1
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Smart A, Gilmer O, Caliskan N. Translation Inhibition Mediated by Interferon-Stimulated Genes during Viral Infections. Viruses 2024; 16:1097. [PMID: 39066259 PMCID: PMC11281336 DOI: 10.3390/v16071097] [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: 04/29/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
Viruses often pose a significant threat to the host through the exploitation of cellular machineries for their own benefit. In the context of immune responses, myriad host factors are deployed to target viral RNAs and inhibit viral protein translation, ultimately hampering viral replication. Understanding how "non-self" RNAs interact with the host translation machinery and trigger immune responses would help in the development of treatment strategies for viral infections. In this review, we explore how interferon-stimulated gene products interact with viral RNA and the translation machinery in order to induce either global or targeted translation inhibition.
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Affiliation(s)
- Alexandria Smart
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
| | - Orian Gilmer
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
| | - Neva Caliskan
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Josef-Schneider-Strasse 2, 97080 Würzburg, Germany; (A.S.); (O.G.)
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
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2
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Nguyen A, Zhao H, Myagmarsuren D, Srinivasan S, Wu D, Chen J, Piszczek G, Schuck P. Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2. eLife 2024; 13:RP94836. [PMID: 38941236 PMCID: PMC11213569 DOI: 10.7554/elife.94836] [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] [Indexed: 06/30/2024] Open
Abstract
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
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Affiliation(s)
- Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Dulguun Myagmarsuren
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
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3
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Singh A, Chimata AV, Deshpande P, Bajpai S, Sangeeth A, Rajput M, Singh A. SARS-CoV2 Nsp3 protein triggers cell death and exacerbates amyloid β42-mediated neurodegeneration. Neural Regen Res 2024; 19:1385-1392. [PMID: 37905889 DOI: 10.4103/1673-5374.382989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/25/2023] [Indexed: 11/02/2023] Open
Abstract
Abstract
JOURNAL/nrgr/04.03/01300535-202406000-00044/inline-graphic1/v/2023-10-30T152229Z/r/image-tiff
Infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) virus, responsible for the coronavirus disease 2019 (COVID-19) pandemic, induces symptoms including increased inflammatory response, severe acute respiratory syndrome (SARS), cognitive dysfunction like brain fog, and cardiovascular defects. Long-term effects of SARS-CoV2 COVID-19 syndrome referred to as post-COVID-19 syndrome on age-related progressive neurodegenerative disorders such as Alzheimer’s disease remain understudied. Using the targeted misexpression of individual SARS-CoV2 proteins in the retinal neurons of the Drosophila
melanogaster eye, we found that misexpression of nonstructural protein 3 (Nsp3), a papain-like protease, ablates the eye and generates dark necrotic spots. Targeted misexpression of Nsp3 in the eye triggers reactive oxygen species production and leads to apoptosis as shown by cell death reporters, terminal deoxynucleotidyl transferase (TdT) dUTP Nick-end labeling (TUNEL) assay, and dihydroethidium staining. Furthermore, Nsp3 misexpression activates both apoptosis and autophagy mechanism(s) to regulate tissue homeostasis. Transient expression of SARS-CoV2 Nsp3 in murine neuroblastoma, Neuro-2a cells, significantly reduced the metabolic activity of these cells and triggers cell death. Misexpression of SARS-CoV2 Nsp3 in an Alzheimer’s disease transgenic fly eye model (glass multiple repeats [GMR]>amyloid β42) further enhances the neurodegenerative rough eye phenotype due to increased cell death. These findings suggest that SARS-CoV2 utilizes Nsp3 protein to potentiate cell death response in a neurodegenerative disease background that has high pre-existing levels of neuroinflammation and cell death.
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Affiliation(s)
- Aditi Singh
- Department of Biology, University of Dayton, Dayton, OH, USA
| | | | | | - Soumya Bajpai
- Department of Biology, University of Dayton, Dayton, OH, USA
| | - Anjali Sangeeth
- Department of Biology, University of Dayton, Dayton, OH, USA
| | | | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, USA
- Premedical Program, University of Dayton, Dayton, OH, USA
- Center for Tissue Regeneration and Engineering at Dayton (TREND), University of Dayton, Dayton, OH, USA
- The Integrative Science and Engineering Center, University of Dayton, Dayton, OH, USA
- Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA
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4
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Meyniel-Schicklin L, de Chassey B. [A biomimetic approach inspired by viruses for the discovery of new drugs]. Med Sci (Paris) 2024; 40:397-399. [PMID: 38819269 DOI: 10.1051/medsci/2024041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024] Open
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5
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Pha K, Mirrashidi K, Sherry J, Tran CJ, Herrera CM, McMahon E, Elwell CA, Engel JN. The Chlamydia effector IncE employs two short linear motifs to reprogram host vesicle trafficking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590830. [PMID: 38712241 PMCID: PMC11071397 DOI: 10.1101/2024.04.23.590830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Chlamydia trachomatis, a leading cause of bacteria sexually transmitted infections, creates a specialized intracellular replicative niche by translocation and insertion of a diverse array of effectors (Incs) into the inclusion membrane. Here, we characterize IncE, a multi-functional Inc that encodes two non-overlapping short linear motifs (SLiMs) within its short cytosolic C-terminus. The proximal SLiM mimics an R-SNARE motif to recruit syntaxin (STX) 7 and 12-containing vesicles to the inclusion. The distal SLiM mimics the Sorting Nexin (SNX) 5 and 6 cargo binding site to recruit SNX6-containing vesicles to the inclusion. By simultaneously binding to two distinct vesicle classes, IncE reprograms host cell trafficking to promote the formation of a class of hybrid vesicles at the inclusion that are required for C. trachomatis intracellular development. Our work suggests that Incs may have evolved SLiMs to facilitate rapid evolution in a limited protein space to disrupt host cell processes.
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6
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Pagano L, Simonetti L, Pennacchietti V, Toto A, Malagrinò F, Ivarsson Y, Gianni S. Exploring the short linear motif-mediated protein-protein interactions of CrkL through ProP-PD. Biochem Biophys Res Commun 2024; 703:149658. [PMID: 38387229 DOI: 10.1016/j.bbrc.2024.149658] [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: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Adaptor proteins play a pivotal role in cellular signaling mediating a multitude of protein-protein interaction critical for cellular homeostasis. Dysregulation of these interactions has been linked to the onset of various cancer pathologies and exploited by viral pathogens during host cell takeover. CrkL is an adaptor protein composed of an N-terminal SH2 domain followed by two SH3 domains that mediate interactions with diverse partners through the recognition of specific binding motifs. In this study, we employed proteomic peptide-phage display (ProP-PD) to comprehensively explore the short linear motif (SLiM)-based interactions of CrkL. Furthermore, we scrutinized how the binding affinity for selected peptides was influenced in the context of the full-length CrkL versus the isolated N-SH3 domain. Importantly, our results provided insights into SLiM-binding sites within previously reported interactors, as well as revealing novel human and viral ligands, expanding our understanding of the interactions mediated by CrkL and highlighting the significance of SLiM-based interactions in mediating adaptor protein function, with implications for cancer and viral pathologies.
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Affiliation(s)
- L Pagano
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185, Rome, Italy
| | - L Simonetti
- Department of Chemistry - BMC, Husargatan 3, 751 23, Uppsala, Sweden
| | - V Pennacchietti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185, Rome, Italy
| | - A Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185, Rome, Italy
| | - F Malagrinò
- Dipartimento di Medicina clinica, sanità pubblica, scienze della vita e dell'ambiente, Università dell'Aquila, Piazzale Salvatore Tommasi 1, L'Aquila, Coppito, 67010, Italy
| | - Y Ivarsson
- Department of Chemistry - BMC, Husargatan 3, 751 23, Uppsala, Sweden.
| | - S Gianni
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Universita di Roma, Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, 00185, Rome, Italy.
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7
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Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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8
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Nguyen A, Zhao H, Myagmarsuren D, Srinivasan S, Wu D, Chen J, Piszczek G, Schuck P. Modulation of Biophysical Properties of Nucleocapsid Protein in the Mutant Spectrum of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.21.568093. [PMID: 38045241 PMCID: PMC10690151 DOI: 10.1101/2023.11.21.568093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also exhibiting functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
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Affiliation(s)
- Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dulguun Myagmarsuren
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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9
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Vieira MFM, Hernandez G, Zhong Q, Arbesú M, Veloso T, Gomes T, Martins ML, Monteiro H, Frazão C, Frankel G, Zanzoni A, Cordeiro TN. The pathogen-encoded signalling receptor Tir exploits host-like intrinsic disorder for infection. Commun Biol 2024; 7:179. [PMID: 38351154 PMCID: PMC10864410 DOI: 10.1038/s42003-024-05856-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
The translocated intimin receptor (Tir) is an essential type III secretion system (T3SS) effector of attaching and effacing pathogens contributing to the global foodborne disease burden. Tir acts as a cell-surface receptor in host cells, rewiring intracellular processes by targeting multiple host proteins. We investigated the molecular basis for Tir's binding diversity in signalling, finding that Tir is a disordered protein with host-like binding motifs. Unexpectedly, also are several other T3SS effectors. By an integrative approach, we reveal that Tir dimerises via an antiparallel OB-fold within a highly disordered N-terminal cytosolic domain. Also, it has a long disordered C-terminal cytosolic domain partially structured at host-like motifs that bind lipids. Membrane affinity depends on lipid composition and phosphorylation, highlighting a previously unrecognised host interaction impacting Tir-induced actin polymerisation and cell death. Furthermore, multi-site tyrosine phosphorylation enables Tir to engage host SH2 domains in a multivalent fuzzy complex, consistent with Tir's scaffolding role and binding promiscuity. Our findings provide insights into the intracellular Tir domains, highlighting the ability of T3SS effectors to exploit host-like protein disorder as a strategy for host evasion.
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Affiliation(s)
- Marta F M Vieira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Guillem Hernandez
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Qiyun Zhong
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Miguel Arbesú
- Department of NMR-supported Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
- InstaDeep Ltd, 5 Merchant Square, London, UK
| | - Tiago Veloso
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Tiago Gomes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Maria L Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Hugo Monteiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Carlos Frazão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Gad Frankel
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Andreas Zanzoni
- Aix-Marseille Université, Inserm, TAGC, UMR_S1090, Marseille, France
| | - Tiago N Cordeiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal.
