1
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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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2
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Klyshko E, Kim JSH, McGough L, Valeeva V, Lee E, Ranganathan R, Rauscher S. Functional protein dynamics in a crystal. Nat Commun 2024; 15:3244. [PMID: 38622111 PMCID: PMC11018856 DOI: 10.1038/s41467-024-47473-4] [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: 07/17/2023] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Proteins are molecular machines and to understand how they work, we need to understand how they move. New pump-probe time-resolved X-ray diffraction methods open up ways to initiate and observe protein motions with atomistic detail in crystals on biologically relevant timescales. However, practical limitations of these experiments demands parallel development of effective molecular dynamics approaches to accelerate progress and extract meaning. Here, we establish robust and accurate methods for simulating dynamics in protein crystals, a nontrivial process requiring careful attention to equilibration, environmental composition, and choice of force fields. With more than seven milliseconds of sampling of a single chain, we identify critical factors controlling agreement between simulation and experiments and show that simulated motions recapitulate ligand-induced conformational changes. This work enables a virtuous cycle between simulation and experiments for visualizing and understanding the basic functional motions of proteins.
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Affiliation(s)
- Eugene Klyshko
- Department of Physics, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Justin Sung-Ho Kim
- Department of Physics, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Victoria Valeeva
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Ethan Lee
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Rama Ranganathan
- Center for Physics of Evolving Systems and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Sarah Rauscher
- Department of Physics, University of Toronto, Toronto, ON, Canada.
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
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3
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Klyshko E, Sung-Ho Kim J, McGough L, Valeeva V, Lee E, Ranganathan R, Rauscher S. Functional Protein Dynamics in a Crystal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.06.548023. [PMID: 37461732 PMCID: PMC10350071 DOI: 10.1101/2023.07.06.548023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Proteins are molecular machines and to understand how they work, we need to understand how they move. New pump-probe time-resolved X-ray diffraction methods open up ways to initiate and observe protein motions with atomistic detail in crystals on biologically relevant timescales. However, practical limitations of these experiments demands parallel development of effective molecular dynamics approaches to accelerate progress and extract meaning. Here, we establish robust and accurate methods for simulating dynamics in protein crystals, a nontrivial process requiring careful attention to equilibration, environmental composition, and choice of force fields. With more than seven milliseconds of sampling of a single chain, we identify critical factors controlling agreement between simulation and experiments and show that simulated motions recapitulate ligand-induced conformational changes. This work enables a virtuous cycle between simulation and experiments for visualizing and understanding the basic functional motions of proteins.
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Affiliation(s)
- Eugene Klyshko
- Department of Physics, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Justin Sung-Ho Kim
- Department of Physics, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Victoria Valeeva
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Ethan Lee
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Rama Ranganathan
- Center for Physics of Evolving Systems and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Sarah Rauscher
- Department of Physics, University of Toronto, Toronto, ON, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
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4
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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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5
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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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6
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Leblanc R, Ghossoub R, Goubard A, Castellano R, Fares J, Camoin L, Audebert S, Balzano M, Bou‐Tayeh B, Fauriat C, Vey N, Garciaz S, Borg J, Collette Y, Aurrand‐Lions M, David G, Zimmermann P. Downregulation of stromal syntenin sustains AML development. EMBO Mol Med 2023; 15:e17570. [PMID: 37819151 PMCID: PMC10630886 DOI: 10.15252/emmm.202317570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023] Open
Abstract
The crosstalk between cancer and stromal cells plays a critical role in tumor progression. Syntenin is a small scaffold protein involved in the regulation of intercellular communication that is emerging as a target for cancer therapy. Here, we show that certain aggressive forms of acute myeloid leukemia (AML) reduce the expression of syntenin in bone marrow stromal cells (BMSC). Stromal syntenin deficiency, in turn, generates a pro-tumoral microenvironment. From serial transplantations in mice and co-culture experiments, we conclude that syntenin-deficient BMSC stimulate AML aggressiveness by promoting AML cell survival and protein synthesis. This pro-tumoral activity is supported by increased expression of endoglin, a classical marker of BMSC, which in trans stimulates AML translational activity. In short, our study reveals a vicious signaling loop potentially at the heart of AML-stroma crosstalk and unsuspected tumor-suppressive effects of syntenin that need to be considered during systemic targeting of syntenin in cancer therapy.
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Affiliation(s)
- Raphael Leblanc
- Team Spatio‐Temporal Regulation of Cell Signaling‐Scaffolds and Phosphoinositides, Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐Calmettes, Aix‐Marseille Université, Inserm, CNRSMarseilleFrance
| | - Rania Ghossoub
- Team Spatio‐Temporal Regulation of Cell Signaling‐Scaffolds and Phosphoinositides, Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐Calmettes, Aix‐Marseille Université, Inserm, CNRSMarseilleFrance
| | - Armelle Goubard
- TrGET Preclinical Platform, Centre de Recherche en Cancérologie de Marseille, Inserm, CNRSAix‐Marseille Université, Institut Paoli‐CalmettesMarseilleFrance
| | - Rémy Castellano
- TrGET Preclinical Platform, Centre de Recherche en Cancérologie de Marseille, Inserm, CNRSAix‐Marseille Université, Institut Paoli‐CalmettesMarseilleFrance
| | - Joanna Fares
- Team Spatio‐Temporal Regulation of Cell Signaling‐Scaffolds and Phosphoinositides, Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐Calmettes, Aix‐Marseille Université, Inserm, CNRSMarseilleFrance
| | - Luc Camoin
- Proteomics and Mass Spectrometry Platform, Centre de Recherche en Cancérologie de MarseilleAix‐Marseille Université, Inserm, CNRS, Institut Paoli CalmettesMarseilleFrance
| | - Stephane Audebert
- Proteomics and Mass Spectrometry Platform, Centre de Recherche en Cancérologie de MarseilleAix‐Marseille Université, Inserm, CNRS, Institut Paoli CalmettesMarseilleFrance
| | - Marielle Balzano
- Team Spatio‐Temporal Regulation of Cell Signaling‐Scaffolds and Phosphoinositides, Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐Calmettes, Aix‐Marseille Université, Inserm, CNRSMarseilleFrance
| | - Berna Bou‐Tayeh
- Team Immunity and Cancer, Centre de Recherche en Cancérologie de MarseilleAix‐Marseille Université, Inserm, CNRS, Institut Paoli CalmettesMarseilleFrance
| | - Cyril Fauriat
- Team Immunity and Cancer, Centre de Recherche en Cancérologie de MarseilleAix‐Marseille Université, Inserm, CNRS, Institut Paoli CalmettesMarseilleFrance
| | - Norbert Vey
- Aix‐Marseille Univ, Inserm, CNRS, Institut Paoli‐Calmettes, CRCMMarseilleFrance
| | - Sylvain Garciaz
- Aix‐Marseille Univ, Inserm, CNRS, Institut Paoli‐Calmettes, CRCMMarseilleFrance
| | - Jean‐Paul Borg
- Proteomics and Mass Spectrometry Platform, Centre de Recherche en Cancérologie de MarseilleAix‐Marseille Université, Inserm, CNRS, Institut Paoli CalmettesMarseilleFrance
| | - Yves Collette
- TrGET Preclinical Platform, Centre de Recherche en Cancérologie de Marseille, Inserm, CNRSAix‐Marseille Université, Institut Paoli‐CalmettesMarseilleFrance
| | - Michel Aurrand‐Lions
- Team Leuko/Stromal Interactions in Normal and Pathological Hematopoiesis, Centre de Recherche en Cancérologie de Marseille, Aix‐Marseille Université, Inserm, CNRS, Institut Paoli CalmettesMarseilleFrance
| | - Guido David
- Team Spatio‐Temporal Regulation of Cell Signaling‐Scaffolds and Phosphoinositides, Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐Calmettes, Aix‐Marseille Université, Inserm, CNRSMarseilleFrance
- Department of Human GeneticsK U LeuvenLeuvenBelgium
| | - Pascale Zimmermann
- Team Spatio‐Temporal Regulation of Cell Signaling‐Scaffolds and Phosphoinositides, Equipe Labellisée Ligue 2018, Centre de Recherche en Cancérologie de Marseille (CRCM)Institut Paoli‐Calmettes, Aix‐Marseille Université, Inserm, CNRSMarseilleFrance
- Department of Human GeneticsK U LeuvenLeuvenBelgium
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7
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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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8
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Sun B, Kekenes-Huskey PM. Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling. Q Rev Biophys 2023; 56:e2. [PMID: 36628457 PMCID: PMC11070111 DOI: 10.1017/s003358352300001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The cardiac sarcomere is a cellular structure in the heart that enables muscle cells to contract. Dozens of proteins belong to the cardiac sarcomere, which work in tandem to generate force and adapt to demands on cardiac output. Intriguingly, the majority of these proteins have significant intrinsic disorder that contributes to their functions, yet the biophysics of these intrinsically disordered regions (IDRs) have been characterized in limited detail. In this review, we first enumerate these myofilament-associated proteins with intrinsic disorder (MAPIDs) and recent biophysical studies to characterize their IDRs. We secondly summarize the biophysics governing IDR properties and the state-of-the-art in computational tools toward MAPID identification and characterization of their conformation ensembles. We conclude with an overview of future computational approaches toward broadening the understanding of intrinsic disorder in the cardiac sarcomere.
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Affiliation(s)
- Bin Sun
- Research Center for Pharmacoinformatics (The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, China
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9
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Gautier C, Gianni S. A short structural extension dictates the early stages of folding of a PDZ domain. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140852. [PMID: 36055518 DOI: 10.1016/j.bbapap.2022.140852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/16/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
PDZ domains are highly abundant protein-protein interaction modules in human. One of the most extensively characterized PDZ domain, the third PDZ domain from PSD-95 (PDZ3), contains an α-helical C-terminal extension that has a key role in the function of the domain. Here we compared the folding of PDZ3 with a truncated variant (PDZ3Δα3), lacking the additional helix, by means of the so-called Φ-value analysis, an experimental technique that allows inferring the structure of folding transition states. Experiments reveal subtle but detectable differences in the folding of PDZ3Δα3 versus PDZ3, as probed by structural characterization of the folding transition states. These differences appear more remarkable in the early stages of folding, with a detectable shift of the folding nucleus. The presented results allow demonstrating that the native state exerts a weak bias at the early stages of folding, which appear to be characterized by alternative pathways.
