1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Javorsky A, Humbert PO, Kvansakul M. Viral manipulation of cell polarity signalling. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119536. [PMID: 37437846 DOI: 10.1016/j.bbamcr.2023.119536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/24/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
Cell polarity refers to the asymmetric distribution of biomacromolecules that enable the correct orientation of a cell in a particular direction. It is thus an essential component for appropriate tissue development and function. Viral infections can lead to dysregulation of polarity. This is associated with a poor prognosis due to viral interference with core cell polarity regulatory scaffolding proteins that often feature PDZ (PSD-95, DLG, and ZO-1) domains including Scrib, Dlg, Pals1, PatJ, Par3 and Par6. PDZ domains are also promiscuous, binding to several different partners through their C-terminal region which contain PDZ-binding motifs (PBM). Numerous viruses encode viral effector proteins that target cell polarity regulators for their benefit and include papillomaviruses, flaviviruses and coronaviruses. A better understanding of the mechanisms of action utilised by viral effector proteins to subvert host cell polarity sigalling will provide avenues for future therapeutic intervention, while at the same time enhance our understanding of cell polarity regulation and its role tissue homeostasis.
Collapse
Affiliation(s)
- Airah Javorsky
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Patrick O Humbert
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia; Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria 3086, Australia; Department of Biochemistry & Pharmacology, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Marc Kvansakul
- Department of Biochemistry & Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia; Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria 3086, Australia.
| |
Collapse
|
4
|
Wang Y, Wang Y, Wu Y, Suo Y, Guo H, Yu Y, Yin R, Xi R, Wu J, Hua N, Zhang Y, Zhang S, Jin Z, He L, Ma G. Using the inner membrane of Escherichia coli as a scaffold to anchor enzymes for metabolic flux enhancement. Eng Life Sci 2023; 23:e2200034. [PMID: 36751472 PMCID: PMC9893748 DOI: 10.1002/elsc.202200034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 01/11/2023] Open
Abstract
Clustering enzymes in the same metabolic pathway is a natural strategy to enhance productivity. Synthetic protein, RNA and DNA scaffolds have been designed to artificially cluster multiple enzymes in the cell, which require complex construction processes and possess limited slots for target enzymes. We utilized the Escherichia coli inner cell membrane as a native scaffold to cluster four fatty acid synthases (FAS) and achieved to improve the efficiency of fatty acid synthesis in vivo. The construction strategy is as simple as fusing target enzymes to the N-terminus or C-terminus of the membrane anchor protein (Lgt), and the number of anchored enzymes is not restricted. This novel device not only presents a similar efficiency in clustering multiple enzymes to that of other artificial scaffolds but also promotes the product secretion, driving the entire metabolic flux forward and further increasing the gross yield compared with that in a cytoplasmic scaffold system.
Collapse
Affiliation(s)
- You Wang
- Bio‐X‐Renji Hospital Research CenterRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP.R. China,Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China,2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Yushu Wang
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Yuqi Wu
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China,2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Yang Suo
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China,2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Huaqing Guo
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China,2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Yineng Yu
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China,2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Ruonan Yin
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China,2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Rui Xi
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China,2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Jiajie Wu
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China,2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Nan Hua
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China,2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Yuehan Zhang
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China,2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Shaobo Zhang
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China,2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Zhenming Jin
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China,2012 SJTU‐BioX‐Shanghai Team for The International Genetically Engineered Machine Competition (iGEM)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Lin He
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
| | - Gang Ma
- Bio‐X‐Renji Hospital Research CenterRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiP.R. China,Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education)Shanghai Jiao Tong UniversityShanghaiP.R. China
| |
Collapse
|
5
|
Schoeman D, Cloete R, Fielding BC. The Flexible, Extended Coil of the PDZ-Binding Motif of the Three Deadly Human Coronavirus E Proteins Plays a Role in Pathogenicity. Viruses 2022; 14:v14081707. [PMID: 36016329 PMCID: PMC9416557 DOI: 10.3390/v14081707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/22/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023] Open
Abstract
The less virulent human (h) coronaviruses (CoVs) 229E, NL63, OC43, and HKU1 cause mild, self-limiting respiratory tract infections, while the more virulent SARS-CoV-1, MERS-CoV, and SARS-CoV-2 have caused severe outbreaks. The CoV envelope (E) protein, an important contributor to the pathogenesis of severe hCoV infections, may provide insight into this disparate severity of the disease. We, therefore, generated full-length E protein models for SARS-CoV-1 and -2, MERS-CoV, HCoV-229E, and HCoV-NL63 and docked C-terminal peptides of each model to the PDZ domain of the human PALS1 protein. The PDZ-binding motif (PBM) of the SARS-CoV-1 and -2 and MERS-CoV models adopted a more flexible, extended coil, while the HCoV-229E and HCoV-NL63 models adopted a less flexible alpha helix. All the E peptides docked to PALS1 occupied the same binding site and the more virulent hCoV E peptides generally interacted more stably with PALS1 than the less virulent ones. We hypothesize that the increased flexibility of the PBM in the more virulent hCoVs facilitates more stable binding to various host proteins, thereby contributing to more severe disease. This is the first paper to model full-length 3D structures for both the more virulent and less virulent hCoV E proteins, providing novel insights for possible drug and/or vaccine development.
