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Waszkiewicz R, Michaś A, Białobrzewski MK, Klepka BP, Cieplak-Rotowska MK, Staszałek Z, Cichocki B, Lisicki M, Szymczak P, Niedzwiecka A. Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation. J Phys Chem Lett 2024; 15:5024-5033. [PMID: 38696815 PMCID: PMC11103702 DOI: 10.1021/acs.jpclett.4c00312] [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: 01/31/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/04/2024]
Abstract
The diffusion coefficients of globular and fully unfolded proteins can be predicted with high accuracy solely from their mass or chain length. However, this approach fails for intrinsically disordered proteins (IDPs) containing structural domains. We propose a rapid predictive methodology for estimating the diffusion coefficients of IDPs. The methodology uses accelerated conformational sampling based on self-avoiding random walks and includes hydrodynamic interactions between coarse-grained protein subunits, modeled using the generalized Rotne-Prager-Yamakawa approximation. To estimate the hydrodynamic radius, we rely on the minimum dissipation approximation recently introduced by Cichocki et al. Using a large set of experimentally measured hydrodynamic radii of IDPs over a wide range of chain lengths and domain contributions, we demonstrate that our predictions are more accurate than the Kirkwood approximation and phenomenological approaches. Our technique may prove to be valuable in predicting the hydrodynamic properties of both fully unstructured and multidomain disordered proteins.
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Affiliation(s)
- Radost Waszkiewicz
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Agnieszka Michaś
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Michał K. Białobrzewski
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Barbara P. Klepka
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | | | - Zuzanna Staszałek
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Bogdan Cichocki
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Maciej Lisicki
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Piotr Szymczak
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Anna Niedzwiecka
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
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2
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Białobrzewski MK, Klepka BP, Michaś A, Cieplak-Rotowska MK, Staszałek Z, Niedźwiecka A. Diversity of hydrodynamic radii of intrinsically disordered proteins. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:607-618. [PMID: 37831084 PMCID: PMC10618399 DOI: 10.1007/s00249-023-01683-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/08/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023]
Abstract
Intrinsically disordered proteins (IDPs) form an important class of biomolecules regulating biological processes in higher organisms. The lack of a fixed spatial structure facilitates them to perform their regulatory functions and allows the efficiency of biochemical reactions to be controlled by temperature and the cellular environment. From the biophysical point of view, IDPs are biopolymers with a broad configuration state space and their actual conformation depends on non-covalent interactions of its amino acid side chain groups at given temperature and chemical conditions. Thus, the hydrodynamic radius (Rh) of an IDP of a given polymer length (N) is a sequence- and environment-dependent variable. We have reviewed the literature values of hydrodynamic radii of IDPs determined experimentally by SEC, AUC, PFG NMR, DLS, and FCS, and complement them with our FCS results obtained for a series of protein fragments involved in the regulation of human gene expression. The data collected herein show that the values of hydrodynamic radii of IDPs can span the full space between the folded globular and denatured proteins in the Rh(N) diagram.
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Affiliation(s)
- Michał K Białobrzewski
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Barbara P Klepka
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Agnieszka Michaś
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Maja K Cieplak-Rotowska
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, PL-02093, Warsaw, Poland
- The International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Flisa 6, PL-02247, Warsaw, Poland
| | - Zuzanna Staszałek
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Anna Niedźwiecka
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland.
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3
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Kulkarni P, Brocca S, Dunker AK, Longhi S. Per Aspera ad Chaos: Vladimir Uversky's Odyssey through the Strange World of Intrinsically Disordered Proteins. Biomolecules 2023; 13:1015. [PMID: 37371595 DOI: 10.3390/biom13061015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Until the late 1990s, we believed that protein function required a unique, well-defined 3D structure encrypted in the amino acid sequence [...].
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA 91010, USA
- Department of Systems Biology, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy
| | - A Keith Dunker
- Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sonia Longhi
- Architecture and Function of Biological Macromolecules (AFMB), UMR 7257, Aix Marseille University and CNRS, 13288 Marseille, France
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4
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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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Ando T. Functional Implications of Dynamic Structures of Intrinsically Disordered Proteins Revealed by High-Speed AFM Imaging. Biomolecules 2022; 12:biom12121876. [PMID: 36551304 PMCID: PMC9776203 DOI: 10.3390/biom12121876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/09/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
The unique functions of intrinsically disordered proteins (IDPs) depend on their dynamic protean structure that often eludes analysis. High-speed atomic force microscopy (HS-AFM) can conduct this difficult analysis by directly visualizing individual IDP molecules in dynamic motion at sub-molecular resolution. After brief descriptions of the microscopy technique, this review first shows that the intermittent tip-sample contact does not alter the dynamic structure of IDPs and then describes how the number of amino acids contained in a fully disordered region can be estimated from its HS-AFM images. Next, the functional relevance of a dumbbell-like structure that has often been observed on IDPs is discussed. Finally, the dynamic structural information of two measles virus IDPs acquired from their HS-AFM and NMR analyses is described together with its functional implications.
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Affiliation(s)
- Toshio Ando
- Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
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Shafat Z, Ahmed A, Parvez MK, Parveen S. Role of "dual-personality" fragments in HEV adaptation-analysis of Y-domain region. J Genet Eng Biotechnol 2021; 19:154. [PMID: 34637041 PMCID: PMC8511232 DOI: 10.1186/s43141-021-00238-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/30/2021] [Indexed: 01/06/2023]
Abstract
BACKGROUND Hepatitis E is a liver disease caused by the pathogen hepatitis E virus (HEV). The largest polyprotein open reading frame 1 (ORF1) contains a nonstructural Y-domain region (YDR) whose activity in HEV adaptation remains uncharted. The specific role of disordered regions in several nonstructural proteins has been demonstrated to participate in the multiplication and multiple regulatory functions of the viruses. Thus, intrinsic disorder of YDR including its structural and functional annotation was comprehensively studied by exploiting computational methodologies to delineate its role in viral adaptation. RESULTS Based on our findings, it was evident that YDR contains significantly higher levels of ordered regions with less prevalence of disordered residues. Sequence-based analysis of YDR revealed it as a "dual personality" (DP) protein due to the presence of both structured and unstructured (intrinsically disordered) regions. The evolution of YDR was shaped by pressures that lead towards predominance of both disordered and regularly folded amino acids (Ala, Arg, Gly, Ile, Leu, Phe, Pro, Ser, Tyr, Val). Additionally, the predominance of characteristic DP residues (Thr, Arg, Gly, and Pro) further showed the order as well as disorder characteristic possessed by YDR. The intrinsic disorder propensity analysis of YDR revealed it as a moderately disordered protein. All the YDR sequences consisted of molecular recognition features (MoRFs), i.e., intrinsic disorder-based protein-protein interaction (PPI) sites, in addition to several nucleotide-binding sites. Thus, the presence of molecular recognition (PPI, RNA binding, and DNA binding) signifies the YDR's interaction with specific partners, host membranes leading to further viral infection. The presence of various disordered-based phosphorylation sites further signifies the role of YDR in various biological processes. Furthermore, functional annotation of YDR revealed it as a multifunctional-associated protein, due to its susceptibility in binding to a wide range of ligands and involvement in various catalytic activities. CONCLUSIONS As DP are targets for regulation, thus, YDR contributes to cellular signaling processes through PPIs. As YDR is incompletely understood, therefore, our data on disorder-based function could help in better understanding its associated functions. Collectively, our novel data from this comprehensive investigation is the first attempt to delineate YDR role in the regulation and pathogenesis of HEV.
