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EswarKumar N, Yang CH, Tewary S, Peng WH, Chen GC, Yeh YQ, Yang HC, Ho MC. An integrative approach unveils a distal encounter site for rPTPε and phospho-Src complex formation. Structure 2023; 31:1567-1577.e5. [PMID: 37794594 DOI: 10.1016/j.str.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/10/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023]
Abstract
The structure determination of protein tyrosine phosphatase (PTP): phospho-protein complexes, which is essential to understand how specificity is achieved at the amino acid level, remains a significant challenge for protein crystallography and cryoEM due to the transient nature of binding interactions. Using rPTPεD1 and phospho-SrcKD as a model system, we have established an integrative workflow to address this problem, by means of which we generate a protein:phospho-protein complex model using predetermined protein structures, SAXS and pTyr-tailored MD simulations. Our model reveals transient protein-protein interactions between rPTPεD1 and phospho-SrcKD and is supported by three independent experimental validations. Measurements of the association rate between rPTPεD1 and phospho-SrcKD showed that mutations on the rPTPεD1: SrcKD complex interface disrupts these transient interactions, resulting in a reduction in protein-protein association rate and, eventually, phosphatase activity. This integrative approach is applicable to other PTP: phospho-protein complexes and the characterization of transient protein-protein interface interactions.
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Affiliation(s)
- Nadendla EswarKumar
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - Sunilkumar Tewary
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wen-Hsin Peng
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Guang-Chao Chen
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsin-Chu 300, Taiwan
| | - Hsiao-Ching Yang
- Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan.
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.
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2
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Godbold GD, Hewitt FC, Kappell AD, Scholz MB, Agar SL, Treangen TJ, Ternus KL, Sandbrink JB, Koblentz GD. Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern. Front Bioeng Biotechnol 2023; 11:1124100. [PMID: 37180048 PMCID: PMC10167326 DOI: 10.3389/fbioe.2023.1124100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
Regulation of research on microbes that cause disease in humans has historically been focused on taxonomic lists of 'bad bugs'. However, given our increased knowledge of these pathogens through inexpensive genome sequencing, 5 decades of research in microbial pathogenesis, and the burgeoning capacity of synthetic biologists, the limitations of this approach are apparent. With heightened scientific and public attention focused on biosafety and biosecurity, and an ongoing review by US authorities of dual-use research oversight, this article proposes the incorporation of sequences of concern (SoCs) into the biorisk management regime governing genetic engineering of pathogens. SoCs enable pathogenesis in all microbes infecting hosts that are 'of concern' to human civilization. Here we review the functions of SoCs (FunSoCs) and discuss how they might bring clarity to potentially problematic research outcomes involving infectious agents. We believe that annotation of SoCs with FunSoCs has the potential to improve the likelihood that dual use research of concern is recognized by both scientists and regulators before it occurs.
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Affiliation(s)
| | | | | | | | - Stacy L. Agar
- Signature Science, LLC, Charlottesville, VA, United States
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, United States
| | | | - Jonas B. Sandbrink
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gregory D. Koblentz
- Schar School of Policy and Government, George Mason University, Arlington, VA, United States
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3
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Shi G, Song C, Torres Robles J, Salichos L, Lou HJ, Lam TT, Gerstein M, Turk BE. Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Sci Signal 2023; 16:eabm5518. [PMID: 36626580 PMCID: PMC9995140 DOI: 10.1126/scisignal.abm5518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Essential functions of mitogen-activated protein kinases (MAPKs) depend on their capacity to selectively phosphorylate a limited repertoire of substrates. MAPKs harbor a conserved groove located outside of the catalytic cleft that binds to short linear sequence motifs found in substrates and regulators. However, the weak and transient nature of these "docking" interactions poses a challenge to defining MAPK interactomes and associated sequence motifs. Here, we describe a yeast-based genetic screening pipeline to evaluate large collections of MAPK docking sequences in parallel. Using this platform, we analyzed a combinatorial library based on the docking sequences from the MAPK kinases MKK6 and MKK7, defining features critical for binding to the stress-activated MAPKs JNK1 and p38α. Our screen of a library consisting of ~12,000 sequences from the human proteome revealed multiple MAPK-selective interactors, including many that did not conform to previously defined docking motifs. Analysis of p38α/JNK1 exchange mutants identified specific docking groove residues that mediate selective binding. Last, we verified that docking sequences identified in the screen functioned in substrate recruitment in vitro and in cultured cells. Together, these studies establish an approach to characterize MAPK docking sequences and provide a resource for future investigation of signaling downstream of p38 and JNK.