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Affiliation(s)
- Candice Gautier
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy.
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10
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Lindqvist R, Benz C, Sereikaite V, Maassen L, Laursen L, Jemth P, Strømgaard K, Ivarsson Y, Överby AK. A Syntenin Inhibitor Blocks Endosomal Entry of SARS-CoV-2 and a Panel of RNA Viruses. Viruses 2022; 14:v14102202. [PMID: 36298757 PMCID: PMC9610207 DOI: 10.3390/v14102202] [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: 08/18/2022] [Revised: 09/26/2022] [Accepted: 10/01/2022] [Indexed: 11/16/2022] Open
Abstract
Viruses are dependent on host factors in order to efficiently establish an infection and replicate. Targeting the interactions of such host factors provides an attractive strategy to develop novel antivirals. Syntenin is a protein known to regulate the architecture of cellular membranes by its involvement in protein trafficking and has previously been shown to be important for human papilloma virus (HPV) infection. Here, we show that a highly potent and metabolically stable peptide inhibitor that binds to the PDZ1 domain of syntenin inhibits severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by blocking the endosomal entry of the virus. Furthermore, we found that the inhibitor also hampered chikungunya infection and strongly reduced flavivirus infection, which is completely dependent on receptor-mediated endocytosis for their entry. In conclusion, we have identified a novel broad spectrum antiviral inhibitor that efficiently targets a broad range of RNA viruses.
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Affiliation(s)
- Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90185 Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186 Umeå, Sweden
| | - Caroline Benz
- Department of Chemistry—BMC, Uppsala University, Box 576, Husargatan 3, 75123 Uppsala, Sweden
| | - Vita Sereikaite
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Lars Maassen
- Department of Chemistry—BMC, Uppsala University, Box 576, Husargatan 3, 75123 Uppsala, Sweden
| | - Louise Laursen
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 75123 Uppsala, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 75123 Uppsala, Sweden
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Ylva Ivarsson
- Department of Chemistry—BMC, Uppsala University, Box 576, Husargatan 3, 75123 Uppsala, Sweden
- Correspondence: (Y.I.); (A.K.Ö.)
| | - Anna K. Överby
- Department of Clinical Microbiology, Umeå University, 90185 Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186 Umeå, Sweden
- Correspondence: (Y.I.); (A.K.Ö.)
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11
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Malagrinò F, Fusco G, Pennacchietti V, Toto A, Nardella C, Pagano L, de Simone A, Gianni S. Cryptic binding properties of a transient folding intermediate in a PDZ tandem repeat. Protein Sci 2022; 31:e4396. [PMID: 36040267 PMCID: PMC9375522 DOI: 10.1002/pro.4396] [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: 03/16/2022] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 12/17/2022]
Abstract
PDZ domains are the most diffused protein-protein interaction modules of the human proteome and are often present in tandem repeats. An example is PDZD2, a protein characterized by the presence of six PDZ domains that undergoes a proteolytic cleavage producing sPDZD2, comprising a tandem of two PDZ domains, namely PDZ5 and PDZ6. Albeit the physiopathological importance of sPDZD2 is well-established, the interaction with endogenous ligands has been poorly characterized. To understand the determinants of the stability and function of sPDZD2, we investigated its folding pathway. Our data highlights the presence of a complex scenario involving a transiently populated folding intermediate that may be accumulated from the concurrent denaturation of both PDZ5 and PDZ6 domains. Importantly, double jump kinetic experiments allowed us to pinpoint the ability of this transient intermediate to bind the physiological ligand of sPDZD2 with increased affinity compared to the native state. In summary, our results provide an interesting example of a functionally competent misfolded intermediate, which may exert a cryptic function that is not captured from the analysis of the native state only.
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Affiliation(s)
- Francesca Malagrinò
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNRSapienza Università di RomaRomeItaly
| | - Giuliana Fusco
- Centre for Misfolding Diseases, Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Valeria Pennacchietti
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNRSapienza Università di RomaRomeItaly
| | - Angelo Toto
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNRSapienza Università di RomaRomeItaly
| | - Caterina Nardella
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNRSapienza Università di RomaRomeItaly
| | - Livia Pagano
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNRSapienza Università di RomaRomeItaly
| | - Alfonso de Simone
- Dipartimento di FarmaciaUniversità degli Studi di Napoli Federico IINaplesItaly
| | - Stefano Gianni
- Dipartimento di FarmaciaUniversità degli Studi di Napoli Federico IINaplesItaly
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12
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Deafness-related protein PDZD7 forms complex with the C-terminal tail of FCHSD2. Biochem J 2022; 479:1393-1405. [PMID: 35695292 PMCID: PMC9317961 DOI: 10.1042/bcj20220147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022]
Abstract
In cochlea, deafness-related protein PDZD7 is an indispensable component of the ankle link complex, which is critical for the maturation of inner-ear hair cell for sound perception. Ankle links, connecting the different rows of cochlear stereocilia, are essential for the staircase-like development of stereocilia. However, the molecular mechanism of how PDZD7 governs stereociliary development remains unknown. Here, we reported a novel PDZD7-binding partner, FCHSD2, identified by yeast two-hybrid screening. FCHSD2 was reported to be expressed in hair cell, where it co-operated with CDC42 and N-WASP to regulate the formation of cell protrusion. The association between FCHSD2 and PDZD7 was further confirmed in COS-7 cells. More importantly, we solved the complex structure of FCHSD2 tail with PDZD7 PDZ3 domain at 2.0 Å resolution. The crystal structure shows that PDZD7 PDZ3 adopts a typical PDZ domain topology, comprising five β strands and two α helixes. The PDZ-binding motif of FCHSD2 tail stretches through the αB/βB groove of PDZD7 PDZ3. Our study not only uncovers the interaction between FCHSD2 tail and PDZD7 PDZ3 at the atomic level, but also provides clues of connecting the ankle link complex with cytoskeleton dynamics for exploiting the molecular mechanism of stereociliary development.
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13
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Human Serine Racemase Weakly Binds the Third PDZ Domain of PSD-95. Int J Mol Sci 2022; 23:ijms23094959. [PMID: 35563349 PMCID: PMC9105370 DOI: 10.3390/ijms23094959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/13/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Human serine racemase (hSR) is a pyridoxal-5'-phosphate (PLP)-dependent dimer that catalyzes the formation of D-serine from L-serine, as well as the dehydration of both L- and D-serine to pyruvate and ammonia. As D-serine is a co-agonist of N-methyl-D-aspartate receptors (NMDARs), hSR is a key enzyme in glutamatergic neurotransmission. hSR activity is finely regulated by Mg2+, ATP, post-translational modifications, and the interaction with protein partners. In particular, the C-terminus of murine SR binds the third PDZ domain (PDZ3) of postsynaptic density protein 95 (PSD-95), a member of the membrane-associated guanylate kinase (MAGUK) family involved in the trafficking and localization of glutamate receptors. The structural details of the interaction and the stability of the complex have not been elucidated yet. We evaluated the binding of recombinant human PSD-95 PDZ3 to hSR by glutaraldehyde cross-linking, pull-down assays, isothermal titration calorimetry, nuclear magnetic resonance, and enzymatic assays. Overall, a weak interaction was observed, confirming the binding for the human orthologs but supporting the hypothesis that a third protein partner (i.e., stargazin) is required for the regulation of hSR activity by PSD-95 and to stabilize their interaction.
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14
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Lee A, Klinkradt S, McCombe P, Pow D. Cloning of a new form of EAAT2/GLT-1 from human and rodent brains. Neurosci Lett 2022; 780:136637. [DOI: 10.1016/j.neulet.2022.136637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 11/15/2022]
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15
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Inagaki N. Processing of D1 Protein: A Mysterious Process Carried Out in Thylakoid Lumen. Int J Mol Sci 2022; 23:2520. [PMID: 35269663 PMCID: PMC8909930 DOI: 10.3390/ijms23052520] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022] Open
Abstract
In oxygenic photosynthetic organisms, D1 protein, a core subunit of photosystem II (PSII), displays a rapid turnover in the light, in which D1 proteins are distinctively damaged and immediately removed from the PSII. In parallel, as a repair process, D1 proteins are synthesized and simultaneously assembled into the PSII. On this flow, the D1 protein is synthesized as a precursor with a carboxyl-terminal extension, and the D1 processing is defined as a step for proteolytic removal of the extension by a specific protease, CtpA. The D1 processing plays a crucial role in appearance of water-oxidizing capacity of PSII, because the main chain carboxyl group at carboxyl-terminus of the D1 protein, exposed by the D1 processing, ligates a manganese and a calcium atom in the Mn4CaO5-cluster, a special equipment for water-oxidizing chemistry of PSII. This review focuses on the D1 processing and discusses it from four angles: (i) Discovery of the D1 processing and recognition of its importance: (ii) Enzyme involved in the D1 processing: (iii) Efforts for understanding significance of the D1 processing: (iv) Remaining mysteries in the D1 processing. Through the review, I summarize the current status of our knowledge on and around the D1 processing.
