022.899578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/07/2022] [Indexed: 11/29/2022] Open
Abstract
Directed evolution is a widely-used engineering strategy for improving the stabilities or biochemical functions of proteins by repeated rounds of mutation and selection. A protein of interest is selected as the template and expressed on a molecular display platform such as a bacteriophage for engineering. Initially, the surface-displayed protein template needs to be checked against the desired target via ELISA to examine whether the functions of the displayed template remain intact. The ELISA signal is subject to the protein-target binding affinity. A low-affinity results in a weak ELISA signal which makes it difficult to determine whether the weak signal is because of low affinity or because of poor expression of the protein. Using a methyllysine-binding chromodomain protein Cbx1 that weakly binds to the histone H3K9me3 peptide, we developed and compared three different approaches to increase the signal-to-background ratio of ELISA measurements. We observed that the specific peptide-binding signal was enhanced by increasing the Cbx1 phage concentration on the ELISA plate. The introduction of previously known gain-of-function mutations to the Cbx1 protein significantly increased the ELISA signals. Moreover, we demonstrated that the H3K9me3-specific binding signal was enhanced by fusing Cbx1 with a high-affinity phosphotyrosine-binding protein and by coating the ELISA plate with a mixture of H3K9me3 and phosphotyrosine peptides. This approach also worked with binding to a lower affinity momomethyllysine peptide H3K9me1. These approaches may help improve ELISA experiments when dealing with low-affinity ligand-protein interactions.
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Affiliation(s)
- Chenglong Ma
- College of Life Sciences, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Chunyang Jiang
- School of Basic Medicine, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Dongping Zhao
- School of Basic Medicine, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Shuhao Li
- School of Basic Medicine, Qingdao Medical College, Qingdao University, Qingdao, China
| | - Ronggui Li
- College of Life Sciences, Qingdao University, Qingdao, China
| | - Lei Li
- School of Basic Medicine, Qingdao Medical College, Qingdao University, Qingdao, China
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3
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Fan M, Pan T, Jin W, Sun J, Zhang S, Du Y, Chen X, Chen Q, Xu W, Choo SW, Zhu G, Chen Y, Zhou J. FGF4, A New Potential Regulator in Gestational Diabetes Mellitus. Front Pharmacol 2022; 13:827617. [PMID: 35317005 PMCID: PMC8934430 DOI: 10.3389/fphar.2022.827617] [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: 12/02/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Gestational diabetes mellitus (GDM) is associated with adverse maternal and neonatal outcomes, however the underlying mechanisms remain elusive. The aim of this study was to find efficient regulator of FGFs in response to the pathogenesis of GDM and explore the role of the FGFs in GDM.Methods: We performed a systematic screening of placental FGFs in GDM patients and further in two different GDM mouse models to investigate their expression changes. Significant changed FGF4 was selected, engineered, purified, and used to treat GDM mice in order to examine whether it can regulate the adverse metabolic phenotypes of the diabetic mice and protect their fetus.Results: We found FGF4 expression was elevated in GDM patients and its level was positively correlated to blood glucose, indicating a physiological relevance of FGF4 with respect to the development of GDM. Recombinant FGF4 (rFGF4) treatment could effectively normalize the adverse metabolic phenotypes in high fat diet induced GDM mice but not in STZ induced GDM mice. However, rFGF4 was highly effective in reduce of neural tube defects (NTDs) of embryos in both the two GDM models. Mechanistically, rFGF4 treatment inhibits pro-inflammatory signaling cascades and neuroepithelial cell apoptosis of both GDM models, which was independent of glucose regulation.Conclusions/interpretation: Our study provides novel insight into the important roles of placental FGF4 and suggests that it may serve as a promising diagnostic factor and therapeutic target for GDM.