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Affiliation(s)
- Guangda Shi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Claire Song
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jaylissa Torres Robles
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Leonidas Salichos
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA.,Keck MS and Proteomics Resource, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
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4
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Zuo Z, Liu J, Sun Z, Silverstein R, Zou M, Finkel T, Bugge TH, Leppla SH, Liu S. A potent tumor-selective ERK pathway inactivator with high therapeutic index. PNAS NEXUS 2022; 1:pgac104. [PMID: 35899070 PMCID: PMC9308561 DOI: 10.1093/pnasnexus/pgac104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/28/2022] [Indexed: 02/05/2023]
Abstract
FDA-approved BRAF and MEK small molecule inhibitors have demonstrated some level of efficacy in patients with metastatic melanomas. However, these "targeted" therapeutics have a very low therapeutic index, since these agents affect normal cells, causing undesirable, even fatal, side effects. To address these significant drawbacks, here, we have reengineered the anthrax toxin-based protein delivery system to develop a potent, tumor-selective MEK inactivator. This toxin-based MEK inactivator exhibits potent activity against a wide range of solid tumors, with the highest activity seen when directed toward tumors containing the BRAFV600E mutation. We demonstrate that this reengineered MEK inactivator also exhibits an extremely high therapeutic index (>15), due to its in vitro and in vivo activity being strictly dependent on the expression of multiple tumor-associated factors including tumor-associated proteases matrix metalloproteinase, urokinase plasminogen activator, and anthrax toxin receptor capillary morphogenesis protein-2. Furthermore, we have improved the specificity of this MEK inactivator, restricting its enzymatic activity to only target the ERK pathway, thereby greatly diminishing off-target toxicity. Together, these data suggest that engineered bacterial toxins can be modified to have significant in vitro and in vivo therapeutic effects with high therapeutic index.
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Affiliation(s)
| | | | - Zhihao Sun
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Rachel Silverstein
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Meijuan Zou
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA
| | - Toren Finkel
- Aging Institute of University of Pittsburgh and University of Pittsburgh Medical Center, Pittsburgh, PA 15219, USA,Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Thomas H Bugge
- Proteases and Tissue Remodeling Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen H Leppla
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shihui Liu
- To whom correspondence should be addressed:
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5
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Banihashemi SR, Rahbarizadeh F, Zavaran Hosseini A, Ahmadvand D, Khoshtinat Nikkhoi S. Liposome-based nanocarriers loaded with anthrax lethal factor and armed with anti-CD19 VHH for effectively inhibiting MAPK pathway in B cells. Int Immunopharmacol 2021; 100:107927. [PMID: 34500284 DOI: 10.1016/j.intimp.2021.107927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 01/26/2023]
Abstract
OBJECTIVE One of the vital signaling pathways in cancer development and metastasis is mitogen-activated protein kinases (MAPKs). Bacillus anthracis Lethal Toxin (LT) is a potent MAPK signaling inhibitor. This toxin is comprised of two distinct domains, Lethal Factor (LF), MAPK inhibitor, and Protective Antigen (PA). To enter various cell lines, LF must be associated with the protective antigen (PA), which facilitates LF delivery. In the current study, to block MAPK signaling, LF was loaded into anti-CD19 immunoliposomes nanoparticle to deliver the cargo to Raji B cells. METHODS The liposome nanoparticle was prepared using classical lipid film formation, then conjugated to anti-CD19 VHH. The binding efficiency was measured through flow cytometry. The targeted cytotoxicity of LF immunoliposome was confirmed by BrdU lymphoproliferation assay. This was followed by Real-Time PCR to assess the effect of formulation on pro-apoptotic genes. The inhibitory effect of LF on MAPK signaling was confirmed by western blot. RESULTS Liposome nano-formulation was optimized to reach the maximum LF encapsulation and targeted delivery. Next, phosphorylation of MAPK pathway mediators like MEK1/2, P38 and JNK were inhibited following the treatment of Raji cells with LF-immunoliposome. The treatment also upregulated caspase genes, clearly illustrating cell death induced by LF through pyroptosis and caspase-dependent apoptosis. CONCLUSIONS In conclusion, anti-CD19 VHH immunoliposome was loaded with LF, a potent MAPK inhibitor targeting B cells, which curbs proliferation and ushers B cells toward apoptosis. Thus, immunoliposome presents as a versatile nanoparticle for delivery of LF to block aberrant MAPK activation. To use LF as a therapy, it would be necessary to materialize LF without PA. In the current study, PA was substituted with anti-CD19 immunoliposome to make it targeted to CD19+ while keeping the normal cells intact.