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Affiliation(s)
- Noritoshi Inagaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8518, Japan
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16
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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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17
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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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18
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Liu Q, Lin J, Wen L, Wang S, Zhou P, Mei L, Shang S. Systematic Modeling, Prediction, and Comparison of Domain-Peptide Affinities: Does it Work Effectively With the Peptide QSAR Methodology? Front Genet 2022; 12:800857. [PMID: 35096016 PMCID: PMC8795790 DOI: 10.3389/fgene.2021.800857] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
The protein-protein association in cellular signaling networks (CSNs) often acts as weak, transient, and reversible domain-peptide interaction (DPI), in which a flexible peptide segment on the surface of one protein is recognized and bound by a rigid peptide-recognition domain from another. Reliable modeling and accurate prediction of DPI binding affinities would help to ascertain the diverse biological events involved in CSNs and benefit our understanding of various biological implications underlying DPIs. Traditionally, peptide quantitative structure-activity relationship (pQSAR) has been widely used to model and predict the biological activity of oligopeptides, which employs amino acid descriptors (AADs) to characterize peptide structures at sequence level and then statistically correlate the resulting descriptor vector with observed activity data via regression. However, the QSAR has not yet been widely applied to treat the direct binding behavior of large-scale peptide ligands to their protein receptors. In this work, we attempted to clarify whether the pQSAR methodology can work effectively for modeling and predicting DPI affinities in a high-throughput manner? Over twenty thousand short linear motif (SLiM)-containing peptide segments involved in SH3, PDZ and 14-3-3 domain-medicated CSNs were compiled to define a comprehensive sequence-based data set of DPI affinities, which were represented by the Boehringer light units (BLUs) derived from previous arbitrary light intensity assays following SPOT peptide synthesis. Four sophisticated MLMs (MLMs) were then utilized to perform pQSAR modeling on the set described with different AADs to systematically create a variety of linear and nonlinear predictors, and then verified by rigorous statistical test. It is revealed that the genome-wide DPI events can only be modeled qualitatively or semiquantitatively with traditional pQSAR strategy due to the intrinsic disorder of peptide conformation and the potential interplay between different peptide residues. In addition, the arbitrary BLUs used to characterize DPI affinity values were measured via an indirect approach, which may not very reliable and may involve strong noise, thus leading to a considerable bias in the modeling. The R prd 2 = 0.7 can be considered as the upper limit of external generalization ability of the pQSAR methodology working on large-scale DPI affinity data.
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Affiliation(s)
- Qian Liu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Jing Lin
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Li Wen
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Shaozhou Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Peng Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Li Mei
- Institute of Culinary, Sichuan Tourism University, Chengdu, China
| | - Shuyong Shang
- Institute of Ecological Environment Protection, Chengdu Normal University, Chengdu, China
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19
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Kliche J, Ivarsson Y. Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs. Biochem J 2022; 479:1-22. [PMID: 34989786 PMCID: PMC8786283 DOI: 10.1042/bcj20200714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022]
Abstract
Cellular function is based on protein-protein interactions. A large proportion of these interactions involves the binding of short linear motifs (SLiMs) by folded globular domains. These interactions are regulated by post-translational modifications, such as phosphorylation, that create and break motif binding sites or tune the affinity of the interactions. In addition, motif-based interactions are involved in targeting serine/threonine kinases and phosphatases to their substrate and contribute to the specificity of the enzymatic actions regulating which sites are phosphorylated. Here, we review how SLiM-based interactions assist in determining the specificity of serine/threonine kinases and phosphatases, and how phosphorylation, in turn, affects motif-based interactions. We provide examples of SLiM-based interactions that are turned on/off, or are tuned by serine/threonine phosphorylation and exemplify how this affects SLiM-based protein complex formation.
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Affiliation(s)
- Johanna Kliche
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
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20
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Bozovic O, Jankovic B, Hamm P. Using azobenzene photocontrol to set proteins in motion. Nat Rev Chem 2021; 6:112-124. [PMID: 37117294 DOI: 10.1038/s41570-021-00338-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 02/06/2023]
Abstract
Controlling the activity of proteins with azobenzene photoswitches is a potent tool for manipulating their biological function. With the help of light, it is possible to change binding affinities, control allostery or manipulate complex biological processes, for example. Additionally, owing to their intrinsically fast photoisomerization, azobenzene photoswitches can serve as triggers that initiate out-of-equilibrium processes. Such switching of the activity initiates a cascade of conformational events that can be accessed with time-resolved methods. In this Review, we show how the potency of azobenzene photoswitching can be combined with transient spectroscopic techniques to disclose the order of events and experimentally observe biomolecular interactions in real time. This strategy will further our understanding of how a protein can accommodate, adapt and readjust its structure to answer an incoming signal, revealing more of the dynamical character of proteins.
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21
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Abstract
Background: Iodide transport defect is an uncommon cause of dyshormonogenic congenital hypothyroidism due to homozygous or compound heterozygous pathogenic variants in the SLC5A5 gene, which encodes the sodium/iodide symporter (NIS), causing deficient iodide accumulation in thyroid follicular cells, thus impairing thyroid hormonogenesis. Methods:SLC5A5 gene variants were compiled from public databases and research articles exploring the molecular bases of congenital hypothyroidism. Using a dataset of 198 missense NIS variants classified as either benign or pathogenic, we developed and validated a machine learning-based NIS-specific variant classifier to predict the impact of missense NIS variants. Results: We generated a manually curated dataset containing 7793 unique SLC5A5 variants. As most databases compiled exome sequencing data, variant mapping revealed an increased density of variants in SLC5A5 coding exons. Based on allele frequency (AF) analysis, we established an AF threshold of 1:10,000 above which a variant should be considered benign. Most pathogenic NIS variants were located in the protein-coding region, as most patients were genetically diagnosed by using a candidate gene strategy limited to this region. Significantly, we evidenced that 94.5% of missense NIS variants were classified as of uncertain significance. Therefore, we developed an NIS-specific variant classifier to improve the prediction of pathogenicity of missense variants. Our classifier predicted the clinical outcome of missense variants with high accuracy (90%), outperforming state-of-the-art pathogenicity predictors, such as REVEL, PolyPhen-2, and SIFT. Based on the excellent performance of our classifier, we predicted the mutational landscape of NIS. The analysis of the mutational landscape revealed that most missense variants located in transmembrane segments are frequently pathogenic. Moreover, we predicted that ∼28% of all single-nucleotide variants that could cause missense NIS variants are pathogenic, thus putatively leading to congenital hypothyroidism if present in homozygous or compound heterozygous state. Conclusions: We reported the first NIS-specific variant classifier aiming at improving the interpretation of missense NIS variants in clinical practice. Deciphering the mutational landscape for every protein involved in thyroid hormonogenesis is a relevant task for a deep understanding of the molecular mechanisms causing dyshormonogenic congenital hypothyroidism.
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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 Consejo Nacional de Investigaciones Científicas y Técnicas (CIBICI-CONICET), Córdoba, Argentina
| | - 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 Consejo Nacional de Investigaciones Científicas y Técnicas (CIBICI-CONICET), Córdoba, Argentina
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22
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Gutiérrez-González LH, Rivas-Fuentes S, Guzmán-Beltrán S, Flores-Flores A, Rosas-García J, Santos-Mendoza T. Peptide Targeting of PDZ-Dependent Interactions as Pharmacological Intervention in Immune-Related Diseases. Molecules 2021; 26:molecules26216367. [PMID: 34770776 PMCID: PMC8588348 DOI: 10.3390/molecules26216367] [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: 09/22/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022] Open
Abstract
PDZ (postsynaptic density (PSD95), discs large (Dlg), and zonula occludens (ZO-1)-dependent interactions are widely distributed within different cell types and regulate a variety of cellular processes. To date, some of these interactions have been identified as targets of small molecules or peptides, mainly related to central nervous system disorders and cancer. Recently, the knowledge of PDZ proteins and their interactions has been extended to various cell types of the immune system, suggesting that their targeting by viral pathogens may constitute an immune evasion mechanism that favors viral replication and dissemination. Thus, the pharmacological modulation of these interactions, either with small molecules or peptides, could help in the control of some immune-related diseases. Deeper structural and functional knowledge of this kind of protein–protein interactions, especially in immune cells, will uncover novel pharmacological targets for a diversity of clinical conditions.
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Affiliation(s)
- Luis H. Gutiérrez-González
- Department of Virology and Mycology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Selma Rivas-Fuentes
- Department of Research on Biochemistry, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Silvia Guzmán-Beltrán
- Department of Microbiology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico;
| | - Angélica Flores-Flores
- Laboratory of Immunopharmacology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (A.F.-F.); (J.R.-G.)
| | - Jorge Rosas-García
- Laboratory of Immunopharmacology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (A.F.-F.); (J.R.-G.)
- Department of Molecular Biomedicine, Centro de Investigación y de Estudios Avanzados, Mexico City 07360, Mexico
| | - Teresa Santos-Mendoza
- Laboratory of Immunopharmacology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (A.F.-F.); (J.R.-G.)
- Correspondence: ; Tel.: +52-55-54871700 (ext. 5243)
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23
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Kotelevets L, Chastre E. A New Story of the Three Magi: Scaffolding Proteins and lncRNA Suppressors of Cancer. Cancers (Basel) 2021; 13:4264. [PMID: 34503076 PMCID: PMC8428372 DOI: 10.3390/cancers13174264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 12/16/2022] Open
Abstract
Scaffolding molecules exert a critical role in orchestrating cellular response through the spatiotemporal assembly of effector proteins as signalosomes. By increasing the efficiency and selectivity of intracellular signaling, these molecules can exert (anti/pro)oncogenic activities. As an archetype of scaffolding proteins with tumor suppressor property, the present review focuses on MAGI1, 2, and 3 (membrane-associated guanylate kinase inverted), a subgroup of the MAGUK protein family, that mediate networks involving receptors, junctional complexes, signaling molecules, and the cytoskeleton. MAGI1, 2, and 3 are comprised of 6 PDZ domains, 2 WW domains, and 1 GUK domain. These 9 protein binding modules allow selective interactions with a wide range of effectors, including the PTEN tumor suppressor, the β-catenin and YAP1 proto-oncogenes, and the regulation of the PI3K/AKT, the Wnt, and the Hippo signaling pathways. The frequent downmodulation of MAGIs in various human malignancies makes these scaffolding molecules and their ligands putative therapeutic targets. Interestingly, MAGI1 and MAGI2 genetic loci generate a series of long non-coding RNAs that act as a tumor promoter or suppressor in a tissue-dependent manner, by selectively sponging some miRNAs or by regulating epigenetic processes. Here, we discuss the different paths followed by the three MAGIs to control carcinogenesis.
