51
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Habchi J, Longhi S. Structural Disorder within Paramyxoviral Nucleoproteins and Phosphoproteins in Their Free and Bound Forms: From Predictions to Experimental Assessment. Int J Mol Sci 2015; 16:15688-726. [PMID: 26184170 PMCID: PMC4519920 DOI: 10.3390/ijms160715688] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 01/10/2023] Open
Abstract
We herein review available computational and experimental data pointing to the abundance of structural disorder within the nucleoprotein (N) and phosphoprotein (P) from three paramyxoviruses, namely the measles (MeV), Nipah (NiV) and Hendra (HeV) viruses. We provide a detailed molecular description of the mechanisms governing the disorder-to-order transition that the intrinsically disordered C-terminal domain (NTAIL) of their N proteins undergoes upon binding to the C-terminal X domain (PXD) of the homologous P proteins. We also show that NTAIL-PXD complexes are "fuzzy", i.e., they possess a significant residual disorder, and discuss the possible functional significance of this fuzziness. Finally, we emphasize the relevance of N-P interactions involving intrinsically disordered proteins as promising targets for new antiviral approaches, and end up summarizing the general functional advantages of disorder for viruses.
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Affiliation(s)
- Johnny Habchi
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 163, Avenue de Luminy, Case 932, 13288 Marseille, France.
- Centre National pour la Recherche Scientifique (CNRS), AFMB UMR 7257, 163, Avenue de Luminy, Case 932, 13288 Marseille, France.
| | - Sonia Longhi
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 163, Avenue de Luminy, Case 932, 13288 Marseille, France.
- Centre National pour la Recherche Scientifique (CNRS), AFMB UMR 7257, 163, Avenue de Luminy, Case 932, 13288 Marseille, France.
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52
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Longhi S. Structural disorder within paramyxoviral nucleoproteins. FEBS Lett 2015; 589:2649-59. [PMID: 26071376 DOI: 10.1016/j.febslet.2015.05.055] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 12/21/2022]
Abstract
In this review I summarize available data pointing to the abundance of structural disorder within the nucleoprotein (N) from three paramyxoviruses, namely the measles (MeV), Nipah (NiV) and Hendra (HeV) viruses. I provide a detailed description of the molecular mechanisms that govern the disorder-to-order transition that the intrinsically disordered C-terminal domain (NTAIL) of their N proteins undergoes upon binding to the C-terminal X domain (XD) of the homologous phosphoproteins. I also show that a significant flexibility persists within NTAIL-XD complexes, which makes them illustrative examples of "fuzziness". Finally, I discuss the functional implications of structural disorder for viral transcription and replication in light of the promiscuity of disordered regions and of the considerable reach they confer to the components of the replicative machinery.
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Affiliation(s)
- Sonia Longhi
- Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France.
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53
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Cox R, Plemper RK. The paramyxovirus polymerase complex as a target for next-generation anti-paramyxovirus therapeutics. Front Microbiol 2015; 6:459. [PMID: 26029193 PMCID: PMC4428208 DOI: 10.3389/fmicb.2015.00459] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/27/2015] [Indexed: 12/04/2022] Open
Abstract
The paramyxovirus family includes major human and animal pathogens, including measles virus, mumps virus, and human respiratory syncytial virus (RSV), as well as the emerging zoonotic Hendra and Nipah viruses. In the U.S., RSV is the leading cause of infant hospitalizations due to viral infectious disease. Despite their clinical significance, effective drugs for the improved management of paramyxovirus disease are lacking. The development of novel anti-paramyxovirus therapeutics is therefore urgently needed. Paramyxoviruses contain RNA genomes of negative polarity, necessitating a virus-encoded RNA-dependent RNA polymerase (RdRp) complex for replication and transcription. Since an equivalent enzymatic activity is absent in host cells, the RdRp complex represents an attractive druggable target, although structure-guided drug development campaigns are hampered by the lack of high-resolution RdRp crystal structures. Here, we review the current structural and functional insight into the paramyxovirus polymerase complex in conjunction with an evaluation of the mechanism of activity and developmental status of available experimental RdRp inhibitors. Our assessment spotlights the importance of the RdRp complex as a premier target for therapeutic intervention and examines how high-resolution insight into the organization of the complex will pave the path toward the structure-guided design and optimization of much-needed next-generation paramyxovirus RdRp blockers.