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Affiliation(s)
- Miaojuan Fan
- Department of Infectious Diseases & Zhejiang Provincial Key laboratory of Liver Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- Baoji Maternal and Child Health Hospital, Baoji, China
| | - Tongtong Pan
- Department of Infectious Diseases & Zhejiang Provincial Key laboratory of Liver Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wei Jin
- Department of Infectious Diseases & Zhejiang Provincial Key laboratory of Liver Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Jian Sun
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shujun Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yali Du
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xinwei Chen
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qiong Chen
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Wenxin Xu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Siew Woh Choo
- College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Guanghui Zhu
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Guanghui Zhu, ; Yongping Chen, ; Jie Zhou,
| | - Yongping Chen
- Department of Infectious Diseases & Zhejiang Provincial Key laboratory of Liver Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Guanghui Zhu, ; Yongping Chen, ; Jie Zhou,
| | - Jie Zhou
- Department of Infectious Diseases & Zhejiang Provincial Key laboratory of Liver Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Guanghui Zhu, ; Yongping Chen, ; Jie Zhou,
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4
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Yasui N, Nakamura K, Yamashita A. A sweet protein monellin as a non-antibody scaffold for synthetic binding proteins. J Biochem 2021; 169:585-599. [PMID: 33386843 DOI: 10.1093/jb/mvaa147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022] Open
Abstract
Synthetic binding proteins that have the ability to bind with molecules can be generated using various protein domains as non-antibody scaffolds. These designer proteins have been used widely in research studies, as their properties overcome the disadvantages of using antibodies. Here, we describe the first application of a phage display to generate synthetic binding proteins using a sweet protein, monellin, as a non-antibody scaffold. Single-chain monellin (scMonellin), in which two polypeptide chains of natural monellin are connected by a short linker, has two loops on one side of the molecule. We constructed phage display libraries of scMonellin, in which the amino acid sequence of the two loops is diversified. To validate the performance of these libraries, we sorted them against the folding mutant of the green fluorescent protein variant (GFPuv) and yeast small ubiquitin-related modifier. We successfully obtained scMonellin variants exhibiting moderate but significant affinities for these target proteins. Crystal structures of one of the GFPuv-binding variants in complex with GFPuv revealed that the two diversified loops were involved in target recognition. scMonellin, therefore, represents a promising non-antibody scaffold in the design and generation of synthetic binding proteins. We termed the scMonellin-derived synthetic binding proteins 'SWEEPins'.
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Affiliation(s)
- Norihisa Yasui
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Kazuaki Nakamura
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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5
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Wang W, Miao Y, Sui S, Wang Y, Wu S, Cao Q, Duan H, Qi X, Zhou Q, Pan X, Zhang J, Chen X, Han Y, Wang N, Kuehn MH, Zhu W. Xeno- and Feeder-Free Differentiation of Human iPSCs to Trabecular Meshwork-Like Cells by Recombinant Cytokines. Transl Vis Sci Technol 2021; 10:27. [PMID: 34015102 PMCID: PMC8142710 DOI: 10.1167/tvst.10.6.27] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Purpose Stem cell-based therapy has the potential to become one approach to regenerate the damaged trabecular meshwork (TM) in glaucoma. Co-culture of induced pluripotent stem cells (iPSCs) with human TM cells has been a successful approach to generate autologous TM resembling cells. However, the differentiated cells generated using this approach are still problematic for clinical usage. This study aimed to develop a clinically applicable strategy for generating TM-like cells from iPSCs. Methods Highly expressed receptors during iPSC differentiation were identified by AutoSOME, Gene Ontology, and reverse transcription polymerase chain reaction (RT-PCR) analysis. The recombinant cytokines that bind to these receptors were used to generate a new differentiation protocol. The resultant TM-like cells were characterized morphologically, immunohistochemically, and transcriptionally. Results We first determined two stages of iPSC differentiation and identified highly expressed receptors associated with the differentiation at each stage. The expression of these receptors was further confirmed by RT-PCR analysis. Exposure to the recombinant cytokines that bind to these receptors, including transforming growth factor beta 1, nerve growth factor beta, erythropoietin, prostaglandin F2 alpha, and epidermal growth factor, can efficiently differentiate iPSCs into TM-like cells, which express TM biomarkers and can form dexamethasone-inducible CLANs. Conclusions We successfully generated a xeno- and feeder-free differentiation protocol with recombinant cytokines to generate the TM progenitor and TM-like cells from human iPSCs. Translational Relevance The new approach minimizes the risks from contamination and also improves the differentiation efficiency and consistency, which are particularly crucial for clinical use of stem cells in glaucoma treatment.
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Affiliation(s)
- Wenyan Wang
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Yongzhen Miao
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China
| | - Shangru Sui
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China
| | - Yanan Wang
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Shen Wu
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital Eye Center, Beijing, China
| | - Qilong Cao
- Qingdao Haier Biotech Co. Ltd., Qingdao, China
| | - Haoyun Duan
- Qingdao Eye Hospital, Shandong Eye Institute, Shandong Academy of Medical Sciences, Qingdao, China
| | - Xia Qi
- Qingdao Eye Hospital, Shandong Eye Institute, Shandong Academy of Medical Sciences, Qingdao, China
| | - Qingjun Zhou
- Qingdao Eye Hospital, Shandong Eye Institute, Shandong Academy of Medical Sciences, Qingdao, China
| | - Xiaojing Pan
- Qingdao Eye Hospital, Shandong Eye Institute, Shandong Academy of Medical Sciences, Qingdao, China
| | - Jingxue Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital Eye Center, Beijing, China
| | - Xuehong Chen
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Yantao Han
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Ningli Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital Eye Center, Beijing, China
| | - Markus H Kuehn
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA.,Center for the Prevention and Treatment of Visual Loss, Iowa City Veterans Affairs Medical Center, Iowa City, IA, USA
| | - Wei Zhu
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China.,Advanced Innovation Center for Big Data-Based Precision Medicine, Beijing University of Aeronautics and Astronautics-Capital Medical University, Beijing, China
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6
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Nian Q, Zeng J, He L, Chen Y, Zhang Z, Rodrigues-Lima F, Zhao L, Feng X, Shi J. A small molecule inhibitor targeting SHP2 mutations for the lung carcinoma. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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7
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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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8
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Abstract
Proteins are versatile macromolecules with diverse structure, charge, and function. They are ideal building blocks for biomaterials for drug delivery, biosensing, or tissue engineering applications. Simultaneously, the need to develop green alternatives to chemical processes has led to renewed interest in multienzyme biocatalytic routes to fine, specialty, and commodity chemicals. Therefore, a method to reliably assemble protein complexes using protein-protein interactions would facilitate the rapid production of new materials. Here we show a method for modular assembly of protein materials using a supercharged protein as a scaffolding "hub" onto which target proteins bearing oppositely charged domains have been self-assembled. The physical properties of the material can be tuned through blending and heating and disassembly triggered using changes in pH or salt concentration. The system can be extended to the synthesis of living materials. Our modular method can be used to reliably direct the self-assembly of proteins using small charged tag domains that can be easily encoded in a fusion protein.