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10
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Sisk TR, Robustelli P. Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model. Proc Natl Acad Sci U S A 2024; 121:e2313360121. [PMID: 38294935 PMCID: PMC10861926 DOI: 10.1073/pnas.2313360121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/22/2023] [Indexed: 02/02/2024] Open
Abstract
A central challenge in the study of intrinsically disordered proteins is the characterization of the mechanisms by which they bind their physiological interaction partners. Here, we utilize a deep learning-based Markov state modeling approach to characterize the folding-upon-binding pathways observed in a long timescale molecular dynamics simulation of a disordered region of the measles virus nucleoprotein NTAIL reversibly binding the X domain of the measles virus phosphoprotein complex. We find that folding-upon-binding predominantly occurs via two distinct encounter complexes that are differentiated by the binding orientation, helical content, and conformational heterogeneity of NTAIL. We observe that folding-upon-binding predominantly proceeds through a multi-step induced fit mechanism with several intermediates and do not find evidence for the existence of canonical conformational selection pathways. We observe four kinetically separated native-like bound states that interconvert on timescales of eighty to five hundred nanoseconds. These bound states share a core set of native intermolecular contacts and stable NTAIL helices and are differentiated by a sequential formation of native and non-native contacts and additional helical turns. Our analyses provide an atomic resolution structural description of intermediate states in a folding-upon-binding pathway and elucidate the nature of the kinetic barriers between metastable states in a dynamic and heterogenous, or "fuzzy", protein complex.
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Affiliation(s)
- Thomas R. Sisk
- Department of Chemistry, Dartmouth College, Hanover, NH03755
| | - Paul Robustelli
- Department of Chemistry, Dartmouth College, Hanover, NH03755
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11
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Garvanska DH, Alvarado RE, Mundt FO, Lindqvist R, Duel JK, Coscia F, Nilsson E, Lokugamage K, Johnson BA, Plante JA, Morris DR, Vu MN, Estes LK, McLeland AM, Walker J, Crocquet-Valdes PA, Mendez BL, Plante KS, Walker DH, Weisser MB, Överby AK, Mann M, Menachery VD, Nilsson J. The NSP3 protein of SARS-CoV-2 binds fragile X mental retardation proteins to disrupt UBAP2L interactions. EMBO Rep 2024; 25:902-926. [PMID: 38177924 PMCID: PMC10897489 DOI: 10.1038/s44319-023-00043-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
Viruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these interactions. Here, we uncover a novel interaction between the viral NSP3 protein and the fragile X mental retardation proteins (FMRPs: FMR1, FXR1-2). SARS-CoV-2 NSP3 mutant viruses preventing FMRP binding have attenuated replication in vitro and reduced levels of viral antigen in lungs during the early stages of infection. We show that a unique peptide motif in NSP3 binds directly to the two central KH domains of FMRPs and that this interaction is disrupted by the I304N mutation found in a patient with fragile X syndrome. NSP3 binding to FMRPs disrupts their interaction with the stress granule component UBAP2L through direct competition with a peptide motif in UBAP2L to prevent FMRP incorporation into stress granules. Collectively, our results provide novel insight into how SARS-CoV-2 hijacks host cell proteins and provides molecular insight into the possible underlying molecular defects in fragile X syndrome.
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Affiliation(s)
- Dimitriya H Garvanska
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - R Elias Alvarado
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Filip Oskar Mundt
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Josephine Kerzel Duel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Coscia
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emma Nilsson
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Kumari Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Dorothea R Morris
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Michelle N Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Leah K Estes
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Alyssa M McLeland
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jordyn Walker
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Blanca Lopez Mendez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - David H Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Melanie Bianca Weisser
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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12
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Dhayalan M, Wang W, Riyaz SUM, Dinesh RA, Shanmugam J, Irudayaraj SS, Stalin A, Giri J, Mallik S, Hu R. Advances in functional lipid nanoparticles: from drug delivery platforms to clinical applications. 3 Biotech 2024; 14:57. [PMID: 38298556 PMCID: PMC10825110 DOI: 10.1007/s13205-023-03901-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/18/2023] [Indexed: 02/02/2024] Open
Abstract
Since Doxil's first clinical approval in 1995, lipid nanoparticles have garnered great interest and shown exceptional therapeutic efficacy. It is clear from the licensure of two RNA treatments and the mRNA-COVID-19 vaccination that lipid nanoparticles have immense potential for delivering nucleic acids. The review begins with a list of lipid nanoparticle types, such as liposomes and solid lipid nanoparticles. Then it moves on to the earliest lipid nanoparticle forms, outlining how lipid is used in a variety of industries and how it is used as a versatile nanocarrier platform. Lipid nanoparticles must then be functionally modified. Various approaches have been proposed for the synthesis of lipid nanoparticles, such as High-Pressure Homogenization (HPH), microemulsion methods, solvent-based emulsification techniques, solvent injection, phase reversal, and membrane contractors. High-pressure homogenization is the most commonly used method. All of the methods listed above follow four basic steps, as depicted in the flowchart below. Out of these four steps, the process of dispersing lipids in an aqueous medium to produce liposomes is the most unpredictable step. A short outline of the characterization of lipid nanoparticles follows discussions of applications for the trapping and transporting of various small molecules. It highlights the use of rapamycin-coated lipid nanoparticles in glioblastoma and how lipid nanoparticles function as a conjugator in the delivery of anticancer-targeting nucleic acids. High biocompatibility, ease of production, scalability, non-toxicity, and tailored distribution are just a meager of the enticing allowances of using lipid nanoparticles as drug delivery vehicles. Due to the present constraints in drug delivery, more research is required to utterly realize the potential of lipid nanoparticles for possible clinical and therapeutic purposes.
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Affiliation(s)
- Manikandan Dhayalan
- Department of Prosthodontics, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences (Saveetha University), Chennai, Tamil Nadu 600 077 India
- College of Public Health Sciences (CPHS), Chulalongkorn University, 254 Phyathai Road, Pathumwan, Bangkok 10330 Thailand
| | - Wei Wang
- Beidahuang Industry Group General Hospital, Harbin, 150001 China
| | - S. U. Mohammed Riyaz
- Department of Prosthodontics, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences (Saveetha University), Chennai, Tamil Nadu 600 077 India
- PG & Research Department of Biotechnology, Islamiah College (Autonomous), Vaniyambadi, Tamil Nadu 635752 India
| | - Rakshi Anuja Dinesh
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072 Australia
| | - Jayashree Shanmugam
- Department of Biotechnology, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu India
| | | | - Antony Stalin
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, 610054 China
| | - Jayant Giri
- Department of Mechanical Engineering, Yeshwantrao Chavan College of Engineering, Nagpur, India
| | - Saurav Mallik
- Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, MA USA
| | - Ruifeng Hu
- Department of Neurology, Harvard Medical School, Boston, MA USA
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13
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Meyniel-Schicklin L, Amaudrut J, Mallinjoud P, Guillier F, Mangeot PE, Lines L, Aublin-Gex A, Scholtes C, Punginelli C, Joly S, Vasseur F, Manet E, Gruffat H, Henry T, Halitim F, Paparin JL, Machin P, Darteil R, Sampson D, Mikaelian I, Lane L, Navratil V, Golinelli-Cohen MP, Terzi F, André P, Lotteau V, Vonderscher J, Meldrum EC, de Chassey B. Viruses traverse the human proteome through peptide interfaces that can be biomimetically leveraged for drug discovery. Proc Natl Acad Sci U S A 2024; 121:e2308776121. [PMID: 38252831 PMCID: PMC10835127 DOI: 10.1073/pnas.2308776121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
We present a drug design strategy based on structural knowledge of protein-protein interfaces selected through virus-host coevolution and translated into highly potential small molecules. This approach is grounded on Vinland, the most comprehensive atlas of virus-human protein-protein interactions with annotation of interacting domains. From this inspiration, we identified small viral protein domains responsible for interaction with human proteins. These peptides form a library of new chemical entities used to screen for replication modulators of several pathogens. As a proof of concept, a peptide from a KSHV protein, identified as an inhibitor of influenza virus replication, was translated into a small molecule series with low nanomolar antiviral activity. By targeting the NEET proteins, these molecules turn out to be of therapeutic interest in a nonalcoholic steatohepatitis mouse model with kidney lesions. This study provides a biomimetic framework to design original chemistries targeting cellular proteins, with indications going far beyond infectious diseases.
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Affiliation(s)
| | | | | | | | - Philippe E. Mangeot
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | | | - Anne Aublin-Gex
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Caroline Scholtes
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Claire Punginelli
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | | | - Florence Vasseur
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département “Croissance et Signalisation”, Paris75015, France
| | - Evelyne Manet
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Henri Gruffat
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Thomas Henry
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | | | | | | | | | | | - Ivan Mikaelian
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon69373, France
| | - Lydie Lane
- Computer and Laboratory Investigation of Proteins of Human Origin Group, Swiss Institute of Bioinformatics, Lausanne1015, Switzerland
| | - Vincent Navratil
- Pôle Rhône-Alpes de bioinformatique, Rhône-Alpes Bioinformatics Center, Université Lyon 1, Villeurbanne69622, France
- European Virus Bio-informatiques Center, Jena07743, Germany
- Institut Français de Bioinformatique, IFB-core, UMS 3601, Évry91057, France
| | - Marie-Pierre Golinelli-Cohen
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Unité Propre de Recherche 2301, Gif-sur-Yvette91198, France
| | - Fabiola Terzi
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département “Croissance et Signalisation”, Paris75015, France
| | - Patrice André
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Vincent Lotteau
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
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14
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Guerin N, Childs H, Zhou P, Donald BR. DexDesign: an OSPREY-based algorithm for designing de novo D-peptide inhibitors. Protein Eng Des Sel 2024; 37:gzae007. [PMID: 38757573 PMCID: PMC11099876 DOI: 10.1093/protein/gzae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains play a central role in modulating polarization, signaling, and trafficking pathways. Mutations in PDZ domains lead to diseases such as cancer and cystic fibrosis, making PDZ domains attractive targets for therapeutic intervention. D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. Here, we introduce DexDesign, a novel OSPREY-based algorithm for computationally designing de novo D-peptide inhibitors. DexDesign leverages three novel techniques that are broadly applicable to computational protein design: the Minimum Flexible Set, K*-based Mutational Scan, and Inverse Alanine Scan. We apply these techniques and DexDesign to generate novel D-peptide inhibitors of two biomedically important PDZ domain targets: CAL and MAST2. We introduce a framework for analyzing de novo peptides-evaluation along a replication/restitution axis-and apply it to the DexDesign-generated D-peptides. Notably, the peptides we generated are predicted to bind their targets tighter than their targets' endogenous ligands, validating the peptides' potential as lead inhibitors. We also provide an implementation of DexDesign in the free and open source computational protein design software OSPREY.