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Affiliation(s)
- Robert Cox
- Institute for Biomedical Sciences, Petit Science Center, Georgia State University, Atlanta, GA USA
| | - Richard K Plemper
- Institute for Biomedical Sciences, Petit Science Center, Georgia State University, Atlanta, GA USA
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54
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Egelman EH. Three-dimensional reconstruction of helical polymers. Arch Biochem Biophys 2015; 581:54-8. [PMID: 25912526 DOI: 10.1016/j.abb.2015.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/06/2015] [Accepted: 04/14/2015] [Indexed: 11/18/2022]
Abstract
The field of three-dimensional electron microscopy began more than 45years ago with a reconstruction of a helical phage tail, and helical polymers continue to be important objects for three-dimensional reconstruction due to the centrality of helical protein and nucleoprotein polymers in all aspects of biology. We are now witnessing a fundamental revolution in this area, made possible by direct electron detectors, which has led to near-atomic resolution for a number of important helical structures. Most importantly, the possibility of achieving such resolution routinely for a vast number of helical samples is within our reach. One of the main problems in helical reconstruction, ambiguities in assigning the helical symmetry, is overcome when one reaches a resolution where secondary structure is clearly visible. However, obstacles still exist due to the intrinsic variability within many helical filaments.
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Affiliation(s)
- Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Box 800733, Charlottesville, VA 22908, USA.
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55
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Dosnon M, Bonetti D, Morrone A, Erales J, di Silvio E, Longhi S, Gianni S. Demonstration of a folding after binding mechanism in the recognition between the measles virus NTAIL and X domains. ACS Chem Biol 2015; 10:795-802. [PMID: 25511246 DOI: 10.1021/cb5008579] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In the past decade, a wealth of experimental data has demonstrated that a large fraction of proteins, while functional, are intrinsically disordered at physiological conditions. Many intrinsically disordered proteins (IDPs) undergo a disorder-to-order transition upon binding to their biological targets, a phenomenon known as induced folding. Induced folding may occur through two extreme mechanisms, namely conformational selection and folding after binding. Although the pre-existence of ordered structures in IDPs is a prerequisite for conformational selection, it does not necessarily commit to this latter mechanism, and kinetic studies are needed to discriminate between the two possible scenarios. So far, relatively few studies have addressed this issue from an experimental perspective. Here, we analyze the interaction kinetics between the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) and the X domain (XD) of the viral phosphoprotein. Data reveal that NTAIL recognizes XD by first forming a weak encounter complex in a disordered conformation, which is subsequently locked-in by a folding step; i.e., binding precedes folding. The implications of our kinetic results, in the context of previously reported equilibrium data, are discussed. These results contribute to enhancing our understanding of the molecular mechanisms by which IDPs recognize their partners and represent a paradigmatic example of the need of kinetic methods to discriminate between reaction mechanisms.
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Affiliation(s)
- Marion Dosnon
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 13288, Marseille, France
- CNRS, AFMB UMR 7257, 13288, Marseille, France
| | - Daniela Bonetti
- Istituto
Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli” and Istituto di Biologia e Patologia
Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Angela Morrone
- Istituto
Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli” and Istituto di Biologia e Patologia
Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Jenny Erales
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 13288, Marseille, France
- CNRS, AFMB UMR 7257, 13288, Marseille, France
| | - Eva di Silvio
- Istituto
Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli” and Istituto di Biologia e Patologia
Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Sonia Longhi
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 13288, Marseille, France
- CNRS, AFMB UMR 7257, 13288, Marseille, France
| | - Stefano Gianni
- Istituto
Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli” and Istituto di Biologia e Patologia
Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
- Department
of Chemistry, University of Cambridge, Cambridge CB21EW, United Kingdom
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Beltrandi M, Blocquel D, Erales J, Barbier P, Cavalli A, Longhi S. Insights into the coiled-coil organization of the Hendra virus phosphoprotein from combined biochemical and SAXS studies. Virology 2015; 477:42-55. [PMID: 25637789 DOI: 10.1016/j.virol.2014.12.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 10/21/2014] [Accepted: 12/19/2014] [Indexed: 10/24/2022]
Abstract
Nipah and Hendra viruses are recently emerged paramyxoviruses belonging to the Henipavirus genus. The Henipavirus phosphoprotein (P) consists of a large intrinsically disordered domain and a C-terminal domain (PCT) containing alternating disordered and ordered regions. Among these latter is the P multimerization domain (PMD). Using biochemical, analytical ultracentrifugation and small-angle X-ray scattering (SAXS) studies, we show that Hendra virus (HeV) PMD forms an elongated coiled-coil homotrimer in solution, in agreement with our previous findings on Nipah virus (NiV) PMD. However, the orientation of the N-terminal region differs from that observed in solution for NiV PMD, consistent with the ability of this region to adopt different conformations. SAXS studies provided evidence for a trimeric organization also in the case of PCT, thus extending and strengthening our findings on PMD. The present results are discussed in light of conflicting reports in the literature pointing to a tetrameric organization of paramyxoviral P proteins.