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Affiliation(s)
- James A. J. Arpino
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Karen Marie Polizzi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
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9
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Wang C, Gong Z, Huang X, Wang J, Xia K, Ying L, Shu J, Yu C, Zhou X, Li F, Liang C, Chen Q. An injectable heparin-Laponite hydrogel bridge FGF4 for spinal cord injury by stabilizing microtubule and improving mitochondrial function. Am J Cancer Res 2019; 9:7016-7032. [PMID: 31660084 PMCID: PMC6815951 DOI: 10.7150/thno.37601] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 07/25/2019] [Indexed: 12/13/2022] Open
Abstract
Rationale: Spinal cord injury (SCI) remains a critical clinical challenge. The controlled release of FGF4, a novel neuroprotective factor, from a versatile Laponite hydrogel to the injured site was a promising strategy to promote axon regeneration and motor functional recovery after SCI. Methods: Characterization of Laponite, Laponite/Heparin (Lap/Hep) and Laponite/Heparin loaded with FGF4 (Lap/Hep@FGF4) hydrogels were measured by rheometer. Multiple comprehensive evaluations were used to detect motor functional recovery and the axonal rehabilitation after Lap/Hep@FGF4 treatment in vivo (SCI rat model). Moreover, microtubule dynamic and energy transportation, which regulated axonal regeneration was evaluated by Lap/Hep@FGF4 gel in vitro (primary neuron). Results: FGF4 released from Lap/Hep gel locally achieves strong protection and regeneration after SCI. The Lap/Hep@FGF4 group revealed remarkable motor functional recovery and axonal regrowth after SCI through suppressing inflammatory reaction, increasing remyelination and reducing glial/fibrotic scars. Furthermore, the underlying mechanism of axonal rehabilitation were demonstrated via enhancing microtubule stability and regulating mitochondrial localization after Lap/Hep@FGF4 treatment. Conclusion: This promising sustained release system provides a synergistic effective approach to enhance recovery after SCI underlying a novel mechanism of axonal rehabilitation, and shows a translational prospect for the clinical treatment of SCI.
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10
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Hober S, Lindbo S, Nilvebrant J. Bispecific applications of non-immunoglobulin scaffold binders. Methods 2019; 154:143-152. [DOI: 10.1016/j.ymeth.2018.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/24/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
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11
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Liu H, Huang H, Voss C, Kaneko T, Qin WT, Sidhu S, Li SSC. Surface Loops in a Single SH2 Domain Are Capable of Encoding the Spectrum of Specificity of the SH2 Family. Mol Cell Proteomics 2019; 18:372-382. [PMID: 30482845 PMCID: PMC6356082 DOI: 10.1074/mcp.ra118.001123] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/05/2018] [Indexed: 12/15/2022] Open
Abstract
Src homology 2 (SH2) domains play an essential role in cellular signal transduction by binding to proteins phosphorylated on Tyr residue. Although Tyr phosphorylation (pY) is a prerequisite for binding for essentially all SH2 domains characterized to date, different SH2 domains prefer specific sequence motifs C-terminal to the pY residue. Because all SH2 domains adopt the same structural fold, it is not well understood how different SH2 domains have acquired the ability to recognize distinct sequence motifs. We have shown previously that the EF and BG loops that connect the secondary structure elements on an SH2 domain dictate its specificity. In this study, we investigated if these surface loops could be engineered to encode diverse specificities. By characterizing a group of SH2 variants selected by different pY peptides from phage-displayed libraries, we show that the EF and BG loops of the Fyn SH2 domain can encode a wide spectrum of specificities, including all three major specificity classes (p + 2, p + 3 and p + 4) of the SH2 domain family. Furthermore, we found that the specificity of a given variant correlates with the sequence feature of the bait peptide used for its isolation, suggesting that an SH2 domain may acquire specificity by co-evolving with its ligand. Intriguingly, we found that the SH2 variants can employ a variety of different mechanisms to confer the same specificity, suggesting the EF and BG loops are highly flexible and adaptable. Our work provides a plausible mechanism for the SH2 domain to acquire the wide spectrum of specificity observed in nature through loop variation with minimal disturbance to the SH2 fold. It is likely that similar mechanisms may have been employed by other modular interaction domains to generate diversity in specificity.