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Affiliation(s)
- Larissa Kotelevets
- Sorbonne Université, INSERM, UMR_S938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
| | - Eric Chastre
- Sorbonne Université, INSERM, UMR_S938, Centre de Recherche Saint-Antoine (CRSA), 75012 Paris, France
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24
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Vincenzi M, Mercurio FA, Leone M. Protein Interaction Domains: Structural Features and Drug Discovery Applications (Part 2). Curr Med Chem 2021; 28:854-892. [PMID: 31942846 DOI: 10.2174/0929867327666200114114142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Proteins present a modular organization made up of several domains. Apart from the domains playing catalytic functions, many others are crucial to recruit interactors. The latter domains can be defined as "PIDs" (Protein Interaction Domains) and are responsible for pivotal outcomes in signal transduction and a certain array of normal physiological and disease-related pathways. Targeting such PIDs with small molecules and peptides able to modulate their interaction networks, may represent a valuable route to discover novel therapeutics. OBJECTIVE This work represents a continuation of a very recent review describing PIDs able to recognize post-translationally modified peptide segments. On the contrary, the second part concerns with PIDs that interact with simple peptide sequences provided with standard amino acids. METHODS Crucial structural information on different domain subfamilies and their interactomes was gained by a wide search in different online available databases (including the PDB (Protein Data Bank), the Pfam (Protein family), and the SMART (Simple Modular Architecture Research Tool)). Pubmed was also searched to explore the most recent literature related to the topic. RESULTS AND CONCLUSION PIDs are multifaceted: they have all diverse structural features and can recognize several consensus sequences. PIDs can be linked to different diseases onset and progression, like cancer or viral infections and find applications in the personalized medicine field. Many efforts have been centered on peptide/peptidomimetic inhibitors of PIDs mediated interactions but much more work needs to be conducted to improve drug-likeness and interaction affinities of identified compounds.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
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25
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Ali M, Simonetti L, Ivarsson Y. Screening Intrinsically Disordered Regions for Short Linear Binding Motifs. Methods Mol Biol 2021; 2141:529-552. [PMID: 32696376 DOI: 10.1007/978-1-0716-0524-0_27] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The intrinsically disordered regions of the proteome are enriched in short linear motifs (SLiMs) that serve as binding sites for peptide binding proteins. These interactions are often of low-to-mid micromolar affinities and are challenging to screen for experimentally. However, a range of dedicated methods have been developed recently, which open for screening of SLiM-based interactions on large scale. A variant of phage display, termed proteomic peptide phage display (ProP-PD), has proven particularly useful for the purpose. Here, we describe a complete high-throughput ProP-PD protocol for screening intrinsically disordered regions for SLiMs. The protocol requires some basic bioinformatics skills for the design of the library and for data analysis but can be performed in a standard biochemistry lab. The protocol starts from the construction of a library, followed by the high-throughput expression and purification of bait proteins, the phage selection, and the analysis of the binding-enriched phage pools using next-generation sequencing. As the protocol generates rather large data sets, we also emphasize the importance of data management and storage.
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Molecular Basis of the Versatile Regulatory Mechanism of HtrA-Type Protease AlgW from Pseudomonas aeruginosa. mBio 2021; 12:mBio.03299-20. [PMID: 33622718 PMCID: PMC8545111 DOI: 10.1128/mbio.03299-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
AlgW, a membrane-bound periplasmic serine protease belonging to the HtrA protein family, is a key regulator of the regulated intramembrane proteolysis (RIP) pathway and is responsible for transmitting the envelope stress signals in Pseudomonas aeruginosa. The AlgW PDZ domain senses and binds the C-terminal of mis-localized outer membrane proteins (OMPs) or periplasmic protein MucE, leading to catalytic activation of the protease domain. While AlgW is functionally well studied, its exact activation mechanism remains to be elucidated. Here, we show that AlgW is a novel HtrA protease that can be biochemically activated by both peptide and lipid signals. Compared with the corresponding homologue DegS in Escherichia coli, AlgW exhibits a distinct substrate specificity and regulation mechanism. Structural, biochemical, and mutagenic analyses revealed that, by specifically binding to the C-terminal decapeptide of MucE, AlgW could adopt more relaxed conformation and obtain higher activity than with tripeptide activation. We also investigated the regulatory mechanism of the LA loop in AlgW and proved that the unique structural feature of this region was responsible for the distinct enzymatic property of AlgW. These results demonstrate the unique and diverse activation mechanism of AlgW, which P. aeruginosa may utilize to enhance its adaptability to environmental stress.
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Carr HS, Chang JT, Frost JA. The PDZ Domain Protein SYNJ2BP Regulates GRK-Dependent Sst2A Phosphorylation and Downstream MAPK Signaling. Endocrinology 2021; 162:6031468. [PMID: 33313679 PMCID: PMC7799432 DOI: 10.1210/endocr/bqaa229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 11/19/2022]
Abstract
The somatostatin receptor 2A (SST2) is a G-protein-coupled receptor (GPCR) that is expressed in neuroendocrine tissues within the gastrointestinal tract and brain, and is commonly overexpressed in many neuroendocrine tumors. Moreover, SST2 agonists are used clinically as the primary pharmacological treatment to suppress excess hormone secretion in a variety of neuroendocrine tumors. Despite its wide clinical use, mechanisms controlling the trafficking and signaling of SST2 are not fully understood. SST2 contains a C-terminal post-synaptic density 95, Drosophila discs large, zona-occludens 1 (PDZ) domain-binding motif that has been shown to interact with 3 different PDZ domain-containing proteins. However, the consequences of these interactions are not well understood, nor is it known whether additional PDZ domain proteins interact with SST2. Through unbiased screening we have identified 10 additional PDZ domain proteins that interact with SST2. We chose one of these, SYNJ2BP, for further study. We observed that SYNJ2BP interacted with SST2 in an agonist-dependent manner, and that this required the PDZ binding site of SST2. Importantly, overexpression of SYNJ2BP enhanced ligand-stimulated receptor internalization. Mechanistically, SYNJ2BP interacted with G-protein-coupled receptor kinase 2 (GRK2) and promoted GRK-dependent phosphorylation of the receptor after somatostatin stimulation. Interaction with GRK2 required the C-terminus of SYNJ2BP. Binding to SYNJ2BP did not affect the ability of SST2 to suppress 3',5'-cyclic adenosine 5'-monophosphate production, but was required for optimal agonist-stimulated extracellularly regulated kinase 1/2 activation. These data indicated that SYNJ2BP is an SST2-interacting protein that modulates agonist-stimulated receptor regulation and downstream signaling.
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Affiliation(s)
- Heather S Carr
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jeffrey A Frost
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas, USA
- Correspondence: Jeffrey A. Frost, PhD, Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, 6431 Fannin St, Houston, TX 77030, USA.
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Jurásek M, Kumar J, Paclíková P, Kumari A, Tripsianes K, Bryja V, Vácha R. Phosphorylation-induced changes in the PDZ domain of Dishevelled 3. Sci Rep 2021; 11:1484. [PMID: 33452274 PMCID: PMC7810883 DOI: 10.1038/s41598-020-79398-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/04/2020] [Indexed: 01/29/2023] Open
Abstract
The PDZ domain of Dishevelled 3 protein belongs to a highly abundant protein recognition motif which typically binds short C-terminal peptides. The affinity of the PDZ towards the peptides could be fine-tuned by a variety of post-translation modifications including phosphorylation. However, how phosphorylations affect the PDZ structure and its interactions with ligands remains elusive. Combining molecular dynamics simulations, NMR titration, and biological experiments, we explored the role of previously reported phosphorylation sites and their mimetics in the Dishevelled PDZ domain. Our observations suggest three major roles for phosphorylations: (1) acting as an on/off PDZ binding switch, (2) allosterically affecting the binding groove, and (3) influencing the secondary binding site. Our simulations indicated that mimetics had similar but weaker effects, and the effects of distinct sites were non-additive. This study provides insight into the Dishevelled regulation by PDZ phosphorylation. Furthermore, the observed effects could be used to elucidate the regulation mechanisms in other PDZ domains.
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Affiliation(s)
- Miroslav Jurásek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Jitender Kumar
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Petra Paclíková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Alka Kumari
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Konstantinos Tripsianes
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Brno, 612 65, Czech Republic
| | - Robert Vácha
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
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Kliche J, Kuss H, Ali M, Ivarsson Y. Cytoplasmic short linear motifs in ACE2 and integrin β 3 link SARS-CoV-2 host cell receptors to mediators of endocytosis and autophagy. Sci Signal 2021; 14:14/665/eabf1117. [PMID: 33436498 PMCID: PMC7928716 DOI: 10.1126/scisignal.abf1117] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SARS-CoV-2, the virus that causes COVID-19, enters cells through endocytosis upon binding to the cell surface receptor ACE2 and potentially others, including integrins. Using bioinformatics, Mészáros et al. predicted the presence of short amino acid sequences, called short linear motifs (SLiMs), in the cytoplasmic tails of ACE2 and various integrins that may engage the endocytic and autophagic machinery. Using affinity binding assays, Kliche et al. not only confirmed that many of these predicted SLiMs interacted with target peptides in various components of the endocytosis and autophagy machinery, but also found that these interactions were regulated by the phosphorylation of SLiM-adjacent amino acids. Together, these findings have identified a potential link between autophagy and integrin signaling and could lead to new ways to prevent viral infection. The spike protein of SARS-CoV-2 binds the angiotensin-converting enzyme 2 (ACE2) on the host cell surface and subsequently enters host cells through receptor-mediated endocytosis. Additional cell receptors may be directly or indirectly involved, including integrins. The cytoplasmic tails of ACE2 and integrins contain several predicted short linear motifs (SLiMs) that may facilitate internalization of the virus as well as its subsequent propagation through processes such as autophagy. Here, we measured the binding affinity of predicted interactions between SLiMs in the cytoplasmic tails of ACE2 and integrin β3 with proteins that mediate endocytic trafficking and autophagy. We validated that a class I PDZ-binding motif mediated binding of ACE2 to the scaffolding proteins SNX27, NHERF3, and SHANK, and that a binding site for the clathrin adaptor AP2 μ2 in ACE2 overlaps with a phospho-dependent binding site for the SH2 domains of Src family tyrosine kinases. Furthermore, we validated that an LC3-interacting region (LIR) in integrin β3 bound to the ATG8 domains of the autophagy receptors MAP1LC3 and GABARAP in a manner enhanced by LIR-adjacent phosphorylation. Our results provide molecular links between cell receptors and mediators of endocytosis and autophagy that may facilitate viral entry and propagation.