Collapse
Affiliation(s)
- Dewald Schoeman
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
| | - Ruben Cloete
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
| | - Burtram C. Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa;
- Correspondence:
| |
Collapse
|
6
|
Zhu Y, Alvarez F, Wolff N, Mechaly A, Brûlé S, Neitthoffer B, Etienne-Manneville S, Haouz A, Boëda B, Caillet-Saguy C. Interactions of Severe Acute Respiratory Syndrome Coronavirus 2 Protein E With Cell Junctions and Polarity PSD-95/Dlg/ZO-1-Containing Proteins. Front Microbiol 2022; 13:829094. [PMID: 35283834 PMCID: PMC8909127 DOI: 10.3389/fmicb.2022.829094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/06/2022] [Indexed: 12/24/2022] Open
Abstract
The C-terminus of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protein E contains a PBM (PDZ-binding motif) targeting PDZ (PSD-95/Dlg/ZO-1) domains, which is identical to the PBM of SARS-CoV. The latter is involved in the pathogenicity of the virus. Recently, we identified 10 human PDZ-containing proteins showing significant interactions with SARS-CoV-2 protein E PBM. We selected several of them involved in cellular junctions and cell polarity (TJP1, PARD3, MLLT4, and LNX2) and MPP5/PALS1 previously shown to interact with SARS-CoV E PBM. Targeting cellular junctions and polarity components is a common strategy by viruses to hijack cell machinery to their advantage. In this study, we showed that these host PDZ domains TJP1, PARD3, MLLT4, LNX2, and MPP5/PALS1 interact in a PBM-dependent manner in vitro and colocalize with the full-length E protein in cellulo, sequestrating the PDZ domains to the Golgi compartment. We solved three crystal structures of complexes between human LNX2, MLLT4, and MPP5 PDZs and SARS-CoV-2 E PBM highlighting its binding preferences for several cellular targets. Finally, we showed different affinities for the PDZ domains with the original SARS-CoV-2 C-terminal sequence containing the PBM and the one of the beta variant that contains a mutation close to the PBM. The acquired mutations in the E protein localized near the PBM might have important effects both on the structure and the ion-channel activity of the E protein and on the host machinery targeted by the variants during the infection.
Collapse
Affiliation(s)
- Yanlei Zhu
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Flavio Alvarez
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Nicolas Wolff
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| | - Ariel Mechaly
- Crystallography Platform-C2RT, CNRS, UMR 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Sébastien Brûlé
- Molecular Biophysics Platform-C2RT, CNRS, UMR 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Benoit Neitthoffer
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR 3691 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR 3691 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Ahmed Haouz
- Crystallography Platform-C2RT, CNRS, UMR 3528, Institut Pasteur, Université de Paris, Paris, France
| | - Batiste Boëda
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR 3691 CNRS, Université de Paris, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Célia Caillet-Saguy
- Channel Receptors Unit, CNRS, UMR 3571, Institut Pasteur, Université de Paris, Paris, France
| |
Collapse
|
7
|
Javorsky A, Humbert PO, Kvansakul M. Structural basis of coronavirus E protein interactions with human PALS1 PDZ domain. Commun Biol 2021; 4:724. [PMID: 34117354 PMCID: PMC8196010 DOI: 10.1038/s42003-021-02250-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/20/2021] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 infection leads to coronavirus disease 2019 (COVID-19), which is associated with severe and life-threatening pneumonia and respiratory failure. However, the molecular basis of these symptoms remains unclear. SARS-CoV-1 E protein interferes with control of cell polarity and cell-cell junction integrity in human epithelial cells by binding to the PALS1 PDZ domain, a key component of the Crumbs polarity complex. We show that C-terminal PDZ binding motifs of SARS-CoV-1 and SARS-CoV-2 E proteins bind the PALS1 PDZ domain with 29.6 and 22.8 μM affinity, whereas the related sequence from MERS-CoV did not bind. We then determined crystal structures of PALS1 PDZ domain bound to both SARS-CoV-1 and SARS-CoV-2 E protein PDZ binding motifs. Our findings establish the structural basis for SARS-CoV-1/2 mediated subversion of Crumbs polarity signalling and serve as a platform for the development of small molecule inhibitors to suppress SARS-CoV-1/2 mediated disruption of polarity signalling in epithelial cells. Airah Javorsky et al. present the crystal structures of SARS-CoV-1 and SARS-CoV-2 E proteins in complex with the PALS1 PDZ domain. Their results suggest that the coronavirus E protein can interfere with normal PALS1 binding, potentially disrupting epithelial tissue integrity, and may provide future insight into the development of small molecule inhibitors against SARS-CoV-1/2.