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Affiliation(s)
- Nathan Guerin
- Department of Computer Science, Duke University, 308 Research Drive, Durham, NC 27708, United States
| | - Henry Childs
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, United States
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 22710, United States
| | - Bruce R Donald
- Department of Computer Science, Duke University, 308 Research Drive, Durham, NC 27708, United States
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, United States
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 22710, United States
- Department of Mathematics, Duke University, 120 Science Drive, Durham, NC 27708, United States
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15
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Kumar M, Michael S, Alvarado-Valverde J, Zeke A, Lazar T, Glavina J, Nagy-Kanta E, Donagh J, Kalman Z, Pascarelli S, Palopoli N, Dobson L, Suarez C, Van Roey K, Krystkowiak I, Griffin J, Nagpal A, Bhardwaj R, Diella F, Mészáros B, Dean K, Davey N, Pancsa R, Chemes L, Gibson T. ELM-the Eukaryotic Linear Motif resource-2024 update. Nucleic Acids Res 2024; 52:D442-D455. [PMID: 37962385 PMCID: PMC10767929 DOI: 10.1093/nar/gkad1058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Short Linear Motifs (SLiMs) are the smallest structural and functional components of modular eukaryotic proteins. They are also the most abundant, especially when considering post-translational modifications. As well as being found throughout the cell as part of regulatory processes, SLiMs are extensively mimicked by intracellular pathogens. At the heart of the Eukaryotic Linear Motif (ELM) Resource is a representative (not comprehensive) database. The ELM entries are created by a growing community of skilled annotators and provide an introduction to linear motif functionality for biomedical researchers. The 2024 ELM update includes 346 novel motif instances in areas ranging from innate immunity to both protein and RNA degradation systems. In total, 39 classes of newly annotated motifs have been added, and another 17 existing entries have been updated in the database. The 2024 ELM release now includes 356 motif classes incorporating 4283 individual motif instances manually curated from 4274 scientific publications and including >700 links to experimentally determined 3D structures. In a recent development, the InterPro protein module resource now also includes ELM data. ELM is available at: http://elm.eu.org.
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Affiliation(s)
- Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Sushama Michael
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Jesús Alvarado-Valverde
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Germany
| | - András Zeke
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Tamas Lazar
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Pleinlaan 2, 1050 Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Juliana Glavina
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CP 1650, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 San Martín, Buenos Aires, Argentina
| | - Eszter Nagy-Kanta
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest 1083, Hungary
| | - Juan Mac Donagh
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bernal, Buenos Aires, Argentina
| | - Zsofia E Kalman
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest 1083, Hungary
| | - Stefano Pascarelli
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bernal, Buenos Aires, Argentina
| | - László Dobson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 7, Budapest 1094, Hungary
| | - Carmen Florencia Suarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CP 1650, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 San Martín, Buenos Aires, Argentina
| | - Kim Van Roey
- Health Services Research, Sciensano, Brussels, Belgium
| | - Izabella Krystkowiak
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Juan Esteban Griffin
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Bernal, Buenos Aires, Argentina
| | - Anurag Nagpal
- Department of Biological Sciences, BITS Pilani, K. K. Birla Goa campus, Zuarinagar, Goa 403726, India
| | - Rajesh Bhardwaj
- Inselspital, University of Bern, Freiburgstrasse 15, CH-3010 Bern, Switzerland
| | - Francesca Diella
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Bálint Mészáros
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Kellie Dean
- School of Biochemistry and Cell Biology, 3.91 Western Gateway Building, University College Cork, Cork, Ireland
| | - Norman E Davey
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Rd, Chelsea, London SW3 6JB, UK
| | - Rita Pancsa
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest 1117, Hungary
| | - Lucía B Chemes
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CP 1650, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad Nacional de San Martín, Av. 25 de Mayo y Francia, CP1650 San Martín, Buenos Aires, Argentina
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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16
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Mezghrani A, Simon J, Reys V, Labesse G. Detection and Analysis of Short Linear Motif-Based Protein-Protein Interactions with SLiMAn2 Web Server. Methods Mol Biol 2024; 2836:253-281. [PMID: 38995545 DOI: 10.1007/978-1-0716-4007-4_14] [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: 07/13/2024]
Abstract
Interactomics is bringing a deluge of data regarding protein-protein interactions (PPIs) which are involved in various molecular processes in all types of cells. However, this information does not easily translate into direct and precise molecular interfaces. This limits our understanding of each interaction network and prevents their efficient modulation. A lot of the detected interactions involve recognition of short linear motifs (SLiMs) by a folded domain while others rely on domain-domain interactions. Functional SLiMs hide among a lot of spurious ones, making deeper analysis of interactomes tedious. Hence, actual contacts and direct interactions are difficult to identify.Consequently, there is a need for user-friendly bioinformatic tools, enabling rapid molecular and structural analysis of SLiM-based PPIs in a protein network. In this chapter, we describe the use of the new webserver SLiMAn to help digging into SLiM-based PPIs in an interactive fashion.
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Affiliation(s)
- Alexandre Mezghrani
- Centre de Biologie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Juliette Simon
- Centre de Biologie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Victor Reys
- Centre de Biologie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier, France.
| | - Gilles Labesse
- Centre de Biologie Structurale (CBS), CNRS, INSERM, University of Montpellier, Montpellier, France.
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17
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Schuck P, Zhao H. Diversity of short linear interaction motifs in SARS-CoV-2 nucleocapsid protein. mBio 2023; 14:e0238823. [PMID: 38018991 PMCID: PMC10746173 DOI: 10.1128/mbio.02388-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Short linear motifs (SLiMs) are 3-10 amino acid long binding motifs in intrinsically disordered protein regions (IDRs) that serve as ubiquitous protein-protein interaction modules in eukaryotic cells. Through molecular mimicry, viruses hijack these sequence motifs to control host cellular processes. It is thought that the small size of SLiMs and the high mutation frequencies of viral IDRs allow rapid host adaptation. However, a salient characteristic of RNA viruses, due to high replication errors, is their obligate existence as mutant swarms. Taking advantage of the uniquely large genomic database of SARS-CoV-2, here, we analyze the role of sequence diversity in the presentation of SLiMs, focusing on the highly abundant, multi-functional nucleocapsid protein. We find that motif mimicry is a highly dynamic process that produces an abundance of motifs transiently present in subsets of mutant species. This diversity allows the virus to efficiently explore eukaryotic motifs and evolve the host-virus interface.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
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18
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Tessier TM, King CR, Mymryk JS. Exploiting the endogenous yeast nuclear proteome to identify short linear motifs in vivo. CELL REPORTS METHODS 2023; 3:100637. [PMID: 37949066 PMCID: PMC10694487 DOI: 10.1016/j.crmeth.2023.100637] [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: 05/17/2023] [Revised: 09/01/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023]
Abstract
Peptide-domain interactions mediated by short linear motifs (SLiMs) play crucial roles in cellular biology. The simplicity of SLiMs poses challenges in their computational identification. Existing high-throughput methods for discovering SLiMs lack cellular context as they are typically performed in vitro. We developed a functional selection method using yeast to identify peptides that interact with the endogenous yeast nuclear proteome. Remarkably, peptides selected for in yeast also mediated nuclear import in human cells. Notably, the identified peptides did not resemble classical nuclear localization sequences. This platform has the potential to identify and investigate motifs that interact with the nuclear proteome of yeast and human and to aid in the identification and understanding of alternative protein nuclear import mechanisms.
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Affiliation(s)
- Tanner M Tessier
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Cason R King
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Joe S Mymryk
- Department of Microbiology and Immunology, Western University, London, ON, Canada; Department of Oncology, Western University, London, ON, Canada; Department of Otolaryngology, Western University, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
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19
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Tusnády GE, Zeke A, Kálmán ZE, Fatoux M, Ricard-Blum S, Gibson TJ, Dobson L. LeishMANIAdb: a comparative resource for Leishmania proteins. Database (Oxford) 2023; 2023:baad074. [PMID: 37935582 PMCID: PMC10627299 DOI: 10.1093/database/baad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/09/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023]
Abstract
Leishmaniasis is a detrimental disease causing serious changes in quality of life and some forms can lead to death. The disease is spread by the parasite Leishmania transmitted by sandfly vectors and their primary hosts are vertebrates including humans. The pathogen penetrates host cells and secretes proteins (the secretome) to repurpose cells for pathogen growth and to alter cell signaling via host-pathogen protein-protein interactions). Here, we present LeishMANIAdb, a database specifically designed to investigate how Leishmania virulence factors may interfere with host proteins. Since the secretomes of different Leishmania species are only partially characterized, we collated various experimental evidence and used computational predictions to identify Leishmania secreted proteins to generate a user-friendly unified web resource allowing users to access all information available on experimental and predicted secretomes. In addition, we manually annotated host-pathogen interactions of 211 proteins and the localization/function of 3764 transmembrane (TM) proteins of different Leishmania species. We also enriched all proteins with automatic structural and functional predictions that can provide new insights in the molecular mechanisms of infection. Our database may provide novel insights into Leishmania host-pathogen interactions and help to identify new therapeutic targets for this neglected disease. Database URL https://leishmaniadb.ttk.hu/.
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Affiliation(s)
- Gábor E Tusnády
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest 1117, Hungary
- Department of Bioinformatics, Semmelweis University, Tűzoltó u. 7, Budapest 1094, Hungary
| | - András Zeke
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest 1117, Hungary
| | - Zsófia E Kálmán
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, Budapest 1083, Hungary
| | - Marie Fatoux
- ICBMS UMR CNRS 5246, University Lyon 1, Rue Victor Grignard, Villeurbanne 69622, France
- UMR CNRS 5086, University Lyon 1, 7 Passage du Vercors, Lyon 69367, France
| | - Sylvie Ricard-Blum
- ICBMS UMR CNRS 5246, University Lyon 1, Rue Victor Grignard, Villeurbanne 69622, France
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany
| | - Laszlo Dobson
- Protein Bioinformatics Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Magyar Tudósok körútja 2, Budapest 1117, Hungary
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg 69117, Germany
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20
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Idrees S, Paudel KR, Sadaf T, Hansbro PM. How different viruses perturb host cellular machinery via short linear motifs. EXCLI JOURNAL 2023; 22:1113-1128. [PMID: 38054205 PMCID: PMC10694346 DOI: 10.17179/excli2023-6328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023]
Abstract
The virus interacts with its hosts by developing protein-protein interactions. Most viruses employ protein interactions to imitate the host protein: A viral protein with the same amino acid sequence or structure as the host protein attaches to the host protein's binding partner and interferes with the host protein's pathways. Being opportunistic, viruses have evolved to manipulate host cellular mechanisms by mimicking short linear motifs. In this review, we shed light on the current understanding of mimicry via short linear motifs and focus on viral mimicry by genetically different viral subtypes by providing recent examples of mimicry evidence and how high-throughput methods can be a reliable source to study SLiM-mediated viral mimicry.