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Affiliation(s)
- Matilde Beltrandi
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - David Blocquel
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Jenny Erales
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France
| | - Pascale Barbier
- Aix-Marseille University, INSERM, CRO2 UMR_S911, Faculté de Pharmacie, 13385 Marseille, France
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland; Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
| | - Sonia Longhi
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, 13288 Marseille, France; CNRS, AFMB UMR 7257, 13288 Marseille, France.
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57
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Order and Disorder in the Replicative Complex of Paramyxoviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:351-81. [PMID: 26387109 DOI: 10.1007/978-3-319-20164-1_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this review we summarize available data showing the abundance of structural disorder within the nucleoprotein (N) and phosphoprotein (P) from three paramyxoviruses, namely the measles (MeV), Nipah (NiV) and Hendra (HeV) viruses. We provide a detailed description of the molecular mechanisms that govern the disorder-to-order transition that the intrinsically disordered C-terminal domain (NTAIL) of their N proteins undergoes upon binding to the C-terminal X domain (XD) of the homologous P proteins. We also show that a significant flexibility persists within NTAIL-XD complexes, which therefore provide illustrative examples of "fuzziness". The functional implications of structural disorder for viral transcription and replication are discussed in light of the ability of disordered regions to establish a complex molecular partnership and to confer a considerable reach to the elements of the replicative machinery.
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58
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Duro N, Miskei M, Fuxreiter M. Fuzziness endows viral motif-mimicry. MOLECULAR BIOSYSTEMS 2015; 11:2821-9. [DOI: 10.1039/c5mb00301f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The local dynamics of host and viral peptide motifs suggests a different scenario for partner recognition. Host peptide motifs serve as molecular recognition elements, while viral motifs preserve the structural heterogeneity and remain fuzzy when bound to the host.
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Affiliation(s)
- Norbert Duro
- MTA-DE Momentum
- Laboratory of Protein Dynamics
- Department of Biochemistry and Molecular Biology
- University of Debrecen
- Hungary
| | - Marton Miskei
- MTA-DE Momentum
- Laboratory of Protein Dynamics
- Department of Biochemistry and Molecular Biology
- University of Debrecen
- Hungary
| | - Monika Fuxreiter
- MTA-DE Momentum
- Laboratory of Protein Dynamics
- Department of Biochemistry and Molecular Biology
- University of Debrecen
- Hungary
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59
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Dolan PT, Roth AP, Xue B, Sun R, Dunker AK, Uversky VN, LaCount DJ. Intrinsic disorder mediates hepatitis C virus core-host cell protein interactions. Protein Sci 2014; 24:221-35. [PMID: 25424537 DOI: 10.1002/pro.2608] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 11/19/2014] [Indexed: 12/18/2022]
Abstract
Viral proteins bind to numerous cellular and viral proteins throughout the infection cycle. However, the mechanisms by which viral proteins interact with such large numbers of factors remain unknown. Cellular proteins that interact with multiple, distinct partners often do so through short sequences known as molecular recognition features (MoRFs) embedded within intrinsically disordered regions (IDRs). In this study, we report the first evidence that MoRFs in viral proteins play a similar role in targeting the host cell. Using a combination of evolutionary modeling, protein-protein interaction analyses and forward genetic screening, we systematically investigated two computationally predicted MoRFs within the N-terminal IDR of the hepatitis C virus (HCV) Core protein. Sequence analysis of the MoRFs showed their conservation across all HCV genotypes and the canine and equine Hepaciviruses. Phylogenetic modeling indicated that the Core MoRFs are under stronger purifying selection than the surrounding sequence, suggesting that these modules have a biological function. Using the yeast two-hybrid assay, we identified three cellular binding partners for each HCV Core MoRF, including two previously characterized cellular targets of HCV Core (DDX3X and NPM1). Random and site-directed mutagenesis demonstrated that the predicted MoRF regions were required for binding to the cellular proteins, but that different residues within each MoRF were critical for binding to different partners. This study demonstrated that viruses may use intrinsic disorder to target multiple cellular proteins with the same amino acid sequence and provides a framework for characterizing the binding partners of other disordered regions in viral and cellular proteomes.