Collapse
Affiliation(s)
- Airah Javorsky
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Vic, Australia
| | - Patrick O Humbert
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Vic, Australia. .,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Vic, Australia. .,Department of Biochemistry & Molecular Biology, University of Melbourne, Melbourne, Vic, Australia. .,Department of Clinical Pathology, University of Melbourne, Melbourne, Vic, Australia.
| | - Marc Kvansakul
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Vic, Australia. .,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Vic, Australia.
| |
Collapse
|
8
|
Lo Cascio E, Toto A, Babini G, De Maio F, Sanguinetti M, Mordente A, Della Longa S, Arcovito A. Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. Comput Struct Biotechnol J 2021; 19:1838-1847. [PMID: 33758649 PMCID: PMC7970798 DOI: 10.1016/j.csbj.2021.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/13/2021] [Accepted: 03/13/2021] [Indexed: 12/21/2022] Open
Abstract
Short Linear Motifs (SLiMs) are functional protein microdomains that typically mediate interactions between a short linear region in one protein and a globular domain in another. Surface Plasmon Resonance assays have been performed to determine the binding affinity between PDZ domain of wild type human PALS1 protein and tetradecapeptides representing the SLiMs sequences of SARS-CoV-1 and SARS-CoV-2 E proteins (E-SLiMs). SARS-CoV-2 E-SLiM binds to the human target protein with a higher affinity compared to SARS-CoV-1, showing a difference significantly greater than previously reported using the F318W mutant of PALS1 protein and shorter target peptides. Moreover, molecular dynamics simulations have provided clear evidence of the structural determinants driving this binding process. Specifically, the Arginine 69 residue in the SARS-CoV-2 E-SLiM is the key residue able to both enhance the specific polar interaction with negatively charged pockets of the PALS1 PDZ domain and reduce significantly the mobility of the viral peptide. These experimental and computational data are reinforced by the comparison of the interaction between the PALS1 PDZ domain with the natural ligand CRB1, as well as the corresponding E-SLiMs of other coronavirus members such as MERS and OCF43. Our results provide a model at the molecular level of the strategies used to mimic the endogenous SLiM peptide in the binding of the tight junctions of the host cell, explaining one of the possible reasons of the severity of the infection and pulmonary inflammation by SARS-CoV-2.
Collapse
Affiliation(s)
- Ettore Lo Cascio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Angelo Toto
- 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
| | - Gabriele Babini
- Dipartimento di Scienze della Salute della Donna, del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy
| | - Flavio De Maio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy
| | - Alvaro Mordente
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy.,Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy
| | - Stefano Della Longa
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Alessandro Arcovito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy.,Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy
| |
Collapse
|
9
|
Martin E, Girardello R, Dittmar G, Ludwig A. New insights into the organization and regulation of the apical polarity network in mammalian epithelial cells. FEBS J 2021; 288:7073-7095. [DOI: 10.1111/febs.15710] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 12/11/2022]
Affiliation(s)
- Eleanor Martin
- School of Biological Sciences Nanyang Technological University Singapore City Singapore
- Proteomics of Cellular Signaling Luxembourg Institute of Health Strassen Luxembourg
| | - Rossana Girardello
- School of Biological Sciences Nanyang Technological University Singapore City Singapore
- Proteomics of Cellular Signaling Luxembourg Institute of Health Strassen Luxembourg
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling Luxembourg Institute of Health Strassen Luxembourg
- Department of Life Sciences and Medicine University of Luxembourg Luxembourg
| | - Alexander Ludwig
- School of Biological Sciences Nanyang Technological University Singapore City Singapore
- NTU Institute of Structural Biology (NISB) Experimental Medicine Building Nanyang Technological University Singapore City Singapore
| |
Collapse
|
10
|
Chytła A, Gajdzik-Nowak W, Olszewska P, Biernatowska A, Sikorski AF, Czogalla A. Not Just Another Scaffolding Protein Family: The Multifaceted MPPs. Molecules 2020; 25:molecules25214954. [PMID: 33114686 PMCID: PMC7662862 DOI: 10.3390/molecules25214954] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/16/2020] [Accepted: 10/20/2020] [Indexed: 01/03/2023] Open
Abstract
Membrane palmitoylated proteins (MPPs) are a subfamily of a larger group of multidomain proteins, namely, membrane-associated guanylate kinases (MAGUKs). The ubiquitous expression and multidomain structure of MPPs provide the ability to form diverse protein complexes at the cell membranes, which are involved in a wide range of cellular processes, including establishing the proper cell structure, polarity and cell adhesion. The formation of MPP-dependent complexes in various cell types seems to be based on similar principles, but involves members of different protein groups, such as 4.1-ezrin-radixin-moesin (FERM) domain-containing proteins, polarity proteins or other MAGUKs, showing their multifaceted nature. In this review, we discuss the function of the MPP family in the formation of multiple protein complexes. Notably, we depict their significant role for cell physiology, as the loss of interactions between proteins involved in the complex has a variety of negative consequences. Moreover, based on recent studies concerning the mechanism of membrane raft formation, we shed new light on a possible role played by MPPs in lateral membrane organization.
