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Bütikofer M, Stadler GR, Kadavath H, Cadalbert R, Torres F, Riek R. Rapid Protein-Ligand Affinity Determination by Photoinduced Hyperpolarized NMR. J Am Chem Soc 2024; 146:17974-17985. [PMID: 38957136 DOI: 10.1021/jacs.4c04000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
The binding affinity determination of protein-ligand complexes is a cornerstone of drug design. State-of-the-art techniques are limited by lengthy and expensive processes. Building upon our recently introduced novel screening method utilizing photochemically induced dynamic nuclear polarization (photo-CIDNP) NMR, we provide the methodological framework to determine binding affinities within 5-15 min using 0.1 mg of protein. The accuracy of our method is demonstrated for the affinity constants of peptides binding to a PDZ domain and fragment ligands binding to the protein PIN1. The method can also be extended to measure the affinity of nonphoto-CIDNP-polarizable ligands in competition binding experiments. Finally, we demonstrate a strong correlation between the ligand-reduced signals in photo-CIDNP-based NMR fragment screening and the well-established saturation transfer difference (STD) NMR. Thus, our methodology measures protein-ligand affinities in the micro- to millimolar range in only a few minutes and informs on the binding epitope in a single-scan experiment, opening new avenues for early stage drug discovery approaches.
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Affiliation(s)
- Matthias Bütikofer
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Gabriela R Stadler
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Harindranath Kadavath
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Riccardo Cadalbert
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Felix Torres
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
- NexMR AG, Wiesenstrasse 10A, 8952 Schlieren, Switzerland
| | - Roland Riek
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
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Wang Q, Ji C, Ali A, Ding I, Wang Y, McCulloch CA. TRPV4 mediates IL-1-induced Ca 2+ signaling, ERK activation and MMP expression. FASEB J 2024; 38:e23731. [PMID: 38855909 DOI: 10.1096/fj.202400031r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/14/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
Ca2+ permeation through TRPV4 in fibroblasts is associated with pathological matrix degradation. In human gingival fibroblasts, IL-1β binding to its signaling receptor (IL-1R1) induces activation of extracellular regulated kinase (ERK) and MMP1 expression, processes that require Ca2+ flux across the plasma membrane. It is not known how IL-1R1, which does not conduct Ca2+, generates Ca2+ signals in response to IL-1. We examined whether TRPV4 mediates the Ca2+ fluxes required for ERK signaling in IL-1 stimulated gingival fibroblasts. TRPV4 was immunostained in fibroblasts of human gingival connective tissue and in focal adhesions of cultured mouse gingival fibroblasts. Human gingival fibroblasts treated with IL-1β showed no change of TRPV4 expression but there was increased MMP1 expression. In mouse, gingival fibroblasts expressing TRPV4, IL-1 strongly increased [Ca2+]i. Pre-incubation of cells with IL-1 Receptor Antagonist blocked Ca2+ entry induced by IL-1 or the TRPV4 agonist GSK101. Knockout of TRPV4 or expression of a non-Ca2+-conducting TRPV4 pore-mutant or pre-incubation with the TRPV4 inhibitor RN1734, blocked IL-1-induced Ca2+ transients and expression of the mouse interstitial collagenase, MMP13. Treatment of mouse gingival fibroblasts with GSK101 phenocopied Ca2+ and ERK responses induced by IL-1; these responses were absent in TRPV4-null cells or cells expressing a non-conducting TRPV4 pore-mutant. Immunostained IL-1R1 localized with TRPV4 in adhesions within cell extensions. While TRPV4 immunoprecipitates analyzed by mass spectrometry showed no association with IL-1R1, TRPV4 associated with Src-related proteins and Src co-immunoprecipitated with TRPV4. Src inhibition reduced IL-1-induced Ca2+ responses. The functional linkage of TRPV4 with IL-1R1 expands its repertoire of innate immune signaling processes by mediating IL-1-driven Ca2+ responses that drive matrix remodeling in fibroblasts. Thus, inhibiting TRPV4 activity may provide a new pharmacological approach for blunting matrix degradation in inflammatory diseases.
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Affiliation(s)
- Qin Wang
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Chenfan Ji
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Aiman Ali
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Isabel Ding
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Yongqiang Wang
- Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
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Omble A, Mahajan S, Bhoite A, Kulkarni K. Dishevelled2 activates WGEF via its interaction with a unique internal peptide motif of the GEF. Commun Biol 2024; 7:543. [PMID: 38714795 PMCID: PMC11076555 DOI: 10.1038/s42003-024-06194-6] [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: 11/04/2023] [Accepted: 04/15/2024] [Indexed: 05/10/2024] Open
Abstract
The Wnt-planar cell polarity (Wnt-PCP) pathway is crucial in establishing cell polarity during development and tissue homoeostasis. This pathway is found to be dysregulated in many pathological conditions, including cancer and autoimmune disorders. The central event in Wnt-PCP pathway is the activation of Weak-similarity guanine nucleotide exchange factor (WGEF) by the adapter protein Dishevelled (Dvl). The PDZ domain of Dishevelled2 (Dvl2PDZ) binds and activates WGEF by releasing it from its autoinhibitory state. However, the actual Dvl2PDZ binding site of WGEF and the consequent activation mechanism of the GEF have remained elusive. Using biochemical and molecular dynamics studies, we show that a unique "internal-PDZ binding motif" (IPM) of WGEF mediates the WGEF-Dvl2PDZ interaction to activate the GEF. The residues at P2, P0, P-2 and P-3 positions of IPM play an important role in stabilizing the WGEFpep-Dvl2PDZ interaction. Furthermore, MD simulations of modelled Dvl2PDZ-WGEFIPM peptide complexes suggest that WGEF-Dvl2PDZ interaction may differ from the reported Dvl2PDZ-IPM interactions. Additionally, the apo structure of human Dvl2PDZ shows conformational dynamics different from its IPM peptide bound state, suggesting an induced fit mechanism for the Dvl2PDZ-peptide interaction. The current study provides a model for Dvl2 induced activation of WGEF.
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Affiliation(s)
- Aishwarya Omble
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shrutika Mahajan
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Ashwini Bhoite
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kiran Kulkarni
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Yang F, Yang M, Liu Y, Zhou C, Chen Y, Wu J, Zhang X, Xiao S. PDLIM7 Promotes Tumor Metastasis in Papillary Thyroid Carcinoma via Stabilizing Focal Adhesion Kinase Protein. Thyroid 2024; 34:598-610. [PMID: 38243825 DOI: 10.1089/thy.2023.0497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
Background: As an actin cytoskeleton interactor, PDZ (postsynaptic density 65-discs large-zonula occludens 1) and LIM (abnormal cell lineage 11-isket 1-mechanosensory abnormal 3) domain protein 7 (PDLIM7) was supposed to play an essential role modulating cytoskeleton. Focal adhesions (FAs), which are located at the cytomembrane terminus of actin cytoskeleton, function as a force sensor and can transform the mechanical signal to a biochemical signal. Focal adhesion kinase (FAK) localizes to and regulates signal transduction in FAs, which play an essential role in cell polarity, migration, and invasion. However, whether PDLIM7 is involved in FAs-associated signal transduction and its role in tumor invasion and metastasis remains largely unknown. Methods: A cohort of 80 patients with papillary thyroid carcinoma (PTC) at The Second Affiliated Hospital of Guilin Medical University, as well as 512 PTC samples from The Cancer Genome Atlas thyroid cancer database was utilized to analyze the expression of PDLIM7 and its association with prognosis. Survival data were assessed using Kaplan-Meier curves, whereas clinicopathological characteristics such as age, sex, tumor size, multilocality, extrathyroidal extension, lymph metastases, Hashimoto's thyroiditis, distant metastasis, and TNM stage were considered. Functional assays were performed in vitro and in a xenograft mouse model to assess the role of PDLIM7 in PTC cell lines. The colocalization of PDLIM7 with FAK and integrin alpha V (ITGAV) was determined using immunofluorescence assay and immunoprecipitation assay. Protein expression levels in cell and tissue biopsies were measured through Western blotting and immunohistochemistry. Results: (1) The PDLIM7 protein frequently upregulated in both PTC tissues and cells, and overexpression of PDLIM7 is associated with advanced clinicopathological characteristics. (2) Knockdown of PDLIM7 effectively inhibits cell proliferation, migration, and invasion in PTC cell lines in vitro. (3) Knockdown of PDLIM7 hinders the growth and metastasis of TPC-1 xenografts in vivo. (4) PDLIM7 demonstrates colocalization with both FAK and the FA molecule ITGAV and the knockdown of PDLIM7 resulted in disassembly of FAs and proteosome-dependent degradation of FAK in PTC cell lines. Conclusions: PDLIM7 function as an oncoprotein in PTC to promote metastasis, and a novel underlying mechanism is proposed that PDLIM7 keeps FAK protein from proteosome-dependent degradation.
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Affiliation(s)
- Fan Yang
- Department of Pathology, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Mingqing Yang
- Department of Pathology, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Yi Liu
- Department of Physiology, Faculty of Basic Medical Sciences, Guilin, China
| | - Chen Zhou
- Department of Pathology, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Yongbei Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Jiacai Wu
- School of Biotechnology, Guilin Medical University, Guilin, China
| | - Xiaoling Zhang
- Department of Physiology, Faculty of Basic Medical Sciences, Guilin, China
| | - Shengjun Xiao
- Department of Pathology, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
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Montserrat-Gomez M, Gogl G, Carrasco K, Betzi S, Durbesson F, Cousido-Siah A, Kostmann C, Essig DJ, Strømgaard K, Østergaard S, Morelli X, Trave G, Vincentelli R, Bailly E, Borg JP. PDZome-wide and structural characterization of the PDZ-binding motif of VANGL2. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140989. [PMID: 38142947 DOI: 10.1016/j.bbapap.2023.140989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
VANGL2 is a core component of the non-canonical Wnt/Planar Cell Polarity signaling pathway that uses its highly conserved carboxy-terminal type 1 PDZ-binding motif (PBM) to bind a variety of PDZ proteins. In this study, we characterize and quantitatively assess the largest VANGL2 PDZome-binding profile documented so far, using orthogonal methods. The results of our holdup approach support VANGL2 interactions with a large panel of both long-recognized and unprecedented PDZ domains. Truncation and point mutation analyses of the VANGL2 PBM establish that, beyond the strict requirement of the P-0 / V521 and P-2 / T519 amino acids, upstream residues, including E518, Q516 and R514 at, respectively, P-3, P-5 and P-7 further contribute to the robustness of VANGL2 interactions with two distinct PDZ domains, SNX27 and SCRIBBLE-PDZ3. In agreement with these data, incremental amino-terminal deletions of the VANGL2 PBM causes its overall affinity to progressively decline. Moreover, the holdup data establish that the PDZome binding repertoire of VANGL2 starts to diverge significantly with the truncation of E518. A structural analysis of the SYNJ2BP-PDZ/VANGL2 interaction with truncated PBMs identifies a major conformational change in the binding direction of the PBM peptide after the P-2 position. Finally, we report that the PDZome binding profile of VANGL2 is dramatically rearranged upon phosphorylation of S517, T519 and S520. Our crystallographic approach illustrates how SYNJ2BP accommodates a S520-phosphorylated PBM peptide through the ideal positioning of two basic residues, K48 and R86. Altogether our data provides a comprehensive view of the VANGL2 PDZ network and how this network specifically responds to the post-translation modification of distinct PBM residues. These findings should prove useful in guiding future functional and molecular studies of the key PCP component VANGL2.
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Affiliation(s)
- Marta Montserrat-Gomez
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France
| | - Gergo Gogl
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Kendall Carrasco
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Stephane Betzi
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Fabien Durbesson
- Aix Marseille Université, CNRS, Architecture et fonction des macromolécules biologiques (AFMB), Marseille, France
| | - Alexandra Cousido-Siah
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Camille Kostmann
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Dominic J Essig
- Center for Biopharmaceuticals, Jagtvej 162, 2100 Copenhagen, Denmark; Global Research Technologies, Novo Nordisk Research Park, 2760 Maaloev, Denmark
| | | | - Søren Østergaard
- Global Research Technologies, Novo Nordisk Research Park, 2760 Maaloev, Denmark
| | - Xavier Morelli
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Gilles Trave
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Renaud Vincentelli
- Aix Marseille Université, CNRS, Architecture et fonction des macromolécules biologiques (AFMB), Marseille, France.
| | - Eric Bailly
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France.
| | - Jean-Paul Borg
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France; Institut Universitaire de France (IUF), France.