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Affiliation(s)
- Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
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Karami Y, Saighi P, Vanderhaegen R, Gerlier D, Longhi S, Laine E, Carbone A. Predicting substitutions to modulate disorder and stability in coiled-coils. BMC Bioinformatics 2020; 21:573. [PMID: 33349244 PMCID: PMC7751101 DOI: 10.1186/s12859-020-03867-x] [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: 10/29/2020] [Accepted: 11/09/2020] [Indexed: 11/20/2022] Open
Abstract
Background Coiled-coils are described as stable structural motifs, where two or more helices wind around each other. However, coiled-coils are associated with local mobility and intrinsic disorder. Intrinsically disordered regions in proteins are characterized by lack of stable secondary and tertiary structure under physiological conditions in vitro. They are increasingly recognized as important for protein function. However, characterizing their behaviour in solution and determining precisely the extent of disorder of a protein region remains challenging, both experimentally and computationally. Results In this work, we propose a computational framework to quantify the extent of disorder within a coiled-coil in solution and to help design substitutions modulating such disorder. Our method relies on the analysis of conformational ensembles generated by relatively short all-atom Molecular Dynamics (MD) simulations. We apply it to the phosphoprotein multimerisation domains (PMD) of Measles virus (MeV) and Nipah virus (NiV), both forming tetrameric left-handed coiled-coils. We show that our method can help quantify the extent of disorder of the C-terminus region of MeV and NiV PMDs from MD simulations of a few tens of nanoseconds, and without requiring an extensive exploration of the conformational space. Moreover, this study provided a conceptual framework for the rational design of substitutions aimed at modulating the stability of the coiled-coils. By assessing the impact of four substitutions known to destabilize coiled-coils, we derive a set of rules to control MeV PMD structural stability and cohesiveness. We therefore design two contrasting substitutions, one increasing the stability of the tetramer and the other increasing its flexibility. Conclusions Our method can be considered as a platform to reason about how to design substitutions aimed at regulating flexibility and stability.
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Affiliation(s)
- Yasaman Karami
- CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005, Paris, France. .,Institute of Computing and Data Sciences (ISCD), Sorbonne Université, 75005, Paris, France.
| | - Paul Saighi
- CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005, Paris, France
| | - Rémy Vanderhaegen
- CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005, Paris, France
| | - Denis Gerlier
- CIRI, International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Univ Lyon, Lyon, France
| | - Sonia Longhi
- CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix-Marseille University, Marseille, France
| | - Elodie Laine
- CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005, Paris, France.
| | - Alessandra Carbone
- CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005, Paris, France. .,Institut Universitaire de France, 75005, Paris, France.
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8
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Relevance of Electrostatic Charges in Compactness, Aggregation, and Phase Separation of Intrinsically Disordered Proteins. Int J Mol Sci 2020; 21:ijms21176208. [PMID: 32867340 PMCID: PMC7503639 DOI: 10.3390/ijms21176208] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/22/2020] [Accepted: 08/23/2020] [Indexed: 12/20/2022] Open
Abstract
The abundance of intrinsic disorder in the protein realm and its role in a variety of physiological and pathological cellular events have strengthened the interest of the scientific community in understanding the structural and dynamical properties of intrinsically disordered proteins (IDPs) and regions (IDRs). Attempts at rationalizing the general principles underlying both conformational properties and transitions of IDPs/IDRs must consider the abundance of charged residues (Asp, Glu, Lys, and Arg) that typifies these proteins, rendering them assimilable to polyampholytes or polyelectrolytes. Their conformation strongly depends on both the charge density and distribution along the sequence (i.e., charge decoration) as highlighted by recent experimental and theoretical studies that have introduced novel descriptors. Published experimental data are revisited herein in the frame of this formalism, in a new and possibly unitary perspective. The physicochemical properties most directly affected by charge density and distribution are compaction and solubility, which can be described in a relatively simplified way by tools of polymer physics. Dissecting factors controlling such properties could contribute to better understanding complex biological phenomena, such as fibrillation and phase separation. Furthermore, this knowledge is expected to have enormous practical implications for the design, synthesis, and exploitation of bio-derived materials and the control of natural biological processes.
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The Intrinsically Disordered W Protein Is Multifunctional during Henipavirus Infection, Disrupting Host Signalling Pathways and Nuclear Import. Cells 2020; 9:cells9081913. [PMID: 32824665 PMCID: PMC7465373 DOI: 10.3390/cells9081913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 12/20/2022] Open
Abstract
Nipah and Hendra viruses are highly pathogenic, zoonotic henipaviruses that encode proteins that inhibit the host’s innate immune response. The W protein is one of four products encoded from the P gene and binds a number of host proteins to regulate signalling pathways. The W protein is intrinsically disordered, a structural attribute that contributes to its diverse host protein interactions. Here, we review the role of W in innate immune suppression through inhibition of both pattern recognition receptor (PRR) pathways and interferon (IFN)-responsive signalling. PRR stimulation leading to activation of IRF-3 and IFN release is blocked by henipavirus W, and unphosphorylated STAT proteins are sequestered within the nucleus of host cells by W, thereby inhibiting the induction of IFN stimulated genes. We examine the critical role of nuclear transport in multiple functions of W and how specific binding of importin-alpha (Impα) isoforms, and the 14-3-3 group of regulatory proteins suggests further modulation of these processes. Overall, the disordered nature and multiple functions of W warrant further investigation to understand henipavirus pathogenesis and may reveal insights aiding the development of novel therapeutics.
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The Measles Virus V Protein Binding Site to STAT2 Overlaps That of IRF9. J Virol 2020; 94:JVI.01169-20. [PMID: 32581091 DOI: 10.1128/jvi.01169-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 06/13/2020] [Indexed: 12/25/2022] Open
Abstract
Measles virus (MeV) is a highly immunotropic and contagious pathogen that can even diminish preexisting antibodies and remains a major cause of childhood morbidity and mortality worldwide despite the availability of effective vaccines. MeV is one of the most extensively studied viruses with respect to the mechanisms of JAK-STAT antagonism. Of the three proteins translated from the MeV P gene, P and V are essential for inactivation of this pathway. However, the lack of data from direct analyses of the underlying interactions means that the detailed molecular mechanism of antagonism remains unresolved. Here, we prepared recombinant MeV V protein, which is responsible for human JAK-STAT antagonism, and a panel of variants, enabling the biophysical characterization of V protein, including direct V/STAT1 and V/STAT2 interaction assays. Unambiguous direct interactions between the host and viral factors, in the absence of other factors such as Jak1 or Tyk2, were observed, and the dissociation constants were quantified for the first time. Our data indicate that interactions between the C-terminal region of V and STAT2 is 1 order of magnitude stronger than that of the N-terminal region of V and STAT1. We also clarified that these interactions are completely independent of each other. Moreover, results of size exclusion chromatography demonstrated that addition of MeV-V displaces STAT2-core, a rigid region of STAT2 lacking the N- and C-terminal domains, from preformed complexes of STAT2-core/IRF-associated domain (IRF9). These results provide a novel model whereby MeV-V can not only inhibit the STAT2/IRF9 interaction but also disrupt preassembled interferon-stimulated gene factor 3.IMPORTANCE To evade host immunity, many pathogenic viruses inactivate host Janus kinase signal transducer and activator of transcription (STAT) signaling pathways using diverse strategies. Measles virus utilizes P and V proteins to counteract this signaling pathway. Data derived largely from cell-based assays have indicated several amino acid residues of P and V proteins as important. However, biophysical properties of V protein or its direct interaction with STAT molecules using purified proteins have not been studied. We have developed novel molecular tools enabling us to identify a novel molecular mechanism for immune evasion whereby V protein disrupts critical immune complexes, providing a clear strategy by which measles virus can suppress interferon-mediated antiviral gene expression.