Collapse
Affiliation(s)
- Agnieszka Chytła
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland; (A.C.); (W.G.-N.); (P.O.); (A.B.)
| | - Weronika Gajdzik-Nowak
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland; (A.C.); (W.G.-N.); (P.O.); (A.B.)
| | - Paulina Olszewska
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland; (A.C.); (W.G.-N.); (P.O.); (A.B.)
| | - Agnieszka Biernatowska
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland; (A.C.); (W.G.-N.); (P.O.); (A.B.)
| | - Aleksander F. Sikorski
- Research and Development Center, Regional Specialist Hospital, Kamieńskiego 73a, 51-154 Wroclaw, Poland;
| | - Aleksander Czogalla
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland; (A.C.); (W.G.-N.); (P.O.); (A.B.)
- Correspondence: ; Tel.: +48-71375-6356
| |
Collapse
|
11
|
De Maio F, Lo Cascio E, Babini G, Sali M, Della Longa S, Tilocca B, Roncada P, Arcovito A, Sanguinetti M, Scambia G, Urbani A. Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis. Microbes Infect 2020; 22:592-597. [PMID: 32891874 PMCID: PMC7473260 DOI: 10.1016/j.micinf.2020.08.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 12/14/2022]
Abstract
The Envelope (E) protein of SARS-CoV-2 is the most enigmatic protein among the four structural ones. Most of its current knowledge is based on the direct comparison to the SARS E protein, initially mistakenly undervalued and subsequently proved to be a key factor in the ER-Golgi localization and in tight junction disruption. We compared the genomic sequences of E protein of SARS-CoV-2, SARS-CoV and the closely related genomes of bats and pangolins obtained from the GISAID and GenBank databases. When compared to the known SARS E protein, we observed a significant difference in amino acid sequence in the C-terminal end of SARS-CoV-2 E protein. Subsequently, in silico modelling analyses of E proteins conformation and docking provide evidences of a strengthened binding of SARS-CoV-2 E protein with the tight junction-associated PALS1 protein. Based on our computational evidences and on data related to SARS-CoV, we believe that SARS-CoV-2 E protein interferes more stably with PALS1 leading to an enhanced epithelial barrier disruption, amplifying the inflammatory processes, and promoting tissue remodelling. These findings raise a warning on the underestimated role of the E protein in the pathogenic mechanism and open the route to detailed experimental investigations.
Collapse
Affiliation(s)
- Flavio De Maio
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Ettore Lo Cascio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie - Sezione di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Gabriele Babini
- Dipartimento di Scienze della Salute della Donna, del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy.