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Affiliation(s)
- Sobia Idrees
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Tayyaba Sadaf
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, New South Wales, Australia
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21
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Tayal S, Bhatnagar S. Role of molecular mimicry in the SARS-CoV-2-human interactome for pathogenesis of cardiovascular diseases: An update to ImitateDB. Comput Biol Chem 2023; 106:107919. [PMID: 37463554 DOI: 10.1016/j.compbiolchem.2023.107919] [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: 01/15/2023] [Revised: 06/13/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Mimicry of host proteins is a strategy employed by pathogens to hijack host functions. Domain and motif mimicry was explored in the experimental and predicted SARS-CoV-2-human interactome. The host first interactor proteins were also added to capture the continuum of the interactions. The domains and motifs of the proteins were annotated using NCBI CD Search and ScanProsite, respectively. Host and pathogen proteins with a common host interactor and similar domain/motif constitute a mimicry pair indicating global structural similarity (domain mimicry pair; DMP) or local sequence similarity (motif mimicry pair; MMP). 593 DMPs and 7,02,472 MMPs were determined. AAA, DEXDc and Macro domains were frequent among DMPs whereas glycosylation, myristoylation and RGD motifs were abundant among MMP. The proteins involved in mimicry were visualised as a SARS-CoV-2 mimicry interaction network. The host proteins were enriched in multiple CVD pathways indicating the role of mimicry in COVID-19 associated CVDs. Bridging nodes were identified as potential drug targets. Approved antihypertensive and anti-inflammatory drugs are proposed for repurposing against COVID-19 associated CVDs. The SARS-CoV-2 mimicry data has been updated in ImitateDB (http://imitatedb.sblab-nsit.net/SARSCoV2Mimicry). Determination of key mechanisms, proteins, pathways, drug targets and repurposing candidates is critical for developing therapeutics for SARS CoV-2 associated CVDs.
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Affiliation(s)
- Sonali Tayal
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi 110078, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi 110078, India.
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22
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Nagamine T, Sako Y. A SLiM-dependent conformational change in baculovirus IE1 controls its focus formation ability. J Gen Virol 2023; 104. [PMID: 37877992 DOI: 10.1099/jgv.0.001910] [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: 10/26/2023] Open
Abstract
The baculovirus IE1 gene encodes a multifunctional protein that is essential for both DNA replication and RNA transcription of the virus. Prior to viral DNA replication, IE1 promotes early gene transcription when localized in hr-dependent foci. During viral DNA replication, the IE1 foci expand and fuse to generate the virogenic stroma (VS) with IE1 found in the VS reticulum. To explore the IE1 structural features essential for this coordinated localization, we constructed various IE1 mutants based on three putative domains (N, I, and C). We determined that a BDI motif located in the intrinsic disorder region (IDR) between the N and I domains acts as a nuclear localization signal, whereas BDII and HLH in the C domain are required for VS localization in infected cells or for chromosomal association in uninfected mitotic cells. Deletion of the SLiM (short linear motif) located in the I domain restrains both nuclear- and VS localization. Intra-molecular fluorescence resonance energy transfer (FRET) probes of IE1 mutants revealed a conformational change of the I-C two-domain fragment during infection, which was inhibited by aphidicolin, suggesting that IE1 undergoes a stage-dependent conformational change. Further, homo-dimerization of the I domain and stage-dependent conformational changes require an intact SLiM. Mutational analysis of SLiM revealed that VS localization and chromosomal association were retained following S291A and S291E substitutions, but hr-dependent focus formation differed between the two mutations. These results suggest that coordinated IE1 localization is controlled by SLiM-dependent conformational changes that are potentially switched by the phosphorylation state of the SLiM.
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23
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Mihalič F, Benz C, Kassa E, Lindqvist R, Simonetti L, Inturi R, Aronsson H, Andersson E, Chi CN, Davey NE, Överby AK, Jemth P, Ivarsson Y. Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets. Nat Commun 2023; 14:5636. [PMID: 37704626 PMCID: PMC10499821 DOI: 10.1038/s41467-023-41312-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
The virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (KD ∼ 7-300 μM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.
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Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eszter Kassa
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Hanna Aronsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187, Umeå, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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24
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Garvanska DH, Alvarado RE, Mundt FO, Nilsson E, Duel JK, Coscia F, Lindqvist R, Lokugamage K, Johnson BA, Plante JA, Morris DR, Vu MN, Estes LK, McLeland AM, Walker J, Crocquet-Valdes PA, Mendez BL, Plante KS, Walker DH, Weisser MB, Overby AK, Mann M, Menachery VD, Nilsson J. SARS-CoV-2 hijacks fragile X mental retardation proteins for efficient infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555899. [PMID: 37693415 PMCID: PMC10491247 DOI: 10.1101/2023.09.01.555899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Viruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these interactions. Here, we uncover a novel interaction between the viral NSP3 protein and the fragile X mental retardation proteins (FMRPs: FMR1 and FXR1-2). SARS-CoV-2 NSP3 mutant viruses preventing FMRP binding have attenuated replication in vitro and have delayed disease onset in vivo. We show that a unique peptide motif in NSP3 binds directly to the two central KH domains of FMRPs and that this interaction is disrupted by the I304N mutation found in a patient with fragile X syndrome. NSP3 binding to FMRPs disrupts their interaction with the stress granule component UBAP2L through direct competition with a peptide motif in UBAP2L to prevent FMRP incorporation into stress granules. Collectively, our results provide novel insight into how SARS-CoV-2 hijacks host cell proteins for efficient infection and provides molecular insight to the possible underlying molecular defects in fragile X syndrome.
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Affiliation(s)
- Dimitriya H Garvanska
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rojelio E Alvarado
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, United States
| | - Filip Oskar Mundt
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emma Nilsson
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Josephine Kerzel Duel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Coscia
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Kumari Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, United States
| | - Dorothea R Morris
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, United States
| | - Michelle N Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Leah K Estes
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Alyssa M McLeland
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jordyn Walker
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, United States
| | | | - Blanca Lopez Mendez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, United States
| | - David H Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Melanie Bianca Weisser
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna K Overby
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, United States
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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25
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Schuck P, Zhao H. Diversity of Short Linear Interaction Motifs in SARS-CoV-2 Nucleocapsid Protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551467. [PMID: 37790474 PMCID: PMC10542142 DOI: 10.1101/2023.08.01.551467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Molecular mimicry of short linear interaction motifs has emerged as a key mechanism for viral proteins binding host domains and hijacking host cell processes. Here, we examine the role of RNA-virus sequence diversity in the dynamics of the virus-host interface, by analyzing the uniquely vast sequence record of viable SARS-CoV-2 species with focus on the multi-functional nucleocapsid protein. We observe the abundant presentation of motifs encoding several essential host protein interactions, alongside a majority of possibly non-functional and randomly occurring motif sequences absent in subsets of viable virus species. A large number of motifs emerge ex nihilo through transient mutations relative to the ancestral consensus sequence. The observed mutational landscape implies an accessible motif space that spans at least 25% of known eukaryotic motifs. This reveals motif mimicry as a highly dynamic process with the capacity to broadly explore host motifs, allowing the virus to rapidly evolve the virus-host interface.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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26
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Gunnarsson PA, Babu MM. Predicting evolutionary outcomes through the probability of accessing sequence variants. SCIENCE ADVANCES 2023; 9:eade2903. [PMID: 37506212 PMCID: PMC10381947 DOI: 10.1126/sciadv.ade2903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
Natural selection can only operate on available genetic variation. Thus, determining the probability of accessing different sequence variants from a starting sequence can help predict evolutionary trajectories and outcomes. We define the concept of "variant accessibility" as the probability that a set of genotypes encoding a particular protein function will arise through mutations before subject to natural selection. This probability is shaped by the mutational biases of nucleotides and the structure of the genetic code. Using the influenza A virus as a model, we discuss how a more accessible but less fit variant can emerge as an adaptation rather than a more fit variant. We describe a genotype-accessibility landscape, complementary to the genotype-fitness landscape, that informs the likelihood of a starting sequence reaching different parts of genotype space. The proposed framework lays the foundation for predicting the emergence of adaptive genotypes in evolving systems such as viruses and tumors.
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Affiliation(s)
- P. Alexander Gunnarsson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Department of Structural Biology and Center of Excellence for Data-Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - M. Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Department of Structural Biology and Center of Excellence for Data-Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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27
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Sisk T, Robustelli P. Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.550103. [PMID: 37546728 PMCID: PMC10401938 DOI: 10.1101/2023.07.21.550103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
A central challenge in the study of intrinsically disordered proteins is the characterization of the mechanisms by which they bind their physiological interaction partners. Here, we utilize a deep learning based Markov state modeling approach to characterize the folding-upon-binding pathways observed in a long-time scale molecular dynamics simulation of a disordered region of the measles virus nucleoprotein NTAIL reversibly binding the X domain of the measles virus phosphoprotein complex. We find that folding-upon-binding predominantly occurs via two distinct encounter complexes that are differentiated by the binding orientation, helical content, and conformational heterogeneity of NTAIL. We do not, however, find evidence for the existence of canonical conformational selection or induced fit binding pathways. We observe four kinetically separated native-like bound states that interconvert on time scales of eighty to five hundred nanoseconds. These bound states share a core set of native intermolecular contacts and stable NTAIL helices and are differentiated by a sequential formation of native and non-native contacts and additional helical turns. Our analyses provide an atomic resolution structural description of intermediate states in a folding-upon-binding pathway and elucidate the nature of the kinetic barriers between metastable states in a dynamic and heterogenous, or "fuzzy", protein complex.
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Affiliation(s)
- Thomas Sisk
- Dartmouth College, Department of Chemistry, Hanover, NH, 03755
| | - Paul Robustelli
- Dartmouth College, Department of Chemistry, Hanover, NH, 03755
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28
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Dyson HJ. Vital for Viruses: Intrinsically Disordered Proteins. J Mol Biol 2023; 435:167860. [PMID: 37330280 PMCID: PMC10656058 DOI: 10.1016/j.jmb.2022.167860] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/19/2023]
Abstract
Viruses infect all kingdoms of life; their genomes vary from DNA to RNA and in size from 2kB to 1 MB or more. Viruses frequently employ disordered proteins, that is, protein products of virus genes that do not themselves fold into independent three-dimensional structures, but rather, constitute a versatile molecular toolkit to accomplish a range of functions necessary for viral infection, assembly, and proliferation. Interestingly, disordered proteins have been discovered in almost all viruses so far studied, whether the viral genome consists of DNA or RNA, and whatever the configuration of the viral capsid or other outer covering. In this review, I present a wide-ranging set of stories illustrating the range of functions of IDPs in viruses. The field is rapidly expanding, and I have not tried to include everything. What is included is meant to be a survey of the variety of tasks that viruses accomplish using disordered proteins.