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Fujiwara-Tani R, Sasaki T, Bhawal UK, Mori S, Ogata R, Sasaki R, Ikemoto A, Kishi S, Fujii K, Ohmori H, Sho M, Kuniyasu H. Nuclear MAST4 Suppresses FOXO3 through Interaction with AKT3 and Induces Chemoresistance in Pancreatic Ductal Carcinoma. Int J Mol Sci 2024; 25:4056. [PMID: 38612866 PMCID: PMC11012408 DOI: 10.3390/ijms25074056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/24/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is highly malignant, with a 5-year survival rate of less than 10%. Furthermore, the acquisition of anticancer drug resistance makes PDAC treatment difficult. We established MIA-GEM cells, a PDAC cell line resistant to gemcitabine (GEM), a first-line anticancer drug, using the human PDAC cell line-MIA-PaCa-2. Microtubule-associated serine/threonine kinase-4 (MAST4) expression was increased in MIA-GEM cells compared with the parent cell line. Through inhibitor screening, dysregulated AKT signaling was identified in MIA-GEM cells with overexpression of AKT3. MAST4 knockdown effectively suppressed AKT3 overexpression, and both MAST4 and AKT3 translocation into the nucleus, phosphorylating forkhead box O3a (FOXO3) in MIA-GEM cells. Modulating FOXO3 target gene expression in these cells inhibited apoptosis while promoting stemness and proliferation. Notably, nuclear MAST4 demonstrated higher expression in GEM-resistant PDAC cases compared with that in the GEM-sensitive cases. Elevated MAST4 expression correlated with a poorer prognosis in PDAC. Consequently, nuclear MAST4 emerges as a potential marker for GEM resistance and poor prognosis, representing a novel therapeutic target for PDAC.
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Grants
- 19K16564 Ministry of Education, Culture, Sports, Science and Technology
- 20K21659 Ministry of Education, Culture, Sports, Science and Technology
- 23K10481 Ministry of Education, Culture, Sports, Science and Technology
- 22K11396 Ministry of Education, Culture, Sports, Science and Technology
- 21K11223 Ministry of Education, Culture, Sports, Science and Technology
- 22H04922 Ministry of Education, Culture, Sports, Science and Technology
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Affiliation(s)
- Rina Fujiwara-Tani
- Department of Molecular Pathology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Nara, Japan; (T.S.); (S.M.); (R.O.); (A.I.); (S.K.); (K.F.); (H.O.)
| | - Takamitsu Sasaki
- Department of Molecular Pathology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Nara, Japan; (T.S.); (S.M.); (R.O.); (A.I.); (S.K.); (K.F.); (H.O.)
| | - Ujjal Kumar Bhawal
- Research Institute of Oral Science, Nihon University School of Dentistry at Matsudo, Matsudo 271-8587, Chiba, Japan;
| | - Shiori Mori
- Department of Molecular Pathology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Nara, Japan; (T.S.); (S.M.); (R.O.); (A.I.); (S.K.); (K.F.); (H.O.)
| | - Ruiko Ogata
- Department of Molecular Pathology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Nara, Japan; (T.S.); (S.M.); (R.O.); (A.I.); (S.K.); (K.F.); (H.O.)
| | - Rika Sasaki
- Department of Molecular Pathology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Nara, Japan; (T.S.); (S.M.); (R.O.); (A.I.); (S.K.); (K.F.); (H.O.)
| | - Ayaka Ikemoto
- Department of Molecular Pathology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Nara, Japan; (T.S.); (S.M.); (R.O.); (A.I.); (S.K.); (K.F.); (H.O.)
| | - Shingo Kishi
- Department of Molecular Pathology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Nara, Japan; (T.S.); (S.M.); (R.O.); (A.I.); (S.K.); (K.F.); (H.O.)
- Pathology Laboratory, Research Institute, Tokushukai Nozaki Hospital, 2-10-50 Tanigawa, Daito 574-0074, Osaka, Japan
| | - Kiyomu Fujii
- Department of Molecular Pathology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Nara, Japan; (T.S.); (S.M.); (R.O.); (A.I.); (S.K.); (K.F.); (H.O.)
| | - Hitoshi Ohmori
- Department of Molecular Pathology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Nara, Japan; (T.S.); (S.M.); (R.O.); (A.I.); (S.K.); (K.F.); (H.O.)
| | - Masayuki Sho
- Department of Surgery, Nara Medical University, Kashihara 634-8522, Nara, Japan;
| | - Hiroki Kuniyasu
- Department of Molecular Pathology, Nara Medical University, 840 Shijo-cho, Kashihara 634-8521, Nara, Japan; (T.S.); (S.M.); (R.O.); (A.I.); (S.K.); (K.F.); (H.O.)
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Dibyachintan S, Dube AK, Bradley D, Lemieux P, Dionne U, Landry CR. Cryptic genetic variation shapes the fate of gene duplicates in a protein interaction network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.23.581840. [PMID: 38464075 PMCID: PMC10925128 DOI: 10.1101/2024.02.23.581840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Paralogous genes are often redundant for long periods of time before they diverge in function. While their functions are preserved, paralogous proteins can accumulate mutations that, through epistasis, could impact their fate in the future. By quantifying the impact of all single-amino acid substitutions on the binding of two myosin proteins to their interaction partners, we find that the future evolution of these proteins is highly contingent on their regulatory divergence and the mutations that have silently accumulated in their protein binding domains. Differences in the promoter strength of the two paralogs amplify the impact of mutations on binding in the lowly expressed one. While some mutations would be sufficient to non-functionalize one paralog, they would have minimal impact on the other. Our results reveal how functionally equivalent protein domains could be destined to specific fates by regulatory and cryptic coding sequence changes that currently have little to no functional impact.
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Affiliation(s)
- Soham Dibyachintan
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
| | - Alexandre K Dube
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - David Bradley
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - Pascale Lemieux
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
| | - Ugo Dionne
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Current affiliation: Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Christian R Landry
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
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Shao X, Volk L. PICK1 links KIBRA and AMPA receptors in coiled-coil-driven supramolecular complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584494. [PMID: 38558978 PMCID: PMC10980033 DOI: 10.1101/2024.03.12.584494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The human memory-associated protein KIBRA regulates synaptic plasticity and trafficking of AMPA-type glutamate receptors, and is implicated in multiple neuropsychiatric and cognitive disorders. How KIBRA forms complexes with and regulates AMPA receptors remains unclear. Here, we show that KIBRA does not interact directly with the AMPA receptor subunit GluA2, but that PICK1, a key regulator of AMPA receptor trafficking, can serve as a bridge between KIBRA and GluA2. We identified structural determinants of KIBRA-PICK1-AMPAR complexes by investigating interactions and cellular expression patterns of different combinations of KIBRA and PICK1 domain mutants. We find that the PICK1 BAR domain, a coiled-coil structure, is sufficient for interaction with KIBRA, whereas mutation of the BAR domain disrupts KIBRA-PICK1-GluA2 complex formation. In addition, KIBRA recruits PICK1 into large supramolecular complexes, a process which requires KIBRA coiled-coil domains. These findings reveal molecular mechanisms by which KIBRA can organize key synaptic signaling complexes.
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Guerin N, Childs H, Zhou P, Donald BR. DexDesign: A new OSPREY-based algorithm for designing de novo D-peptide inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579944. [PMID: 38405797 PMCID: PMC10888900 DOI: 10.1101/2024.02.12.579944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains play a central role in modulating polarization, signaling, and trafficking pathways. Mutations in PDZ domains lead to diseases such as cancer and cystic fibrosis, making PDZ domains attractive targets for therapeutic intervention. D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. Here, we introduce DexDesign, a novel OSPREY-based algorithm for computationally designing de novo D-peptide inhibitors. DexDesign leverages three novel techniques that are broadly applicable to computational protein design: the Minimum Flexible Set, K*-based Mutational Scan, and Inverse Alanine Scan, which enable exponential reductions in the size of the peptide sequence search space. We apply these techniques and DexDesign to generate novel D-peptide inhibitors of two biomedically important PDZ domain targets: CAL and MAST2. We introduce a new framework for analyzing de novo peptides-evaluation along a replication/restitution axis-and apply it to the DexDesign-generated D-peptides. Notably, the peptides we generated are predicted to bind their targets tighter than their targets' endogenous ligands, validating the peptides' potential as lead therapeutic candidates. We provide an implementation of DexDesign in the free and open source computational protein design software OSPREY.
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10
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George JL, Agbavor C, Cabo LF, Cahoon LA. Streptococcus pneumoniae secretion chaperones PrsA, SlrA, and HtrA are required for competence, antibiotic resistance, colonization, and invasive disease. Infect Immun 2024; 92:e0049023. [PMID: 38226817 PMCID: PMC10863415 DOI: 10.1128/iai.00490-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 01/17/2024] Open
Abstract
Streptococcus pneumoniae is a Gram-positive bacterium and a significant health threat with the populations most at risk being children, the elderly, and the immuno-compromised. To colonize and transition into an invasive infectious organism, S. pneumoniae secretes virulence factors that are translocated across the bacterial membrane and destined for surface exposure, attachment to the cell wall, or secretion into the host. The surface exposed protein chaperones PrsA, SlrA, and HtrA facilitate S. pneumoniae protein secretion; however, the distinct roles contributed by each of these secretion chaperones have not been well defined. Tandem Mass-Tagged Mass Spectrometry and virulence, adhesion, competence, and cell wall integrity assays were used to interrogate the individual and collective contributions of PrsA, SlrA, and HtrA to multiple aspects of S. pneumoniae physiology and virulence. PrsA, SlrA, and HtrA were found to play critical roles in S. pneumoniae host cell infection and competence, and the absence of each of these secretion chaperones significantly altered the S. pneumoniae secretome in distinct ways. PrsA and SlrA were additionally found to contribute to cell wall assembly and resistance to cell wall-active antimicrobials and were important for enabling S. pneumoniae host cell adhesion during colonization and invasive infection. These findings serve to further illustrate the pivotal contributions of PrsA, SlrA, and HtrA to S. pneumoniae protein secretion and virulence.
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Affiliation(s)
- Jada L. George
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Charles Agbavor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leah F. Cabo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Laty A. Cahoon
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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11
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Song Y, Zhang H, Liu S, Chang Y, Zhang Y, Feng H, Zhang X, Sun M, Sha W, Li Y, Dai S. Na2CO3-responsive mechanism insight from quantitative proteomics and SlRUB gene function in Salix linearistipularis seedlings. TREE PHYSIOLOGY 2024; 44:tpae011. [PMID: 38263488 DOI: 10.1093/treephys/tpae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/28/2023] [Accepted: 01/07/2024] [Indexed: 01/25/2024]
Abstract
Mongolian willow (Salix linearistipularis) is a naturally occurring woody dioecious plant in the saline soils of north-eastern China, which has a high tolerance to alkaline salts. Although transcriptomics studies have identified a large number of salinity-responsive genes, the mechanism of salt tolerance in Mongolian willow is not clear. Here, we found that in response to Na2CO3 stress, Mongolian willow regulates osmotic homeostasis by accumulating proline and soluble sugars and scavenges reactive oxygen species (ROS) by antioxidant enzymes and non-enzymatic antioxidants. Our quantitative proteomics study identified 154 salt-sensitive proteins mainly involved in maintaining the stability of the photosynthetic system and ROS homeostasis to cope with Na2CO3 stress. Among them, Na2CO3-induced rubredoxin (RUB) was predicted to be associated with 122 proteins for the modulation of these processes. The chloroplast-localized S. linearistipularis rubredoxin (SlRUB) was highly expressed in leaves and was significantly induced under Na2CO3 stress. Phenotypic analysis of overexpression, mutation and complementation materials of RUB in Arabidopsis suggests that SlRUB is critical for the regulation of photosynthesis, ROS scavenging and other metabolisms in the seedlings of Mongolian willow to cope with Na2CO3 stress. This provides more clues to better understand the alkali-responsive mechanism and RUB functions in the woody Mongolian willow.
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Affiliation(s)
- Yingying Song
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, No. 100 Guilin Road, Xuhui District, Shanghai 200234, China
| | - Heng Zhang
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, No. 100 Guilin Road, Xuhui District, Shanghai 200234, China
| | - Shijia Liu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, No. 100 Guilin Road, Xuhui District, Shanghai 200234, China
| | - Yu Chang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Yongxue Zhang
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, No. 100 Guilin Road, Xuhui District, Shanghai 200234, China
| | - Huiting Feng
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, No. 1 Jinming Avenue, Longting District, Kaifeng 475001, China
| | - Meihong Sun
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, No. 100 Guilin Road, Xuhui District, Shanghai 200234, China
| | - Wei Sha
- College of Life Sciences and Agriculture and Forestry, Qiqihar University, No. 42 Wenhua Street, Jianhua District, Qiqihar 161006, China
| | - Ying Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, No. 26 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, No. 100 Guilin Road, Xuhui District, Shanghai 200234, China
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12
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Khalil AM, Nogales A, Martínez-Sobrido L, Mostafa A. Antiviral responses versus virus-induced cellular shutoff: a game of thrones between influenza A virus NS1 and SARS-CoV-2 Nsp1. Front Cell Infect Microbiol 2024; 14:1357866. [PMID: 38375361 PMCID: PMC10875036 DOI: 10.3389/fcimb.2024.1357866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
Following virus recognition of host cell receptors and viral particle/genome internalization, viruses replicate in the host via hijacking essential host cell machinery components to evade the provoked antiviral innate immunity against the invading pathogen. Respiratory viral infections are usually acute with the ability to activate pattern recognition receptors (PRRs) in/on host cells, resulting in the production and release of interferons (IFNs), proinflammatory cytokines, chemokines, and IFN-stimulated genes (ISGs) to reduce virus fitness and mitigate infection. Nevertheless, the game between viruses and the host is a complicated and dynamic process, in which they restrict each other via specific factors to maintain their own advantages and win this game. The primary role of the non-structural protein 1 (NS1 and Nsp1) of influenza A viruses (IAV) and the pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respectively, is to control antiviral host-induced innate immune responses. This review provides a comprehensive overview of the genesis, spatial structure, viral and cellular interactors, and the mechanisms underlying the unique biological functions of IAV NS1 and SARS-CoV-2 Nsp1 in infected host cells. We also highlight the role of both non-structural proteins in modulating viral replication and pathogenicity. Eventually, and because of their important role during viral infection, we also describe their promising potential as targets for antiviral therapy and the development of live attenuated vaccines (LAV). Conclusively, both IAV NS1 and SARS-CoV-2 Nsp1 play an important role in virus-host interactions, viral replication, and pathogenesis, and pave the way to develop novel prophylactic and/or therapeutic interventions for the treatment of these important human respiratory viral pathogens.