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Affiliation(s)
- Johanna Kliche
- Department of Chemistry, BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Hanna Kuss
- Department of Chemistry, BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden.,WWU Münster, Institute for Evolution and Biodiversity, DE-48149 Münster, Germany
| | - Muhammad Ali
- Department of Chemistry, BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry, BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden.
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30
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Ali M, McAuley MM, Lüchow S, Knapp S, Joerger AC, Ivarsson Y. Integrated analysis of Shank1 PDZ interactions with C-terminal and internal binding motifs. Curr Res Struct Biol 2021; 3:41-50. [PMID: 34235485 PMCID: PMC8244488 DOI: 10.1016/j.crstbi.2021.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/02/2021] [Indexed: 12/27/2022] Open
Abstract
PDZ domains constitute a large family of modular domains that are well-known for binding C-terminal motifs of target proteins. Some of them also bind to internal PDZ binding motifs (PDZbms), but this aspect of the PDZ interactome is poorly studied. Here we explored internal PDZbm-mediated interactions using the PDZ domain of Shank1 as a model. We identified a series of human Shank1 ligands with C-terminal or internal PDZbms using proteomic peptide-phage display, and established that while the consensus sequence of C-terminal ligands is x-T-x-(L/F)-COOH, the consensus of internal PDZbm is exclusively x-T-x-F-x, where x is any amino acid. We found that the affinities of PDZbm interactions are in the low micromolar range. The crystal structure of the complex between Shank1 PDZ and an internal PDZbm revealed that the binding mode of internal PDZbms was similar to that of C-terminal ligands. Pull-down experiments confirmed that both C-terminal and internal PDZbm interactions can occur in the context of full-length proteins. Our study expands the interactome of Shank1 and hints at a largely unexplored interaction space of PDZ domains.
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Affiliation(s)
- Muhammad Ali
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - Mishal Mariam McAuley
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Susanne Lüchow
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Andreas C. Joerger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Ylva Ivarsson
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
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31
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Daulat AM, Audebert S, Wagner M, Camoin L, Borg JP. Identification of PDZ Interactions by Affinity Purification and Mass Spectrometry Analysis. Methods Mol Biol 2021; 2256:17-40. [PMID: 34014514 DOI: 10.1007/978-1-0716-1166-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Identification of protein networks becomes indispensable for determining the function of a given protein of interest. Some proteins harbor a PDZ binding motif (PDZBM) located at the carboxy-terminus end. This motif is necessary to recruit PDZ domain proteins which are involved in signaling, trafficking, and maintenance of cell architecture. In the present chapter, we present two complementary approaches (immunopurification and peptide-based purification procedures) followed by mass spectrometry analysis to identify PDZ domain proteins associated to a given protein of interest. As proof of example, we focus our attention on TANC1 which is a scaffold protein harboring a PDZBM at its carboxy-terminus. Using these two approaches, we identified several PDZ domain containing proteins. Some of them were found with both approaches, and some were specifically identified using peptide-based purification procedure. This exemplifies advantages and differences of both strategies to identify PDZ interactions.
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Affiliation(s)
- Avais M Daulat
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France
| | - Stéphane Audebert
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Mônica Wagner
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Luc Camoin
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Jean-Paul Borg
- Institut Universitaire de France (IUF), Paris, France.
- Centre de Recherche en Cancérologie de Marseille, Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, Marseille, France.
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32
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Leblanc R, Kashyap R, Barral K, Egea-Jimenez AL, Kovalskyy D, Feracci M, Garcia M, Derviaux C, Betzi S, Ghossoub R, Platonov M, Roche P, Morelli X, Hoffer L, Zimmermann P. Pharmacological inhibition of syntenin PDZ2 domain impairs breast cancer cell activities and exosome loading with syndecan and EpCAM cargo. J Extracell Vesicles 2020; 10:e12039. [PMID: 33343836 PMCID: PMC7737769 DOI: 10.1002/jev2.12039] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 11/02/2020] [Accepted: 11/14/2020] [Indexed: 12/17/2022] Open
Abstract
Exosomes support cell-to-cell communication in physiology and disease, including cancer. We currently lack tools, such as small chemicals, capable of modifying exosome composition and activity in a specific manner. Building on our previous understanding of how syntenin, and its PDZ partner syndecan (SDC), impact on exosome composition we optimized a small chemical compound targeting the PDZ2 domain of syntenin. In vitro , in tests on MCF-7 breast carcinoma cells, this compound is non-toxic and impairs cell proliferation, migration and primary sphere formation. It does not affect the size or the number of secreted particles, yet it decreases the amounts of exosomal syntenin, ALIX and SDC4 while leaving other exosomal markers unaffected. Interestingly, it also blocks the sorting of EpCAM, a bona fide target used for carcinoma exosome immunocapture. Our study highlights the first characterization of a small pharmacological inhibitor of the syntenin-exosomal pathway, of potential interest for exosome research and oncology.
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Affiliation(s)
- R Leblanc
- Equipe labellisée Ligue 2018 Centre de Recherche en Cancérologie de Marseille (CRCM) Aix-Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes Marseille France
| | - R Kashyap
- Equipe labellisée Ligue 2018 Centre de Recherche en Cancérologie de Marseille (CRCM) Aix-Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes Marseille France
| | - K Barral
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - A L Egea-Jimenez
- Equipe labellisée Ligue 2018 Centre de Recherche en Cancérologie de Marseille (CRCM) Aix-Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes Marseille France
| | - D Kovalskyy
- Enamine Ltd. Kyiv Ukraine.,Taras Shevchenko National University of Kyiv Kyiv Ukraine
| | - M Feracci
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - M Garcia
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - C Derviaux
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - S Betzi
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - R Ghossoub
- Equipe labellisée Ligue 2018 Centre de Recherche en Cancérologie de Marseille (CRCM) Aix-Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes Marseille France
| | - M Platonov
- Enamine Ltd. Kyiv Ukraine.,Institute of Molecular Biology and Genetics National Academy of Sciences of Ukraine Kyiv Ukraine
| | - P Roche
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - X Morelli
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - L Hoffer
- Centre de Recherche en Cancérologie de Marseille Integrative Structural & Chemical Biology Aix-Marseille Université, Inserm, CNRS, Institut Paoli Calmettes Marseille France
| | - Pascale Zimmermann
- Equipe labellisée Ligue 2018 Centre de Recherche en Cancérologie de Marseille (CRCM) Aix-Marseille Université, Inserm, CNRS, Institut Paoli-Calmettes Marseille France.,Department of Human Genetics K. U. Leuven Leuven Belgium
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Zheng L, Li S, Zheng X, Guo R, Qu W. AHNAK2 is a novel prognostic marker and correlates with immune infiltration in papillary thyroid cancer: Evidence from integrated analysis. Int Immunopharmacol 2020; 90:107185. [PMID: 33218938 DOI: 10.1016/j.intimp.2020.107185] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022]
Abstract
Papillary thyroid cancer (PTC) is the most prevalent endocrine tumor, and its incidence is still increasing. The mechanisms of PTC dedifferentiation and malignant progression remain unclear. In this study, we identified AHNAK2 as a key gene in PTC by differential expression analysis among four GEO datasets and validated its overexpression profile by data from the Oncomine, TCGA, and HPA databases and IHC staining analysis. AHNAK2 upregulation significantly correlated with advanced grades, stages, and lymph node events. Survival analysis suggested that AHNAK2 overexpression was coupled with poor overall survival. The immune infiltration analysis by TIMER and CIBERSORT indicated that AHNAK2 expression tightly correlated with the infiltration of diverse immune cell types, especially T cell subtypes. In addition, AHNAK2 is correlated with the expression of other conventional key genes of TC, such as PIK3CA, MAPK1, CTNNB1, and SLC5A5. AHNAK2 may be a novel prognostic marker for PTC.
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Affiliation(s)
- Long Zheng
- Department of Nuclear Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, Shaanxi, China
| | - Shanshan Li
- Department of Epidemiology and Health Statistics, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, Shaanxi, China
| | - Xianghong Zheng
- Department of Nuclear Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, Shaanxi, China
| | - Rong Guo
- Department of Nuclear Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, Shaanxi, China
| | - Wei Qu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, Shaanxi, China.
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34
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The Conformational Plasticity Vista of PDZ Domains. Life (Basel) 2020; 10:life10080123. [PMID: 32726937 PMCID: PMC7460260 DOI: 10.3390/life10080123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/19/2020] [Accepted: 07/25/2020] [Indexed: 02/01/2023] Open
Abstract
The PDZ domain (PSD95-Discs large-ZO1) is a widespread modular domain present in the living organisms. A prevalent function in the PDZ family is to serve as scaffolding and adaptor proteins connecting multiple partners in signaling pathways. An explanation of the flexible functionality in this domain family, based just on a static perspective of the structure-activity relationship, might fall short. More dynamic and conformational aspects in the protein fold can be the reasons for such functionality. Folding studies indeed showed an ample and malleable folding landscape for PDZ domains where multiple intermediate states were experimentally detected. Allosteric phenomena that resemble energetic coupling between residues have also been found in PDZ domains. Additionally, several PDZ domains are modulated by post-translational modifications, which introduce conformational switches that affect binding. Altogether, the ability to connect diverse partners might arise from the intrinsic plasticity of the PDZ fold.