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Affiliation(s)
- Huadong Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China;; Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1
| | - Haiming Huang
- Donnelly Centre for Cellular and Biomolecular Research, 160 College St., Toronto ON M5S 3E1, Canada
| | - Courtney Voss
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1
| | - Tomonori Kaneko
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1
| | - Wen Tao Qin
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1
| | - Sachdev Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, 160 College St., Toronto ON M5S 3E1, Canada.
| | - Shawn S-C Li
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1;.
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12
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Wang R, Leung PYM, Huang F, Tang Q, Kaneko T, Huang M, Li Z, Li SSC, Wang Y, Xia J. Reverse Binding Mode of Phosphotyrosine Peptides with SH2 Protein. Biochemistry 2018; 57:5257-5269. [PMID: 30091902 DOI: 10.1021/acs.biochem.8b00677] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Discerning the different interaction states during dynamic protein-ligand binding is difficult. Here we apply site-specific cysteine-α-chloroacetyl cross-linking to scrutinize the binding between the Src homology 2 (SH2) domain and phosphotyrosine (pY) peptides, a highly dynamic interaction that is a key to cellular signal transduction. From a model SH2 protein to a set of representative SH2 domains, we showed here that a proximity-induced cysteine-α-chloroacetyl reaction cross-linked two spatially adjacent chemical groups as a result of the binding interaction, and reciprocally, the information about the interaction states can be deduced from the cross-linked products. To our surprise, we found SH2 domains can adopt a reverse binding mode with "single-pronged", "two-pronged", and "half" pY peptides. This finding was further supported by a set of 500 ns molecular dynamics simulations. This serendipitous finding defies the canonical theory of SH2 binding, suggests a possible answer about the source of the versatility of SH2 signaling, and sets a model for other protein binding interactions.
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Affiliation(s)
- Rui Wang
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
| | | | | | | | - Tomonori Kaneko
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
| | - Mei Huang
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
| | - Zigang Li
- School of Chemical Biology and Biotechnology , Shenzhen Graduate School of Peking University , Shenzhen 518055 , China
| | - Shawn S C Li
- Department of Biochemistry and Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry , Western University , London , Ontario N6A 5C1 , Canada
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13
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SHP2-Mediated Signal Networks in Stem Cell Homeostasis and Dysfunction. Stem Cells Int 2018; 2018:8351374. [PMID: 29983715 PMCID: PMC6015663 DOI: 10.1155/2018/8351374] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/16/2018] [Accepted: 05/28/2018] [Indexed: 12/17/2022] Open
Abstract
Stem cells, including embryonic stem cells (ESCs) and adult stem cells, play a central role in mammal organism development and homeostasis. They have two unique properties: the capacity for self-renewal and the ability to differentiate into many specialized cell types. Src homology region 2- (SH2-) containing protein tyrosine phosphatase 2 (SHP-2), a nonreceptor protein tyrosine phosphatase encoded by protein tyrosine phosphatase nonreceptor type 11 gene (PTPN11), regulates multicellular differentiation, proliferation, and survival through numerous conserved signal pathways. Gain-of-function (GOF) or loss-of-function (LOF) SHP2 in various cells, especially for stem cells, disrupt organism self-balance and lead to a plethora of diseases, such as cancer, maldevelopment, and excessive hyperblastosis. However, the exact mechanisms of SHP2 dysfunction in stem cells remain unclear. In this review, we intended to raise the attention and clarify the framework of SHP2-mediated signal pathways in various stem cells. Establishment of integrated signal architecture, from ESCs to adult stem cells, will help us to understand the changes of dynamic, multilayered pathways in response to SHP2 dysfunction. Overall, better understanding the functions of SHP2 in stem cells provides a new avenue to treat SHP2-associated diseases.
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14
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Next-generation antibodies for post-translational modifications. Curr Opin Struct Biol 2018; 51:141-148. [PMID: 29753204 DOI: 10.1016/j.sbi.2018.04.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 04/24/2018] [Indexed: 01/08/2023]
Abstract
Despite increasing demands for antibodies to post-translational modifications (PTMs), fundamental difficulties in molecular recognition of PTMs hinder the generation of highly functional anti-PTM antibodies using conventional methods. Recently, advanced approaches in protein engineering and design that have been established for biologics development were applied to successfully generating highly functional anti-PTM antibodies. Furthermore, structural analyses of anti-PTM antibodies revealed unprecedented binding modes that substantially increased the antigen-binding surface. These features deepen the understanding of mechanisms underlying specific recognition of PTMs, which may lead to more effective approaches for generating anti-PTM antibodies with exquisite specificity and high affinity.