| | - Michela Sali
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Stefano Della Longa
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Bruno Tilocca
- Department of Health Science, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Paola Roncada
- Department of Health Science, University "Magna Græcia" of Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Alessandro Arcovito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie - Sezione di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy; Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie - Sezione di Microbiologia, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Giovanni Scambia
- Dipartimento di Scienze della Salute della Donna, del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; Dipartimento di Scienze della Vita e Sanità Pubblica - Sezione di Ginecologia ed Ostetricia, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Andrea Urbani
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy; Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie - Sezione di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| |
Collapse
|
12
|
Aguilar-Aragon M, Fletcher G, Thompson BJ. The cytoskeletal motor proteins Dynein and MyoV direct apical transport of Crumbs. Dev Biol 2020; 459:126-137. [PMID: 31881198 PMCID: PMC7090908 DOI: 10.1016/j.ydbio.2019.12.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022]
Abstract
Crumbs (Crb in Drosophila; CRB1-3 in mammals) is a transmembrane determinant of epithelial cell polarity and a regulator of Hippo signalling. Crb is normally localized to apical cell-cell contacts, just above adherens junctions, but how apical trafficking of Crb is regulated in epithelial cells remains unclear. We use the Drosophila follicular epithelium to demonstrate that polarized trafficking of Crb is mediated by transport along microtubules by the motor protein Dynein and along actin filaments by the motor protein Myosin-V (MyoV). Blocking transport of Crb-containing vesicles by Dynein or MyoV leads to accumulation of Crb within Rab11 endosomes, rather than apical delivery. The final steps of Crb delivery and stabilisation at the plasma membrane requires the exocyst complex and three apical FERM domain proteins - Merlin, Moesin and Expanded - whose simultaneous loss disrupts apical localization of Crb. Accordingly, a knock-in deletion of the Crb FERM-binding motif (FBM) also impairs apical localization. Finally, overexpression of Crb challenges this system, creating a sensitized background to identify components involved in cytoskeletal polarization, apical membrane trafficking and stabilisation of Crb at the apical domain.
Collapse
Affiliation(s)
- M Aguilar-Aragon
- The Francis Crick Institute, 1 Midland Rd, NW1 1AT, London, United Kingdom
| | - G Fletcher
- The Francis Crick Institute, 1 Midland Rd, NW1 1AT, London, United Kingdom
| | - B J Thompson
- The Francis Crick Institute, 1 Midland Rd, NW1 1AT, London, United Kingdom; The John Curtin School of Medical Research, The Australian National University, 131 Garran Rd, Acton, ACT 2601, Canberra, Australia.
| |
Collapse
|
13
|
Heinemann U, Schuetz A. Structural Features of Tight-Junction Proteins. Int J Mol Sci 2019; 20:E6020. [PMID: 31795346 PMCID: PMC6928914 DOI: 10.3390/ijms20236020] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022] Open
Abstract
Tight junctions are complex supramolecular entities composed of integral membrane proteins, membrane-associated and soluble cytoplasmic proteins engaging in an intricate and dynamic system of protein-protein interactions. Three-dimensional structures of several tight-junction proteins or their isolated domains have been determined by X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy. These structures provide direct insight into molecular interactions that contribute to the formation, integrity, or function of tight junctions. In addition, the known experimental structures have allowed the modeling of ligand-binding events involving tight-junction proteins. Here, we review the published structures of tight-junction proteins. We show that these proteins are composed of a limited set of structural motifs and highlight common types of interactions between tight-junction proteins and their ligands involving these motifs.
Collapse
Affiliation(s)
- Udo Heinemann
- Macromolecular Structure and Interaction Laboratory, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Anja Schuetz
- Protein Production & Characterization Platform, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| |
Collapse
|
14
|
Lattner J, Leng W, Knust E, Brankatschk M, Flores-Benitez D. Crumbs organizes the transport machinery by regulating apical levels of PI(4,5)P 2 in Drosophila. eLife 2019; 8:e50900. [PMID: 31697234 PMCID: PMC6881148 DOI: 10.7554/elife.50900] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
An efficient vectorial intracellular transport machinery depends on a well-established apico-basal polarity and is a prerequisite for the function of secretory epithelia. Despite extensive knowledge on individual trafficking pathways, little is known about the mechanisms coordinating their temporal and spatial regulation. Here, we report that the polarity protein Crumbs is essential for apical plasma membrane phospholipid-homeostasis and efficient apical secretion. Through recruiting βHeavy-Spectrin and MyosinV to the apical membrane, Crumbs maintains the Rab6-, Rab11- and Rab30-dependent trafficking and regulates the lipid phosphatases Pten and Ocrl. Crumbs knock-down results in increased apical levels of PI(4,5)P2 and formation of a novel, Moesin- and PI(4,5)P2-enriched apical membrane sac containing microvilli-like structures. Our results identify Crumbs as an essential hub required to maintain the organization of the apical membrane and the physiological activity of the larval salivary gland.