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Affiliation(s)
- Patrick T Dolan
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, 47907
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60
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Baronti L, Erales J, Habchi J, Felli IC, Pierattelli R, Longhi S. Dynamics of the Intrinsically Disordered C-Terminal Domain of the Nipah Virus Nucleoprotein and Interaction with the X Domain of the Phosphoprotein as Unveiled by NMR Spectroscopy. Chembiochem 2014; 16:268-76. [DOI: 10.1002/cbic.201402534] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Indexed: 12/12/2022]
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61
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Structural studies on the authentic mumps virus nucleocapsid showing uncoiling by the phosphoprotein. Proc Natl Acad Sci U S A 2014; 111:15208-13. [PMID: 25288750 DOI: 10.1073/pnas.1413268111] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mumps virus (MuV) is a highly contagious pathogen, and despite extensive vaccination campaigns, outbreaks continue to occur worldwide. The virus has a negative-sense, single-stranded RNA genome that is encapsidated by the nucleocapsid protein (N) to form the nucleocapsid (NC). NC serves as the template for both transcription and replication. In this paper we solved an 18-Å-resolution structure of the authentic MuV NC using cryo-electron microscopy. We also observed the effects of phosphoprotein (P) binding on the MuV NC structure. The N-terminal domain of P (PNTD) has been shown to bind NC and appeared to induce uncoiling of the helical NC. Additionally, we solved a 25-Å-resolution structure of the authentic MuV NC bound with the C-terminal domain of P (PCTD). The location of the encapsidated viral genomic RNA was defined by modeling crystal structures of homologous negative strand RNA virus Ns in NC. Both the N-terminal and C-terminal domains of MuV P bind NC to participate in access to the genomic RNA by the viral RNA-dependent-RNA polymerase. These results provide critical insights on the structure-function of the MuV NC and the structural alterations that occur through its interactions with P.
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62
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Structure of Nipah virus unassembled nucleoprotein in complex with its viral chaperone. Nat Struct Mol Biol 2014; 21:754-9. [DOI: 10.1038/nsmb.2868] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 07/03/2014] [Indexed: 11/08/2022]
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63
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Affiliation(s)
- Johnny Habchi
- Aix-Marseille Université , Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 13288, Marseille, France
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64
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Reddy KD, DeForte S, Uversky VN. Digested disorder: Quarterly intrinsic disorder digest (July-August-September, 2013). INTRINSICALLY DISORDERED PROTEINS 2014; 2:e27833. [PMID: 28232877 PMCID: PMC5314876 DOI: 10.4161/idp.27833] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 01/13/2014] [Indexed: 12/26/2022]
Abstract
The current literature on intrinsically disordered proteins grows fast. To keep interested readers up to speed with this literature, we continue a "Digested Disorder" project and represent a new issue of reader's digest of the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the third quarter of 2013; i.e., during the period of June, July, and September of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
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Affiliation(s)
- Krishna D Reddy
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Shelly DeForte
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA; Department of Biological Sciences; Faculty of Science; King Abdulaziz University; Jeddah, Saudi Arabia; Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
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65
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Xue B, Blocquel D, Habchi J, Uversky AV, Kurgan L, Uversky VN, Longhi S. Structural disorder in viral proteins. Chem Rev 2014; 114:6880-911. [PMID: 24823319 DOI: 10.1021/cr4005692] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, College of Fine Arts and Sciences, and ‡Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida , Tampa, Florida 33620, United States
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66
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Communie G, Ruigrok RWH, Jensen MR, Blackledge M. Intrinsically disordered proteins implicated in paramyxoviral replication machinery. Curr Opin Virol 2014; 5:72-81. [DOI: 10.1016/j.coviro.2014.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 02/01/2014] [Accepted: 02/04/2014] [Indexed: 10/25/2022]
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