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15
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Hale AJ, den Hertog J. Shp2-Mitogen-Activated Protein Kinase Signaling Drives Proliferation during Zebrafish Embryo Caudal Fin Fold Regeneration. Mol Cell Biol 2018; 38:e00515-17. [PMID: 29203641 PMCID: PMC5789028 DOI: 10.1128/mcb.00515-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/18/2017] [Accepted: 11/23/2017] [Indexed: 11/25/2022] Open
Abstract
Regeneration of the zebrafish caudal fin following amputation occurs through wound healing, followed by formation of a blastema, which produces cells to replace the lost tissue in the final phase of regenerative outgrowth. We show that ptpn11a-/- ptpn11b-/- zebrafish embryos, lacking functional Shp2, fail to regenerate their caudal fin folds. Rescue experiments indicated that Shp2a has a functional signaling role, requiring its catalytic activity and SH2 domains but not the two C-terminal tyrosine phosphorylation sites. Surprisingly, expression of Shp2a variants with increased and reduced catalytic activity, respectively, rescued caudal fin fold regeneration to similar extents. Expression of mmp9 and junbb, indicative of formation of the wound epidermis and distal blastema, respectively, suggested that these processes occurred in ptpn11a-/- ptpn11b-/- zebrafish embryos. However, cell proliferation and MAPK phosphorylation were reduced. Pharmacological inhibition of MEK1 in wild-type zebrafish embryos phenocopied loss of Shp2. Our results suggest an essential role for Shp2a-mitogen-activated protein kinase (MAPK) signaling in promoting cell proliferation during zebrafish embryo caudal fin fold regeneration.
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Affiliation(s)
- Alexander James Hale
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
- Institute Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Jeroen den Hertog
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands
- Institute Biology Leiden, Leiden University, Leiden, the Netherlands
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16
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Blacklock KM, Yang L, Mulligan VK, Khare SD. A computational method for the design of nested proteins by loop-directed domain insertion. Proteins 2018; 86:354-369. [PMID: 29250820 DOI: 10.1002/prot.25445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 12/04/2017] [Accepted: 12/15/2017] [Indexed: 12/23/2022]
Abstract
The computational design of novel nested proteins-in which the primary structure of one protein domain (insert) is flanked by the primary structure segments of another (parent)-would enable the generation of multifunctional proteins. Here we present a new algorithm, called Loop-Directed Domain Insertion (LooDo), implemented within the Rosetta software suite, for the purpose of designing nested protein domain combinations connected by flexible linker regions. Conformational space for the insert domain is sampled using large libraries of linker fragments for linker-to-parent domain superimposition followed by insert-to-linker superimposition. The relative positioning of the two domains (treated as rigid bodies) is sampled efficiently by a grid-based, mutual placement compatibility search. The conformations of the loop residues, and the identities of loop as well as interface residues, are simultaneously optimized using a generalized kinematic loop closure algorithm and Rosetta EnzymeDesign, respectively, to minimize interface energy. The algorithm was found to consistently sample near-native conformations and interface sequences for a benchmark set of structurally similar but functionally divergent domain-inserted enzymes from the α/β hydrolase superfamily, and discriminates well between native and nonnative conformations and sequences, although loop conformations tended to deviate from the native conformations. Furthermore, in cross-domain placement tests, native insert-parent domain combinations were ranked as the best-scoring structures compared to nonnative domain combinations. This algorithm should be broadly applicable to the design of multi-domain protein complexes with any combination of inserted or tandem domain connections.
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Affiliation(s)
- Kristin M Blacklock
- Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Center for Integrative Proteomics Research, Rutgers The State University of New Jersey, Piscataway, New Jersey
| | - Lu Yang
- Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Center for Integrative Proteomics Research, Rutgers The State University of New Jersey, Piscataway, New Jersey
| | - Vikram K Mulligan
- Institute for Protein Design and Department of Biochemistry, University of Washington, Seattle, Washington
| | - Sagar D Khare
- Institute for Quantitative Biomedicine, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, New Jersey.,Center for Integrative Proteomics Research, Rutgers The State University of New Jersey, Piscataway, New Jersey
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17
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Abstract
Over the past two decades, hundreds of new somatic mutations have been identified in tumours, and a few dozen novel cancer therapeutics that selectively target these mutated oncoproteins have entered clinical practice. This development has resulted in clinical breakthroughs for a few tumour types, but more commonly patients' overall survival has not improved because of the development of drug resistance. Furthermore, only a very limited number of oncoproteins, largely protein kinases, are successfully targeted, whereas most non-kinase oncoproteins inside cancer cells remain untargeted. Engineered small protein inhibitors offer great promise in targeting a larger variety of oncoproteins with better efficacy and higher selectivity. In this article, I focus on a promising class of synthetic binding proteins, termed monobodies, that we have shown to inhibit previously untargetable protein-protein interactions in different oncoproteins. I will discuss the great promise alongside the technical challenges inherent in converting monobodies from potent pre-clinical target validation tools to next-generation protein-based therapeutics.