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Intrinsically disordered proteins of viruses: Involvement in the mechanism of cell regulation and pathogenesis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:1-78. [PMID: 32828463 PMCID: PMC7129803 DOI: 10.1016/bs.pmbts.2020.03.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) possess the property of inherent flexibility and can be distinguished from other proteins in terms of lack of any fixed structure. Such dynamic behavior of IDPs earned the name "Dancing Proteins." The exploration of these dancing proteins in viruses has just started and crucial details such as correlation of rapid evolution, high rate of mutation and accumulation of disordered contents in viral proteome at least understood partially. In order to gain a complete understanding of this correlation, there is a need to decipher the complexity of viral mediated cell hijacking and pathogenesis in the host organism. Further there is necessity to identify the specific patterns within viral and host IDPs such as aggregation; Molecular recognition features (MoRFs) and their association to virulence, host range and rate of evolution of viruses in order to tackle the viral-mediated diseases. The current book chapter summarizes the aforementioned details and suggests the novel opportunities for further research of IDPs senses in viruses.
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12
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Schramm A, Bignon C, Brocca S, Grandori R, Santambrogio C, Longhi S. An arsenal of methods for the experimental characterization of intrinsically disordered proteins - How to choose and combine them? Arch Biochem Biophys 2019; 676:108055. [PMID: 31356778 DOI: 10.1016/j.abb.2019.07.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/16/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Abstract
In this review, we detail the most common experimental approaches to assess and characterize protein intrinsic structural disorder, with the notable exception of NMR and EPR spectroscopy, two ideally suited approaches that will be described in depth in two other reviews within this special issue. We discuss the advantages, the limitations, as well as the caveats of the various methods. We also describe less common and more demanding approaches that enable achieving further insights into the conformational properties of IDPs. Finally, we present recent developments that have enabled assessment of structural disorder in living cells, and discuss the currently available methods to model IDPs as conformational ensembles.
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Affiliation(s)
- Antoine Schramm
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Christophe Bignon
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Sonia Longhi
- CNRS and Aix-Marseille Univ, Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Marseille, France.
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IgA targeting on the α-molecular recognition element (α-MoRE) of viral phosphoprotein inhibits measles virus replication by interrupting formation and function of P-N complex intracellularly. Antiviral Res 2019; 161:144-153. [DOI: 10.1016/j.antiviral.2018.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 11/25/2018] [Accepted: 11/26/2018] [Indexed: 12/21/2022]
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14
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Troilo F, Bignon C, Gianni S, Fuxreiter M, Longhi S. Experimental Characterization of Fuzzy Protein Assemblies: Interactions of Paramyxoviral NTAIL Domains With Their Functional Partners. Methods Enzymol 2018; 611:137-192. [DOI: 10.1016/bs.mie.2018.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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15
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Tedeschi G, Mangiagalli M, Chmielewska S, Lotti M, Natalello A, Brocca S. Aggregation properties of a disordered protein are tunable by pH and depend on its net charge per residue. Biochim Biophys Acta Gen Subj 2017; 1861:2543-2550. [PMID: 28890401 DOI: 10.1016/j.bbagen.2017.09.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 12/30/2022]
Abstract
Intrinsically disordered proteins (IDPs) possess a peculiar amino acid composition that makes them very soluble. Nevertheless, they can encounter aggregation in physiological and pathological contexts. In this work, we addressed the issue of how electrostatic charges can influence aggregation propensity by using the N-terminus moiety of the measles virus phosphoprotein, PNT, as a model IDP. Taking advantage of the high sequence designability of IDPs, we have produced an array of PNT variants sharing the same hydrophobicity, but differing in net charges per residue and isoelectric points (pI). The solubility and conformational properties of these proteins were analysed through biochemical and biophysical techniques in a wide range of pH values and compared with those of the green fluorescence protein (GFP), a globular protein with lower net charge per residue, but similar hydrophobicity. Tested proteins showed a solubility minimum close to their pI, as expected, but the pH-dependent decrease of solubility was not uniform and driven by the net charge per residue of each variant. A parallel behaviour was observed also in fusion proteins between PNT variants and GFP, which minimally contributes to the solubility of chimeras. Our data suggest that the overall solubility of a protein can be dictated by protein regions endowed with higher net charge per residue and, hence, prompter to respond to pH changes. This finding could be exploited for biotechnical purposes, such as the design of solubility/aggregation tags, and in studies aimed to clarify the pathological and physiological behaviour of IDPs.
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Affiliation(s)
- Giulia Tedeschi
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Milano, Italy
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Milano, Italy
| | - Sara Chmielewska
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Milano, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Milano, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Milano, Italy.
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Milano, Italy.
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16
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Longhi S, Bloyet LM, Gianni S, Gerlier D. How order and disorder within paramyxoviral nucleoproteins and phosphoproteins orchestrate the molecular interplay of transcription and replication. Cell Mol Life Sci 2017; 74:3091-3118. [PMID: 28600653 PMCID: PMC11107670 DOI: 10.1007/s00018-017-2556-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 01/01/2023]
Abstract
In this review, we summarize computational and experimental data gathered so far showing that structural disorder is abundant within paramyxoviral nucleoproteins (N) and phosphoproteins (P). In particular, we focus on measles, Nipah, and Hendra viruses and highlight both commonalities and differences with respect to the closely related Sendai virus. The molecular mechanisms that control the disorder-to-order transition undergone by the intrinsically disordered C-terminal domain (NTAIL) of their N proteins upon binding to the C-terminal X domain (XD) of the homologous P proteins are described in detail. By having a significant residual disorder, NTAIL-XD complexes are illustrative examples of "fuzziness", whose possible functional significance is discussed. Finally, the relevance of N-P interactions as promising targets for innovative antiviral approaches is underscored, and the functional advantages of structural disorder for paramyxoviruses are pinpointed.
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Affiliation(s)
- Sonia Longhi
- Aix-Marseille Univ, AFMB UMR 7257, 163, avenue de Luminy, Case 932, 13288, Marseille Cedex 09, France.
- CNRS, AFMB UMR 7257, 13288, Marseille, France.
| | - Louis-Marie Bloyet
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- INSERM, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Stefano Gianni
- Istituto Pasteur, Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185, Rome, Italy
| | - Denis Gerlier
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- INSERM, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
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17
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The Identification and Characterization of Two Novel Epitopes on the Nucleocapsid Protein of the Porcine Epidemic Diarrhea Virus. Sci Rep 2016; 6:39010. [PMID: 27991537 PMCID: PMC5171872 DOI: 10.1038/srep39010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/16/2016] [Indexed: 01/08/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly contagious coronavirus that causes severe diarrhea and death, particularly in neonatal piglets. The nucleocapsid protein (N protein) of PEDV presents strong immunogenicity and contributes to the cross-reactivity between PEDV and TGEV. However, the characterization of epitopes on the PEDV N protein remains largely unknown. Here, two monoclonal antibodies (MAbs) specific to the N protein of a PEDV strain, FJzz1/2011, were generated and screened against a partially overlapping library of 24 GST-fusion N protein-truncated constructs. We confirmed that residues 18–133 (designated NEP-D4) and residues 252–262 (designated NEP-D6) were the epitopes targeted by MAbs PN-D4 and PN-D6, respectively. Sequence analysis revealed that these two epitopes were highly conserved among PEDV strains but were significantly different from other members of the Coronavirinae subfamily. Western blot analysis showed that they could be specifically recognized by PEDV antisera but could not be recognized by TGEV hyperimmune antisera. Indirect immunofluorescence (IFA) assays confirmed no cross-reaction between these two MAbs and TGEV. In addition, the freeze-thaw cycle and protease treatment results indicated that NEP-D4 was intrinsically disordered. All these results suggest that these two novel epitopes and their cognate MAbs could serve as the basis for the development of precise diagnostic assays for PEDV.