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Affiliation(s)
- Ahmed Magdy Khalil
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Department of Zoonotic Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Aitor Nogales
- Center for Animal Health Research, CISA-INIA-CSIC, Madrid, Spain
| | - Luis Martínez-Sobrido
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ahmed Mostafa
- Disease Intervention & Prevention and Host Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
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13
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Zambo B, Gogl G, Morlet B, Eberling P, Negroni L, Moine H, Travé G. Comparative analysis of PDZ-binding motifs in the diacylglycerol kinase family. FEBS J 2024; 291:690-704. [PMID: 37942667 DOI: 10.1111/febs.16994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/26/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Diacylglycerol kinases (DGKs) control local and temporal amounts of diacylglycerol (DAG) and phosphatidic acid (PA) by converting DAG to PA through phosphorylation in cells. Certain DGK enzymes possess C-terminal sequences that encode potential PDZ-binding motifs (PBMs), which could be involved in their recruitment into supramolecular signaling complexes. In this study, we used two different interactomic approaches, quantitative native holdup (nHU) and qualitative affinity purification (AP), both coupled to mass spectrometry (MS) to investigate the PDZ partners associated with the potential PBMs of DGKs. Complementing these results with site-specific affinity interactomic data measured on isolated PDZ domain fragments and PBM motifs, as well as evolutionary conservation analysis of the PBMs of DGKs, we explored functional differences within different DGK groups. All our results indicate that putative PBM sequences of type II enzymes, namely DGKδ, DGKη, and DGKκ, are likely to be nonfunctional. In contrast, type IV enzymes, namely DGKζ and DGKι, possess highly promiscuous PBMs that interact with a set of PDZ proteins with very similar affinity interactomes. The combination of various interactomic assays and evolutionary analyses provides a useful strategy for identifying functional domains and motifs within diverse enzyme families.
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Affiliation(s)
- Boglarka Zambo
- Équipe Labellisée Ligue contre le cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Gergo Gogl
- Équipe Labellisée Ligue contre le cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Pascal Eberling
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Hervé Moine
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Gilles Travé
- Équipe Labellisée Ligue contre le cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
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14
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Guerin N, Childs H, Zhou P, Donald BR. DexDesign: an OSPREY-based algorithm for designing de novo D-peptide inhibitors. Protein Eng Des Sel 2024; 37:gzae007. [PMID: 38757573 PMCID: PMC11099876 DOI: 10.1093/protein/gzae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains play a central role in modulating polarization, signaling, and trafficking pathways. Mutations in PDZ domains lead to diseases such as cancer and cystic fibrosis, making PDZ domains attractive targets for therapeutic intervention. D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. Here, we introduce DexDesign, a novel OSPREY-based algorithm for computationally designing de novo D-peptide inhibitors. DexDesign leverages three novel techniques that are broadly applicable to computational protein design: the Minimum Flexible Set, K*-based Mutational Scan, and Inverse Alanine Scan. We apply these techniques and DexDesign to generate novel D-peptide inhibitors of two biomedically important PDZ domain targets: CAL and MAST2. We introduce a framework for analyzing de novo peptides-evaluation along a replication/restitution axis-and apply it to the DexDesign-generated D-peptides. Notably, the peptides we generated are predicted to bind their targets tighter than their targets' endogenous ligands, validating the peptides' potential as lead inhibitors. We also provide an implementation of DexDesign in the free and open source computational protein design software OSPREY.
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Affiliation(s)
- Nathan Guerin
- Department of Computer Science, Duke University, 308 Research Drive, Durham, NC 27708, United States
| | - Henry Childs
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, United States
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 22710, United States
| | - Bruce R Donald
- Department of Computer Science, Duke University, 308 Research Drive, Durham, NC 27708, United States
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, United States
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 22710, United States
- Department of Mathematics, Duke University, 120 Science Drive, Durham, NC 27708, United States
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15
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Healy MD, Collins BM. The PDLIM family of actin-associated proteins and their emerging role in membrane trafficking. Biochem Soc Trans 2023; 51:2005-2016. [PMID: 38095060 PMCID: PMC10754285 DOI: 10.1042/bst20220804] [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: 09/29/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
The PDZ and LIM domain (PDLIM) proteins are associated with the actin cytoskeleton and have conserved in roles in metazoan actin organisation and function. They primarily function as scaffolds linking various proteins to actin and its binding partner α-actinin via two conserved domains; an N-terminal postsynaptic density 95, discs large and zonula occludens-1 (PDZ) domain, and either single or multiple C-terminal LIN-11, Isl-1 and MEC-3 (LIM) domains in the actinin-associated LIM protein (ALP)- and Enigma-related proteins, respectively. While their role in actin organisation, such as in stress fibres or in the Z-disc of muscle fibres is well known, emerging evidence also suggests a role in actin-dependent membrane trafficking in the endosomal system. This is mediated by a recently identified interaction with the sorting nexin 17 (SNX17) protein, an adaptor for the trafficking complex Commander which is itself intimately linked to actin-directed formation of endosomal recycling domains. In this review we focus on the currently understood structural basis for PDLIM function. The PDZ domains mediate direct binding to distinct classes of PDZ-binding motifs (PDZbms), including α-actinin and other actin-associated proteins, and a highly specific interaction with the type III PDZbm such as the one found in the C-terminus of SNX17. The structures of the LIM domains are less well characterised and how they engage with their ligands is completely unknown. Despite the lack of experimental structural data, we find that recently developed machine learning-based structure prediction methods provide insights into their potential interactions and provide a template for further studies of their molecular functions.
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Affiliation(s)
- Michael D. Healy
- The University of Queensland, Institute for Molecular Bioscience, St Lucia, Queensland 4072, Australia
| | - Brett M. Collins
- The University of Queensland, Institute for Molecular Bioscience, St Lucia, Queensland 4072, Australia
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16
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Alla JA, Nerger E, Langer A, Quitterer U. Identification of membrane palmitoylated protein 1 (MPP1) as a heart-failure-promoting protein triggered by cardiovascular risk factors and aging. Biochem Pharmacol 2023; 217:115789. [PMID: 37683843 DOI: 10.1016/j.bcp.2023.115789] [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: 07/14/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
Membrane-Associated Guanylate Kinase (MAGUK) proteins are scaffold proteins with well-established functions in the neuronal system. A role of MAGUK protein up-regulation in the pathogenesis of heart failure is not established. This study identified the up-regulation of the MAGUK family protein MPP1 (Membrane Palmitoylated Protein 1), in cardiac transcriptome data of three different heart failure models. MPP1 was up-regulated in failing hearts of B6 mice with long-term chronic pressure overload, in failing hearts of aged Apoe-/- mice with long-term atherosclerosis, and in failing hearts of RKIP-transgenic mice with cardiotoxic lipid overload. MPP1-transgenic mice revealed that moderately (2-fold) increased cardiac MPP1 levels caused symptoms of heart failure with a significantly reduced left ventricular ejection fraction of 39.0 ± 6.9 % in Tg-MPP1 mice compared to 55.2 ± 3.7 % of non-transgenic B6 controls. Echocardiographic and histological analyses detected cardiac enlargement and cardiac dilation in Tg-MPP1 mice. The angiotensin II AT1 receptor (AGTR1) and MPP1 were co-localized on sarcolemmal membranes in vivo, and Tg-MPP1 mice had increased levels of cardiac AGTR1, which has an established heart failure-promoting function. The increased AGTR1 protein could be directly triggered by elevated MPP1 because MPP1 also increased the AGTR1 protein in non-cardiomyocyte HEK cells, which was detected by fluorescence measurement of AGTR1eYFP. MPP1 was not only up-regulated by major cardiovascular risk factors but also by old age, which is a major contributor to heart failure. Thus, the aging-induced MPP1 exerts a previously unrecognized role in heart failure pathogenesis by upregulation of the angiotensin II AT1 receptor (AGTR1) protein.
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Affiliation(s)
- Joshua Abd Alla
- Molecular Pharmacology, Department of Chemistry and Applied Biosciences, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Eric Nerger
- Molecular Pharmacology, Department of Chemistry and Applied Biosciences, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Langer
- Molecular Pharmacology, Department of Chemistry and Applied Biosciences, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Ursula Quitterer
- Molecular Pharmacology, Department of Chemistry and Applied Biosciences, ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland; Institute of Pharmacology and Toxicology, University of Zurich, CH-8057 Zurich, Switzerland
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17
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Javorsky A, Humbert PO, Kvansakul M. Viral manipulation of cell polarity signalling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119536. [PMID: 37437846 DOI: 10.1016/j.bbamcr.2023.119536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/24/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
Cell polarity refers to the asymmetric distribution of biomacromolecules that enable the correct orientation of a cell in a particular direction. It is thus an essential component for appropriate tissue development and function. Viral infections can lead to dysregulation of polarity. This is associated with a poor prognosis due to viral interference with core cell polarity regulatory scaffolding proteins that often feature PDZ (PSD-95, DLG, and ZO-1) domains including Scrib, Dlg, Pals1, PatJ, Par3 and Par6. PDZ domains are also promiscuous, binding to several different partners through their C-terminal region which contain PDZ-binding motifs (PBM). Numerous viruses encode viral effector proteins that target cell polarity regulators for their benefit and include papillomaviruses, flaviviruses and coronaviruses. A better understanding of the mechanisms of action utilised by viral effector proteins to subvert host cell polarity sigalling will provide avenues for future therapeutic intervention, while at the same time enhance our understanding of cell polarity regulation and its role tissue homeostasis.
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Affiliation(s)
- Airah Javorsky
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Patrick O Humbert
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia; Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria 3086, Australia; Department of Biochemistry & Pharmacology, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Marc Kvansakul
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia; Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria 3086, Australia.
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18
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Singh AK, Dadey DY, Rau MJ, Fitzpatrick J, Shah HK, Saikia M, Townsend R, Thotala D, Hallahan DE, Kapoor V. Blocking the functional domain of TIP1 by antibodies sensitizes cancer to radiation therapy. Biomed Pharmacother 2023; 166:115341. [PMID: 37625322 DOI: 10.1016/j.biopha.2023.115341] [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: 06/25/2023] [Revised: 08/11/2023] [Accepted: 08/19/2023] [Indexed: 08/27/2023] Open
Abstract
Non-small-cell lung cancer (NSCLC) and glioblastoma (GB) have poor prognoses. Discovery of new molecular targets is needed to improve therapy. Tax interacting protein 1 (TIP1), which plays a role in cancer progression, is overexpressed and radiation-inducible in NSCLC and GB. We evaluated the effect of an anti-TIP1 antibody alone and in combination with ionizing radiation (XRT) on NSCLC and GB in vitro and in vivo. NSCLC and GB cells were treated with anti-TIP1 antibodies and evaluated for proliferation, colony formation, endocytosis, and cell death. The efficacy of anti-TIP1 antibodies in combination with XRT on tumor growth was measured in mouse models of NSCLC and GB. mRNA sequencing was performed to understand the molecular mechanisms involved in the action of anti-TIP1 antibodies. We found that targeting the functional domain of TIP1 leads to endocytosis of the anti-TIP1 antibody followed by reduced proliferation and increased apoptosis-mediated cell death. Anti-TIP1 antibodies bound specifically (with high affinity) to cancer cells and synergized with XRT to significantly increase cytotoxicity in vitro and reduce tumor growth in mouse models of NSCLC and GB. Importantly, downregulation of cancer survival signaling pathways was found in vitro and in vivo following treatment with anti-TIP1 antibodies. TIP1 is a new therapeutic target for cancer treatment. Antibodies targeting the functional domain of TIP1 exhibited antitumor activity and enhanced the efficacy of radiation both in vitro and in vivo. Anti-TIP1 antibodies interrupt TIP1 function and are effective cancer therapy alone or in combination with XRT in mouse models of human cancer.
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Affiliation(s)
- Abhay K Singh
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - David Ya Dadey
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Rau
- Center for Cellular Imaging, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - James Fitzpatrick
- Center for Cellular Imaging, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Departments of Cell Biology & Physiology and Neuroscience, Washington University School of Medicine, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO,USA
| | - Harendra K Shah
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Minakshi Saikia
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Reid Townsend
- Department of Medicine, Washington University in St. Louis, St. Louis, MO,USA; Siteman Cancer Center, St. Louis, MO, USA
| | - Dinesh Thotala
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Siteman Cancer Center, St. Louis, MO, USA
| | - Dennis E Hallahan
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Siteman Cancer Center, St. Louis, MO, USA.
| | - Vaishali Kapoor
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Siteman Cancer Center, St. Louis, MO, USA.