Collapse
Affiliation(s)
- Johanna Lattner
- Max-Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)DresdenGermany
| | - Weihua Leng
- Max-Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)DresdenGermany
| | - Elisabeth Knust
- Max-Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)DresdenGermany
| | - Marko Brankatschk
- The Biotechnological Center of the TU Dresden (BIOTEC)DresdenGermany
| | - David Flores-Benitez
- Max-Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG)DresdenGermany
| |
Collapse
|
15
|
Srivastava A, Karthick T, Joshi BD, Mishra R, Tandon P, Ayala AP, Ellena J. Spectroscopic (far or terahertz, mid-infrared and Raman) investigation, thermal analysis and biological activity of piplartine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 184:368-381. [PMID: 28538206 DOI: 10.1016/j.saa.2017.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 06/07/2023]
Abstract
Research in the field of medicinal plants including Piper species like long pepper (Piper longum L.- Piperaceae) is increasing all over the world due to its use in traditional and Ayurvedic medicine. Piplartine (piperlongumine, 5,6-dihydro-1-[(2E)-1-oxo-3-(3,4,5-trimethoxyphenyl)-2-propenyl]-2(1H)-pyridinone), a biologically active alkaloid/amide was isolated from the phytochemical investigations of Piper species, as long pepper. This alkaloid has cytotoxic, anti-fungal, anti-diabetic, anti-platelet aggregation, anti-tumoral, anxiolytic, anti-depressant, anti-leishmanial, and genotoxic activities, but, its anticancer property is the most promising and has been widely explored. The main purpose of the work is to present a solid state characterization of PPTN using thermal analysis and vibrational spectroscopy. Quantum mechanical calculations based on the density functional theory was also applied to investigate the molecular conformation and vibrational spectrum, which was compared with experimental results obtained by Raman scattering, far (terahertz) and mid-infrared adsorption spectroscopy. NBO analysis has been performed which predict that most intensive interactions in PPTN are the hyperconjugative interactions between n(1) N6 and π*(O1C7) having delocalization energy of 50.53kcal/mol, Topological parameters have been analyzed using 'AIM' analysis which governs the three bond critical points (BCPs), one di-hydrogen, and four ring critical points (RCPs). MEP surface has been plotted which forecast that the most negative region is associated with the electronegative oxygen atoms (sites for nucleophilic activity). Theoretically, to confirm that the title compound has anti-cancer, anti-diabetic and anti-platelet aggregation activities, it was analyzed by molecular docking interactions with the corresponding target receptors. The obtained values of H-bonding parameters and binding affinity prove that its anti-cancer activity is the more prominent than the other properties.
Collapse
Affiliation(s)
- Anubha Srivastava
- Department of Physics, University of Lucknow, University Road, Lucknow 226 007, Uttar Pradesh, India.
| | - T Karthick
- Department of Physics, University of Lucknow, University Road, Lucknow 226 007, Uttar Pradesh, India
| | - B D Joshi
- Department of Physics, Tribhuvan University, Siddhanath Sc. Campus, Nepal 10400, India; Departamento de Física, Universidade Federal do Ceará, C. P. 6030, 60.455-900 Fortaleza, CE, Brazil
| | - Rashmi Mishra
- Department of Physics, University of Lucknow, University Road, Lucknow 226 007, Uttar Pradesh, India; Department of Physics, Seth G.B. Podar College, Nawalgarh, Rajasthan, India
| | - Poonam Tandon
- Department of Physics, University of Lucknow, University Road, Lucknow 226 007, Uttar Pradesh, India.
| | - A P Ayala
- Departamento de Física, Universidade Federal do Ceará, C. P. 6030, 60.455-900 Fortaleza, CE, Brazil
| | - Javier Ellena
- Instituto de Física de São Carlos, Universidade de São Paulo, CP. 369, 13560-970, São Carlos, SP, Brazil
| |
Collapse
|
16
|
Zhong B, Zhang C, Guo S, Zhang C. Rational design of cyclic peptides to disrupt TGF-Β/SMAD7 signaling in heterotopic ossification. J Mol Graph Model 2017; 72:25-31. [DOI: 10.1016/j.jmgm.2016.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/17/2016] [Accepted: 12/05/2016] [Indexed: 12/20/2022]
|
17
|
Hall G, Cullen E, Sawmynaden K, Arnold J, Fox S, Cowan R, Muskett FW, Matthews D, Merritt A, Kettleborough C, Cruikshank W, Taylor D, Bayliss R, Carr MD. Structure of a Potential Therapeutic Antibody Bound to Interleukin-16 (IL-16): MECHANISTIC INSIGHTS AND NEW THERAPEUTIC OPPORTUNITIES. J Biol Chem 2016; 291:16840-8. [PMID: 27231345 DOI: 10.1074/jbc.m115.709303] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Indexed: 01/19/2023] Open
Abstract
Interleukin-16 (IL-16) is reported to be a chemoattractant cytokine and modulator of T-cell activation, and has been proposed as a ligand for the co-receptor CD4. The secreted active form of IL-16 has been detected at sites of TH1-mediated inflammation, such as those seen in autoimmune diseases, ischemic reperfusion injury (IRI), and tissue transplant rejection. Neutralization of IL-16 recruitment to its receptor, using an anti-IL16 antibody, has been shown to significantly attenuate inflammation and disease pathology in IRI, as well as in some autoimmune diseases. The 14.1 antibody is a monoclonal anti-IL-16 antibody, which when incubated with CD4(+) cells is reported to cause a reduction in the TH1-type inflammatory response. Secreted IL-16 contains a characteristic PDZ domain. PDZ domains are typically characterized by a defined globular structure, along with a peptide-binding site located in a groove between the αB and βB structural elements and a highly conserved carboxylate-binding loop. In contrast to other reported PDZ domains, the solution structure previously reported for IL-16 reveals a tryptophan residue obscuring the recognition groove. We have solved the structure of the 14.1Fab fragment in complex with IL-16, revealing that binding of the antibody requires a conformational change in the IL-16 PDZ domain. This involves the rotation of the αB-helix, accompanied movement of the peptide groove obscuring tryptophan residue, and consequent opening up of the binding site for interaction. Our study reveals a surprising mechanism of action for the antibody and identifies new opportunities for the development of IL-16-targeted therapeutics, including small molecules that mimic the interaction of the antibody.