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Affiliation(s)
- S Reza Banihashemi
- Department of Medical Immunology, Faculty of Medical Sciences, Tarbiat Modarres University, Tehran, Iran; Department of Immunology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modarres University, Tehran, Iran.
| | - Ahmad Zavaran Hosseini
- Department of Medical Immunology, Faculty of Medical Sciences, Tarbiat Modarres University, Tehran, Iran
| | - Davoud Ahmadvand
- School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
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Cho E, Lou HJ, Kuruvilla L, Calderwood DA, Turk BE. PPP6C negatively regulates oncogenic ERK signaling through dephosphorylation of MEK. Cell Rep 2021; 34:108928. [PMID: 33789117 PMCID: PMC8068315 DOI: 10.1016/j.celrep.2021.108928] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/26/2021] [Accepted: 03/10/2021] [Indexed: 12/21/2022] Open
Abstract
Flux through the RAF-MEK-ERK protein kinase cascade is shaped by phosphatases acting on the core components of the pathway. Despite being an established drug target and a hub for crosstalk regulation, little is known about dephosphorylation of MEK, the central kinase within the cascade. Here, we identify PPP6C, a phosphatase frequently mutated or downregulated in melanoma, as a major MEK phosphatase in cells exhibiting oncogenic ERK pathway activation. Recruitment of MEK to PPP6C occurs through an interaction with its associated regulatory subunits. Loss of PPP6C causes hyperphosphorylation of MEK at activating and crosstalk phosphorylation sites, promoting signaling through the ERK pathway and decreasing sensitivity to MEK inhibitors. Recurrent melanoma-associated PPP6C mutations cause MEK hyperphosphorylation, suggesting that they promote disease at least in part by activating the core oncogenic pathway driving melanoma. Collectively, our studies identify a key negative regulator of ERK signaling that may influence susceptibility to targeted cancer therapies. Through an shRNA screen, Cho et al. identify PPP6C as a phosphatase that inactivates the kinase MEK, sensitizing tumor cells to clinical MEK inhibitors. This study suggests that cancer-associated loss-of-function PPP6C mutations prevalent in melanoma serve to activate the core oncogenic RAF-MEK-ERK pathway that drives the disease.
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Affiliation(s)
- Eunice Cho
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Leena Kuruvilla
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - David A Calderwood
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA; Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA.
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Anthrax lethal factor cleaves regulatory subunits of phosphoinositide-3 kinase to contribute to toxin lethality. Nat Microbiol 2020; 5:1464-1471. [PMID: 32895527 DOI: 10.1038/s41564-020-0782-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 07/28/2020] [Indexed: 11/08/2022]
Abstract
Anthrax lethal toxin (LT), produced by Bacillus anthracis, comprises a receptor-binding moiety, protective antigen and the lethal factor (LF) protease1,2. Although LF is known to cleave mitogen-activated protein kinase kinases (MEKs/MKKs) and some variants of the NLRP1 inflammasome sensor, targeting of these pathways does not explain the lethality of anthrax toxin1,2. Here we report that the regulatory subunits of phosphoinositide-3 kinase (PI3K)-p85α (PIK3R1) and p85β (PIK3R2)3,4-are substrates of LF. Cleavage of these proteins in a proline-rich region between their N-terminal Src homology and Bcr homology domains disrupts homodimer formation and impacts PI3K signalling. Mice carrying a mutated p85α that cannot be cleaved by LF show a greater resistance to anthrax toxin challenge. The LF(W271A) mutant cleaves p85α with lower efficiency and is non-toxic to mice but can regain lethality when combined with PI3K pathway inhibitors. We provide evidence that LF targets two signalling pathways that are essential for growth and metabolism and that the disabling of both pathways is likely necessary for lethal anthrax infection.
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8
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Turk BE. Exceptionally Selective Substrate Targeting by the Metalloprotease Anthrax Lethal Factor. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1111:189-203. [PMID: 30267305 DOI: 10.1007/5584_2018_273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The zinc-dependent metalloprotease anthrax lethal factor (LF) is the enzymatic component of a toxin thought to have a major role in Bacillus anthracis infections. Like many bacterial toxins, LF is a secreted protein that functions within host cells. LF is a highly selective protease that cleaves a limited number of substrates in a site-specific manner, thereby impacting host signal transduction pathways. The major substrates of LF are mitogen-activated protein kinase kinases (MKKs), which lie in the middle of three-component phosphorylation cascades mediating numerous functions in a variety of cells and tissues. How LF targets its limited substrate repertoire has been an active area of investigation. LF recognizes a specific sequence motif surrounding the scissile bonds of substrate proteins. X-ray crystallography of the protease in complex with peptide substrates has revealed the structural basis of selectivity for the LF cleavage site motif. In addition to having interactions proximal to the cleavage site, LF binds directly to a more distal region in its substrates through a so-called exosite interaction. This exosite has been mapped to a surface within a non-catalytic domain of LF with previously unknown function. A putative LF-binding site has likewise been identified on the catalytic domains of MKKs. Here we review our current state of understanding of LF-substrate interactions and discuss the implications for the design and discovery of inhibitors that may have utility as anthrax therapeutics.
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Affiliation(s)
- Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
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