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Affiliation(s)
- H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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29
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Simonetti L, Nilsson J, McInerney G, Ivarsson Y, Davey NE. SLiM-binding pockets: an attractive target for broad-spectrum antivirals. Trends Biochem Sci 2023; 48:420-427. [PMID: 36623987 DOI: 10.1016/j.tibs.2022.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 01/08/2023]
Abstract
Short linear motif (SLiM)-mediated interactions offer a unique strategy for viral intervention due to their compact interfaces, ease of convergent evolution, and key functional roles. Consequently, many viruses extensively mimic host SLiMs to hijack or deregulate cellular pathways and the same motif-binding pocket is often targeted by numerous unrelated viruses. A toolkit of therapeutics targeting commonly mimicked SLiMs could provide prophylactic and therapeutic broad-spectrum antivirals and vastly improve our ability to treat ongoing and future viral outbreaks. In this opinion article, we discuss the therapeutic relevance of SLiMs, advocating their suitability as targets for broad-spectrum antiviral inhibitors.
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Affiliation(s)
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Husargatan 3, 751 23 Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
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30
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Mihalič F, Simonetti L, Giudice G, Sander MR, Lindqvist R, Peters MBA, Benz C, Kassa E, Badgujar D, Inturi R, Ali M, Krystkowiak I, Sayadi A, Andersson E, Aronsson H, Söderberg O, Dobritzsch D, Petsalaki E, Överby AK, Jemth P, Davey NE, Ivarsson Y. Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs. Nat Commun 2023; 14:2409. [PMID: 37100772 PMCID: PMC10132805 DOI: 10.1038/s41467-023-38015-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Viruses mimic host short linear motifs (SLiMs) to hijack and deregulate cellular functions. Studies of motif-mediated interactions therefore provide insight into virus-host dependencies, and reveal targets for therapeutic intervention. Here, we describe the pan-viral discovery of 1712 SLiM-based virus-host interactions using a phage peptidome tiling the intrinsically disordered protein regions of 229 RNA viruses. We find mimicry of host SLiMs to be a ubiquitous viral strategy, reveal novel host proteins hijacked by viruses, and identify cellular pathways frequently deregulated by viral motif mimicry. Using structural and biophysical analyses, we show that viral mimicry-based interactions have similar binding strength and bound conformations as endogenous interactions. Finally, we establish polyadenylate-binding protein 1 as a potential target for broad-spectrum antiviral agent development. Our platform enables rapid discovery of mechanisms of viral interference and the identification of potential therapeutic targets which can aid in combating future epidemics and pandemics.
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Affiliation(s)
- Filip Mihalič
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Girolamo Giudice
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Marie Rubin Sander
- Department of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, Box 591, SE-751 24, Uppsala, Sweden
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90187, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Marie Berit Akpiroro Peters
- Department of Clinical Microbiology, Umeå University, 90187, 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, 751 23, Uppsala, Sweden
| | - Eszter Kassa
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Dilip Badgujar
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Muhammad Ali
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Izabella Krystkowiak
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Ahmed Sayadi
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Hanna Aronsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, Box 591, SE-751 24, Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, CB10 1SD, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90187, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, Husargatan 3, 751 23, Uppsala, Sweden.
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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31
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Nawaz M, Heydarkhan‐Hagvall S, Tangruksa B, González‐King Garibotti H, Jing Y, Maugeri M, Kohl F, Hultin L, Reyahi A, Camponeschi A, Kull B, Christoffersson J, Grimsholm O, Jennbacken K, Sundqvist M, Wiseman J, Bidar AW, Lindfors L, Synnergren J, Valadi H. Lipid Nanoparticles Deliver the Therapeutic VEGFA mRNA In Vitro and In Vivo and Transform Extracellular Vesicles for Their Functional Extensions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206187. [PMID: 36806740 PMCID: PMC10131815 DOI: 10.1002/advs.202206187] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/19/2022] [Indexed: 05/19/2023]
Abstract
Lipid nanoparticles (LNPs) are currently used to transport functional mRNAs, such as COVID-19 mRNA vaccines. The delivery of angiogenic molecules, such as therapeutic VEGF-A mRNA, to ischemic tissues for producing new blood vessels is an emerging strategy for the treatment of cardiovascular diseases. Here, the authors deliver VEGF-A mRNA via LNPs and study stoichiometric quantification of their uptake kinetics and how the transport of exogenous LNP-mRNAs between cells is functionally extended by cells' own vehicles called extracellular vesicles (EVs). The results show that cellular uptake of LNPs and their mRNA molecules occurs quickly, and that the translation of exogenously delivered mRNA begins immediately. Following the VEGF-A mRNA delivery to cells via LNPs, a fraction of internalized VEGF-A mRNA is secreted via EVs. The overexpressed VEGF-A mRNA is detected in EVs secreted from three different cell types. Additionally, RNA-Seq analysis reveals that as cells' response to LNP-VEGF-A mRNA treatment, several overexpressed proangiogenic transcripts are packaged into EVs. EVs are further deployed to deliver VEGF-A mRNA in vitro and in vivo. Upon equal amount of VEGF-A mRNA delivery via three EV types or LNPs in vitro, EVs from cardiac progenitor cells are the most efficient in promoting angiogenesis per amount of VEGF-A protein produced. Intravenous administration of luciferase mRNA shows that EVs could distribute translatable mRNA to different organs with the highest amounts of luciferase detected in the liver. Direct injections of VEGF-A mRNA (via EVs or LNPs) into mice heart result in locally produced VEGF-A protein without spillover to liver and circulation. In addition, EVs from cardiac progenitor cells cause minimal production of inflammatory cytokines in cardiac tissue compared with all other treatment types. Collectively, the data demonstrate that LNPs transform EVs as functional extensions to distribute therapeutic mRNA between cells, where EVs deliver this mRNA differently than LNPs.
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Affiliation(s)
- Muhammad Nawaz
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburg41346Sweden
| | - Sepideh Heydarkhan‐Hagvall
- BioPharmaceuticals R&DEarly CardiovascularRenal and Metabolism (CVRM)Bioscience CardiovascularAstraZenecaGothenburgMölndal43183Sweden
- Systems Biology Research CenterSchool of BioscienceUniversity of SkövdeSkövdeSE‐54128Sweden
| | - Benyapa Tangruksa
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburg41346Sweden
- Systems Biology Research CenterSchool of BioscienceUniversity of SkövdeSkövdeSE‐54128Sweden
| | - Hernán González‐King Garibotti
- BioPharmaceuticals R&DEarly CardiovascularRenal and Metabolism (CVRM)Bioscience CardiovascularAstraZenecaGothenburgMölndal43183Sweden
| | - Yujia Jing
- Advanced Drug DeliveryPharmaceutical SciencesBioPharmaceuticals R&DAstraZenecaGothenburgMölndal43183Sweden
| | - Marco Maugeri
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburg41346Sweden
- Safety InnovationsClinical Pharmacology and Safety SciencesR&D AstraZenecaGothenburgMölndal43183Sweden
| | - Franziska Kohl
- BioPharmaceuticals R&DDiscovery SciencesTranslational GenomicsAstraZenecaGothenburgMölndal43183Sweden
- Department of Medical Biochemistry and BiophysicsKarolinska InstituteSolnaStockholm17177Sweden
| | - Leif Hultin
- BioPharmaceuticals R&DClinical Pharmacology and Safety ScienceImaging and Data AnalyticsAstraZenecaGothenburgMölndal43183Sweden
| | - Azadeh Reyahi
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburg41346Sweden
| | - Alessandro Camponeschi
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburg41346Sweden
| | - Bengt Kull
- BioPharmaceuticals R&DEarly CardiovascularRenal and Metabolism (CVRM)Bioscience CardiovascularAstraZenecaGothenburgMölndal43183Sweden
| | - Jonas Christoffersson
- BioPharmaceuticals R&DEarly CardiovascularRenal and Metabolism (CVRM)Bioscience CardiovascularAstraZenecaGothenburgMölndal43183Sweden
- Systems Biology Research CenterSchool of BioscienceUniversity of SkövdeSkövdeSE‐54128Sweden
| | - Ola Grimsholm
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburg41346Sweden
- Institute of Pathophysiology and Allergy ResearchMedical University of ViennaVienna1090Austria
| | - Karin Jennbacken
- BioPharmaceuticals R&DEarly CardiovascularRenal and Metabolism (CVRM)Bioscience CardiovascularAstraZenecaGothenburgMölndal43183Sweden
| | - Martina Sundqvist
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburg41346Sweden
| | - John Wiseman
- BioPharmaceuticals R&DDiscovery SciencesTranslational GenomicsAstraZenecaGothenburgMölndal43183Sweden
| | - Abdel Wahad Bidar
- BioPharmaceuticals R&DDiscovery SciencesTranslational GenomicsAstraZenecaGothenburgMölndal43183Sweden
| | - Lennart Lindfors
- Advanced Drug DeliveryPharmaceutical SciencesBioPharmaceuticals R&DAstraZenecaGothenburgMölndal43183Sweden
| | - Jane Synnergren
- Systems Biology Research CenterSchool of BioscienceUniversity of SkövdeSkövdeSE‐54128Sweden
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska AcademyUniversity of GothenburgGothenburg41345Sweden
| | - Hadi Valadi
- Department of Rheumatology and Inflammation ResearchInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburg41346Sweden
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32
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Cai M, Xiao B, Wang Y, Wang K, Luo W, Fu J, Wang S, Deng S, Li B, Gong L, Zhong J, Hu L, Pan L, Wang L, Liu Y, Huang C, Li X, Zeng Q, Kang H, Li L, Zan J, Peng T, Yang H, Li M. Epstein-Barr virus envelope glycoprotein 110 inhibits NF-κB activation by interacting with NF-κB subunit p65. J Biol Chem 2023; 299:104613. [PMID: 36931391 PMCID: PMC10173782 DOI: 10.1016/j.jbc.2023.104613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
Epstein-Barr virus (EBV) is a member of the lymphotropic virus family, and is highly correlated with some human malignant tumors. It has been reported that envelope glycoprotein 110 (gp110) plays an essential role in viral fusion, DNA replication, and nucleocapsid assembly of EBV. However, it has not been established whether gp110 is involved in regulating the host's innate immunity. In this study, we found that gp110 inhibits tumor necrosis factor α (TNF-α)-mediated NF-κB promoter activity and the downstream production of NF-κB-regulated cytokines under physiological conditions. Using dual-luciferase reporter assays, we showed that gp110 might impede the NF-κB promoter activation downstream of NF-κB transactivational subunit p65. Subsequently, we used co-immunoprecipitation assays to demonstrate that gp110 interacts with p65 during EBV lytic infection, and that the C-terminal cytoplasmic region of gp110 is the key interaction domain with p65. Furthermore, we determined gp110 can bind to the N-terminal Rel homologous and C-terminal domains of p65. Alternatively, gp110 might not disturb the association of p65 with non-transactivational subunit p50, but we showed it restrains activational phosphorylation (at Ser536) and nuclear translocation of p65, which we also found to be executed by the C-terminal cytoplasmic region of gp110. Altogether, these data suggest that the surface protein gp110 may be a vital component for EBV to antagonize the host's innate immune response, which is also helpful for revealing the infectivity and pathogenesis of EBV.