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Affiliation(s)
- Oliver Hantschel
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
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18
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Grb2 regulates the proliferation of hematopoietic stem and progenitors cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2449-2459. [PMID: 28964849 DOI: 10.1016/j.bbamcr.2017.09.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 08/31/2017] [Accepted: 09/26/2017] [Indexed: 01/13/2023]
Abstract
Although Hematopoietic Stem and Progenitor Cell (HSPC) proliferation, survival and expansion have been shown to be supported by the cooperative action of different cytokines, little is known about the intracellular signaling pathways that are activated by cytokines upon binding to their receptors. Our study showed that Growth factor receptor-bound protein 2 (Grb2) mRNAs are preferentially expressed in HSC compared to progenitors and differentiated cells of the myeloid and erythroid lineages. Conditional deletion of Grb2 induced a rapid decline of erythroid and myeloid progenitors and a progressive decline of HSC numbers in steady state conditions. We showed that when transplanted, Grb2 deleted bone marrow cells could not reconstitute irradiated recipients. Strinkingly, Grb2 deletion did not modify HSPC quiescence, but impaired LT-HSC and progenitors ability to respond a proliferative signal induced by 5FU in vivo and by various cytokines in vitro. We showed finally that Grb2 links IL3 signaling to the ERK/MAPK proliferative pathway and that both SH2 and SH3 domains of Grb2 are crucial for IL3 signaling in progenitor cells. Our findings position Grb2 as a key adaptor that integrates various cytokines response in cycling HSPC.
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19
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Chen C, Nimlamool W, Miller CJ, Lou HJ, Turk BE. Rational Redesign of a Functional Protein Kinase-Substrate Interaction. ACS Chem Biol 2017; 12:1194-1198. [PMID: 28314095 PMCID: PMC5442603 DOI: 10.1021/acschembio.7b00089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Eukaryotic
protein kinases typically phosphorylate substrates in
the context of specific sequence motifs, contributing to specificity
essential for accurate signal transmission. Protein kinases recognize
their target sequences through complementary interactions within the
active site cleft. As a step toward the construction of orthogonal
kinase signaling systems, we have re-engineered the protein kinase
Pim1 to alter its phosphorylation consensus sequence. Residues in
the Pim1 catalytic domain interacting directly with a critical arginine
residue in the substrate were substituted to produce a kinase mutant
that instead accommodates a hydrophobic residue. We then introduced
a compensating mutation into a Pim1 substrate, the pro-apoptotic protein
BAD, to reconstitute phosphorylation both in vitro and in living cells. Coexpression of the redesigned kinase with
its substrate in cells protected them from apoptosis. Such orthogonal
kinase–substrate pairs provide tools to probe the functional
consequences of specific phosphorylation events in living cells and
to design synthetic signaling pathways.
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Affiliation(s)
- Catherine Chen
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Wutigri Nimlamool
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Chad J. Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Benjamin E. Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
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20
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Sha F, Salzman G, Gupta A, Koide S. Monobodies and other synthetic binding proteins for expanding protein science. Protein Sci 2017; 26:910-924. [PMID: 28249355 PMCID: PMC5405424 DOI: 10.1002/pro.3148] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/20/2023]
Abstract
Synthetic binding proteins are constructed using nonantibody molecular scaffolds. Over the last two decades, in‐depth structural and functional analyses of synthetic binding proteins have improved combinatorial library designs and selection strategies, which have resulted in potent platforms that consistently generate binding proteins to diverse targets with affinity and specificity that rival those of antibodies. Favorable attributes of synthetic binding proteins, such as small size, freedom from disulfide bond formation and ease of making fusion proteins, have enabled their unique applications in protein science, cell biology and beyond. Here, we review recent studies that illustrate how synthetic binding proteins are powerful probes that can directly link structure and function, often leading to new mechanistic insights. We propose that synthetic proteins will become powerful standard tools in diverse areas of protein science, biotechnology and medicine.
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Affiliation(s)
- Fern Sha
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Gabriel Salzman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Ankit Gupta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016.,Department of Biochemistry and Molecular Pharmacology New York University School of Medicine, New York, NY, 10016
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21
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Abstract
The Src Homology 2 (SH2) domain is the prototypical protein interaction module that lies at the heart of phosphotyrosine signaling. Since its serendipitous discovery, there has been a tremendous advancement in technologies and an array of techniques available for studying SH2 domains and phosphotyrosine signaling. In this chapter, we provide a glimpse of the history of SH2 domains and describe many of the tools and techniques that have been developed along the way and discuss future directions for SH2 domain studies. We highlight the gist of each chapter in this volume in the context of: the structural biology and phosphotyrosine binding; characterizing SH2 specificity and generating prediction models; systems biology and proteomics; SH2 domains in signal transduction; and SH2 domains in disease, diagnostics, and therapeutics. Many of the individual chapters provide an in-depth approach that will allow scientists to interrogate the function and role of SH2 domains.