Collapse
Affiliation(s)
- Gareth Hall
- From the Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 9HN, United Kingdom,
| | - Eilish Cullen
- MRC Technology, Centre for Therapeutics Discovery, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom, and
| | - Kovilen Sawmynaden
- MRC Technology, Centre for Therapeutics Discovery, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom, and
| | - Joanne Arnold
- MRC Technology, Centre for Therapeutics Discovery, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom, and
| | - Simon Fox
- MRC Technology, Centre for Therapeutics Discovery, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom, and
| | - Richard Cowan
- From the Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 9HN, United Kingdom
| | - Frederick W Muskett
- From the Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 9HN, United Kingdom
| | - David Matthews
- MRC Technology, Centre for Therapeutics Discovery, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom, and
| | - Andrew Merritt
- MRC Technology, Centre for Therapeutics Discovery, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom, and
| | - Catherine Kettleborough
- MRC Technology, Centre for Therapeutics Discovery, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom, and
| | | | - Debra Taylor
- MRC Technology, Centre for Therapeutics Discovery, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, United Kingdom, and
| | - Richard Bayliss
- From the Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 9HN, United Kingdom
| | - Mark D Carr
- From the Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 9HN, United Kingdom,
| |
Collapse
|
18
|
Horn AHC, Sticht H. Synthetic Protein Scaffolds Based on Peptide Motifs and Cognate Adaptor Domains for Improving Metabolic Productivity. Front Bioeng Biotechnol 2015; 3:191. [PMID: 26636078 PMCID: PMC4655305 DOI: 10.3389/fbioe.2015.00191] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/05/2015] [Indexed: 01/01/2023] Open
Abstract
The efficiency of many cellular processes relies on the defined interaction among different proteins within the same metabolic or signaling pathway. Consequently, a spatial colocalization of functionally interacting proteins has frequently emerged during evolution. This concept has been adapted within the synthetic biology community for the purpose of creating artificial scaffolds. A recent advancement of this concept is the use of peptide motifs and their cognate adaptor domains. SH2, SH3, GBD, and PDZ domains have been used most often in research studies to date. The approach has been successfully applied to the synthesis of a variety of target molecules including catechin, D-glucaric acid, H2, hydrochinone, resveratrol, butyrate, gamma-aminobutyric acid, and mevalonate. Increased production levels of up to 77-fold have been observed compared to non-scaffolded systems. A recent extension of this concept is the creation of a covalent linkage between peptide motifs and adaptor domains, which leads to a more stable association of the scaffolded systems and thus bears the potential to further enhance metabolic productivity.