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18
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Noval MG, Esperante SA, Molina IG, Chemes LB, Prat-Gay GD. Intrinsic Disorder to Order Transitions in the Scaffold Phosphoprotein P from the Respiratory Syncytial Virus RNA Polymerase Complex. Biochemistry 2016; 55:1441-54. [PMID: 26901160 DOI: 10.1021/acs.biochem.5b01332] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intrinsic disorder is at the center of biochemical regulation and is particularly overrepresented among the often multifunctional viral proteins. Replication and transcription of the respiratory syncytial virus (RSV) relies on a RNA polymerase complex with a phosphoprotein cofactor P as the structural scaffold, which consists of a four-helix bundle tetramerization domain flanked by two domains predicted to be intrinsically disordered. Because intrinsic disorder cannot be reduced to a defined atomic structure, we tackled the experimental dissection of the disorder-order transitions of P by a domain fragmentation approach. P remains as a tetramer above 70 °C but shows a pronounced reversible secondary structure transition between 10 and 60 °C. While the N-terminal module behaves as a random coil-like IDP in a manner independent of tetramerization, the isolated C-terminal module displays a cooperative and reversible metastable transition. When linked to the tetramerization domain, the C-terminal module becomes markedly more structured and stable, with strong ANS binding. Therefore, the tertiary structure in the C-terminal module is not compact, conferring "late" molten globule-like IDP properties, stabilized by interactions favored by tetramerization. The presence of a folded structure highly sensitive to temperature, reversibly and almost instantly formed and broken, suggests a temperature sensing activity. The marginal stability allows for exposure of protein binding sites, offering a thermodynamic and kinetic fine-tuning in order-disorder transitions, essential for the assembly and function of the RSV RNA polymerase complex.
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Affiliation(s)
- María G Noval
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Sebastian A Esperante
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Ivana G Molina
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Lucía B Chemes
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina
| | - Gonzalo de Prat-Gay
- Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and IIBBA-CONICET , Av. Patricias Argentinas 435, 1405 Buenos Aires, Argentina.,CNPq, Laboratório de Genômica Estrutural, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro , Rio de Janeiro, RJ, Brazil
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19
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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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20
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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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21
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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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22
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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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23
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Blocquel D, Habchi J, Durand E, Sevajol M, Ferron F, Erales J, Papageorgiou N, Longhi S. Coiled-coil deformations in crystal structures: the measles virus phosphoprotein multimerization domain as an illustrative example. ACTA ACUST UNITED AC 2014; 70:1589-603. [PMID: 24914970 DOI: 10.1107/s139900471400234x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 01/31/2014] [Indexed: 01/02/2023]
Abstract
The structures of two constructs of the measles virus (MeV) phosphoprotein (P) multimerization domain (PMD) are reported and are compared with a third structure published recently by another group [Communie et al. (2013), J. Virol. 87, 7166-7169]. Although the three structures all have a tetrameric and parallel coiled-coil arrangement, structural comparison unveiled considerable differences in the quaternary structure and unveiled that the three structures suffer from significant structural deformation induced by intermolecular interactions within the crystal. These results show that crystal packing can bias conclusions about function and mechanism based on analysis of a single crystal structure, and they challenge to some extent the assumption according to which coiled-coil structures can be reliably predicted from the amino-acid sequence. Structural comparison also highlighted significant differences in the extent of disorder in the C-terminal region of each monomer. The differential flexibility of the C-terminal region is also supported by size-exclusion chromatography and small-angle X-ray scattering studies, which showed that MeV PMD exists in solution as a dynamic equilibrium between two tetramers of different compaction. Finally, the possible functional implications of the flexibility of the C-terminal region of PMD are discussed.
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Affiliation(s)
- David Blocquel
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - Johnny Habchi
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - Eric Durand
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - Marion Sevajol
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - François Ferron
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | - Jenny Erales
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
| | | | - Sonia Longhi
- Aix-Marseille University, AFMB UMR 7257, 13288 Marseille, France
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24
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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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25
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Lo MK, Søgaard TM, Karlin DG. Evolution and structural organization of the C proteins of paramyxovirinae. PLoS One 2014; 9:e90003. [PMID: 24587180 PMCID: PMC3934983 DOI: 10.1371/journal.pone.0090003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 01/24/2014] [Indexed: 12/21/2022] Open
Abstract
The phosphoprotein (P) gene of most Paramyxovirinae encodes several proteins in overlapping frames: P and V, which share a common N-terminus (PNT), and C, which overlaps PNT. Overlapping genes are of particular interest because they encode proteins originated de novo, some of which have unknown structural folds, challenging the notion that nature utilizes only a limited, well-mapped area of fold space. The C proteins cluster in three groups, comprising measles, Nipah, and Sendai virus. We predicted that all C proteins have a similar organization: a variable, disordered N-terminus and a conserved, α-helical C-terminus. We confirmed this predicted organization by biophysically characterizing recombinant C proteins from Tupaia paramyxovirus (measles group) and human parainfluenza virus 1 (Sendai group). We also found that the C of the measles and Nipah groups have statistically significant sequence similarity, indicating a common origin. Although the C of the Sendai group lack sequence similarity with them, we speculate that they also have a common origin, given their similar genomic location and structural organization. Since C is dispensable for viral replication, unlike PNT, we hypothesize that C may have originated de novo by overprinting PNT in the ancestor of Paramyxovirinae. Intriguingly, in measles virus and Nipah virus, PNT encodes STAT1-binding sites that overlap different regions of the C-terminus of C, indicating they have probably originated independently. This arrangement, in which the same genetic region encodes simultaneously a crucial functional motif (a STAT1-binding site) and a highly constrained region (the C-terminus of C), seems paradoxical, since it should severely reduce the ability of the virus to adapt. The fact that it originated twice suggests that it must be balanced by an evolutionary advantage, perhaps from reducing the size of the genetic region vulnerable to mutations.
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Affiliation(s)
- Michael K. Lo
- Centers for Disease Control and Prevention, Viral Special Pathogens Branch, Atlanta, Georgia, United States of America
| | - Teit Max Søgaard
- Division of Structural Biology, Oxford University, Oxford, United Kingdom
| | - David G. Karlin
- Division of Structural Biology, Oxford University, Oxford, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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26
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Breton NL, Martinho M, Kabytaev K, Topin J, Mileo E, Blocquel D, Habchi J, Longhi S, Rockenbauer A, Golebiowski J, Guigliarelli B, Marque SRA, Belle V. Diversification of EPR signatures in site directed spin labeling using a β-phosphorylated nitroxide. Phys Chem Chem Phys 2014; 16:4202-9. [DOI: 10.1039/c3cp54816c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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27
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Devaux P, Priniski L, Cattaneo R. The measles virus phosphoprotein interacts with the linker domain of STAT1. Virology 2013; 444:250-6. [PMID: 23856440 DOI: 10.1016/j.virol.2013.06.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/14/2013] [Accepted: 06/20/2013] [Indexed: 02/07/2023]
Abstract
The measles virus (MV) phosphoprotein (P) and V proteins block the interferon (IFN) response by impeding phosphorylation of the signal transducer and activator of transcription 1 (STAT1) by the Janus kinase 1 (JAK1). We characterized how STAT1 mutants interact with P and JAK1 phosphorylation. Certain mutants of the linker, the Src-homology 2 domain (SH2), or the transactivation domain had reduced or abolished phosphorylation through JAK1 after IFN treatment. Other mutants, mainly localized in the linker, failed to interact with P as documented by the lack of interference with nuclear translocation. Thus the functional footprint of P on STAT1 localizes mainly to the linker domain; there is also some overlap with the STAT1 phosphorylation functional footprint on the SH2 domain. Based on these observations, we discuss how the MV-P might operate to inhibit the JAK/STAT pathway.