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Affiliation(s)
- Bernard A Liu
- Broad Institute of Harvard and MIT, 415 Main St., 5175 JJ, Cambridge, MA, 02142, USA.
| | - Kazuya Machida
- Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Ave., Farmington, CT, 06030, USA.
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22
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Carlin KB, Cruz-Teran CA, Kumar JP, Gomes C, Rao BM. Combinatorial Pairwise Assembly Efficiently Generates High Affinity Binders and Enables a "Mix-and-Read" Detection Scheme. ACS Synth Biol 2016; 5:1348-1354. [PMID: 27268028 DOI: 10.1021/acssynbio.6b00034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We show that a combinatorial library constructed by random pairwise assembly of low affinity binders can efficiently generate binders with increased affinity. Such a library based on the Sso7d scaffold, from a pool of low affinity binders subjected to random mutagenesis, contained putative high affinity clones for a model target (lysozyme) at higher frequency than a library of monovalent mutants generated by random mutagenesis alone. Increased binding affinity was due to intramolecular avidity generated by linking binders targeting nonoverlapping epitopes; individual binders of KD ∼ 1.3 μM and 250 nM produced a bivalent binder with apparent KD ∼ 2 nM. Furthermore, the bivalent protein retained thermal stability (TM = 84.5 °C) and high recombinant expression yields in E. coli. Finally, when binders comprising the bivalent protein are fused to two of the three fragments of tripartite split-green fluorescent protein (GFP), target-dependent reconstitution of fluorescence occurs, thereby enabling a "mix-and-read" assay for target quantification.
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Affiliation(s)
- Kevin B. Carlin
- Department of Chemical
and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carlos A. Cruz-Teran
- Department of Chemical
and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jay Prakash Kumar
- Institute of Stem Cell Biology and Regenerative Medicine, NCBS-TIFR, Bangalore 560065, Karnataka, India
- School of Chemical & Biotechnology, SASTRA University, Thanjavur 613401, Tamil Nadu, India
| | - Catherina Gomes
- Department of Chemical
and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Balaji M. Rao
- Department of Chemical
and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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23
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Liu S, Wu X, Zong M, Tempel W, Loppnau P, Liu Y. Structural basis for a novel interaction between TXNIP and Vav2. FEBS Lett 2016; 590:857-65. [DOI: 10.1002/1873-3468.12110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/08/2016] [Accepted: 02/17/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Shasha Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; College of Life Science; Central China Normal University; Wuhan China
| | - Xue Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; College of Life Science; Central China Normal University; Wuhan China
| | - Minru Zong
- China-Japan Union Hospital of Jilin University; Changchun China
| | - Wolfram Tempel
- Structural Genomics Consortium; University of Toronto; Ontario Canada
| | - Peter Loppnau
- Structural Genomics Consortium; University of Toronto; Ontario Canada
| | - Yanli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology; College of Life Science; Central China Normal University; Wuhan China
- Structural Genomics Consortium; University of Toronto; Ontario Canada
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24
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Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Proc Natl Acad Sci U S A 2016; 113:2092-7. [PMID: 26862167 DOI: 10.1073/pnas.1522691113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antibodies have a well-established modular architecture wherein the antigen-binding site residing in the antigen-binding fragment (Fab or Fv) is an autonomous and complete unit for antigen recognition. Here, we describe antibodies departing from this paradigm. We developed recombinant antibodies to trimethylated lysine residues on histone H3, important epigenetic marks and challenging targets for molecular recognition. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications. Surprisingly, crystal structures and biophysical analyses revealed that two antigen-binding sites of these antibodies form a head-to-head dimer and cooperatively recognize the antigen in the dimer interface. This "antigen clasping" produced an expansive interface where trimethylated Lys bound to an unusually extensive aromatic cage in one Fab and the histone N terminus to a pocket in the other, thereby rationalizing the high specificity. A long-neck antibody format with a long linker between the antigen-binding module and the Fc region facilitated antigen clasping and achieved both high specificity and high potency. Antigen clasping substantially expands the paradigm of antibody-antigen recognition and suggests a strategy for developing extremely specific antibodies.
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25
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Speltz EB, Nathan A, Regan L. Design of Protein-Peptide Interaction Modules for Assembling Supramolecular Structures in Vivo and in Vitro. ACS Chem Biol 2015; 10:2108-15. [PMID: 26131725 DOI: 10.1021/acschembio.5b00415] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Synthetic biology and protein origami both require protein building blocks that behave in a reliable, predictable fashion. In particular, we require protein interaction modules with known specificity and affinity. Here, we describe three designed TRAP (Tetratricopeptide Repeat Affinity Protein)-peptide interaction pairs that are functional in vivo. We show that each TRAP binds to its cognate peptide and exhibits low cross-reactivity with the peptides bound by the other TRAPs. In addition, we demonstrate that the TRAP-peptide interactions are functional in many cellular contexts. In extensions of these designs, we show that the binding affinity of a TRAP-peptide pair can be systematically varied. The TRAP-peptide pairs we present thus represent a powerful set of new building blocks that are suitable for a variety of applications.