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Affiliation(s)
- Mingsheng Cai
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China; Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Bin Xiao
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Yuanfang Wang
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China; The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Kezhen Wang
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Wenqi Luo
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Jiangqin Fu
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Shuai Wang
- Institutes of Biology and Medical Science, Soochow University, Suzhou, Jiangsu, China
| | - Shenyu Deng
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Bolin Li
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Lan Gong
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Jiayi Zhong
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Li Hu
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Lingxia Pan
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Liding Wang
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Yintao Liu
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Chen Huang
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Xiaoqing Li
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Qiyuan Zeng
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Haoran Kang
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Linhai Li
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China
| | - Jie Zan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, China.
| | - Tao Peng
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong, China; Guangdong South China Vaccine, Guangzhou, Guangdong, China.
| | - Haidi Yang
- Department of Otolaryngology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Institute of Hearing and Speech-Language Science, Guangzhou Xinhua University, Guangzhou, Guangdong, China.
| | - Meili Li
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital; State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Qingyuan, Guangdong, China; Department of Pathogenic Biology and Immunology, Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China.
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33
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Evaluation of affinity-purification coupled to mass spectrometry approaches for capture of short linear motif-based interactions. Anal Biochem 2023; 663:115017. [PMID: 36526023 DOI: 10.1016/j.ab.2022.115017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Low affinity and transient protein-protein interactions, such as short linear motif (SLiM)-based interactions, require dedicated experimental tools for discovery and validation. Here, we evaluated and compared biotinylated peptide pulldown and protein interaction screen on peptide matrix (PRISMA) coupled to mass-spectrometry (MS) using a set of peptides containing interaction motifs. Eight different peptide sequences that engage in interactions with three distinct protein domains (KEAP1 Kelch, MDM2 SWIB, and TSG101 UEV) with a wide range of affinities were tested. We found that peptide pulldown can be an effective approach for SLiM validation, however, parameters such as protein abundance and competitive interactions can prevent the capture of known interactors. The use of tandem peptide repeats improved the capture and preservation of some interactions. When testing PRISMA, it failed to provide comparable results for model peptides that successfully pulled down known interactors using biotinylated peptide pulldown. Overall, in our hands, we find that albeit more laborious, biotin-peptide pulldown was more successful in terms of validation of known interactions. Our results highlight that the tested affinity-capture MS-based methods for validation of SLiM-based interactions from cell lysates are suboptimal, and we identified parameters for consideration for method development.
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34
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Iuchi H, Kawasaki J, Kubo K, Fukunaga T, Hokao K, Yokoyama G, Ichinose A, Suga K, Hamada M. Bioinformatics approaches for unveiling virus-host interactions. Comput Struct Biotechnol J 2023; 21:1774-1784. [PMID: 36874163 PMCID: PMC9969756 DOI: 10.1016/j.csbj.2023.02.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
The coronavirus disease-2019 (COVID-19) pandemic has elucidated major limitations in the capacity of medical and research institutions to appropriately manage emerging infectious diseases. We can improve our understanding of infectious diseases by unveiling virus-host interactions through host range prediction and protein-protein interaction prediction. Although many algorithms have been developed to predict virus-host interactions, numerous issues remain to be solved, and the entire network remains veiled. In this review, we comprehensively surveyed algorithms used to predict virus-host interactions. We also discuss the current challenges, such as dataset biases toward highly pathogenic viruses, and the potential solutions. The complete prediction of virus-host interactions remains difficult; however, bioinformatics can contribute to progress in research on infectious diseases and human health.
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Affiliation(s)
- Hitoshi Iuchi
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan
| | - Junna Kawasaki
- Faculty of Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kento Kubo
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.,School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Tsukasa Fukunaga
- Waseda Institute for Advanced Study, Waseda University, Nishi Waseda, Shinjuku-ku, Tokyo 169-0051, Japan
| | - Koki Hokao
- School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Gentaro Yokoyama
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.,School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Akiko Ichinose
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Kanta Suga
- School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan
| | - Michiaki Hamada
- Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.,School of Advanced Science and Engineering, Waseda University, Okubo Shinjuku-ku, Tokyo 169-8555, Japan.,Graduate School of Medicine, Nippon Medical School, Tokyo 113-8602, Japan
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35
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Lundstrom K, Hromić-Jahjefendić A, Bilajac E, Aljabali AAA, Baralić K, Sabri NA, Shehata EM, Raslan M, Ferreira ACBH, Orlandi L, Serrano-Aroca Á, Tambuwala MM, Uversky VN, Azevedo V, Alzahrani KJ, Alsharif KF, Halawani IF, Alzahrani FM, Redwan EM, Barh D. COVID-19 signalome: Pathways for SARS-CoV-2 infection and impact on COVID-19 associated comorbidity. Cell Signal 2023; 101:110495. [PMID: 36252792 PMCID: PMC9568271 DOI: 10.1016/j.cellsig.2022.110495] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic has been the focus of research the past two years. The major breakthrough was made by discovering pathways related to SARS-CoV-2 infection through cellular interaction by angiotensin-converting enzyme (ACE2) and cytokine storm. The presence of ACE2 in lungs, intestines, cardiovascular tissues, brain, kidneys, liver, and eyes shows that SARS-CoV-2 may have targeted these organs to further activate intracellular signalling pathways that lead to cytokine release syndrome. It has also been reported that SARS-CoV-2 can hijack coatomer protein-I (COPI) for S protein retrograde trafficking to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), which, in turn, acts as the assembly site for viral progeny. In infected cells, the newly synthesized S protein in endoplasmic reticulum (ER) is transported first to the Golgi body, and then from the Golgi body to the ERGIC compartment resulting in the formation of specific a motif at the C-terminal end. This review summarizes major events of SARS-CoV-2 infection route, immune response following host-cell infection as an important factor for disease outcome, as well as comorbidity issues of various tissues and organs arising due to COVID-19. Investigations on alterations of host-cell machinery and viral interactions with multiple intracellular signaling pathways could represent a major factor in more effective disease management.
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Affiliation(s)
| | - Altijana Hromić-Jahjefendić
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Hrasnicka Cesta 15, 71000 Sarajevo, Bosnia and Herzegovina.
| | - Esma Bilajac
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Hrasnicka Cesta 15, 71000 Sarajevo, Bosnia and Herzegovina
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, P.O. Box 566, Irbid 21163, Jordan.
| | - Katarina Baralić
- Department of Toxicology "Akademik Danilo Soldatović", University of Belgrade - Faculty of Pharmacy, Vojvode Stepe 450, 11221 Belgrade, Serbia.
| | - Nagwa A Sabri
- Department of Clinical Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo 11865, Egypt.
| | - Eslam M Shehata
- Drug Research Center, Clinical Research and Bioanalysis Department, Cairo 11865, Egypt.
| | - Mohamed Raslan
- Drug Research Center, Clinical Research and Bioanalysis Department, Cairo 11865, Egypt.
| | - Ana Cláudia B H Ferreira
- Campinas State University, Campinas, São Paulo, Brazil; University Center of Lavras (UNILAVRAS), Lavras, Minas Gerais, Brazil.
| | - Lidiane Orlandi
- University Center of Lavras (UNILAVRAS), Lavras, Minas Gerais, Brazil.
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Laboratory, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, c/Guillem de Castro 94, 46001 Valencia, Spain.
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Khalaf F Alsharif
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Ibrahim F Halawani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Fuad M Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia.
| | - Debmalya Barh
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, India.
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36
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Functional benefit of structural disorder for the replication of measles, Nipah and Hendra viruses. Essays Biochem 2022; 66:915-934. [PMID: 36148633 DOI: 10.1042/ebc20220045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022]
Abstract
Measles, Nipah and Hendra viruses are severe human pathogens within the Paramyxoviridae family. Their non-segmented, single-stranded, negative-sense RNA genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that is the substrate used by the viral RNA-dependent-RNA-polymerase (RpRd) for transcription and replication. The RpRd is a complex made of the large protein (L) and of the phosphoprotein (P), the latter serving as an obligate polymerase cofactor and as a chaperon for N. Both the N and P proteins are enriched in intrinsically disordered regions (IDRs), i.e. regions devoid of stable secondary and tertiary structure. N possesses a C-terminal IDR (NTAIL), while P consists of a large, intrinsically disordered N-terminal domain (NTD) and a C-terminal domain (CTD) encompassing alternating disordered and ordered regions. The V and W proteins, two non-structural proteins that are encoded by the P gene via a mechanism of co-transcriptional edition of the P mRNA, are prevalently disordered too, sharing with P the disordered NTD. They are key players in the evasion of the host antiviral response and were shown to phase separate and to form amyloid-like fibrils in vitro. In this review, we summarize the available information on IDRs within the N, P, V and W proteins from these three model paramyxoviruses and describe their molecular partnership. We discuss the functional benefit of disorder to virus replication in light of the critical role of IDRs in affording promiscuity, multifunctionality, fine regulation of interaction strength, scaffolding functions and in promoting liquid-liquid phase separation and fibrillation.