Collapse
Affiliation(s)
- Anselm H C Horn
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg , Erlangen , Germany
| | - Heinrich Sticht
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg , Erlangen , Germany
| |
Collapse
|
19
|
Flores-Benitez D, Knust E. Crumbs is an essential regulator of cytoskeletal dynamics and cell-cell adhesion during dorsal closure in Drosophila. eLife 2015; 4. [PMID: 26544546 PMCID: PMC4718732 DOI: 10.7554/elife.07398] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 11/06/2015] [Indexed: 12/12/2022] Open
Abstract
The evolutionarily conserved Crumbs protein is required for epithelial polarity and morphogenesis. Here we identify a novel role of Crumbs as a negative regulator of actomyosin dynamics during dorsal closure in the Drosophila embryo. Embryos carrying a mutation in the FERM (protein 4.1/ezrin/radixin/moesin) domain-binding motif of Crumbs die due to an overactive actomyosin network associated with disrupted adherens junctions. This phenotype is restricted to the amnioserosa and does not affect other embryonic epithelia. This function of Crumbs requires DMoesin, the Rho1-GTPase, class-I p21-activated kinases and the Arp2/3 complex. Data presented here point to a critical role of Crumbs in regulating actomyosin dynamics, cell junctions and morphogenesis. DOI:http://dx.doi.org/10.7554/eLife.07398.001 A layer of epithelial cells covers the body surface of animals. Epithelial cells have a property known as polarity; this means that they have two different poles, one of which is in contact with the environment. Midway through embryonic development, the Drosophila embryo is covered by two kinds of epithelial sheets; the epidermis on the front, the belly and the sides of the embryo, and the amnioserosa on the back. In the second half of embryonic development, the amnioserosa is brought into the embryo in a process called dorsal closure, while the epidermis expands around the back of the embryo to encompass it. One of the major activities driving dorsal closure is the contraction of amnioserosa cells. This contraction depends on the highly dynamic activity of the protein network that helps give cells their shape, known as the actomyosin cytoskeleton. One major question in the field is how changes in the actomyosin cytoskeleton are controlled as tissues take shape (a process known as “morphogenesis”) and how the integrity of epithelial tissues is maintained during these processes. A key regulator of epidermal and amnioserosa polarity is an evolutionarily conserved protein called Crumbs. The epithelial tissues of mutant embryos that do not produce Crumbs lose polarity and integrity, and the embryos fail to develop properly. Flores-Benitez and Knust have now studied the role of Crumbs in the morphogenesis of the amnioserosa during dorsal closure. This revealed that fly embryos that produce a mutant Crumbs protein that cannot interact with a protein called Moesin (which links the cell membrane and the actomyosin cytoskeleton) are unable to complete dorsal closure. Detailed analyses showed that this failure of dorsal closure is due to the over-activity of the actomyosin cytoskeleton in the amnioserosa. This results in increased and uncoordinated contractions of the cells, and is accompanied by defects in cell-cell adhesion that ultimately cause the amnioserosa to lose integrity. Flores-Benitez and Knust’s genetic analyses further showed that several different signalling systems participate in this process. Flores-Benitez and Knust’s results reveal an unexpected role of Crumbs in coordinating polarity, actomyosin activity and cell-cell adhesion. Further work is now needed to understand the molecular mechanisms and interactions that enable Crumbs to coordinate these processes; in particular, to unravel how Crumbs influences the periodic contractions that drive changes in cell shape. It will also be important to investigate whether Crumbs is involved in similar mechanisms that operate in other developmental events in which actomyosin oscillations have been linked to tissue morphogenesis. DOI:http://dx.doi.org/10.7554/eLife.07398.002
Collapse
Affiliation(s)
| | - Elisabeth Knust
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| |
Collapse
|
20
|
Lin YH, Currinn H, Pocha SM, Rothnie A, Wassmer T, Knust E. AP-2-complex-mediated endocytosis of Drosophila Crumbs regulates polarity by antagonizing Stardust. J Cell Sci 2015; 128:4538-49. [PMID: 26527400 DOI: 10.1242/jcs.174573] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/26/2015] [Indexed: 12/21/2022] Open
Abstract
Maintenance of epithelial polarity depends on the correct localization and levels of polarity determinants. The evolutionarily conserved transmembrane protein Crumbs is crucial for the size and identity of the apical membrane, yet little is known about the molecular mechanisms controlling the amount of Crumbs at the surface. Here, we show that Crumbs levels on the apical membrane depend on a well-balanced state of endocytosis and stabilization. The adaptor protein 2 (AP-2) complex binds to a motif in the cytoplasmic tail of Crumbs that overlaps with the binding site of Stardust, a protein known to stabilize Crumbs on the surface. Preventing endocytosis by mutation of AP-2 causes expansion of the Crumbs-positive plasma membrane domain and polarity defects, which can be partially rescued by removing one copy of crumbs. Strikingly, knocking down both AP-2 and Stardust leads to the retention of Crumbs on the membrane. This study provides evidence for a molecular mechanism, based on stabilization and endocytosis, to adjust surface levels of Crumbs, which are essential for maintaining epithelial polarity.
Collapse
Affiliation(s)
- Ya-Huei Lin
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Heather Currinn
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Shirin Meher Pocha
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| | - Alice Rothnie
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Thomas Wassmer
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Elisabeth Knust
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden 01307, Germany
| |
Collapse
|