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Affiliation(s)
- Patricia Devaux
- Department of Molecular Medicine, and Virology and Gene Therapy Graduate Track, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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28
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Abstract
The phosphoprotein (P) is virally encoded by the Rhabdoviridae and Paramyxoviridae in the order Mononegavirales. P is a self-associated oligomer and forms complexes with the large viral polymerase protein (L), the nucleocapsid protein (N), and the assembled nucleocapsid. P from different viruses has shown structural diversities even though their essential functions are the same. We systematically mapped the domains in mumps virus (MuV) P and investigated their interactions with nucleocapsid-like particles (NLPs). Similar to other P proteins, MuV P contains N-terminal, central, and C-terminal domains with flexible linkers between neighboring domains. By pulldown assays, we discovered that in addition to the previously proposed nucleocapsid binding domain (residues 343 to 391), the N-terminal region of MuV P (residues 1 to 194) could also bind NLPs. Further analysis of binding kinetics was conducted using surface plasmon resonance. This is the first observation that both the N- and C-terminal regions of a negative-strand RNA virus P are involved in binding the nucleocapsid. In addition, we defined the oligomerization domain (POD) of MuV P as residues 213 to 277 and determined its crystal structure. The tetrameric MuV POD is formed by one pair of long parallel α-helices with another pair in opposite orientation. Unlike the parallel orientation of each α-helix in the tetramer of Sendai virus POD, this represents a novel orientation of a POD where both the N- and the C-terminal domains are at either end of the tetramer. This is consistent with the observation that both the N- and the C-terminal domains are involved in binding the nucleocapsid.
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29
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Testa L, Brocca S, Santambrogio C, D'Urzo A, Habchi J, Longhi S, Uversky VN, Grandori R. Extracting structural information from charge-state distributions of intrinsically disordered proteins by non-denaturing electrospray-ionization mass spectrometry. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e25068. [PMID: 28516012 PMCID: PMC5424789 DOI: 10.4161/idp.25068] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/02/2013] [Accepted: 05/16/2013] [Indexed: 11/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) exert key biological functions but tend to escape identification and characterization due to their high structural dynamics and heterogeneity. The possibility to dissect conformational ensembles by electrospray-ionization mass spectrometry (ESI-MS) offers an attracting possibility to develop a signature for this class of proteins based on their peculiar ionization behavior. This review summarizes available data on charge-state distributions (CSDs) obtained for IDPs by non-denaturing ESI-MS, with reference to globular or chemically denatured proteins. The results illustrate the contributions that direct ESI-MS analysis can give to the identification of new putative IDPs and to their conformational investigation.
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Affiliation(s)
- Lorenzo Testa
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Annalisa D'Urzo
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
| | - Johnny Habchi
- Aix-Marseille Université; CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB); Marseille, France
| | - Sonia Longhi
- Aix-Marseille Université; CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB); Marseille, France
| | - Vladimir N Uversky
- Department of Molecular Medicine; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
| | - Rita Grandori
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Milan, Italy
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30
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Motz C, Schuhmann KM, Kirchhofer A, Moldt M, Witte G, Conzelmann KK, Hopfner KP. Paramyxovirus V proteins disrupt the fold of the RNA sensor MDA5 to inhibit antiviral signaling. Science 2013; 339:690-3. [PMID: 23328395 DOI: 10.1126/science.1230949] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) melanoma differentiation-associated protein 5 (MDA5) senses cytoplasmic viral RNA and activates antiviral innate immunity. To reveal how paramyxoviruses counteract this response, we determined the crystal structure of the MDA5 adenosine 5'-triphosphate (ATP)-hydrolysis domain in complex with the viral inhibitor V protein. The V protein unfolded the ATP-hydrolysis domain of MDA5 via a β-hairpin motif and recognized a structural motif of MDA5 that is normally buried in the conserved helicase fold. This leads to disruption of the MDA5 ATP-hydrolysis site and prevention of RNA-bound MDA5 filament formation. The structure explains why V proteins inactivate MDA5, but not RIG-I, and mutating only two amino acids in RIG-I induces robust V protein binding. Our results suggest an inhibition mechanism of RLR signalosome formation by unfolding of receptor and inhibitor.
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Affiliation(s)
- Carina Motz
- Department of Biochemistry and Gene Center, Ludwig-Maximilians-University, Munich, Germany
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31
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The measles virus N(TAIL)-XD complex: an illustrative example of fuzziness. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 725:126-41. [PMID: 22399322 DOI: 10.1007/978-1-4614-0659-4_8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
In this chapter, I focus on the biochemical and structural characterization of the complex between the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (N(TAIL)) and the C-terminal X domain (XD) of the viral phosphoprotein (P). I summarize the main experimental data available so far pointing out the prevalently disordered nature of N(TAIL) even after complex formation and the role of the flexible C-terminal appendage in the binding reaction. I finally discuss the possible functional role of these residual disordered regions within the complex in terms of their ability to capture other regulatory, binding partners.
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32
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Karlin D, Belshaw R. Detecting remote sequence homology in disordered proteins: discovery of conserved motifs in the N-termini of Mononegavirales phosphoproteins. PLoS One 2012; 7:e31719. [PMID: 22403617 PMCID: PMC3293882 DOI: 10.1371/journal.pone.0031719] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 01/18/2012] [Indexed: 11/19/2022] Open
Abstract
Paramyxovirinae are a large group of viruses that includes measles virus and parainfluenza viruses. The viral Phosphoprotein (P) plays a central role in viral replication. It is composed of a highly variable, disordered N-terminus and a conserved C-terminus. A second viral protein alternatively expressed, the V protein, also contains the N-terminus of P, fused to a zinc finger. We suspected that, despite their high variability, the N-termini of P/V might all be homologous; however, using standard approaches, we could previously identify sequence conservation only in some Paramyxovirinae. We now compared the N-termini using sensitive sequence similarity search programs, able to detect residual similarities unnoticeable by conventional approaches. We discovered that all Paramyxovirinae share a short sequence motif in their first 40 amino acids, which we called soyuz1. Despite its short length (11-16aa), several arguments allow us to conclude that soyuz1 probably evolved by homologous descent, unlike linear motifs. Conservation across such evolutionary distances suggests that soyuz1 plays a crucial role and experimental data suggest that it binds the viral nucleoprotein to prevent its illegitimate self-assembly. In some Paramyxovirinae, the N-terminus of P/V contains a second motif, soyuz2, which might play a role in blocking interferon signaling. Finally, we discovered that the P of related Mononegavirales contain similarly overlooked motifs in their N-termini, and that their C-termini share a previously unnoticed structural similarity suggesting a common origin. Our results suggest several testable hypotheses regarding the replication of Mononegavirales and suggest that disordered regions with little overall sequence similarity, common in viral and eukaryotic proteins, might contain currently overlooked motifs (intermediate in length between linear motifs and disordered domains) that could be detected simply by comparing orthologous proteins.