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Affiliation(s)
- Elizabeth B. Speltz
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Aparna Nathan
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Lynne Regan
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
- Integrated Graduate Program in Physical and Engineering Biology, New Haven, Connecticut 06511, United States
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26
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Tsutsui Y, Johnson JM, Demeler B, Kinter MT, Hays FA. Conformation-Dependent Human p52Shc Phosphorylation by Human c-Src. Biochemistry 2015; 54:3469-82. [PMID: 25961473 DOI: 10.1021/acs.biochem.5b00122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Phosphorylation of the human p52Shc adaptor protein is a key determinant in modulating signaling complex assembly in response to tyrosine kinase signaling cascade activation. The underlying mechanisms that govern p52Shc phosphorylation status are unknown. In this study, p52Shc phosphorylation by human c-Src was investigated using purified proteins to define mechanisms that affect the p52Shc phosphorylation state. We conducted biophysical characterizations of both human p52Shc and human c-Src in solution as well as membrane-mimetic environments using the acidic lipid phosphatidylinositol 4-phosphate or a novel amphipathic detergent (2,2-dihexylpropane-1,3-bis-β-D-glucopyranoside). We then identified p52Shc phosphorylation sites under various solution conditions, and the amount of phosphorylation at each identified site was quantified using mass spectrometry. These data demonstrate that the p52Shc phosphorylation level is altered by the solution environment without affecting the fraction of active c-Src. Mass spectrometry analysis of phosphorylated p52Shc implies functional linkage among phosphorylation sites. This linkage may drive preferential coupling to protein binding partners during signaling complex formation, such as during initial binding interactions with the Grb2 adaptor protein leading to activation of the Ras/MAPK signaling cascade. Remarkably, tyrosine residues involved in Grb2 binding were heavily phosphorylated in a membrane-mimetic environment. The increased phosphorylation level in Grb2 binding residues was also correlated with a decrease in the thermal stability of purified human p52Shc. A schematic for the phosphorylation-dependent interaction between p52Shc and Grb2 is proposed. The results of this study suggest another possible therapeutic strategy for altering protein phosphorylation to regulate signaling cascade activation.
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Affiliation(s)
- Yuko Tsutsui
- †Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
| | - Jennifer M Johnson
- †Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
| | - Borries Demeler
- ‡Department of Biochemistry, The University of Texas Health Sciences Center at San Antonio, 7750 Floyd Curl Drive, San Antonio, Texas 78229-3900, United States
| | - Michael T Kinter
- ∥Department of Geriatric Medicine, Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
| | - Franklin A Hays
- †Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States.,⊥Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States.,∇Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, United States
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27
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Stein V, Alexandrov K. Synthetic protein switches: design principles and applications. Trends Biotechnol 2015; 33:101-10. [DOI: 10.1016/j.tibtech.2014.11.010] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/27/2014] [Accepted: 11/29/2014] [Indexed: 12/22/2022]
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28
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Analysis on the interaction domain of VirG and apyrase by pull-down assay. Molecules 2014; 19:18090-101. [PMID: 25379645 PMCID: PMC6271496 DOI: 10.3390/molecules191118090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/19/2014] [Accepted: 10/21/2014] [Indexed: 01/19/2023] Open
Abstract
VirG is outer membrane protein of Shigella and affects the spread of Shigella. Recently it has been reported that apyrase influences the location of VirG, although the underlying mechanism remains poorly understood. The site of interaction between apyrase and VirG is the focus of our research. First we constructed recombinant plasmid pHIS-phoN2 and pS-(v1-1102, v53-758, v759-1102, v53-319, v320-507, v507-758) by denaturation-renaturation, the phoN2:kan mutant of Shigella flexneri 5a M90T by a modified version of the lambda red recombination protocol originally described by Datsenko and Wanner and the complemented strain M90TΔphoN2/pET24a(PhisphoN2). Second, the recombinant plasmid pHIS-phoN2 and the pS-(v1-1102, v53-758, v759-1102, v53-319, v320-507, v507-758) were transformed into E. coli BL21 (DE3) and induced to express the fusion proteins. Third, the fusion proteins were purified and the interaction of VirG and apyrase was identified by pull-down. Fourth, VirG was divided and the interaction site of apyrase and VirG was determined. Finally, how apyrase affects the function of VirG was analyzed by immunofluorescence. Accordingly, the results provided the data supporting the fact that apyrase combines with the α-domain of VirG to influence the function of VirG.
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29
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Miura G. Clampdown. Nat Chem Biol 2014. [DOI: 10.1038/nchembio.1602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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