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37
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Madhu P, Davey NE, Ivarsson Y. How viral proteins bind short linear motifs and intrinsically disordered domains. Essays Biochem 2022; 66:EBC20220047. [PMID: 36504386 DOI: 10.1042/ebc20220047] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 02/11/2024]
Abstract
Viruses are the obligate intracellular parasites that exploit the host cellular machinery to replicate their genome. During the viral life cycle viruses manipulate the host cell through interactions with host proteins. Many of these protein-protein interactions are mediated through the recognition of host globular domains by short linear motifs (SLiMs), or longer intrinsically disordered domains (IDD), in the disordered regions of viral proteins. However, viruses also employ their own globular domains for binding to SLiMs and IDDs present in host proteins or virus proteins. In this review, we focus on the different strategies adopted by viruses to utilize proteins or protein domains for binding to the disordered regions of human or/and viral ligands. With a set of examples, we describe viral domains that bind human SLiMs. We also provide examples of viral proteins that bind to SLiMs, or IDDs, of viral proteins as a part of complex assembly and regulation of protein functions. The protein-protein interactions are often crucial for viral replication, and may thus offer possibilities for innovative inhibitor design.
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Affiliation(s)
- Priyanka Madhu
- Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, London, U.K
| | - Ylva Ivarsson
- Department of Chemistry, BMC, Uppsala University, Uppsala, Sweden
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38
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Evolution of SLiM-mediated hijack functions in intrinsically disordered viral proteins. Essays Biochem 2022; 66:945-958. [DOI: 10.1042/ebc20220059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 12/07/2022]
Abstract
Abstract
Viruses and their hosts are involved in an ‘arms race’ where they continually evolve mechanisms to overcome each other. It has long been proposed that intrinsic disorder provides a substrate for the evolution of viral hijack functions and that short linear motifs (SLiMs) are important players in this process. Here, we review evidence in support of this tenet from two model systems: the papillomavirus E7 protein and the adenovirus E1A protein. Phylogenetic reconstructions reveal that SLiMs appear and disappear multiple times across evolution, providing evidence of convergent evolution within individual viral phylogenies. Multiple functionally related SLiMs show strong coevolution signals that persist across long distances in the primary sequence and occur in unrelated viral proteins. Moreover, changes in SLiMs are associated with changes in phenotypic traits such as host range and tropism. Tracking viral evolutionary events reveals that host switch events are associated with the loss of several SLiMs, suggesting that SLiMs are under functional selection and that changes in SLiMs support viral adaptation. Fine-tuning of viral SLiM sequences can improve affinity, allowing them to outcompete host counterparts. However, viral SLiMs are not always competitive by themselves, and tethering of two suboptimal SLiMs by a disordered linker may instead enable viral hijack. Coevolution between the SLiMs and the linker indicates that the evolution of disordered regions may be more constrained than previously thought. In summary, experimental and computational studies support a role for SLiMs and intrinsic disorder in viral hijack functions and in viral adaptive evolution.
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39
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Piovesan D, Del Conte A, Clementel D, Monzon A, Bevilacqua M, Aspromonte M, Iserte J, Orti FE, Marino-Buslje C, Tosatto SE. MobiDB: 10 years of intrinsically disordered proteins. Nucleic Acids Res 2022; 51:D438-D444. [PMID: 36416266 PMCID: PMC9825420 DOI: 10.1093/nar/gkac1065] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/11/2022] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
The MobiDB database (URL: https://mobidb.org/) is a knowledge base of intrinsically disordered proteins. MobiDB aggregates disorder annotations derived from the literature and from experimental evidence along with predictions for all known protein sequences. MobiDB generates new knowledge and captures the functional significance of disordered regions by processing and combining complementary sources of information. Since its first release 10 years ago, the MobiDB database has evolved in order to improve the quality and coverage of protein disorder annotations and its accessibility. MobiDB has now reached its maturity in terms of data standardization and visualization. Here, we present a new release which focuses on the optimization of user experience and database content. The major advances compared to the previous version are the integration of AlphaFoldDB predictions and the re-implementation of the homology transfer pipeline, which expands manually curated annotations by two orders of magnitude. Finally, the entry page has been restyled in order to provide an overview of the available annotations along with two separate views that highlight structural disorder evidence and functions associated with different binding modes.
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Affiliation(s)
- Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Alessio Del Conte
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Damiano Clementel
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | | | | | - Javier A Iserte
- Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, Argentina
| | - Fernando E Orti
- Bioinformatics Unit, Fundación Instituto Leloir, Buenos Aires, Argentina
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Asim MN, Fazeel A, Ibrahim MA, Dengel A, Ahmed S. MP-VHPPI: Meta predictor for viral host protein-protein interaction prediction in multiple hosts and viruses. Front Med (Lausanne) 2022; 9:1025887. [PMID: 36465911 PMCID: PMC9709337 DOI: 10.3389/fmed.2022.1025887] [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: 08/23/2022] [Accepted: 10/17/2022] [Indexed: 09/19/2023] Open
Abstract
Viral-host protein-protein interaction (VHPPI) prediction is essential to decoding molecular mechanisms of viral pathogens and host immunity processes that eventually help to control the propagation of viral diseases and to design optimized therapeutics. Multiple AI-based predictors have been developed to predict diverse VHPPIs across a wide range of viruses and hosts, however, these predictors produce better performance only for specific types of hosts and viruses. The prime objective of this research is to develop a robust meta predictor (MP-VHPPI) capable of more accurately predicting VHPPI across multiple hosts and viruses. The proposed meta predictor makes use of two well-known encoding methods Amphiphilic Pseudo-Amino Acid Composition (APAAC) and Quasi-sequence (QS) Order that capture amino acids sequence order and distributional information to most effectively generate the numerical representation of complete viral-host raw protein sequences. Feature agglomeration method is utilized to transform the original feature space into a more informative feature space. Random forest (RF) and Extra tree (ET) classifiers are trained on optimized feature space of both APAAC and QS order separate encoders and by combining both encodings. Further predictions of both classifiers are utilized to feed the Support Vector Machine (SVM) classifier that makes final predictions. The proposed meta predictor is evaluated over 7 different benchmark datasets, where it outperforms existing VHPPI predictors with an average performance of 3.07, 6.07, 2.95, and 2.85% in terms of accuracy, Mathews correlation coefficient, precision, and sensitivity, respectively. To facilitate the scientific community, the MP-VHPPI web server is available at https://sds_genetic_analysis.opendfki.de/MP-VHPPI/.
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Affiliation(s)
- Muhammad Nabeel Asim
- Department of Computer Science, Technical University of Kaiserslautern, Kaiserslautern, Germany
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern, Germany
| | - Ahtisham Fazeel
- Department of Computer Science, Technical University of Kaiserslautern, Kaiserslautern, Germany
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern, Germany
| | - Muhammad Ali Ibrahim
- Department of Computer Science, Technical University of Kaiserslautern, Kaiserslautern, Germany
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern, Germany
| | - Andreas Dengel
- Department of Computer Science, Technical University of Kaiserslautern, Kaiserslautern, Germany
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence GmbH, Kaiserslautern, Germany
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Garg A, Singhal N, Kumar M. Investigating the eukaryotic host-like SLiMs in microbial mimitopes and their potential as novel drug targets for treating autoimmune diseases. Front Microbiol 2022; 13:1039188. [DOI: 10.3389/fmicb.2022.1039188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
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Lerer V, Shlezinger N. Inseparable companions: Fungal viruses as regulators of fungal fitness and host adaptation. Front Cell Infect Microbiol 2022; 12:1020608. [PMID: 36310864 PMCID: PMC9606465 DOI: 10.3389/fcimb.2022.1020608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/28/2022] [Indexed: 08/01/2023] Open
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An anti-influenza combined therapy assessed by single cell RNA-sequencing. Commun Biol 2022; 5:1075. [PMID: 36216966 PMCID: PMC9549038 DOI: 10.1038/s42003-022-04013-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/20/2022] [Indexed: 11/08/2022] Open
Abstract
Influenza makes millions of people ill every year, placing a large burden on the healthcare system and the economy. To develop a treatment against influenza, we combined virucidal sialylated cyclodextrins with interferon lambda and demonstrated, in human airway epithelia, that the two compounds inhibit the replication of a clinical H1N1 strain more efficiently when administered together rather than alone. We investigated the mechanism of action of the combined treatment by single cell RNA-sequencing analysis and found that both the single and combined treatments impair viral replication to different extents across distinct epithelial cell types. We showed that each cell type comprises multiple sub-types, whose proportions are altered by H1N1 infection, and assessed the ability of the treatments to restore them. To the best of our knowledge this is the first study investigating the effectiveness of an antiviral therapy against influenza virus by single cell transcriptomic studies. When combined with interferon lambda, virucidal sialylated cyclodextrins inhibit the replication of a clinical H1N1 influenza strain in ex vivo human airway epithelia more efficiently than when delivered alone.
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Kee J, Thudium S, Renner DM, Glastad K, Palozola K, Zhang Z, Li Y, Lan Y, Cesare J, Poleshko A, Kiseleva AA, Truitt R, Cardenas-Diaz FL, Zhang X, Xie X, Kotton DN, Alysandratos KD, Epstein JA, Shi PY, Yang W, Morrisey E, Garcia BA, Berger SL, Weiss SR, Korb E. SARS-CoV-2 disrupts host epigenetic regulation via histone mimicry. Nature 2022; 610:381-388. [PMID: 36198800 PMCID: PMC9533993 DOI: 10.1038/s41586-022-05282-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 08/26/2022] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged at the end of 2019 and caused the devastating global pandemic of coronavirus disease 2019 (COVID-19), in part because of its ability to effectively suppress host cell responses1-3. In rare cases, viral proteins dampen antiviral responses by mimicking critical regions of human histone proteins4-8, particularly those containing post-translational modifications required for transcriptional regulation9-11. Recent work has demonstrated that SARS-CoV-2 markedly disrupts host cell epigenetic regulation12-14. However, how SARS-CoV-2 controls the host cell epigenome and whether it uses histone mimicry to do so remain unclear. Here we show that the SARS-CoV-2 protein encoded by ORF8 (ORF8) functions as a histone mimic of the ARKS motifs in histone H3 to disrupt host cell epigenetic regulation. ORF8 is associated with chromatin, disrupts regulation of critical histone post-translational modifications and promotes chromatin compaction. Deletion of either the ORF8 gene or the histone mimic site attenuates the ability of SARS-CoV-2 to disrupt host cell chromatin, affects the transcriptional response to infection and attenuates viral genome copy number. These findings demonstrate a new function of ORF8 and a mechanism through which SARS-CoV-2 disrupts host cell epigenetic regulation. Further, this work provides a molecular basis for the finding that SARS-CoV-2 lacking ORF8 is associated with decreased severity of COVID-19.