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Affiliation(s)
- David Karlin
- Department of Zoology, University of Oxford, Oxford, United Kingdom.
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Habchi J, Longhi S. Structural disorder within paramyxovirus nucleoproteins and phosphoproteins. ACTA ACUST UNITED AC 2012; 8:69-81. [DOI: 10.1039/c1mb05204g] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Lotti M, Longhi S. Mutual effects of disorder and order in fusion proteins between intrinsically disordered domains and fluorescent proteins. ACTA ACUST UNITED AC 2012; 8:105-13. [DOI: 10.1039/c1mb05244f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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35
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Blocquel D, Habchi J, Gruet A, Blangy S, Longhi S. Compaction and binding properties of the intrinsically disordered C-terminal domain of Henipavirus nucleoprotein as unveiled by deletion studies. ACTA ACUST UNITED AC 2012; 8:392-410. [DOI: 10.1039/c1mb05401e] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Sieber T, Scholz R, Spoerner M, Schumann F, Kalbitzer HR, Dobner T. Intrinsic disorder in the common N-terminus of human adenovirus 5 E1B-55K and its related E1BN proteins indicated by studies on E1B-93R. Virology 2011; 418:133-43. [DOI: 10.1016/j.virol.2011.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 07/13/2011] [Accepted: 07/18/2011] [Indexed: 10/17/2022]
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Testa L, Brocca S, Grandori R. Charge-surface correlation in electrospray ionization of folded and unfolded proteins. Anal Chem 2011; 83:6459-63. [PMID: 21800882 DOI: 10.1021/ac201740z] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electrospray-ionization mass spectrometry (ESI-MS) is widely used for protein studies. It has been shown that the extent of protein ionization under nondenaturing conditions correlates well with the solvent-accessible surface area of the tridimensional structure, for either folded monomers or multimeric complexes. The goal of this study was to test whether this relation holds for unfolded proteins as well. In order to overcome the paucity of structural data, the server ProtSA was used to model the conformational ensembles of proteins in the unfolded state and generate estimates of the average solvent accessibility. The results are analyzed along with literature data or original measurements by ESI-MS. It is found that the charge-to-surface relation holds for proteins in the unfolded state, free from solvent effects. A double-log plot is derived, in close agreement with published data for folded proteins. These results suggest that the solvent-accessible surface area is a key factor determining the extent of protein ionization by electrospray, independent of the conformational state. This conclusion helps rationalizing conformational effects in protein ESI-MS. The here reported relation can be used to predict the average solvent accessibility and, hence, the state of folding of unknown proteins from ESI-MS data.
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Habchi J, Blangy S, Mamelli L, Jensen MR, Blackledge M, Darbon H, Oglesbee M, Shu Y, Longhi S. Characterization of the interactions between the nucleoprotein and the phosphoprotein of Henipavirus. J Biol Chem 2011; 286:13583-602. [PMID: 21317293 PMCID: PMC3075704 DOI: 10.1074/jbc.m111.219857] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 02/10/2011] [Indexed: 01/15/2023] Open
Abstract
The Henipavirus genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that recruits the polymerase complex via the phosphoprotein (P). In a previous study, we reported that in henipaviruses, the N-terminal domain of the phosphoprotein and the C-terminal domain of the nucleoprotein (N(TAIL)) are both intrinsically disordered. Here we show that Henipavirus N(TAIL) domains are also disordered in the context of full-length nucleoproteins. We also report the cloning, purification, and characterization of the C-terminal X domains (P(XD)) of Henipavirus phosphoproteins. Using isothermal titration calorimetry, we show that N(TAIL) and P(XD) form a 1:1 stoichiometric complex that is stable under NaCl concentrations as high as 1 M and has a K(D) in the μM range. Using far-UV circular dichroism and nuclear magnetic resonance, we show that P(XD) triggers an increase in the α-helical content of N(TAIL). Using fluorescence spectroscopy, we show that P(XD) has no impact on the chemical environment of a Trp residue introduced at position 527 of the Henipavirus N(TAIL) domain, thus arguing for the lack of stable contacts between the C termini of N(TAIL) and P(XD). Finally, we present a tentative structural model of the N(TAIL)-P(XD) interaction in which a short, order-prone region of N(TAIL) (α-MoRE; amino acids 473-493) adopts an α-helical conformation and is embedded between helices α2 and α3 of P(XD), leading to a relatively small interface dominated by hydrophobic contacts. The present results provide the first detailed experimental characterization of the N-P interaction in henipaviruses and designate the N(TAIL)-P(XD) interaction as a valuable target for rational antiviral approaches.
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Affiliation(s)
- Johnny Habchi
- From the Laboratoire d' Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Aix-Marseille University, Campus de Luminy, 13288 Marseille Cedex 9, France
| | - Stéphanie Blangy
- From the Laboratoire d' Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Aix-Marseille University, Campus de Luminy, 13288 Marseille Cedex 9, France
| | - Laurent Mamelli
- From the Laboratoire d' Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Aix-Marseille University, Campus de Luminy, 13288 Marseille Cedex 9, France
| | - Malene Ringkjøbing Jensen
- the Protein Dynamics and Flexibility by NMR Group, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, CEA-CNRS-UJF, 41 Rue Jules Horowitz, 38027 Grenoble, France, and
| | - Martin Blackledge
- the Protein Dynamics and Flexibility by NMR Group, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, CEA-CNRS-UJF, 41 Rue Jules Horowitz, 38027 Grenoble, France, and
| | - Hervé Darbon
- From the Laboratoire d' Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Aix-Marseille University, Campus de Luminy, 13288 Marseille Cedex 9, France
| | - Michael Oglesbee
- the Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210
| | - Yaoling Shu
- the Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210
| | - Sonia Longhi
- From the Laboratoire d' Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS, Aix-Marseille University, Campus de Luminy, 13288 Marseille Cedex 9, France
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Sambi I, Gatti-Lafranconi P, Longhi S, Lotti M. How disorder influences order and vice versa - mutual effects in fusion proteins containing an intrinsically disordered and a globular protein. FEBS J 2010; 277:4438-51. [DOI: 10.1111/j.1742-4658.2010.07825.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Habchi J, Mamelli L, Darbon H, Longhi S. Structural disorder within Henipavirus nucleoprotein and phosphoprotein: from predictions to experimental assessment. PLoS One 2010; 5:e11684. [PMID: 20657787 PMCID: PMC2908138 DOI: 10.1371/journal.pone.0011684] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Accepted: 06/21/2010] [Indexed: 12/30/2022] Open
Abstract
Henipaviruses are newly emerged viruses within the Paramyxoviridae family. Their negative-strand RNA genome is packaged by the nucleoprotein (N) within alpha-helical nucleocapsid that recruits the polymerase complex made of the L protein and the phosphoprotein (P). To date structural data on Henipaviruses are scarce, and their N and P proteins have never been characterized so far. Using both computational and experimental approaches we herein show that Henipaviruses N and P proteins possess large intrinsically disordered regions. By combining several disorder prediction methods, we show that the N-terminal domain of P (PNT) and the C-terminal domain of N (NTAIL) are both mostly disordered, although they contain short order-prone segments. We then report the cloning, the bacterial expression, purification and characterization of Henipavirus PNT and NTAIL domains. By combining gel filtration, dynamic light scattering, circular dichroism and nuclear magnetic resonance, we show that both NTAIL and PNT belong to the premolten globule sub-family within the class of intrinsically disordered proteins. This study is the first reported experimental characterization of Henipavirus P and N proteins. The evidence that their respective N-terminal and C-terminal domains are highly disordered under native conditions is expected to be invaluable for future structural studies by helping to delineate N and P protein domains amenable to crystallization. In addition, following previous hints establishing a relationship between structural disorder and protein interactivity, the present results suggest that Henipavirus PNT and NTAIL domains could be involved in manifold protein-protein interactions.