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19
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Sahoo G, Samal D, Khandayataray P, Murthy MK. A Review on Caspases: Key Regulators of Biological Activities and Apoptosis. Mol Neurobiol 2023; 60:5805-5837. [PMID: 37349620 DOI: 10.1007/s12035-023-03433-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 06/06/2023] [Indexed: 06/24/2023]
Abstract
Caspases are proteolytic enzymes that belong to the cysteine protease family and play a crucial role in homeostasis and programmed cell death. Caspases have been broadly classified by their known roles in apoptosis (caspase-3, caspase-6, caspase-7, caspase-8, and caspase-9 in mammals) and in inflammation (caspase-1, caspase-4, caspase-5, and caspase-12 in humans, and caspase-1, caspase-11, and caspase-12 in mice). Caspases involved in apoptosis have been subclassified by their mechanism of action as either initiator caspases (caspase-8 and caspase-9) or executioner caspases (caspase-3, caspase-6, and caspase-7). Caspases that participate in apoptosis are inhibited by proteins known as inhibitors of apoptosis (IAPs). In addition to apoptosis, caspases play a role in necroptosis, pyroptosis, and autophagy, which are non-apoptotic cell death processes. Dysregulation of caspases features prominently in many human diseases, including cancer, autoimmunity, and neurodegenerative disorders, and increasing evidence shows that altering caspase activity can confer therapeutic benefits. This review covers the different types of caspases, their functions, and their physiological and biological activities and roles in different organisms.
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Affiliation(s)
- Gayatri Sahoo
- Department of Zoology, PSSJ College, Banarpal, 759128, Odisha, India
| | - Dibyaranjan Samal
- Department of Biotechnology, Academy of Management and Information Technology (AMIT, affiliated to Utkal University), Khurda, 752057, Odisha, India
| | | | - Meesala Krishna Murthy
- Department of Allied Health Sciences, Chitkara School of Health Sciences, Chitkara University, Rajpura, Punjab, 140401, India.
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20
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Hu Y, Jia K, Zhou Y, Chen L, Wang F, Yi X, Huang Y, Ge Y, Chen X, Liao D, Peng Y, Meng Y, Liu Y, Luo Q, Cheng B, Zhao Y, Lu H, Yuan W. Rutin hydrate relieves neuroinflammation in zebrafish models: Involvement of NF-κB pathway as a central network. FISH & SHELLFISH IMMUNOLOGY 2023; 141:109062. [PMID: 37678480 DOI: 10.1016/j.fsi.2023.109062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/26/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023]
Abstract
Neuroinflammation is prevalent in multiple brain diseases and may also lead to dementia, cognitive impairment, and impaired spatial memory function associated with neurodegenerative diseases. A neuroprotective and antioxidant flavonoid, rutin hydrate (RH), was evaluated for the anti-neuroinflammatory activity mediated by copper sulfate (CuSO4) solution and lipopolysaccharide (LPS) in zebrafish. The results showed that 100 mg/L RH significantly reduced the ratio of neutrophil mobility in caudal hematopoietic tissue (CHT) region caused by CuSO4 and the number of neutrophils co-localized with facial peripheral nerves. In the LPS model, RH co-injection significantly diminished neutrophil and macrophage migration. Therefore, RH exhibited a significant rescue effect on both models. In addition, RH treatment remarkably reduced the effects of neuroinflammation on the locomotor ability, expression levels of genes associated with behavioral disorders, and acetylcholinesterase (AChE) activity. Furthermore, network pharmacology techniques were employed to investigate the potential mechanisms, and the associated genes and enzyme activities were validated in order to elucidate the underlying mechanisms. Network pharmacological analysis and zebrafish model indicated that RH regulated the expressions of NF-κB pathway-related targets (Toll-like receptor 9 (tlr9), nuclear factor kappa B subunit 1 (nfkb1), RELA proto-oncogene (RelA), nitric oxide synthase 2a, inducible (nos2a), tumour necrosis factor alpha-like (tnfα), interleukin 6 (il6), interleukin 1β (il1β), chemokine 8 (cxcl8), and macrophage migration inhibitory factor (mif)) as well as six key factors (arachidonic acid 4 alpha-lipoxygenase (alox4a), arachidonate 5-lipoxygenase a (alox5), prion protein a (prnpa), integrin, beta 2 (itgb2), catalase (CAT), and alkaline phosphatase (ALP) enzymes). Through this study, a thorough understanding of the mechanism underlying the therapeutic effects of RH in neuroinflammation has been achieved, thereby establishing a solid foundation for further research on the potential therapeutic applications of RH in neuroinflammatory disorders.
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Affiliation(s)
- Ying Hu
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Kun Jia
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Yatong Zhou
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Lixin Chen
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Fei Wang
- The First Clinical College of Gannan Medical Uinversity, Ganzhou, 341000, Jiangxi, China
| | - Xiaokun Yi
- The First Clinical College of Gannan Medical Uinversity, Ganzhou, 341000, Jiangxi, China
| | - Yong Huang
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Yurui Ge
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Xiaomei Chen
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Dalong Liao
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Yuyang Peng
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Yunlong Meng
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Ye Liu
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Qiang Luo
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Bo Cheng
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Yan Zhao
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Huiqiang Lu
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China; Affiliated Hospital of Jinggangshan University, Jinggangshan University, Ji'an, 343009, Jiangxi, China.
| | - Wei Yuan
- Ganzhou Key Laboratory for Drug Screening and Discovery, School of Geography and Environmental Engineering, Gannan Normal University, Ganzhou, 341000, Jiangxi, China.
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21
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Castro-Cruz M, Hyka L, Daaboul G, Leblanc R, Meeussen S, Lembo F, Oris A, Van Herck L, Granjeaud S, David G, Zimmermann P. PDZ scaffolds regulate extracellular vesicle production, composition, and uptake. Proc Natl Acad Sci U S A 2023; 120:e2310914120. [PMID: 37695903 PMCID: PMC10515165 DOI: 10.1073/pnas.2310914120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 08/08/2023] [Indexed: 09/13/2023] Open
Abstract
Extracellular vesicles (EVs) are membrane-limited organelles mediating cell-to-cell communication in health and disease. EVs are of high medical interest, but their rational use for diagnostics or therapies is restricted by our limited understanding of the molecular mechanisms governing EV biology. Here, we tested whether PDZ proteins, molecular scaffolds that support the formation, transport, and function of signal transduction complexes and that coevolved with multicellularity, may represent important EV regulators. We reveal that the PDZ proteome (ca. 150 proteins in human) establishes a discrete number of direct interactions with the tetraspanins CD9, CD63, and CD81, well-known EV constituents. Strikingly, PDZ proteins interact more extensively with syndecans (SDCs), ubiquitous membrane proteins for which we previously demonstrated an important role in EV biogenesis, loading, and turnover. Nine PDZ proteins were tested in loss-of-function studies. We document that these PDZ proteins regulate both tetraspanins and SDCs, differentially affecting their steady-state levels, subcellular localizations, metabolism, endosomal budding, and accumulations in EVs. Importantly, we also show that PDZ proteins control the levels of heparan sulfate at the cell surface that functions in EV capture. In conclusion, our study establishes that the extensive networking of SDCs, tetraspanins, and PDZ proteins contributes to EV heterogeneity and turnover, highlighting an important piece of the molecular framework governing intracellular trafficking and intercellular communication.
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Affiliation(s)
- Monica Castro-Cruz
- Department of Human Genetics, Katholieke Universiteit Leuven, B-3000Leuven, Belgium
- Équipe Labellisée Ligue 2018, Aix Marseille Université, INSERM 1068, CNRS 7258, Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille, 13009Marseille, France
| | - Lukas Hyka
- Department of Human Genetics, Katholieke Universiteit Leuven, B-3000Leuven, Belgium
- Équipe Labellisée Ligue 2018, Aix Marseille Université, INSERM 1068, CNRS 7258, Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille, 13009Marseille, France
| | | | - Raphael Leblanc
- Équipe Labellisée Ligue 2018, Aix Marseille Université, INSERM 1068, CNRS 7258, Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille, 13009Marseille, France
| | - Sofie Meeussen
- Department of Human Genetics, Katholieke Universiteit Leuven, B-3000Leuven, Belgium
| | - Frédérique Lembo
- Équipe Labellisée Ligue 2018, Aix Marseille Université, INSERM 1068, CNRS 7258, Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille, 13009Marseille, France
| | - Anouk Oris
- Department of Human Genetics, Katholieke Universiteit Leuven, B-3000Leuven, Belgium
| | - Lore Van Herck
- Department of Human Genetics, Katholieke Universiteit Leuven, B-3000Leuven, Belgium
| | - Samuel Granjeaud
- Équipe Labellisée Ligue 2018, Aix Marseille Université, INSERM 1068, CNRS 7258, Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille, 13009Marseille, France
| | - Guido David
- Department of Human Genetics, Katholieke Universiteit Leuven, B-3000Leuven, Belgium
- Équipe Labellisée Ligue 2018, Aix Marseille Université, INSERM 1068, CNRS 7258, Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille, 13009Marseille, France
| | - Pascale Zimmermann
- Department of Human Genetics, Katholieke Universiteit Leuven, B-3000Leuven, Belgium
- Équipe Labellisée Ligue 2018, Aix Marseille Université, INSERM 1068, CNRS 7258, Institut Paoli Calmettes, Centre de Recherche en Cancérologie de Marseille, 13009Marseille, France
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22
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Maseko SB, Brammerloo Y, Van Molle I, Sogues A, Martin C, Gorgulla C, Plant E, Olivet J, Blavier J, Ntombela T, Delvigne F, Arthanari H, El Hajj H, Bazarbachi A, Van Lint C, Salehi-Ashtiani K, Remaut H, Ballet S, Volkov AN, Twizere JC. Identification of small molecule antivirals against HTLV-1 by targeting the hDLG1-Tax-1 protein-protein interaction. Antiviral Res 2023; 217:105675. [PMID: 37481039 DOI: 10.1016/j.antiviral.2023.105675] [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: 06/24/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
Human T-cell leukemia virus type-1 (HTLV-1) is the first pathogenic retrovirus discovered in human. Although HTLV-1-induced diseases are well-characterized and linked to the encoded Tax-1 oncoprotein, there is currently no strategy to target Tax-1 functions with small molecules. Here, we analyzed the binding of Tax-1 to the human homolog of the drosophila discs large tumor suppressor (hDLG1/SAP97), a multi-domain scaffolding protein involved in Tax-1-transformation ability. We have solved the structures of the PDZ binding motif (PBM) of Tax-1 in complex with the PDZ1 and PDZ2 domains of hDLG1 and assessed the binding of 10 million molecules by virtual screening. Among the 19 experimentally confirmed compounds, one systematically inhibited the Tax-1-hDLG1 interaction in different biophysical and cellular assays, as well as HTLV-1 cell-to-cell transmission in a T-cell model. Thus, our work demonstrates that interactions involving Tax-1 PDZ-domains are amenable to small-molecule inhibition, which provides a framework for the design of targeted therapies for HTLV-1-induced diseases.
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Affiliation(s)
- Sibusiso B Maseko
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | - Yasmine Brammerloo
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | - Inge Van Molle
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Adrià Sogues
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Estelle Plant
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Julien Olivet
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium; Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research and Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Jeremy Blavier
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | | | - Frank Delvigne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liege Belgium
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hiba El Hajj
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ali Bazarbachi
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University of Abu Dhabi, Abu Dhabi United Arab Emirates
| | - Han Remaut
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Alexander N Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium; Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels Belgium.
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium; TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liege Belgium; Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University of Abu Dhabi, Abu Dhabi United Arab Emirates.
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23
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Castro-Cruz M, Lembo F, Borg JP, Travé G, Vincentelli R, Zimmermann P. The Human PDZome 2.0: Characterization of a New Resource to Test for PDZ Interactions by Yeast Two-Hybrid. MEMBRANES 2023; 13:737. [PMID: 37623798 PMCID: PMC10456741 DOI: 10.3390/membranes13080737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/28/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
PSD95-disc large-zonula occludens (PDZ) domains are globular modules of 80-90 amino acids that co-evolved with multicellularity. They commonly bind to carboxy-terminal sequences of a plethora of membrane-associated proteins and influence their trafficking and signaling. We previously built a PDZ resource (PDZome) allowing us to unveil human PDZ interactions by Yeast two-hybrid. Yet, this resource is incomplete according to the current knowledge on the human PDZ proteome. Here we built the PDZome 2.0 library for Yeast two-hybrid, based on a PDZ library manually curated from online resources. The PDZome2.0 contains 305 individual clones (266 PDZ domains in isolation and 39 tandems), for which all boundaries were designed based on available PDZ structures. Using as bait the E6 oncoprotein from HPV16, a known promiscuous PDZ interactor, we show that PDZome 2.0 outperforms the previous resource.