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Affiliation(s)
- John Kee
- Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Samuel Thudium
- Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - David M Renner
- Department of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Karl Glastad
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine Palozola
- Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Zhen Zhang
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Yize Li
- Department of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Yemin Lan
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Cesare
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Anna A Kiseleva
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel Truitt
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Fabian L Cardenas-Diaz
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Konstantinos D Alysandratos
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jonathan A Epstein
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Wenli Yang
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Edward Morrisey
- Department of Medicine at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn-CHOP Lung Biology Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley L Berger
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Biology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Susan R Weiss
- Department of Microbiology at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Penn Center for Research on Coronaviruses and Other Emerging Pathogens at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Erica Korb
- Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
- Epigenetics Institute at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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Gogl G, Zambo B, Kostmann C, Cousido-Siah A, Morlet B, Durbesson F, Negroni L, Eberling P, Jané P, Nominé Y, Zeke A, Østergaard S, Monsellier É, Vincentelli R, Travé G. Quantitative fragmentomics allow affinity mapping of interactomes. Nat Commun 2022; 13:5472. [PMID: 36115835 PMCID: PMC9482650 DOI: 10.1038/s41467-022-33018-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/24/2022] [Indexed: 12/18/2022] Open
Abstract
Human protein networks have been widely explored but most binding affinities remain unknown, hindering quantitative interactome-function studies. Yet interactomes rely on minimal interacting fragments displaying quantifiable affinities. Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. We calculate interactomic distances, identify hot spots for viral interference, generate binding profiles and specificity logos, and explain selected cases by crystallographic studies. Mass spectrometry experiments on cell extracts and literature surveys show that quantitative fragmentomics effectively complements protein interactomics by providing affinities and completeness of coverage, putting a full human interactome affinity survey within reach. Finally, we show that interactome hijacking by the viral PBM of human papillomavirus E6 oncoprotein substantially impacts the host cell proteome beyond immediate E6 binders, illustrating the complex system-wide relationship between interactome and function. Protein networks have been widely explored but most binding affinities remain unknown, limiting the quantitative interpretation of interactomes. Here the authors measure affinities of 65,000 interactions involving human PDZ domains and target sequence motifs relevant for viral infection and cancer.
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Shuler G, Hagai T. Rapidly evolving viral motifs mostly target biophysically constrained binding pockets of host proteins. Cell Rep 2022; 40:111212. [PMID: 35977510 DOI: 10.1016/j.celrep.2022.111212] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/11/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022] Open
Abstract
Evolutionary changes in host-virus interactions can alter the course of infection, but the biophysical and regulatory constraints that shape interface evolution remain largely unexplored. Here, we focus on viral mimicry of host-like motifs that allow binding to host domains and modulation of cellular pathways. We observe that motifs from unrelated viruses preferentially target conserved, widely expressed, and highly connected host proteins, enriched with regulatory and essential functions. The interface residues within these host domains are more conserved and bind a larger number of cellular proteins than similar motif-binding domains that are not known to interact with viruses. In contrast, rapidly evolving viral-binding human proteins form few interactions with other cellular proteins and display high tissue specificity, and their interfaces have few inter-residue contacts. Our results distinguish between conserved and rapidly evolving host-virus interfaces and show how various factors limit host capacity to evolve, allowing for efficient viral subversion of host machineries.
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Affiliation(s)
- Gal Shuler
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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Conformational buffering underlies functional selection in intrinsically disordered protein regions. Nat Struct Mol Biol 2022; 29:781-790. [PMID: 35948766 DOI: 10.1038/s41594-022-00811-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 06/23/2022] [Indexed: 02/02/2023]
Abstract
Many disordered proteins conserve essential functions in the face of extensive sequence variation, making it challenging to identify the mechanisms responsible for functional selection. Here we identify the molecular mechanism of functional selection for the disordered adenovirus early gene 1A (E1A) protein. E1A competes with host factors to bind the retinoblastoma (Rb) protein, subverting cell cycle regulation. We show that two binding motifs tethered by a hypervariable disordered linker drive picomolar affinity Rb binding and host factor displacement. Compensatory changes in amino acid sequence composition and sequence length lead to conservation of optimal tethering across a large family of E1A linkers. We refer to this compensatory mechanism as conformational buffering. We also detect coevolution of the motifs and linker, which can preserve or eliminate the tethering mechanism. Conformational buffering and motif-linker coevolution explain robust functional encoding within hypervariable disordered linkers and could underlie functional selection of many disordered protein regions.
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Basant A, Way M. The relative binding position of Nck and Grb2 adaptors impacts actin-based motility of Vaccinia virus. eLife 2022; 11:74655. [PMID: 35796545 PMCID: PMC9333988 DOI: 10.7554/elife.74655] [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: 10/12/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Phosphotyrosine (pTyr) motifs in unstructured polypeptides orchestrate important cellular processes by engaging SH2-containing adaptors to assemble complex signalling networks. The concept of phase separation has recently changed our appreciation of multivalent networks, however, the role of pTyr motif positioning in their function remains to be explored. We have now investigated this parameter in the operation of the signalling cascade driving actin-based motility and spread of Vaccinia virus. This network involves two pTyr motifs in the viral protein A36 that recruit the adaptors Nck and Grb2 upstream of N-WASP and Arp2/3 complex-mediated actin polymerisation. Manipulating the position of pTyr motifs in A36 and the unrelated p14 from Orthoreovirus, we find that only specific spatial arrangements of Nck and Grb2 binding sites result in robust N-WASP recruitment, Arp2/3 complex driven actin polymerisation and viral spread. This suggests that the relative position of pTyr adaptor binding sites is optimised for signal output. This finding may explain why the relative positions of pTyr motifs are frequently conserved in proteins from widely different species. It also has important implications for regulation of physiological networks, including those undergoing phase transitions.
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Affiliation(s)
- Angika Basant
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Way
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
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49
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A.V.S SK, Sinha S, Donakonda S. Virus-host interaction network analysis in Colorectal cancer identifies core virus network signature and small molecules. Comput Struct Biotechnol J 2022; 20:4025-4039. [PMID: 35983230 PMCID: PMC9356043 DOI: 10.1016/j.csbj.2022.07.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/23/2022] [Accepted: 07/23/2022] [Indexed: 11/15/2022] Open
Abstract
Systematic analysis of virus-host networks identified key pathways in CRC. Core virus-CRC network revealed the growth pathway regulated by viruses. Short linear motif analysis identified druggable regions in virus proteins. Virtual screening revealed key anti-viral molecules against viral proteins. Molecular dynamics simulations showed the effect of anti-viral molecules.
Colorectal cancer (CRC) is a significant contributor to cancer-related deaths caused by an unhealthy lifestyle. Multiple studies reveal that viruses are involved in colorectal tumorigenesis. The viruses such as Human Cytomegalovirus (HCMV), Human papillomaviruses (HPV16 & HPV18), and John Cunningham virus (JCV) are known to cause colorectal cancer. The molecular mechanisms of cancer genesis and maintenance shared by these viruses remain unclear. We analysed the virus-host networks and connected them with colorectal cancer proteome datasets and extracted the core shared interactions in the virus-host CRC network. Our network topology analysis identified prominent virus proteins RL6 (HCMV), VE6 (HPV16 and HPV18), and Large T antigen (JCV). Sequence analysis uncovered short linear motifs (SLiMs) in each viral target. We used these targets to identify the antiviral drugs through a structure-based virtual screening approach. This analysis highlighted that temsavir, pimodivir, famotine, and bictegravir bind to each virus protein target, respectively. We also assessed the effect of drug binding using molecular dynamic simulations, which shed light on the modulatory effect of drug molecules on SLiM regions in viral targets. Hence, our systematic screening of virus-host networks revealed viral targets, which could be crucial for cancer therapy.
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Affiliation(s)
- Sai Krishna A.V.S
- Department of Biotechnology, Faculty of Life and Allied Health Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, India
| | - Swati Sinha
- Department of Biotechnology, Faculty of Life and Allied Health Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, India
| | - Sainitin Donakonda
- Institute of Molecular Immunology and Experimental Oncology, Klinikum Rechts Der Isar, Technical University of Munich, Munich, Germany
- Corresponding author.
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50
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Islan GA, Rodenak-Kladniew B, Noacco N, Duran N, Castro GR. Prodigiosin: a promising biomolecule with many potential biomedical applications. Bioengineered 2022; 13:14227-14258. [PMID: 35734783 PMCID: PMC9342244 DOI: 10.1080/21655979.2022.2084498] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pigments are among the most fascinating molecules found in nature and used by human civilizations since the prehistoric ages. Although most of the bio-dyes reported in the literature were discovered around the eighties, the necessity to explore novel compounds for new biological applications has made them resurface as potential alternatives. Prodigiosin (PG) is an alkaloid red bio-dye produced by diverse microorganisms and composed of a linear tripyrrole chemical structure. PG emerges as a really interesting tool since it shows a wide spectrum of biological activities, such as antibacterial, antifungal, algicidal, anti-Chagas, anti-amoebic, antimalarial, anticancer, antiparasitic, antiviral, and/or immunosuppressive. However, PG vehiculation into different delivery systems has been proposed since possesses low bioavailability because of its high hydrophobic character (XLogP3-AA = 4.5). In the present review, the general aspects of the PG correlated with synthesis, production process, and biological activities are reported. Besides, some of the most relevant PG delivery systems described in the literature, as well as novel unexplored applications to potentiate its biological activity in biomedical applications, are proposed.
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Affiliation(s)
- German A Islan
- Desarrollo en Fermentaciones Industriales (CINDEFI), Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP) -CONICET (CCT La Plata)Laboratorio de Nanobiomateriales, Centro de Investigación y , La Plata, Argentina
| | - Boris Rodenak-Kladniew
- Facultad de Ciencias Médicas, Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), CONICET-UNLP, CCT-La Plata, La Plata, Pcia de Bueos aires, Argentina
| | - Nehuen Noacco
- Desarrollo en Fermentaciones Industriales (CINDEFI), Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP) -CONICET (CCT La Plata)Laboratorio de Nanobiomateriales, Centro de Investigación y , La Plata, Argentina
| | - Nelson Duran
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, Biological Institute, Department of Structural and Functional Biology, University of Campinas, Campinas, Brazil.,Nanomedicine Research Unit (Nanomed), Federal University of Abc (Ufabc), Santo André, Brazil
| | - Guillermo R Castro
- Laboratory of Urogenital Carcinogenesis and Immunotherapy, Biological Institute, Department of Structural and Functional Biology, University of Campinas, Campinas, Brazil.,. Partner Laboratory of the Max Planck Institute for Biophysical Chemistry (MPIbpC, MPG). Centro de Estudios Interdisciplinarios (CEI), Universidad Nacional de RosarioMax Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPIbpC), Rosario, Argentina
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