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35
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Genovese I, Carotti A, Ilari A, Fiorillo A, Battista T, Colotti G, Ivarsson Y. Profiling calcium-dependent interactions between Sorcin and intrinsically disordered regions of human proteome. Biochim Biophys Acta Gen Subj 2020; 1864:129618. [PMID: 32305337 DOI: 10.1016/j.bbagen.2020.129618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/05/2020] [Accepted: 04/12/2020] [Indexed: 11/18/2022]
Abstract
BACKGROUND Sorcin is a calcium sensor that exerts many calcium-related functions in the cells, e.g. it regulates calcium concentration in the cytoplasm, endoplasmic reticulum (ER) and mitochondria, by interacting with calcium pumps, exchangers and channels. Albeit Sorcin is an interesting potential cancer target, little is known about its interactors upon calcium-mediated activation. Our previous study suggested that Sorcin may recognize short linear binding motifs as the crystal structure revealed a self-interaction with a GYYPGG stretch in its N-terminus, and combinatorial peptide-phage display provided support for peptide-mediated interactions. METHODS In this study we screened for motif-based interactions between Sorcin and intrinsically disordered regions of the human proteome using proteomic peptide phage display (ProP-PD). We identified a peptide belonging to protein phosphatase 1 regulatory subunit 3G (PPP1R3G) as a potential novel interactor and confirm the interaction through biophysical and cell-based approaches, and provide structural information through molecular dynamics simulations. RESULTS Altogether, we identify a preferred motif in the enriched pool of binders and a peptide belonging to protein phosphatase 1 regulatory subunit 3G (PPP1R3G) as a preferred ligand. CONCLUSION Through this study we gain information on a new Sorcin binding partner and profile Sorcin's motif-based interaction. GENERAL SIGNIFICANCE The interaction between Sorcin and PPP1R3G may suggest a close dependence between glucose homeostasis and calcium concentration in the different cell compartments, opening a completely new and interesting scenery yet to be fully disclosed.
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Affiliation(s)
- Ilaria Genovese
- Department of Medical Sciences, Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, via Fossato di Mortara 70, 44121 Ferrara, Italy; Department of Biochemical Sciences, University Sapienza, P.le Aldo Moro 5, 00185 Rome, Italy; Department of Chemistry - BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden.
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti 48, 06123 Perugia, Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology National Research Council, IBPM-CNR, c/o Department of Biochemical Sciences, University Sapienza, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Annarita Fiorillo
- Department of Biochemical Sciences, University Sapienza, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Theo Battista
- Department of Biochemical Sciences, University Sapienza, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology National Research Council, IBPM-CNR, c/o Department of Biochemical Sciences, University Sapienza, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Husargatan 3, 751 23 Uppsala, Sweden
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36
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Bailly AL, Grenier JMP, Cartier-Michaud A, Bardin F, Balzano M, Goubard A, Lissitzky JC, De Grandis M, Mancini SJC, Serge A, Aurrand-Lions M. GRASP55 Is Dispensable for Normal Hematopoiesis but Necessary for Myc-Dependent Leukemic Growth. THE JOURNAL OF IMMUNOLOGY 2020; 204:2685-2696. [PMID: 32229537 DOI: 10.4049/jimmunol.1901124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/03/2020] [Indexed: 11/19/2022]
Abstract
Grasp55 is a ubiquitous Golgi stacking protein involved in autophagy, protein trafficking, and glucose deprivation sensing. The function of Grasp55 in protein trafficking has been attributed to its PDZ-mediated interaction with the C-terminal PDZ-binding motifs of protein cargos. We have recently shown that such an interaction occurs between Grasp55 and the adhesion molecule Jam-C, which plays a central role in stemness maintenance of hematopoietic and spermatogenic cells. Accordingly, we have found that Grasp55-deficient mice suffer from spermatogenesis defects similar to Jam-C knockout mice. However, whether Grasp55 is involved in the maintenance of immunohematopoietic homeostasis through regulation of protein transport and Jam-C expression remains unknown. In this study, we show that Grasp55 deficiency does not affect hematopoietic stem cell differentiation, engraftment, or mobilization, which are known to depend on expression of Grasp55-dependent protein cargos. In contrast, using an Myc-dependent leukemic model addicted to autophagy, we show that knockdown of Grasp55 in leukemic cells reduces spleen and bone marrow tumor burden upon i.v. leukemic engraftment. This is not due to reduced homing of Grasp55-deficient cells to these organs but to increased spontaneous apoptosis of Grasp55-deficient leukemic cells correlated with increased sensitivity of the cells to glucose deprivation. These results show that Grasp55 plays a role in Myc-transformed hematopoietic cells but not in normal hematopoietic cells in vivo.
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Affiliation(s)
- Anne-Laure Bailly
- Equipe Labellisée Ligue contre le Cancer, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, Cancerology Research Center of Marseille, Marseille 13009, France; and
| | - Julien M P Grenier
- Equipe Labellisée Ligue contre le Cancer, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, Cancerology Research Center of Marseille, Marseille 13009, France; and
| | - Amandine Cartier-Michaud
- Equipe Labellisée Ligue contre le Cancer, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, Cancerology Research Center of Marseille, Marseille 13009, France; and
| | - Florence Bardin
- Equipe Labellisée Ligue contre le Cancer, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, Cancerology Research Center of Marseille, Marseille 13009, France; and
| | - Marielle Balzano
- Equipe Labellisée Ligue contre le Cancer, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, Cancerology Research Center of Marseille, Marseille 13009, France; and
| | - Armelle Goubard
- Equipe Labellisée Ligue contre le Cancer, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, Cancerology Research Center of Marseille, Marseille 13009, France; and
| | - Jean-Claude Lissitzky
- Equipe Labellisée Ligue contre le Cancer, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, Cancerology Research Center of Marseille, Marseille 13009, France; and
| | - Maria De Grandis
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, UMR 7268, Aix Marseille Université, CNRS, Marseille 13005, France
| | - Stéphane J C Mancini
- Equipe Labellisée Ligue contre le Cancer, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, Cancerology Research Center of Marseille, Marseille 13009, France; and
| | - Arnauld Serge
- Equipe Labellisée Ligue contre le Cancer, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, Cancerology Research Center of Marseille, Marseille 13009, France; and
| | - Michel Aurrand-Lions
- Equipe Labellisée Ligue contre le Cancer, Aix Marseille University, CNRS, INSERM, Institut Paoli-Calmettes, Cancerology Research Center of Marseille, Marseille 13009, France; and
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Amacher JF, Brooks L, Hampton TH, Madden DR. Specificity in PDZ-peptide interaction networks: Computational analysis and review. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100022. [PMID: 32289118 PMCID: PMC7138185 DOI: 10.1016/j.yjsbx.2020.100022] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/26/2020] [Accepted: 02/29/2020] [Indexed: 01/03/2023]
Abstract
Globular PDZ domains typically serve as protein-protein interaction modules that regulate a wide variety of cellular functions via recognition of short linear motifs (SLiMs). Often, PDZ mediated-interactions are essential components of macromolecular complexes, and disruption affects the entire scaffold. Due to their roles as linchpins in trafficking and signaling pathways, PDZ domains are attractive targets: both for controlling viral pathogens, which bind PDZ domains and hijack cellular machinery, as well as for developing therapies to combat human disease. However, successful therapeutic interventions that avoid off-target effects are a challenge, because each PDZ domain interacts with a number of cellular targets, and specific binding preferences can be difficult to decipher. Over twenty-five years of research has produced a wealth of data on the stereochemical preferences of individual PDZ proteins and their binding partners. Currently the field lacks a central repository for this information. Here, we provide this important resource and provide a manually curated, comprehensive list of the 271 human PDZ domains. We use individual domain, as well as recent genomic and proteomic, data in order to gain a holistic view of PDZ domains and interaction networks, arguing this knowledge is critical to optimize targeting selectivity and to benefit human health.
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Affiliation(s)
- Jeanine F Amacher
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.,Department of Chemistry, Western Washington University, Bellingham, WA 98225, USA
| | - Lionel Brooks
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Dean R Madden
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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Laursen L, Karlsson E, Gianni S, Jemth P. Functional interplay between protein domains in a supramodular structure involving the postsynaptic density protein PSD-95. J Biol Chem 2019; 295:1992-2000. [PMID: 31831623 DOI: 10.1074/jbc.ra119.011050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/12/2019] [Indexed: 11/06/2022] Open
Abstract
Cell scaffolding and signaling are governed by protein-protein interactions. Although a particular interaction is often defined by two specific domains binding to each other, this interaction often occurs in the context of other domains in multidomain proteins. How such adjacent domains form supertertiary structures and modulate protein-protein interactions has only recently been addressed and is incompletely understood. The postsynaptic density protein PSD-95 contains a three-domain supramodule, denoted PSG, which consists of PDZ, Src homology 3 (SH3), and guanylate kinase-like domains. The PDZ domain binds to the C terminus of its proposed natural ligand, CXXC repeat-containing interactor of PDZ3 domain (CRIPT), and results from previous experiments using only the isolated PDZ domain are consistent with the simplest scenario for a protein-protein interaction; namely, a two-state mechanism. Here we analyzed the binding kinetics of the PSG supramodule with CRIPT. We show that PSG binds CRIPT via a more complex mechanism involving two conformational states interconverting on the second timescale. Both conformational states bound a CRIPT peptide with similar affinities but with different rates, and the distribution of the two conformational states was slightly shifted upon CRIPT binding. Our results are consistent with recent structural findings of conformational changes in PSD-95 and demonstrate how conformational transitions in supertertiary structures can shape the ligand-binding energy landscape and modulate protein-protein interactions.
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Affiliation(s)
- Louise Laursen
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden
| | - Elin Karlsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, 00185 Rome, Italy.
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123 Uppsala, Sweden.