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Affiliation(s)
- Monica Castro-Cruz
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium;
- Équipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, 13009 Marseille, France;
| | - Frédérique Lembo
- Équipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, 13009 Marseille, France;
| | - Jean-Paul Borg
- Marseille Proteomics Platform, CRCM, Institute Paoli-Calmettes, Aix-Marseille Université, Inserm, CNRS, 13009 Marseille, France;
| | - Gilles Travé
- Équipe Labellisée Ligue 2015, Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 67404 Illkirch, France;
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, 13009 Marseille, France;
| | - Pascale Zimmermann
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium;
- Équipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, 13009 Marseille, France;
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24
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Shah K, Cook M. LIMK2: A Multifaceted kinase with pleiotropic roles in human physiology and pathologies. Cancer Lett 2023; 565:216207. [PMID: 37141984 PMCID: PMC10316521 DOI: 10.1016/j.canlet.2023.216207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023]
Abstract
LIMK2, a serine-specific kinase, was discovered as an actin dynamics regulating kinase. Emerging studies have shown its pivotal role in numerous human malignancies and neurodevelopmental disorder. Inducible knockdown of LIMK2 fully reverses tumorigenesis, underscoring its potential as a clinical target. However, the molecular mechanisms leading to its upregulation and its deregulated activity in various diseases largely remain unknown. Similarly, LIMK2's peptide substrate specificity has not been analyzed. This is particularly important for LIMK2, a kinase almost three decades old, as only a handful of its substrates are known to date. As a result, most of LIMK2's physiological and pathological roles have been assigned to its regulation of actin dynamics via cofilin. This review focuses on LIMK2's unique catalytic mechanism, substrate specificity and its upstream regulators at transcriptional, post-transcriptional and post-translational stages. Moreover, emerging studies have unveiled a few tumor suppressors and oncogenes as LIMK2's direct substrates, which in turn have uncovered novel molecular mechanisms by which it plays pleiotropic roles in human physiology and pathologies independent of actin dynamics.
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Affiliation(s)
- Kavita Shah
- Department of Chemistry and Purdue University Center for Cancer Research, 560 Oval Drive, West Lafayette, IN, 47907, USA.
| | - Mason Cook
- Department of Chemistry and Purdue University Center for Cancer Research, 560 Oval Drive, West Lafayette, IN, 47907, USA
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25
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Tahti EF, Blount JM, Jackson SN, Gao M, Gill NP, Smith SN, Pederson NJ, Rumph SN, Struyvenberg SA, Mackley IGP, Madden DR, Amacher JF. Additive energetic contributions of multiple peptide positions determine the relative promiscuity of viral and human sequences for PDZ domain targets. Protein Sci 2023; 32:e4611. [PMID: 36851847 PMCID: PMC10022582 DOI: 10.1002/pro.4611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/13/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
Protein-protein interactions that involve recognition of short peptides are critical in cellular processes. Protein-peptide interaction surface areas are relatively small and shallow, and there are often overlapping specificities in families of peptide-binding domains. Therefore, dissecting selectivity determinants can be challenging. PDZ domains are a family of peptide-binding domains located in several intracellular signaling and trafficking pathways. These domains are also directly targeted by pathogens, and a hallmark of many oncogenic viral proteins is a PDZ-binding motif. However, amidst sequences that target PDZ domains, there is a wide spectrum in relative promiscuity. For example, the viral HPV16 E6 oncoprotein recognizes over double the number of PDZ domain-containing proteins as the cystic fibrosis transmembrane conductance regulator (CFTR) in the cell, despite similar PDZ targeting-sequences and identical motif residues. Here, we determine binding affinities for PDZ domains known to bind either HPV16 E6 alone or both CFTR and HPV16 E6, using peptides matching WT and hybrid sequences. We also use energy minimization to model PDZ-peptide complexes and use sequence analyses to investigate this difference. We find that while the majority of single mutations had marginal effects on overall affinity, the additive effect on the free energy of binding accurately describes the selectivity observed. Taken together, our results describe how complex and differing PDZ interactomes can be programmed in the cell.
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Affiliation(s)
- Elise F. Tahti
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Jadon M. Blount
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Sophie N. Jackson
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Melody Gao
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Nicholas P. Gill
- Department of BiochemistryGeisel School of Medicine at DartmouthHanoverNew HampshireUSA
| | - Sarah N. Smith
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Nick J. Pederson
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | | | | | - Iain G. P. Mackley
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Dean R. Madden
- Department of BiochemistryGeisel School of Medicine at DartmouthHanoverNew HampshireUSA
| | - Jeanine F. Amacher
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
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26
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Baliova M, Jahodova I, Jursky F. A Significant Difference in Core PDZ Interactivity of SARS-CoV, SARS-CoV2 and MERS-CoV Protein E Peptide PDZ Motifs In Vitro. Protein J 2023:10.1007/s10930-023-10103-x. [PMID: 36932261 PMCID: PMC10023026 DOI: 10.1007/s10930-023-10103-x] [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] [Accepted: 03/01/2023] [Indexed: 03/19/2023]
Abstract
Small structural E protein of coronaviruses uses its C-terminal PDZ motif to compromise the cellular PDZ interactome. In this work we compared core PDZ interactivity of small (seven amino acids) peptide PDZ motifs, originating from the envelope proteins of recently transmitted coronaviruses SARS-CoV, SARS-CoV2, and MERS-CoV. As the interaction targets we used 23 domains of the largest PDZ proteins MUPP1/MPDZ and PATJ/INAD. Results revealed exceptional affinity and interaction promiscuity of MERS-CoV PDZ motif in vitro, suggesting an increased probability of potential PDZ targets in vivo. We hypothesize that together with its known ability to enter the cells from both apical and basolateral sites, this might further contribute to its elevated disruption of cellular PDZ pathways and higher virulence.
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Affiliation(s)
- Martina Baliova
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska Cesta 21, 845 51 Bratislava, Slovakia
| | - Iveta Jahodova
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska Cesta 21, 845 51 Bratislava, Slovakia
| | - Frantisek Jursky
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska Cesta 21, 845 51 Bratislava, Slovakia
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27
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Jahodova I, Baliova M, Jursky F. PDZ interaction of the GABA transporter GAT1 with the syntenin-1 in Neuro-2a cells. Neurochem Int 2023; 165:105522. [PMID: 36966820 DOI: 10.1016/j.neuint.2023.105522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/15/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
The GABA transporter GAT1 regulates brain inhibitory neurotransmission and it is considered a potential therapeutic target for the treatment of wide spectrum of neurological diseases including epilepsy, stroke and autism. Syntenin-1 binds to syntaxin 1A, which is known to regulate the plasma membrane insertion of several neurotransmitter transporters. Previously, a direct interaction of syntenin-1 with the glycine transporter GlyT2 was reported. Here, we show that the GABA transporter GAT1 also directly interacts with syntenin-1, involving both unidentified protein interaction interface and the GAT1 C-terminal PDZ binding motif interacting mainly with syntenin-1 PDZ domain 1. The PDZ interaction was eliminated by the mutation of GAT1 isoleucine 599 and tyrosine 598 located in PDZ positions 0 and -1, respectively. This indicates an unconventional PDZ interaction and possible regulation of the transporter PDZ motif via tyrosine phosphorylation. Whole syntenin-1 protein fused to GST protein and immobilised on glutathione resin coprecipitated intact GAT1 transporter from an extract of GAT1 transfected neuroblastoma N2a cells. This coprecipitation was inhibited by tyrosine phosphatases inhibitor pervanadate. The fluorescence tagged GAT1 and syntenin-1 colocalized upon coexpression in N2a cells. The above results show that syntenin-1 might be, in addition to GlyT2, directly involved in the trafficking of GAT1 transporter.
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Affiliation(s)
- Iveta Jahodova
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia
| | - Martina Baliova
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia.
| | - Frantisek Jursky
- Laboratory of Neurobiology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 845 51, Bratislava, Slovakia.
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28
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Cowan B, Beveridge DL, Thayer KM. Allosteric Signaling in PDZ Energetic Networks: Embedding Error Analysis. J Phys Chem B 2023; 127:623-633. [PMID: 36626697 PMCID: PMC9884075 DOI: 10.1021/acs.jpcb.2c06546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/23/2022] [Indexed: 01/12/2023]
Abstract
Allosteric signaling in proteins has been known for some half a century, yet how the signal traverses the protein remains an active area of research. Recently, the importance of electrostatics to achieve long-range signaling has become increasingly appreciated. Our laboratory has been working on developing network approaches to capture such interactions. In this study, we turn our attention to the well-studied allosteric model protein, PDZ. We study the allosteric dynamics on a per-residue basis in key constructs involving the PDZ domain, its allosteric effector, and its peptide ligand. We utilize molecular dynamics trajectories to create the networks for the constructs to explore the allosteric effect by plotting the heat kernel results onto axes defined by principal components. We introduce a new metric to quantitate the volume sampled by a residue in the latent space. We relate our findings to PDZ and the greater field of allostery.
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Affiliation(s)
- Benjamin
S. Cowan
- Department
of Computer Science, Wesleyan University, Middletown, Connecticut06457, United States
- College
of Integrative Sciences, Wesleyan University, Middletown, Connecticut06457, United States
| | - David L. Beveridge
- Molecular
Biophysics Program, Wesleyan University, Middletown, Connecticut06457, United States
- Department
of Chemistry, Wesleyan University, Middletown, Connecticut06457, United States
| | - Kelly M. Thayer
- Department
of Computer Science, Wesleyan University, Middletown, Connecticut06457, United States
- Molecular
Biophysics Program, Wesleyan University, Middletown, Connecticut06457, United States
- Department
of Chemistry, Wesleyan University, Middletown, Connecticut06457, United States
- College
of Integrative Sciences, Wesleyan University, Middletown, Connecticut06457, United States
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29
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Tahti EF, Blount JM, Jackson SN, Gao M, Gill NP, Smith SN, Pederson NJ, Rumph SN, Struyvenberg SA, Mackley IGP, Madden DR, Amacher JF. Additive energetic contributions of multiple peptide positions determine the relative promiscuity of viral and human sequences for PDZ domain targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2022.12.31.522388. [PMID: 36711692 PMCID: PMC9881875 DOI: 10.1101/2022.12.31.522388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Protein-protein interactions that include recognition of short sequences of amino acids, or peptides, are critical in cellular processes. Protein-peptide interaction surface areas are relatively small and shallow, and there are often overlapping specificities in families of peptide-binding domains. Therefore, dissecting selectivity determinants can be challenging. PDZ domains are an example of a peptide-binding domain located in several intracellular signaling and trafficking pathways, which form interactions critical for the regulation of receptor endocytic trafficking, tight junction formation, organization of supramolecular complexes in neurons, and other biological systems. These domains are also directly targeted by pathogens, and a hallmark of many oncogenic viral proteins is a PDZ-binding motif. However, amidst sequences that target PDZ domains, there is a wide spectrum in relative promiscuity. For example, the viral HPV16 E6 oncoprotein recognizes over double the number of PDZ domain-containing proteins as the cystic fibrosis transmembrane conductance regulator (CFTR) in the cell, despite similar PDZ targeting-sequences and identical motif residues. Here, we determine binding affinities for PDZ domains known to bind either HPV16 E6 alone or both CFTR and HPV16 E6, using peptides matching WT and hybrid sequences. We also use energy minimization to model PDZ-peptide complexes and use sequence analyses to investigate this difference. We find that while the majority of single mutations had a marginal effect on overall affinity, the additive effect on the free energy of binding accurately describes the selectivity observed. Taken together, our results describe how complex and differing PDZ interactomes can be programmed in the cell.
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Affiliation(s)
- Elise F. Tahti
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Jadon M. Blount
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Sophie N. Jackson
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Melody Gao
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Nicholas P. Gill
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Sarah N. Smith
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Nick J. Pederson
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Simone N. Rumph
- Department of Biochemistry, Bowdoin College, Brunswick, ME, USA
| | | | - Iain G. P. Mackley
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
| | - Dean R. Madden
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Jeanine F. Amacher
- Department of Chemistry, Western Washington University, Bellingham, WA, USA
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30
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Stevens AO, Kazan IC, Ozkan B, He Y. Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all-atom simulations. Protein Sci 2022; 31:e4474. [PMID: 36251217 PMCID: PMC9667829 DOI: 10.1002/pro.4474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022]
Abstract
The PDZ family is comprised of small modular domains that play critical roles in the allosteric modulation of many cellular signaling processes by binding to the C-terminal tail of different proteins. As dominant modular proteins that interact with a diverse set of peptides, it is of particular interest to explore how different binding partners induce different allosteric effects on the same PDZ domain. Because the PICK1 PDZ domain can bind different types of ligands, it is an ideal test case to answer this question and explore the network of interactions that give rise to dynamic allostery. Here, we use all-atom molecular dynamics simulations to explore dynamic allostery in the PICK1 PDZ domain by modeling two PICK1 PDZ systems: PICK1 PDZ-DAT and PICK1 PDZ-GluR2. Our results suggest that ligand binding to the PICK1 PDZ domain induces dynamic allostery at the αA helix that is similar to what has been observed in other PDZ domains. We found that the PICK1 PDZ-ligand distance is directly correlated with both dynamic changes of the αA helix and the distance between the αA helix and βB strand. Furthermore, our work identifies a hydrophobic core between DAT/GluR2 and I35 as a key interaction in inducing such dynamic allostery. Finally, the unique interaction patterns between different binding partners and the PICK1 PDZ domain can induce unique dynamic changes to the PICK1 PDZ domain. We suspect that unique allosteric coupling patterns with different ligands may play a critical role in how PICK1 performs its biological functions in various signaling networks.