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Affiliation(s)
- Johnny Habchi
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Universités Aix-Marseille I et II, Campus de Luminy, Marseille, France
| | - Laurent Mamelli
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Universités Aix-Marseille I et II, Campus de Luminy, Marseille, France
| | - Hervé Darbon
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Universités Aix-Marseille I et II, Campus de Luminy, Marseille, France
| | - Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Universités Aix-Marseille I et II, Campus de Luminy, Marseille, France
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41
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Foucault M, Mayol K, Receveur-Bréchot V, Bussat MC, Klinguer-Hamour C, Verrier B, Beck A, Haser R, Gouet P, Guillon C. UV and X-ray structural studies of a 101-residue long Tat protein from a HIV-1 primary isolate and of its mutated, detoxified, vaccine candidate. Proteins 2010; 78:1441-56. [PMID: 20034112 DOI: 10.1002/prot.22661] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The 101-residue long Tat protein of primary isolate 133 of the human immunodeficiency virus type 1 (HIV-1), wt-Tat(133) displays a high transactivation activity in vitro, whereas the mutant thereof, STLA-Tat(133), a vaccine candidate for HIV-1, has none. These two proteins were chemically synthesized and their biological activity was validated. Their structural properties were characterized using circular dichroism (CD), fluorescence emission, gel filtration, dynamic light scattering, and small angle X-ray scattering (SAXS) techniques. SAXS studies revealed that both proteins were extended and belong to the family of intrinsically unstructured proteins. CD measurements showed that wt-Tat(133) or STLA-Tat(133) underwent limited structural rearrangements when complexed with specific fragments of antibodies. Crystallization trials have been performed on the two forms, assuming that the Tat(133) proteins might have a better propensity to fold in supersaturated conditions, and small crystals have been obtained. These results suggest that biologically active Tat protein is natively unfolded and requires only a limited gain of structure for its function.
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42
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Gely S, Lowry DF, Bernard C, Jensen MR, Blackledge M, Costanzo S, Bourhis JM, Darbon H, Daughdrill G, Longhi S. Solution structure of the C-terminal X domain of the measles virus phosphoprotein and interaction with the intrinsically disordered C-terminal domain of the nucleoprotein. J Mol Recognit 2010; 23:435-47. [DOI: 10.1002/jmr.1010] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Shaw ML. Henipaviruses employ a multifaceted approach to evade the antiviral interferon response. Viruses 2009; 1:1190-203. [PMID: 21994589 PMCID: PMC3185527 DOI: 10.3390/v1031190] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 12/02/2009] [Accepted: 12/03/2009] [Indexed: 12/13/2022] Open
Abstract
Hendra and Nipah virus, which constitute the genus Henipavirus, are zoonotic paramyxoviruses that have been associated with sporadic outbreaks of severe disease and mortality in humans since their emergence in the late 1990s. Similar to other paramyxoviruses, their ability to evade the host interferon (IFN) response is conferred by the P gene. The henipavirus P gene encodes four proteins; the P, V, W and C proteins, which have all been described to inhibit the antiviral response. Further studies have revealed that these proteins have overlapping but unique properties which enable the virus to block multiple signaling pathways in the IFN response. The best characterized of these is the JAK-STAT signaling pathway which is targeted by the P, V and W proteins via an interaction with the transcription factor STAT1. In addition the V and W proteins can both limit virus-induced induction of IFN but they appear to do this via distinct mechanisms that rely on unique sequences in their C-terminal domains. The ability to generate recombinant Nipah viruses now gives us the opportunity to determine the precise role for each of these proteins and address their contribution to pathogenicity. Additionally, the question of whether these multiple anti-IFN strategies are all active in the different mammalian hosts for henipaviruses, particularly the fruit bat reservoir, warrants further exploration.
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Affiliation(s)
- Megan L Shaw
- Department of Microbiology, Mount Sinai School of Medicine, New York, NY 10029, USA; E-Mail: ; Tel.: +1-212-241-8931
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44
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Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. J Virol 2009; 83:10719-36. [PMID: 19640978 DOI: 10.1128/jvi.00595-09] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is widely assumed that new proteins are created by duplication, fusion, or fission of existing coding sequences. Another mechanism of protein birth is provided by overlapping genes. They are created de novo by mutations within a coding sequence that lead to the expression of a novel protein in another reading frame, a process called "overprinting." To investigate this mechanism, we have analyzed the sequences of the protein products of manually curated overlapping genes from 43 genera of unspliced RNA viruses infecting eukaryotes. Overlapping proteins have a sequence composition globally biased toward disorder-promoting amino acids and are predicted to contain significantly more structural disorder than nonoverlapping proteins. By analyzing the phylogenetic distribution of overlapping proteins, we were able to confirm that 17 of these had been created de novo and to study them individually. Most proteins created de novo are orphans (i.e., restricted to one species or genus). Almost all are accessory proteins that play a role in viral pathogenicity or spread, rather than proteins central to viral replication or structure. Most proteins created de novo are predicted to be fully disordered and have a highly unusual sequence composition. This suggests that some viral overlapping reading frames encoding hypothetical proteins with highly biased composition, often discarded as noncoding, might in fact encode proteins. Some proteins created de novo are predicted to be ordered, however, and whenever a three-dimensional structure of such a protein has been solved, it corresponds to a fold previously unobserved, suggesting that the study of these proteins could enhance our knowledge of protein space.
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45
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Bernard C, Gely S, Bourhis JM, Morelli X, Longhi S, Darbon H. Interaction between the C-terminal domains of N and P proteins of measles virus investigated by NMR. FEBS Lett 2009; 583:1084-9. [PMID: 19275899 DOI: 10.1016/j.febslet.2009.03.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 02/19/2009] [Accepted: 03/02/2009] [Indexed: 11/19/2022]
Abstract
In this paper we investigate the interaction between the C-terminal domains of the measles virus phosphoprotein (XD) and nucleoprotein (N(TAIL)) by using nuclear magnetic resonance chemical shift perturbation experiments. Using both N(TAIL) constructs and peptides, we show that contrary to the conserved Box2 region (N(489-506)), the C-terminal region of N(TAIL) (N(513-525)) does not directly interact with XD, and yet affects binding to XD. We tentatively propose a model where the C-terminus of N(TAIL) would stabilize the N(TAIL)-XD complex either via a functional coupling with N(489-506) or by reducing the entropic penalty associated to the binding-coupled-to-folding process.
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Affiliation(s)
- Cedric Bernard
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Université de Provence et Université de la Méditerranée, Marseille Cedex 9, France.