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Dubreuil B, Matalon O, Levy ED. Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions. J Mol Biol 2019; 431:4978-4992. [PMID: 31442477 PMCID: PMC6941228 DOI: 10.1016/j.jmb.2019.08.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/07/2019] [Accepted: 08/10/2019] [Indexed: 02/07/2023]
Abstract
In eukaryotes, disordered regions cover up to 50% of proteomes and mediate fundamental cellular processes. In contrast to globular domains, where about half of the amino acids are buried in the protein interior, disordered regions show higher solvent accessibility, which makes them prone to engage in non-functional interactions. Such interactions are exacerbated by the law of mass action, prompting the question of how they are minimized in abundant proteins. We find that interaction propensity or "stickiness" of disordered regions negatively correlates with their cellular abundance, both in yeast and human. Strikingly, considering yeast proteins where a large fraction of the sequence is disordered, the correlation between stickiness and abundance reaches R=-0.55. Beyond this global amino-acid composition bias, we identify three rules by which amino-acid composition of disordered regions adjusts with high abundance. First, lysines are preferred over arginines, consistent with the latter amino acid being stickier than the former. Second, compensatory effects exist, whereby a sticky region can be tolerated if it is compensated by a distal non-sticky region. Third, such compensation requires a lower average stickiness at the same abundance when compared to a scenario where stickiness is homogeneous throughout the sequence. We validate these rules experimentally, employing them as different strategies to rescue an otherwise sticky protein fragment from aggregation. Our results highlight that non-functional interactions represent a significant constraint in cellular systems and reveal simple rules by which protein sequences adapt to that constraint. Data from this work are deposited in Figshare, at https://doi.org/10.6084/m9.figshare.8068937.v3.
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Affiliation(s)
- Benjamin Dubreuil
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Or Matalon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Emmanuel D Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Abstract
OTULIN (OTU Deubiquitinase With Linear Linkage Specificity) specifically hydrolyzes methionine1 (Met1)-linked ubiquitin chains conjugated by LUBAC (linear ubiquitin chain assembly complex). Here we report on the mass spectrometric identification of the OTULIN interactor SNX27 (sorting nexin 27), an adaptor of the endosomal retromer complex responsible for protein recycling to the cell surface. The C-terminal PDZ-binding motif (PDZbm) in OTULIN associates with the cargo-binding site in the PDZ domain of SNX27. By solving the structure of the OTU domain in complex with the PDZ domain, we demonstrate that a second interface contributes to the selective, high affinity interaction of OTULIN and SNX27. SNX27 does not affect OTULIN catalytic activity, OTULIN-LUBAC binding or Met1-linked ubiquitin chain homeostasis. However, via association, OTULIN antagonizes SNX27-dependent cargo loading, binding of SNX27 to the VPS26A-retromer subunit and endosome-to-plasma membrane trafficking. Thus, we define an additional, non-catalytic function of OTULIN in the regulation of SNX27-retromer assembly and recycling to the cell surface. OTULIN is a linear ubiquitin hydrolase that regulates ubiquitin homeostasis. Here the authors identify the adaptor of the endosomal retromer complex sorting nexin 27 (SNX27) as a binding partner of OTULIN and determine the structure of the OTULIN-SNX27 complex, which reveals a secondary interface through which OTULIN non-catalytically antagonizes SNX27 retromer assembly and cargo loading.
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Christensen NR, Čalyševa J, Fernandes EFA, Lüchow S, Clemmensen LS, Haugaard‐Kedström LM, Strømgaard K. PDZ Domains as Drug Targets. ADVANCED THERAPEUTICS 2019; 2:1800143. [PMID: 32313833 PMCID: PMC7161847 DOI: 10.1002/adtp.201800143] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/25/2019] [Indexed: 12/14/2022]
Abstract
Protein-protein interactions within protein networks shape the human interactome, which often is promoted by specialized protein interaction modules, such as the postsynaptic density-95 (PSD-95), discs-large, zona occludens 1 (ZO-1) (PDZ) domains. PDZ domains play a role in several cellular functions, from cell-cell communication and polarization, to regulation of protein transport and protein metabolism. PDZ domain proteins are also crucial in the formation and stability of protein complexes, establishing an important bridge between extracellular stimuli detected by transmembrane receptors and intracellular responses. PDZ domains have been suggested as promising drug targets in several diseases, ranging from neurological and oncological disorders to viral infections. In this review, the authors describe structural and genetic aspects of PDZ-containing proteins and discuss the current status of the development of small-molecule and peptide modulators of PDZ domains. An overview of potential new therapeutic interventions in PDZ-mediated protein networks is also provided.
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Affiliation(s)
- Nikolaj R. Christensen
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Jelena Čalyševa
- European Molecular Biology Laboratory (EMBL)Structural and Computational Biology UnitMeyerhofstraße 169117HeidelbergGermany
- EMBL International PhD ProgrammeFaculty of BiosciencesEMBL–Heidelberg UniversityGermany
| | - Eduardo F. A. Fernandes
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Susanne Lüchow
- Department of Chemistry – BMCUppsala UniversityBox 576SE75123UppsalaSweden
| | - Louise S. Clemmensen
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Linda M. Haugaard‐Kedström
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Kristian Strømgaard
- Center for BiopharmaceuticalsDepartment of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
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Predicted amino acid motif repeats in proteins potentially encode extensive multivalent macromolecular assemblies in the human proteome. Curr Opin Struct Biol 2019; 54:171-178. [PMID: 30978654 DOI: 10.1016/j.sbi.2019.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 01/31/2023]
Abstract
There are emerging interests in understanding higher order assemblies of biopolymers within and between cells, such as protein-protein and protein-RNA biomolecular condensates. These biomolecular condensates are thought to assemble/disassemble via multivalent interactions, including those mediated particularly by unique repeated amino acid motifs (URM). We asked how common are proteins with such URMs, their incidence and abundance, by exhaustively enumerating repeating motifs of length 3-10 in the human proteome. We found that URMs are very common and widely distributed across the human proteome. Moreover, the number of repetitions and intervals between them do not correlate with their lengths, which suggests that the number of repeats among proteins in the proteome is independent of length, contrary to the notion that short motifs are more abundant then long motifs. Finally, we describe two examples of URMs in proteins known to form higher order biopolymer assemblies: multi-PDZ domain-containing proteins and the FUS family of RNA binding proteins. For the FUS family, we predicted a known sequence 'grammar', specific motifs and interval sequence compositions that are essential to phase separation and material properties of condensates formed by this family of proteins. In PDZ domain-containing proteins we found a novel repeated motif that was surprisingly both within and between individual PDZ domains. We speculate that these motifs could be binding sites for multivalent interactions, a residual result of the mechanism by which PDZ-domain duplications occurred or that the linker sequences between PDZ domains may encode cryptic PDZ domains.
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Erlendsson S, Thorsen TS, Vauquelin G, Ammendrup-Johnsen I, Wirth V, Martinez KL, Teilum K, Gether U, Madsen KL. Mechanisms of PDZ domain scaffold assembly illuminated by use of supported cell membrane sheets. eLife 2019; 8:39180. [PMID: 30605082 PMCID: PMC6345565 DOI: 10.7554/elife.39180] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 01/02/2019] [Indexed: 01/07/2023] Open
Abstract
PDZ domain scaffold proteins are molecular modules orchestrating cellular signalling in space and time. Here, we investigate assembly of PDZ scaffolds using supported cell membrane sheets, a unique experimental setup enabling direct access to the intracellular face of the cell membrane. Our data demonstrate how multivalent protein-protein and protein-lipid interactions provide critical avidity for the strong binding between the PDZ domain scaffold proteins, PICK1 and PSD-95, and their cognate transmembrane binding partners. The kinetics of the binding were remarkably slow and binding strength two-three orders of magnitude higher than the intrinsic affinity for the isolated PDZ interaction. Interestingly, discrete changes in the intrinsic PICK1 PDZ affinity did not affect overall binding strength but instead revealed dual scaffold modes for PICK1. Our data supported by simulations suggest that intrinsic PDZ domain affinities are finely tuned and encode specific cellular responses, enabling multiplexed cellular functions of PDZ scaffolds. Inside a cell, many different signals carry information that is essential for the cell to remain healthy and perform its role in the body. It is, therefore, very important that the signals are sent to the right places at the right times. Scaffold proteins play an essential role in organizing these signals by bringing specific proteins and other molecules into close contact at particular times and locations within the cell. Defects in scaffolding proteins can lead to cancer, psychiatric disorders and other diseases, so these proteins represent potential new targets for medicinal drugs. Many scaffolding proteins assemble groups of proteins on the surface of the membrane that surrounds the cell. Previous studies have shown that scaffolding proteins are able to bind to several other proteins as well as the membrane itself at the same time. However, the precise way in which scaffolding proteins assemble such groups is not clear because it is technically challenging to study this process in living cells. To overcome this challenge, Erlendsson, Thorsen et al. used a new experimental setup known as supported cell membrane sheets – which provides direct access to the side of the cell membrane that usually faces into the cell – to study two scaffolding proteins known as PICK1 and PSD-95. The experiments show that PICK1 and PSD-95 bind to their partner proteins up to 100 times more strongly than previously observed using other approaches. This is due to the scaffolding proteins binding more strongly to both their partners and the membrane. Unexpectedly, the experiments show that the shape and physical characteristics of the partner protein have no effect on the increase in the strength of the binding. Further experiments suggest that altering the ability of the PDZ domain of PICK1 to bind to partner proteins changes the mode of action of the PICK1 protein so that it can activate different responses in the cell. Together these findings imply that the ability of scaffolding proteins to bind to their partner proteins is finely tuned to encode specific responses in cells in different situations – a hypothesis that Erlendsson, Thorsen et al. are planning to test in intact cells.