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Affiliation(s)
- Amy O. Stevens
- Department of Chemistry and Chemical BiologyThe University of New MexicoAlbuquerqueNew MexicoUSA
| | - I. Can Kazan
- Department of Physics, Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | - Banu Ozkan
- Department of Physics, Center for Biological PhysicsArizona State UniversityTempeArizonaUSA
| | - Yi He
- Department of Chemistry and Chemical BiologyThe University of New MexicoAlbuquerqueNew MexicoUSA
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31
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Fisher LAB, Schöck F. The unexpected versatility of ALP/Enigma family proteins. Front Cell Dev Biol 2022; 10:963608. [PMID: 36531944 PMCID: PMC9751615 DOI: 10.3389/fcell.2022.963608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022] Open
Abstract
One of the most intriguing features of multicellular animals is their ability to move. On a cellular level, this is accomplished by the rearrangement and reorganization of the cytoskeleton, a dynamic network of filamentous proteins which provides stability and structure in a stationary context, but also facilitates directed movement by contracting. The ALP/Enigma family proteins are a diverse group of docking proteins found in numerous cellular milieus and facilitate these processes among others. In vertebrates, they are characterized by having a PDZ domain in combination with one or three LIM domains. The family is comprised of CLP-36 (PDLIM1), Mystique (PDLIM2), ALP (PDLIM3), RIL (PDLIM4), ENH (PDLIM5), ZASP (PDLIM6), and Enigma (PDLIM7). In this review, we will outline the evolution and function of their protein domains which confers their versatility. Additionally, we highlight their role in different cellular environments, focusing specifically on recent advances in muscle research using Drosophila as a model organism. Finally, we show the relevance of this protein family to human myopathies and the development of muscle-related diseases.
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32
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Ashkinadze D, Kadavath H, Pokharna A, Chi CN, Friedmann M, Strotz D, Kumari P, Minges M, Cadalbert R, Königl S, Güntert P, Vögeli B, Riek R. Atomic resolution protein allostery from the multi-state structure of a PDZ domain. Nat Commun 2022; 13:6232. [PMID: 36266302 PMCID: PMC9584909 DOI: 10.1038/s41467-022-33687-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/28/2022] [Indexed: 12/25/2022] Open
Abstract
Recent methodological advances in solution NMR allow the determination of multi-state protein structures and provide insights into structurally and dynamically correlated protein sites at atomic resolution. This is demonstrated in the present work for the well-studied PDZ2 domain of protein human tyrosine phosphatase 1E for which protein allostery had been predicted. Two-state protein structures were calculated for both the free form and in complex with the RA-GEF2 peptide using the exact nuclear Overhauser effect (eNOE) method. In the apo protein, an allosteric conformational selection step comprising almost 60% of the domain was detected with an "open" ligand welcoming state and a "closed" state that obstructs the binding site by changing the distance between the β-sheet 2, α-helix 2, and sidechains of residues Lys38 and Lys72. The observed induced fit-type apo-holo structural rearrangements are in line with the previously published evolution-based analysis covering ~25% of the domain with only a partial overlap with the protein allostery of the open form. These presented structural studies highlight the presence of a dedicated highly optimized and complex dynamic interplay of the PDZ2 domain owed by the structure-dynamics landscape.
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Affiliation(s)
- Dzmitry Ashkinadze
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Harindranath Kadavath
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Aditya Pokharna
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Celestine N. Chi
- grid.8993.b0000 0004 1936 9457Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 75121 Uppsala, Sweden
| | - Michael Friedmann
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Dean Strotz
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Pratibha Kumari
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Martina Minges
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Riccardo Cadalbert
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Stefan Königl
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
| | - Peter Güntert
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland ,grid.7839.50000 0004 1936 9721Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany ,grid.265074.20000 0001 1090 2030Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo 1920397 Japan
| | - Beat Vögeli
- grid.266190.a0000000096214564Biochemistry and Molecular Genetics Department, University of Colorado School of Medicine, Colorado, CO USA
| | - Roland Riek
- grid.5801.c0000 0001 2156 2780Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland
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33
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Murph M, Singh S, Schvarzstein M. A combined in silico and in vivo approach to the structure-function annotation of SPD-2 provides mechanistic insight into its functional diversity. Cell Cycle 2022; 21:1958-1979. [PMID: 35678569 PMCID: PMC9415446 DOI: 10.1080/15384101.2022.2078458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 04/10/2022] [Accepted: 05/04/2022] [Indexed: 11/03/2022] Open
Abstract
Centrosomes are organelles that function as hubs of microtubule nucleation and organization, with key roles in organelle positioning, asymmetric cell division, ciliogenesis, and signaling. Aberrant centrosome number, structure or function is linked to neurodegenerative diseases, developmental abnormalities, ciliopathies, and tumor development. A major regulator of centrosome biogenesis and function in C. elegans is the conserved Spindle-defective protein 2 (SPD-2), a homolog of the human CEP-192 protein. CeSPD-2 is required for centrosome maturation, centriole duplication, spindle assembly and possibly cell polarity establishment. Despite its importance, the specific molecular mechanism of CeSPD-2 regulation and function is poorly understood. Here, we combined computational analysis with cell biology approaches to uncover possible structure-function relationships of CeSPD-2 that may shed mechanistic light on its function. Domain prediction analysis corroborated and refined previously identified coiled-coils and ASH (Aspm-SPD-2 Hydin) domains and identified new domains: a GEF domain, an Ig-like domain, and a PDZ-like domain. In addition to these predicted structural features, CeSPD-2 is also predicted to be intrinsically disordered. Surface electrostatic maps identified a large basic region unique to the ASH domain of CeSPD-2. This basic region overlaps with most of the residues predicted to be involved in protein-protein interactions. In vivo, ASH::GFP localized to centrosomes and centrosome-associated microtubules. Our analysis groups ASH domains, PapD, Usher chaperone domains, and Major Sperm Protein (MSP) domains into a single superfold within the larger Immunoglobulin superfamily. This study lays the groundwork for designing rational hypothesis-based experiments to uncover the mechanisms of CeSPD-2 function in vivo.Abbreviations: AIR, Aurora kinase; ASH, Aspm-SPD-2 Hydin; ASP, Abnormal Spindle Protein; ASPM, Abnormal Spindle-like Microcephaly-associated Protein; CC, coiled-coil; CDK, Cyclin-dependent Kinase; Ce, Caenorhabditis elegans; CEP, Centrosomal Protein; CPAP, centrosomal P4.1-associated protein; D, Drosophila; GAP, GTPase activating protein; GEF, GTPase guanine nucleotide exchange factor; Hs, Homo sapiens/Human; Ig, Immunoglobulin; MAP, Microtubule associated Protein; MSP, Major Sperm Protein; MDP, Major Sperm Domain-Containing Protein; OCRL-1, Golgi endocytic trafficking protein Inositol polyphosphate 5-phosphatase; PAR, abnormal embryonic PARtitioning of the cytosol; PCM, Pericentriolar material; PCMD, pericentriolar matrix deficient; PDZ, PSD95/Dlg-1/zo-1; PLK, Polo like kinase; RMSD, Root Mean Square Deviation; SAS, Spindle assembly abnormal proteins; SPD, Spindle-defective protein; TRAPP, TRAnsport Protein Particle; Xe, Xenopus; ZYG, zygote defective protein.
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Affiliation(s)
- Mikaela Murph
- Department of Biology, City University of New York, Brooklyn College, New York, NY, USA
| | - Shaneen Singh
- Department of Biology, City University of New York, Brooklyn College, New York, NY, USA
- Department of Biology, The Graduate Center at City University of New York, New York, NY, USA
- Department Biochemistry, The Graduate Center at City University of New York, New York, NY, USA
| | - Mara Schvarzstein
- Department of Biology, City University of New York, Brooklyn College, New York, NY, USA
- Department of Biology, The Graduate Center at City University of New York, New York, NY, USA
- Department Biochemistry, The Graduate Center at City University of New York, New York, NY, USA
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34
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Stevens AO, Luo S, He Y. Three Binding Conformations of BIO124 in the Pocket of the PICK1 PDZ Domain. Cells 2022; 11:cells11152451. [PMID: 35954295 PMCID: PMC9368557 DOI: 10.3390/cells11152451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 11/30/2022] Open
Abstract
The PDZ family has drawn attention as possible drug targets because of the domains’ wide ranges of function and highly conserved binding pockets. The PICK1 PDZ domain has been proposed as a possible drug target because the interactions between the PICK1 PDZ domain and the GluA2 subunit of the AMPA receptor have been shown to progress neurodegenerative diseases. BIO124 has been identified as a sub µM inhibitor of the PICK1–GluA2 interaction. Here, we use all-atom molecular dynamics simulations to reveal the atomic-level interaction pattern between the PICK1 PDZ domain and BIO124. Our simulations reveal three unique binding conformations of BIO124 in the PICK1 PDZ binding pocket, referred to here as state 0, state 1, and state 2. Each conformation is defined by a unique hydrogen bonding network and a unique pattern of hydrophobic interactions between BIO124 and the PICK1 PDZ domain. Interestingly, each conformation of BIO124 results in different dynamic changes to the PICK1 PDZ domain. Unlike states 1 and 2, state 0 induces dynamic coupling between BIO124 and the αA helix. Notably, this dynamic coupling with the αA helix is similar to what has been observed in other PDZ–ligand complexes. Our analysis indicates that the interactions formed between BIO124 and I35 may be the key to inducing dynamic coupling with the αA helix. Lastly, we suspect that the conformational shifts observed in our simulations may affect the stability and thus the overall effectiveness of BIO124. We propose that a physically larger inhibitor may be necessary to ensure sufficient interactions that permit stable binding between a drug and the PICK1 PDZ domain.
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Affiliation(s)
- Amy O. Stevens
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Samuel Luo
- Albuquerque Academy, Albuquerque, NM 87131, USA
| | - Yi He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
- Correspondence:
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35
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Rosas-García J, Ramón-Luing LA, Bobadilla K, Meraz-Ríos MA, Sevilla-Reyes EE, Santos-Mendoza T. Distinct Transcriptional Profile of PDZ Genes after Activation of Human Macrophages and Dendritic Cells. Int J Mol Sci 2022; 23:ijms23137010. [PMID: 35806015 PMCID: PMC9266728 DOI: 10.3390/ijms23137010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
The PDZ (PSD95, Dlg and ZO-1) genes encode proteins that primarily function as scaffolds of diverse signaling pathways. To date, 153 PDZ genes have been identified in the human genome, most of which have multiple protein isoforms widely studied in epithelial and neural cells. However, their expression and function in immune cells have been poorly studied. Herein, we aimed to assess the transcriptional profiles of 83 PDZ genes in human macrophages (Mɸ) and dendritic cells (DCs) and changes in their relative expression during cell PRR stimulation. Significantly distinct PDZ gene transcriptional profiles were identified under different stimulation conditions. Furthermore, a distinct PDZ gene transcriptional signature was found in Mɸ and DCs under the same phagocytic stimuli. Notably, more than 40 PDZ genes had significant changes in expression, with potentially relevant functions in antigen-presenting cells (APCs). Given that several PDZ proteins are targeted by viral products, our results support that many of these proteins might be viral targets in APCs as part of evasion mechanisms. Our results suggest a distinct requirement for PDZ scaffolds in Mɸ and DCs signaling pathways activation. More assessments on the functions of PDZ proteins in APCs and their role in immune evasion mechanisms are needed.
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Affiliation(s)
- Jorge Rosas-García
- Laboratory of Transcriptomics and Molecular Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.R.-G.); (K.B.)
- Department of Molecular Biomedicine, CINVESTAV, Mexico City 07360, Mexico;
| | - Lucero A. Ramón-Luing
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Karen Bobadilla
- Laboratory of Transcriptomics and Molecular Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.R.-G.); (K.B.)
| | | | - Edgar E. Sevilla-Reyes
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico
- Correspondence: (E.E.S.-R.); (T.S.-M.)
| | - Teresa Santos-Mendoza
- Laboratory of Transcriptomics and Molecular Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.R.-G.); (K.B.)
- Correspondence: (E.E.S.-R.); (T.S.-M.)