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46
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Belle V, Rouger S, Costanzo S, Liquière E, Strancar J, Guigliarelli B, Fournel A, Longhi S. Mapping alpha-helical induced folding within the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by site-directed spin-labeling EPR spectroscopy. Proteins 2008; 73:973-88. [PMID: 18536007 DOI: 10.1002/prot.22125] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Using site-directed spin-labeling EPR spectroscopy, we mapped the region of the intrinsically disordered C-terminal domain of measles virus nucleoprotein (N(TAIL)) that undergoes induced folding. In addition to four spin-labeled N(TAIL) variants (S407C, S488C, L496C, and V517C) (Morin et al. (2006), J Phys Chem 110: 20596-20608), 10 new single-site cysteine variants were designed, purified from E. coli, and spin-labeled. These 14 spin-labeled variants enabled us to map in detail the gain of rigidity of N(TAIL) in the presence of either the secondary structure stabilizer 2,2,2-trifluoroethanol or the C-terminal domain X (XD) of the viral phosphoprotein. Different regions of N(TAIL) were shown to contribute to a different extent to the binding to XD, while the mobility of the spin labels grafted at positions 407 and 460 was unaffected upon addition of XD; that of the spin labels grafted within the 488-502 and the 505-522 regions was severely and moderately reduced, respectively. Furthermore, EPR experiments in the presence of 30% sucrose allowed us to precisely map to residues 488-502, the N(TAIL) region undergoing alpha-helical folding. The mobility of the 488-502 region was found to be restrained even in the absence of the partner, a behavior that could be accounted for by the existence of a transiently populated folded state. Finally, we show that the restrained motion of the 505-522 region upon binding to XD is due to the alpha-helical transition occurring within the 488-502 region and not to a direct interaction with XD.
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Affiliation(s)
- Valérie Belle
- Bioénergétique et Ingénierie des Protéines, UPR 9036 CNRS et Université Aix-Marseille I et II, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 9, France
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47
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Soares DC, Barlow PN, Porteous DJ, Devon RS. An interrupted beta-propeller and protein disorder: structural bioinformatics insights into the N-terminus of alsin. J Mol Model 2008; 15:113-22. [PMID: 19023603 DOI: 10.1007/s00894-008-0381-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 11/05/2008] [Indexed: 12/11/2022]
Abstract
Defects in the human ALS2 gene, which encodes the 1,657-amino-acid residue protein alsin, are linked to several related motor neuron diseases. We created a structural model for the N-terminal 690-residue region of alsin through comparative modelling based on regulator of chromosome condensation 1 (RCC1). We propose that this alsin region contains seven RCC1-like repeats in a seven-bladed beta-propeller structure. The propeller is formed by a double clasp arrangement containing two segments (residues 1-218 and residues 525-690). The 306-residue insert region, predicted to lie within blade 5 and to be largely disordered, is poorly conserved across species. Surface patches of evolutionary conservation probably indicate locations of binding sites. Both disease-causing missense mutations-Cys157Tyr and Gly540Glu-are buried in the propeller and likely to be structurally disruptive. This study aids design of experimental studies by highlighting the importance of construct length, will enhance interpretation of protein-protein interactions, and enable rational site-directed mutagenesis.
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Affiliation(s)
- Dinesh C Soares
- Medical Genetics Section, Molecular Medicine Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road, Edinburgh EH42XU, UK.
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Caignard G, Bouraï M, Jacob Y, Tangy F, Vidalain PO. Inhibition of IFN-alpha/beta signaling by two discrete peptides within measles virus V protein that specifically bind STAT1 and STAT2. Virology 2008; 383:112-20. [PMID: 19007958 DOI: 10.1016/j.virol.2008.10.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 08/26/2008] [Accepted: 10/09/2008] [Indexed: 12/30/2022]
Abstract
The V protein of measles virus (MV-V) is a potent inhibitor of IFN-alpha/beta signaling pathway. We previously reported that when physically dissociated, the N-terminal and C-terminal regions of MV-V (PNT and VCT, respectively) could independently impair signal transduction. The PNT region inhibited IFN-alpha/beta signaling by interacting with at least two components of this pathway: Jak1 and STAT1. Here we report a direct interaction between the VCT of MV-V and STAT2, a third component of IFN-alpha/beta transduction machinery. This interaction with STAT2 is carried by the cysteine-constrained peptide of 49 amino acids localized in the VCT region, and is essential to the inhibition of IFN-alpha/beta signaling. In parallel, we also mapped STAT1 binding site in the PNT region and identified a minimal peptide of only 11 amino acids. IFN-alpha/beta signaling was impaired in human cells treated with this MV-V peptide fused to a cell-penetrating sequence. Finally, we show that signaling downstream of IFN-lambda, a recently identified cytokine that also relies on STAT1, STAT2 and Jak1 to transduce, is blocked by MV-V. Altogether, our results illustrate how a single viral protein has evolved to achieve a robust inhibition of the antiviral response by interacting with several signaling molecules.
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Affiliation(s)
- Grégory Caignard
- Laboratoire de Génomique Virale et Vaccination, CNRS URA 3015, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
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Abstract
Measles virus belongs to the Paramyxoviridae family within the Mononegavirales order. Its nonsegmented, single-stranded, negative-sense RNA genome is encapsidated by the nucleoprotein (N) to form a helical nucleocapsid. This ribonucleoproteic complex is the substrate for both transcription and replication. The RNA-dependent RNA polymerase binds to the nucleocapsid template via its co-factor, the phosphoprotein (P). This chapter describes the main structural information available on the nucleoprotein, showing that it consists of a structured core (N(CORE)) and an intrinsically disordered C-terminal domain (N(TAIL)). We propose a model where the dynamic breaking and reforming of the interaction between N(TAIL) and P would allow the polymerase complex (L-P) to cartwheel on the nucleocapsid template. We also propose a model where the flexibility of the disordered N and P domains allows the formation of a tripartite complex (No-P-L) during replication, followed by the delivery of N monomers to the newly synthesized genomic RNA chain. Finally, the functional implications of structural disorder are also discussed in light of the ability of disordered regions to establish interactions with multiple partners, thus leading to multiple biological effects.
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Affiliation(s)
- S Longhi
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Universités Aix-Marseille I et II, 163 avenue de Luminy, Case 932, 13288 Marseille Cedex 09, France.
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50
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Haaning S, Radutoiu S, Hoffmann SV, Dittmer J, Giehm L, Otzen DE, Stougaard J. An unusual intrinsically disordered protein from the model legume Lotus japonicus stabilizes proteins in vitro. J Biol Chem 2008; 283:31142-52. [PMID: 18779323 DOI: 10.1074/jbc.m805024200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Intrinsic structural disorder is a prevalent feature of proteins with chaperone activity. Using a complementary set of techniques, we have structurally characterized LjIDP1 (intrinsically disordered protein 1) from the model legume Lotus japonicus, and our results provide the first structural characterization of a member of the Lea5 protein family (PF03242). Contrary to in silico predictions, we show that LjIDP1 is intrinsically disordered and probably exists as an ensemble of conformations with limited residual beta-sheet, turn/loop, and polyproline II secondary structure. Furthermore, we show that LjIDP1 has an inherent propensity to undergo a large conformational shift, adopting a largely alpha-helical structure when it is dehydrated and in the presence of different detergents and alcohols. This is consistent with an overrepresentation of order-promoting residues in LjIDP1 compared with the average of intrinsically disordered proteins. In line with functioning as a chaperone, we show that LjIDP1 effectively prevents inactivation of two model enzymes under conditions that promote protein misfolding and aggregation. The LjIdp1 gene is expressed in all L. japonicus tissues tested. A higher expression level was found in the root tip proximal zone, in roots inoculated with compatible endosymbiotic M. loti, and in functional nitrogen-fixing root nodules. We suggest that the ability of LjIDP1 to prevent protein misfolding and aggregation may play a significant role in tissues, such as symbiotic root nodules, which are characterized by high metabolic activity.
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Affiliation(s)
- Svend Haaning
- Department of Molecular Biology, University of Aarhus, 8000 Aarhus, Denmark
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