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Affiliation(s)
- Simon Erlendsson
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen, Copenhagen, Denmark.,Structural Biology and NMR Laboratory, Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Thor Seneca Thorsen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Georges Vauquelin
- Molecular and Biochemical Pharmacology, Department of Biotechnology, Free University Brussels (VUB), Brussels, Belgium
| | - Ina Ammendrup-Johnsen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Volker Wirth
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, Nano-science Center, University of Copenhagen, Copenhagen, Denmark
| | - Karen L Martinez
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, Nano-science Center, University of Copenhagen, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Ulrik Gether
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth Lindegaard Madsen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
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Pemberton JG, Balla T. Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1111:77-137. [PMID: 30483964 DOI: 10.1007/5584_2018_288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within eukaryotic cells, biochemical reactions need to be organized on the surface of membrane compartments that use distinct lipid constituents to dynamically modulate the functions of integral proteins or influence the selective recruitment of peripheral membrane effectors. As a result of these complex interactions, a variety of human pathologies can be traced back to improper communication between proteins and membrane surfaces; either due to mutations that directly alter protein structure or as a result of changes in membrane lipid composition. Among the known structural lipids found in cellular membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the membrane-anchored precursor of low-abundance regulatory lipids, the polyphosphoinositides (PPIn), which have restricted distributions within specific subcellular compartments. The ability of PPIn lipids to function as signaling platforms relies on both non-specific electrostatic interactions and the selective stereospecific recognition of PPIn headgroups by specialized protein folds. In this chapter, we will attempt to summarize the structural diversity of modular PPIn-interacting domains that facilitate the reversible recruitment and conformational regulation of peripheral membrane proteins. Outside of protein folds capable of capturing PPIn headgroups at the membrane interface, recent studies detailing the selective binding and bilayer extraction of PPIn species by unique functional domains within specific families of lipid-transfer proteins will also be highlighted. Overall, this overview will help to outline the fundamental physiochemical mechanisms that facilitate localized interactions between PPIn lipids and the wide-variety of PPIn-binding proteins that are essential for the coordinate regulation of cellular metabolism and membrane dynamics.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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45
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Probing the Architecture of a Multi-PDZ Domain Protein: Structure of PDZK1 in Solution. Structure 2018; 26:1522-1533.e5. [DOI: 10.1016/j.str.2018.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/12/2018] [Accepted: 07/27/2018] [Indexed: 12/15/2022]
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Phosphorylation of NHERF1 S279 and S301 differentially regulates breast cancer cell phenotype and metastatic organotropism. Biochim Biophys Acta Mol Basis Dis 2018; 1865:26-37. [PMID: 30326259 DOI: 10.1016/j.bbadis.2018.10.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/21/2018] [Accepted: 10/11/2018] [Indexed: 02/08/2023]
Abstract
Metastatic cancer cells are highly plastic for the expression of different tumor phenotype hallmarks and organotropism. This plasticity is highly regulated but the dynamics of the signaling processes orchestrating the shift from one cell phenotype and metastatic organ pattern to another are still largely unknown. The scaffolding protein NHERF1 has been shown to regulate the expression of different neoplastic phenotypes through its PDZ domains, which forms the mechanistic basis for metastatic organotropism. This reprogramming activity was postulated to be dependent on its differential phosphorylation patterns. Here, we show that NHERF1 phosphorylation on S279/S301 dictates several tumor phenotypes such as in vivo invasion, NHE1-mediated matrix digestion, growth and vasculogenic mimicry. Remarkably, injecting mice with cells having differential NHERF1 expression and phosphorylation drove a shift from the predominantly lung colonization (WT NHERF1) to predominately bone colonization (double S279A/S301A mutant), indicating that NHERF1 phosphorylation also acts as a signaling switch in metastatic organotropism.
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47
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Singh KH, Yadav S, Kumar D, Biswal BK. The crystal structure of an essential high-temperature requirement protein HtrA1 (Rv1223) from Mycobacterium tuberculosis reveals its unique features. Acta Crystallogr D Struct Biol 2018; 74:906-921. [PMID: 30198900 DOI: 10.1107/s205979831800952x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 07/03/2018] [Indexed: 11/11/2022] Open
Abstract
High-temperature requirement A (HtrA) proteins, which are members of the heat-shock-induced serine protease family, are involved in extracytoplasmic protein quality control and bacterial survival strategies under stress conditions, and are associated with the virulence of several pathogens; they are therefore major drug targets. Mycobacterium tuberculosis possesses three putative HtrAs: HtrA1 (Rv1223), HtrA2 (Rv0983) and HtrA3 (Rv0125). Each has a cytoplasmic region, a transmembrane helix and a periplasmic region. Here, the crystal structure of the periplasmic region consisting of a protease domain (PD) and a PDZ domain from an M. tuberculosis HtrA1 mutant (mHtrA1S387A) is reported at 2.7 Å resolution. Although the mHtrA1S387A PD shows structural features similar to those of other HtrAs, its loops, particularly L3 and LA, display different conformations. Loop L3 communicates between the PDs of the trimer and the PDZ domains and undergoes a transition from an active to an inactive conformation, as reported for an equivalent HtrA (DegS). Loop LA, which is responsible for higher oligomer formation owing to its length (50 amino acids) in DegP, is very short in mHtrA1S387A (five amino acids), as in mHtrA2 (also five amino acids), and therefore lacks essential interactions for the formation of higher oligomers. Notably, a well ordered loop known as the insertion clamp in the PDZ domain interacts with the protease domain of the adjacent molecule, which possibly aids in the stabilization of a trimeric functional unit of this enzyme. The three-dimensional structure of mHtrA1S387A presented here will be useful in the design of enzyme-specific antituberculosis inhibitors.
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Affiliation(s)
- Khundrakpam Herojit Singh
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Savita Yadav
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Deepak Kumar
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Bichitra Kumar Biswal
- Structural and Functional Biology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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48
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Sundell GN, Arnold R, Ali M, Naksukpaiboon P, Orts J, Güntert P, Chi CN, Ivarsson Y. Proteome-wide analysis of phospho-regulated PDZ domain interactions. Mol Syst Biol 2018; 14:e8129. [PMID: 30126976 PMCID: PMC6100724 DOI: 10.15252/msb.20178129] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 12/13/2022] Open
Abstract
A key function of reversible protein phosphorylation is to regulate protein-protein interactions, many of which involve short linear motifs (3-12 amino acids). Motif-based interactions are difficult to capture because of their often low-to-moderate affinities. Here, we describe phosphomimetic proteomic peptide-phage display, a powerful method for simultaneously finding motif-based interaction and pinpointing phosphorylation switches. We computationally designed an oligonucleotide library encoding human C-terminal peptides containing known or predicted Ser/Thr phosphosites and phosphomimetic variants thereof. We incorporated these oligonucleotides into a phage library and screened the PDZ (PSD-95/Dlg/ZO-1) domains of Scribble and DLG1 for interactions potentially enabled or disabled by ligand phosphorylation. We identified known and novel binders and characterized selected interactions through microscale thermophoresis, isothermal titration calorimetry, and NMR We uncover site-specific phospho-regulation of PDZ domain interactions, provide a structural framework for how PDZ domains accomplish phosphopeptide binding, and discuss ligand phosphorylation as a switching mechanism of PDZ domain interactions. The approach is readily scalable and can be used to explore the potential phospho-regulation of motif-based interactions on a large scale.
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Affiliation(s)
- Gustav N Sundell
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Roland Arnold
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Muhammad Ali
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Piangfan Naksukpaiboon
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Julien Orts
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
- Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
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49
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Mazzotta GM, Bellanda M, Minervini G, Damulewicz M, Cusumano P, Aufiero S, Stefani M, Zambelli B, Mammi S, Costa R, Tosatto SCE. Calmodulin Enhances Cryptochrome Binding to INAD in Drosophila Photoreceptors. Front Mol Neurosci 2018; 11:280. [PMID: 30177872 PMCID: PMC6109769 DOI: 10.3389/fnmol.2018.00280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 07/24/2018] [Indexed: 12/13/2022] Open
Abstract
Light is the main environmental stimulus that synchronizes the endogenous timekeeping systems in most terrestrial organisms. Drosophila cryptochrome (dCRY) is a light-responsive flavoprotein that detects changes in light intensity and wavelength around dawn and dusk. We have previously shown that dCRY acts through Inactivation No Afterpotential D (INAD) in a light-dependent manner on the Signalplex, a multiprotein complex that includes visual-signaling molecules, suggesting a role for dCRY in fly vision. Here, we predict and demonstrate a novel Ca2+-dependent interaction between dCRY and calmodulin (CaM). Through yeast two hybrid, coimmunoprecipitation (Co-IP), nuclear magnetic resonance (NMR) and calorimetric analyses we were able to identify and characterize a CaM binding motif in the dCRY C-terminus. Similarly, we also detailed the CaM binding site of the scaffold protein INAD and demonstrated that CaM bridges dCRY and INAD to form a ternary complex in vivo. Our results suggest a process whereby a rapid dCRY light response stimulates an interaction with INAD, which can be further consolidated by a novel mechanism regulated by CaM.
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Affiliation(s)
| | - Massimo Bellanda
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | | | - Milena Damulewicz
- Department of Cell Biology and Imaging, Institute of Zoology and Biomedical Research, Faculty of Biology and Earth Sciences, Jagiellonian University, Kraków, Poland
| | - Paola Cusumano
- Department of Biology, University of Padova, Padova, Italy
| | - Simona Aufiero
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Monica Stefani
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Barbara Zambelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Stefano Mammi
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Rodolfo Costa
- Department of Biology, University of Padova, Padova, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,CNR Institute of Neuroscience, Padova, Italy
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50
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Ponna SK, Ruskamo S, Myllykoski M, Keller C, Boeckers TM, Kursula P. Structural basis for PDZ domain interactions in the post-synaptic density scaffolding protein Shank3. J Neurochem 2018; 145:449-463. [DOI: 10.1111/jnc.14322] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/07/2018] [Accepted: 02/14/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Srinivas Kumar Ponna
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu; University of Oulu; Oulu Finland
| | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu; University of Oulu; Oulu Finland
| | - Matti Myllykoski
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu; University of Oulu; Oulu Finland
| | - Corinna Keller
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu; University of Oulu; Oulu Finland
| | | | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu; University of Oulu; Oulu Finland
- Department of Biomedicine; University of Bergen; Bergen Norway
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