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36
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Künzel N, Helms V. How Peptides Bind to PSD-95/Discs-Large/ZO-1 Domains. J Chem Theory Comput 2022; 18:3845-3859. [PMID: 35608157 DOI: 10.1021/acs.jctc.1c01140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PSD-95/discs-large/ZO-1 (PDZ) domains form a large family of adaptor proteins that bind to the C-terminal tails of their binding partner proteins. Via extensive molecular dynamics simulations and alchemical free energy calculations, we characterized the binding modi of phosphorylated and unphosphorylated EQVSAV peptides and of a EQVEAV phosphate mimic to the hPTP1E PDZ2 and MAGI1 PDZ1 domains. The simulations reproduced the well-known binding characteristics such as tight coordination of the peptidic carboxyl tail and pronounced hydrogen bonding between the peptide backbone and the backbone atoms of a β-sheet in PDZ. Overall, coordination by hPTP1E PDZ2 appeared tighter than by MAGI1 PDZ1. Simulations of wild-type PDZ and arginine mutants suggest that contacts with Arg79/85 in hPTP1E/MAGI1 are more important for the EQVEAV peptide than for EQVSAV. Alchemical free energy calculations and PaCS-MD simulations could well reproduce the difference in binding free energy between unphosphorylated EQVSAV and EQVEAV peptides and the absolute binding free energy of EQVSAV. However, likely due to small force field inaccuracies, the simulations erroneously favored binding of the phosphorylated peptide instead of its unphosphorylated counterpart, which is in contrast to the experiment.
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Affiliation(s)
- Nicolas Künzel
- Center for Bioinformatics, Saarland University, P.O. Box 15 11 50, D-66041 Saarbrücken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, P.O. Box 15 11 50, D-66041 Saarbrücken, Germany
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37
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Brusa I, Sondo E, Falchi F, Pedemonte N, Roberti M, Cavalli A. Proteostasis Regulators in Cystic Fibrosis: Current Development and Future Perspectives. J Med Chem 2022; 65:5212-5243. [PMID: 35377645 PMCID: PMC9014417 DOI: 10.1021/acs.jmedchem.1c01897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In cystic fibrosis (CF), the deletion of phenylalanine 508 (F508del) in the CF transmembrane conductance regulator (CFTR) leads to misfolding and premature degradation of the mutant protein. These defects can be targeted with pharmacological agents named potentiators and correctors. During the past years, several efforts have been devoted to develop and approve new effective molecules. However, their clinical use remains limited, as they fail to fully restore F508del-CFTR biological function. Indeed, the search for CFTR correctors with different and additive mechanisms has recently increased. Among them, drugs that modulate the CFTR proteostasis environment are particularly attractive to enhance therapy effectiveness further. This Perspective focuses on reviewing the recent progress in discovering CFTR proteostasis regulators, mainly describing the design, chemical structure, and structure-activity relationships. The opportunities, challenges, and future directions in this emerging and promising field of research are discussed, as well.
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Affiliation(s)
- Irene Brusa
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.,Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Elvira Sondo
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | | | | | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.,Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
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38
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SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations. PLoS One 2022; 17:e0265194. [PMID: 35298511 PMCID: PMC8929561 DOI: 10.1371/journal.pone.0265194] [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: 07/16/2021] [Accepted: 02/25/2022] [Indexed: 12/05/2022] Open
Abstract
Computational methods play a key role for investigating allosteric mechanisms in proteins, with the potential of generating valuable insights for innovative drug design. Here we present the SenseNet (“Structure ENSEmble NETworks”) framework for analysis of protein structure networks, which differs from established network models by focusing on interaction timelines obtained by molecular dynamics simulations. This approach is evaluated by predicting allosteric residues reported by NMR experiments in the PDZ2 domain of hPTP1e, a reference system for which previous computational predictions have shown considerable variance. We applied two models based on the mutual information between interaction timelines to estimate the conformational influence of each residue on its local environment. In terms of accuracy our prediction model is comparable to the top performing model published for this system, but by contrast benefits from its independence from NMR structures. Our results are complementary to experimental data and the consensus of previous predictions, demonstrating the potential of our new analysis tool SenseNet. Biochemical interpretation of our model suggests that allosteric residues in the PDZ2 domain form two distinct clusters of contiguous sidechain surfaces. SenseNet is provided as a plugin for the network analysis software Cytoscape, allowing for ease of future application and contributing to a system of compatible tools bridging the fields of system and structural biology.
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Zhu Y, Alvarez F, Wolff N, Mechaly A, Brûlé S, Neitthoffer B, Etienne-Manneville S, Haouz A, Boëda B, Caillet-Saguy C. Interactions of Severe Acute Respiratory Syndrome Coronavirus 2 Protein E With Cell Junctions and Polarity PSD-95/Dlg/ZO-1-Containing Proteins. Front Microbiol 2022; 13:829094. [PMID: 35283834 PMCID: PMC8909127 DOI: 10.3389/fmicb.2022.829094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/06/2022] [Indexed: 12/24/2022] Open
Abstract
The C-terminus of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protein E contains a PBM (PDZ-binding motif) targeting PDZ (PSD-95/Dlg/ZO-1) domains, which is identical to the PBM of SARS-CoV. The latter is involved in the pathogenicity of the virus. Recently, we identified 10 human PDZ-containing proteins showing significant interactions with SARS-CoV-2 protein E PBM. We selected several of them involved in cellular junctions and cell polarity (TJP1, PARD3, MLLT4, and LNX2) and MPP5/PALS1 previously shown to interact with SARS-CoV E PBM. Targeting cellular junctions and polarity components is a common strategy by viruses to hijack cell machinery to their advantage. In this study, we showed that these host PDZ domains TJP1, PARD3, MLLT4, LNX2, and MPP5/PALS1 interact in a PBM-dependent manner in vitro and colocalize with the full-length E protein in cellulo, sequestrating the PDZ domains to the Golgi compartment. We solved three crystal structures of complexes between human LNX2, MLLT4, and MPP5 PDZs and SARS-CoV-2 E PBM highlighting its binding preferences for several cellular targets. Finally, we showed different affinities for the PDZ domains with the original SARS-CoV-2 C-terminal sequence containing the PBM and the one of the beta variant that contains a mutation close to the PBM. The acquired mutations in the E protein localized near the PBM might have important effects both on the structure and the ion-channel activity of the E protein and on the host machinery targeted by the variants during the infection.
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Affiliation(s)
- Yanlei Zhu
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Flavio Alvarez
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Nicolas Wolff
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Ariel Mechaly
- Crystallography Platform-C2RT, CNRS, UMR 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Sébastien Brûlé
- Molecular Biophysics Platform-C2RT, CNRS, UMR 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Benoit Neitthoffer
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR 3691 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR 3691 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Ahmed Haouz
- Crystallography Platform-C2RT, CNRS, UMR 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Batiste Boëda
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR 3691 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Célia Caillet-Saguy
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
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Martín M, Brunello FG, Modenutti CP, Nicola JP, Marti MA. MotSASi: Functional short linear motifs (SLiMs) prediction based on genomic single nucleotide variants and structural data. Biochimie 2022; 197:59-73. [DOI: 10.1016/j.biochi.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/17/2022] [Accepted: 02/02/2022] [Indexed: 11/28/2022]
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41
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Stevens AO, He Y. Allosterism in the PDZ Family. Int J Mol Sci 2022; 23:1454. [PMID: 35163402 PMCID: PMC8836106 DOI: 10.3390/ijms23031454] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 02/05/2023] Open
Abstract
Dynamic allosterism allows the propagation of signal throughout a protein. The PDZ (PSD-95/Dlg1/ZO-1) family has been named as a classic example of dynamic allostery in small modular domains. While the PDZ family consists of more than 200 domains, previous efforts have primarily focused on a few well-studied PDZ domains, including PTP-BL PDZ2, PSD-95 PDZ3, and Par6 PDZ. Taken together, experimental and computational studies have identified regions of these domains that are dynamically coupled to ligand binding. These regions include the αA helix, the αB lower-loop, and the αC helix. In this review, we summarize the specific residues on the αA helix, the αB lower-loop, and the αC helix of PTP-BL PDZ2, PSD-95 PDZ3, and Par6 PDZ that have been identified as participants in dynamic allostery by either experimental or computational approaches. This review can serve as an index for researchers to look back on the previously identified allostery in the PDZ family. Interestingly, our summary of previous work reveals clear consistencies between the domains. While the PDZ family has a low sequence identity, we show that some of the most consistently identified allosteric residues within PTP-BL PDZ2 and PSD-95 PDZ3 domains are evolutionarily conserved. These residues include A46/A347, V61/V362, and L66/L367 on PTP-BL PDZ2 and PSD-95 PDZ3, respectively. Finally, we expose a need for future work to explore dynamic allostery within (1) PDZ domains with multiple binding partners and (2) multidomain constructs containing a PDZ domain.
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Affiliation(s)
| | - Yi He
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, NM 87131, USA;
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42
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Functions of CNKSR2 and Its Association with Neurodevelopmental Disorders. Cells 2022; 11:cells11020303. [PMID: 35053419 PMCID: PMC8774548 DOI: 10.3390/cells11020303] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/05/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
The Connector Enhancer of Kinase Suppressor of Ras-2 (CNKSR2), also known as CNK2 or MAGUIN, is a scaffolding molecule that contains functional protein binding domains: Sterile Alpha Motif (SAM) domain, Conserved Region in CNK (CRIC) domain, PSD-95/Dlg-A/ZO-1 (PDZ) domain, Pleckstrin Homology (PH) domain, and C-terminal PDZ binding motif. CNKSR2 interacts with different molecules, including RAF1, ARHGAP39, and CYTH2, and regulates the Mitogen-Activated Protein Kinase (MAPK) cascade and small GTPase signaling. CNKSR2 has been reported to control the development of dendrite and dendritic spines in primary neurons. CNKSR2 is encoded by the CNKSR2 gene located in the X chromosome. CNKSR2 is now considered as a causative gene of the Houge type of X-linked syndromic mental retardation (MRXHG), an X-linked Intellectual Disability (XLID) that exhibits delayed development, intellectual disability, early-onset seizures, language delay, attention deficit, and hyperactivity. In this review, we summarized molecular features, neuronal function, and neurodevelopmental disorder-related variations of CNKSR2.
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43
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Gul L, Modos D, Fonseca S, Madgwick M, Thomas JP, Sudhakar P, Booth C, Stentz R, Carding SR, Korcsmaros T. Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease. J Extracell Vesicles 2022; 11:e12189. [PMID: 35064769 PMCID: PMC8783345 DOI: 10.1002/jev2.12189] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 10/04/2021] [Accepted: 12/31/2021] [Indexed: 12/14/2022] Open
Abstract
The gastrointestinal (GI) tract harbours a complex microbial community, which contributes to its homeostasis. A disrupted microbiome can cause GI-related diseases, including inflammatory bowel disease (IBD), therefore identifying host-microbe interactions is crucial for better understanding gut health. Bacterial extracellular vesicles (BEVs), released into the gut lumen, can cross the mucus layer and access underlying immune cells. To study BEV-host interactions, we examined the influence of BEVs generated by the gut commensal bacterium, Bacteroides thetaiotaomicron, on host immune cells. Single-cell RNA sequencing data and host-microbe protein-protein interaction networks were used to predict the effect of BEVs on dendritic cells, macrophages and monocytes focusing on the Toll-like receptor (TLR) pathway. We identified biological processes affected in each immune cell type and cell-type specific processes including myeloid cell differentiation. TLR pathway analysis highlighted that BEV targets differ among cells and between the same cells in healthy versus disease (ulcerative colitis) conditions. The in silico findings were validated in BEV-monocyte co-cultures demonstrating the requirement for TLR4 and Toll-interleukin-1 receptor domain-containing adaptor protein (TIRAP) in BEV-elicited NF-kB activation. This study demonstrates that both cell-type and health status influence BEV-host communication. The results and the pipeline could facilitate BEV-based therapies for the treatment of IBD.
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Affiliation(s)
| | - Dezso Modos
- Earlham Institute, NorwichNorwichUK
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - Sonia Fonseca
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - Matthew Madgwick
- Earlham Institute, NorwichNorwichUK
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - John P. Thomas
- Earlham Institute, NorwichNorwichUK
- Department of GastroenterologyNorfolk and Norwich University HospitalNorwichUK
| | - Padhmanand Sudhakar
- Earlham Institute, NorwichNorwichUK
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
- KU Leuven Department of Chronic DiseasesMetabolism and AgeingTranslational Research Centre for Gastrointestinal Disorders (TARGID)LeuvenBelgium
| | | | - Régis Stentz
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
| | - Simon R. Carding
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
- Norwich Medical SchoolUniversity of East AngliaNorwichUK
| | - Tamas Korcsmaros
- Earlham Institute, NorwichNorwichUK
- Gut Microbes and Health Research ProgrammeQuadram Institute BioscienceNorwichUK
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Thomas M, Banks L. The biology of papillomavirus PDZ associations: what do they offer papillomaviruses? Curr Opin Virol 2021; 51:119-126. [PMID: 34655911 DOI: 10.1016/j.coviro.2021.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/10/2021] [Accepted: 09/21/2021] [Indexed: 01/05/2023]
Abstract
The high-risk α-type papillomaviruses have a C-terminal PDZ-binding motif (PBM) on one of the two major oncoproteins E6 or E7; the vast majority on E6. The PBM is essential for the high-risk HPV life cycle, for episomal maintenance of the virus genome, and for maintaining the mitotic stability of the infected cell. The question is why only these viruses have PBMs - are there specific constraints imposed by the mucosal epithelium in which these viruses replicate? However the low-risk α-HPVs, such as HPV-6 and HPV-11 replicate extremely efficiently without a PBM, while viruses of the alpha8 group, such as HPV-40, replicate well with a very primitive PBM. So what does PDZ-binding capacity contribute to the fitness of the virus?
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Affiliation(s)
- Miranda Thomas
- ICGEB, AREA Science Park, Padriciano 99, 34149, Trieste, Italy.
| | - Lawrence Banks
- ICGEB, AREA Science Park, Padriciano 99, 34149, Trieste, Italy
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45
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Domain Analysis and Motif Matcher (DAMM): A Program to Predict Selectivity Determinants in Monosiga brevicollis PDZ Domains Using Human PDZ Data. Molecules 2021; 26:molecules26196034. [PMID: 34641578 PMCID: PMC8512817 DOI: 10.3390/molecules26196034] [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: 09/11/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
Choanoflagellates are single-celled eukaryotes with complex signaling pathways. They are considered the closest non-metazoan ancestors to mammals and other metazoans and form multicellular-like states called rosettes. The choanoflagellate Monosiga brevicollis contains over 150 PDZ domains, an important peptide-binding domain in all three domains of life (Archaea, Bacteria, and Eukarya). Therefore, an understanding of PDZ domain signaling pathways in choanoflagellates may provide insight into the origins of multicellularity. PDZ domains recognize the C-terminus of target proteins and regulate signaling and trafficking pathways, as well as cellular adhesion. Here, we developed a computational software suite, Domain Analysis and Motif Matcher (DAMM), that analyzes peptide-binding cleft sequence identity as compared with human PDZ domains and that can be used in combination with literature searches of known human PDZ-interacting sequences to predict target specificity in choanoflagellate PDZ domains. We used this program, protein biochemistry, fluorescence polarization, and structural analyses to characterize the specificity of A9UPE9_MONBE, a M. brevicollis PDZ domain-containing protein with no homology to any metazoan protein, finding that its PDZ domain is most similar to those of the DLG family. We then identified two endogenous sequences that bind A9UPE9 PDZ with <100 μM affinity, a value commonly considered the threshold for cellular PDZ-peptide interactions. Taken together, this approach can be used to predict cellular targets of previously uncharacterized PDZ domains in choanoflagellates and other organisms. Our data contribute to investigations into choanoflagellate signaling and how it informs metazoan evolution.
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46
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Schuster-Gossler K, Boldt K, Bornhorst D, Delany-Heiken P, Ueffing M, Gossler A. Activity of the mouse Notch ligand DLL1 is sensitive to C-terminal tagging in vivo. BMC Res Notes 2021; 14:383. [PMID: 34583743 PMCID: PMC8477538 DOI: 10.1186/s13104-021-05785-4] [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: 04/15/2021] [Accepted: 09/14/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The mammalian Notch ligand DLL1 has essential functions during development. To visualise DLL1 in tissues, for sorting and enrichment of DLL1-expressing cells, and to efficiently purify DLL1 protein complexes we tagged DLL1 in mice with AcGFPHA or Strep/FLAG. RESULTS We generated constructs to express DLL1 that carried C-terminal in-frame an AcGFPHA tag flanked by loxP sites followed by a Strep/FLAG (SF) tag out of frame. Cre-mediated recombination replaced AcGFP-HA by SF. The AcGFPHAstopSF cassette was added to DLL1 for tests in cultured cells and introduced into endogenous DLL1 in mice by homologous recombination. Tagged DLL1 protein was detected by antibodies against GFP and HA or Flag, respectively, both in CHO cells and embryo lysates. In CHO cells the AcGFP fluorophore fused to DLL1 was functional. In vivo AcGFP expression was below the level of detection by direct fluorescence. However, the SF tag allowed us to specifically purify DLL1 complexes from embryo lysates. Homozygous mice expressing AcGFPHA or SF-tagged DLL1 revealed a vertebral column phenotype reminiscent of disturbances in AP polarity during somitogenesis, a process most sensitive to reduced DLL1 function. Thus, even small C-terminal tags can impinge on sensitive developmental processes requiring DLL1 activity.
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Affiliation(s)
- Karin Schuster-Gossler
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Karsten Boldt
- Institute of Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076, Tübingen, Germany
| | - Dorothee Bornhorst
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.,Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, USA
| | - Patricia Delany-Heiken
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Marius Ueffing
- Institute of Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076, Tübingen, Germany
| | - Achim Gossler
- Institute for Molecular Biology, OE5250, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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Heimhalt M, Berndt A, Wagstaff J, Anandapadamanaban M, Perisic O, Maslen S, McLaughlin S, Yu CWH, Masson GR, Boland A, Ni X, Yamashita K, Murshudov GN, Skehel M, Freund SM, Williams RL. Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace. eLife 2021; 10:e68799. [PMID: 34519269 PMCID: PMC8439657 DOI: 10.7554/elife.68799] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/31/2021] [Indexed: 12/16/2022] Open
Abstract
The mTORC1 kinase complex regulates cell growth, proliferation, and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted mTORC1 with DEPTOR to understand its function. We find that DEPTOR is a unique partial mTORC1 inhibitor that may have evolved to preserve feedback inhibition of PI3K. Counterintuitively, mTORC1 activated by RHEB or oncogenic mutation is much more potently inhibited by DEPTOR. Although DEPTOR partially inhibits mTORC1, mTORC1 prevents this inhibition by phosphorylating DEPTOR, a mutual antagonism that requires no exogenous factors. Structural analyses of the mTORC1/DEPTOR complex showed DEPTOR's PDZ domain interacting with the mTOR FAT region, and the unstructured linker preceding the PDZ binding to the mTOR FRB domain. The linker and PDZ form the minimal inhibitory unit, but the N-terminal tandem DEP domains also significantly contribute to inhibition.
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Affiliation(s)
- Maren Heimhalt
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Alex Berndt
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Jane Wagstaff
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | | | - Olga Perisic
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Sarah Maslen
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | | | | | - Glenn R Masson
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Andreas Boland
- Department of Molecular Biology, University of GenevaGenevaSwitzerland
| | - Xiaodan Ni
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | | | | | - Mark Skehel
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
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Drummond HA. What Evolutionary Evidence Implies About the Identity of the Mechanoelectrical Couplers in Vascular Smooth Muscle Cells. Physiology (Bethesda) 2021; 36:292-306. [PMID: 34431420 DOI: 10.1152/physiol.00008.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Loss of pressure-induced vasoconstriction increases susceptibility to renal and cerebral vascular injury. Favored paradigms underlying initiation of the response include transient receptor potential channels coupled to G protein-coupled receptors or integrins as transducers. Degenerin channels may also mediate the response. This review addresses the 1) evolutionary role of these molecules in mechanosensing, 2) limitations to identifying mechanosensitive molecules, and 3) paradigm shifting molecular model for a VSMC mechanosensor.
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Affiliation(s)
- Heather A Drummond
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi
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49
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Tutzauer J, Gonzalez de Valdivia E, Swärd K, Alexandrakis Eilard I, Broselid S, Kahn R, Olde B, Leeb-Lundberg LMF. Ligand-independent G protein-coupled Estrogen Receptor (GPER)/GPR30 Activity: Lack of receptor-dependent effects of G-1 and 17β-estradiol.. Mol Pharmacol 2021; 100:271-282. [PMID: 34330822 PMCID: PMC8626787 DOI: 10.1124/molpharm.121.000259] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/06/2021] [Indexed: 11/22/2022] Open
Abstract
G protein–coupled receptor 30 (GPR30) is a membrane receptor reported to bind 17β-estradiol (E2) and mediate rapid nongenomic estrogen responses, hence also named G protein–coupled estrogen receptor. G-1 is a proposed GPR30-specific agonist that has been used to implicate the receptor in several pathophysiological events. However, controversy surrounds the role of GPR30 in G-1 and E2 responses. We investigated GPR30 activity in the absence and presence of G-1 and E2 in several eukaryotic systems ex vivo and in vitro in the absence and presence of the receptor. Ex vivo activity was addressed using the caudal artery from wild-type (WT) and GPR30 knockout (KO) mice, and in vitro activity was addressed using a HeLa cell line stably expressing a synthetic multifunctional promoter (nuclear factor κB, signal transducer and activator of transcription, activator protein 1)–luciferase construct (HFF11 cells) and a human GPR30-inducible T-REx system (T-REx HFF11 cells), HFF11 and human embryonic kidney 293 cells transiently expressing WT GPR30 and GPR30 lacking the C-terminal PDZ (postsynaptic density-95/discs-large /zonula occludens-1 homology) motif SSAV, and yeast Saccharomyces cerevisiae transformed to express GPR30. WT and KO arteries exhibited similar contractile responses to 60 mM KCl and 0.3 μM cirazoline, and G-1 relaxed both arteries with the same potency and efficacy. Furthermore, expression of GPR30 did not introduce any responses to 1 μM G-1 and 0.1 μM E2 in vitro. On the other hand, receptor expression caused considerable ligand-independent activity in vitro, which was receptor PDZ motif-dependent in mammalian cells. We conclude from these results that GPR30 exhibits ligand-independent activity in vitro but no G-1– or E2-stimulated activity in any of the systems used.
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Affiliation(s)
- Julia Tutzauer
- Department of Experimental Medical Science, Lund University, Sweden
| | | | - Karl Swärd
- Department of Experimental Medical Science, Lund University, Sweden
| | | | - Stefan Broselid
- Department of Experimental Medical Science, Lund University, Sweden
| | - Robin Kahn
- Department of Clinical Sciences Lund, Lund University, Sweden
| | - Björn Olde
- Department of Clinical Sciences Lund, Lund University, Sweden
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50
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Martín M, Salleron L, Peyret V, Geysels RC, Darrouzet E, Lindenthal S, Bernal Barquero CE, Masini-Repiso AM, Pourcher T, Nicola JP. The PDZ protein SCRIB regulates sodium/iodide symporter (NIS) expression at the basolateral plasma membrane. FASEB J 2021; 35:e21681. [PMID: 34196428 DOI: 10.1096/fj.202100303r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/27/2021] [Accepted: 05/06/2021] [Indexed: 01/25/2023]
Abstract
The sodium/iodide symporter (NIS) expresses at the basolateral plasma membrane of the thyroid follicular cell and mediates iodide accumulation required for normal thyroid hormonogenesis. Loss-of-function NIS variants cause congenital hypothyroidism due to impaired iodide accumulation in thyroid follicular cells underscoring the significance of NIS for thyroid physiology. Here we report novel findings derived from the thorough characterization of the nonsense NIS mutant p.R636* NIS-leading to a truncated protein missing the last eight amino acids-identified in twins with congenital hypothyroidism. R636* NIS is severely mislocalized into intracellular vesicular compartments due to the lack of a conserved carboxy-terminal type 1 PDZ-binding motif. As a result, R636* NIS is barely targeted to the plasma membrane and therefore iodide transport is reduced. Deletion of the PDZ-binding motif causes NIS accumulation into late endosomes and lysosomes. Using PDZ domain arrays, we revealed that the PDZ-domain containing protein SCRIB binds to the carboxy-terminus of NIS by a PDZ-PDZ interaction. Furthermore, in CRISPR/Cas9-based SCRIB deficient cells, NIS expression at the basolateral plasma membrane is compromised, leading to NIS localization into intracellular vesicular compartments. We conclude that the PDZ-binding motif is a plasma membrane retention signal that participates in the polarized expression of NIS by selectively interacting with the PDZ-domain containing protein SCRIB, thus retaining the transporter at the basolateral plasma membrane. Our data provide insights into the molecular mechanisms that regulate NIS expression at the plasma membrane, a topic of great interest in the thyroid cancer field considering the relevance of NIS-mediated radioactive iodide therapy for differentiated thyroid carcinoma.
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Affiliation(s)
- Mariano Martín
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Lisa Salleron
- Transporteurs, Imagerie et Radiothérapie en Oncologie, Faculté de médecine, Direction de la Recherche Fondamentale, Commissariat à l'Energie Atomique et aux énergies alternatives, Université Côte d'Azur, Institut des sciences du vivant Fréderic Joliot, Nice, France
| | - Victoria Peyret
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Romina Celeste Geysels
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Elisabeth Darrouzet
- Transporteurs, Imagerie et Radiothérapie en Oncologie, Faculté de médecine, Direction de la Recherche Fondamentale, Commissariat à l'Energie Atomique et aux énergies alternatives, Université Côte d'Azur, Institut des sciences du vivant Fréderic Joliot, Nice, France
| | - Sabine Lindenthal
- Transporteurs, Imagerie et Radiothérapie en Oncologie, Faculté de médecine, Direction de la Recherche Fondamentale, Commissariat à l'Energie Atomique et aux énergies alternatives, Université Côte d'Azur, Institut des sciences du vivant Fréderic Joliot, Nice, France
| | - Carlos Eduardo Bernal Barquero
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Ana María Masini-Repiso
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
| | - Thierry Pourcher
- Transporteurs, Imagerie et Radiothérapie en Oncologie, Faculté de médecine, Direction de la Recherche Fondamentale, Commissariat à l'Energie Atomique et aux énergies alternatives, Université Côte d'Azur, Institut des sciences du vivant Fréderic Joliot, Nice, France
| | - Juan Pablo Nicola
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.,Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
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