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Sisk TR, Robustelli P. Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model. Proc Natl Acad Sci U S A 2024; 121:e2313360121. [PMID: 38294935 PMCID: PMC10861926 DOI: 10.1073/pnas.2313360121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/22/2023] [Indexed: 02/02/2024] Open
Abstract
A central challenge in the study of intrinsically disordered proteins is the characterization of the mechanisms by which they bind their physiological interaction partners. Here, we utilize a deep learning-based Markov state modeling approach to characterize the folding-upon-binding pathways observed in a long timescale molecular dynamics simulation of a disordered region of the measles virus nucleoprotein NTAIL reversibly binding the X domain of the measles virus phosphoprotein complex. We find that folding-upon-binding predominantly occurs via two distinct encounter complexes that are differentiated by the binding orientation, helical content, and conformational heterogeneity of NTAIL. We observe that folding-upon-binding predominantly proceeds through a multi-step induced fit mechanism with several intermediates and do not find evidence for the existence of canonical conformational selection pathways. We observe four kinetically separated native-like bound states that interconvert on timescales of eighty to five hundred nanoseconds. These bound states share a core set of native intermolecular contacts and stable NTAIL helices and are differentiated by a sequential formation of native and non-native contacts and additional helical turns. Our analyses provide an atomic resolution structural description of intermediate states in a folding-upon-binding pathway and elucidate the nature of the kinetic barriers between metastable states in a dynamic and heterogenous, or "fuzzy", protein complex.
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Affiliation(s)
- Thomas R. Sisk
- Department of Chemistry, Dartmouth College, Hanover, NH03755
| | - Paul Robustelli
- Department of Chemistry, Dartmouth College, Hanover, NH03755
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2
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Sisk T, Robustelli P. Folding-upon-binding pathways of an intrinsically disordered protein from a deep Markov state model. bioRxiv 2023:2023.07.21.550103. [PMID: 37546728 PMCID: PMC10401938 DOI: 10.1101/2023.07.21.550103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
A central challenge in the study of intrinsically disordered proteins is the characterization of the mechanisms by which they bind their physiological interaction partners. Here, we utilize a deep learning based Markov state modeling approach to characterize the folding-upon-binding pathways observed in a long-time scale molecular dynamics simulation of a disordered region of the measles virus nucleoprotein NTAIL reversibly binding the X domain of the measles virus phosphoprotein complex. We find that folding-upon-binding predominantly occurs via two distinct encounter complexes that are differentiated by the binding orientation, helical content, and conformational heterogeneity of NTAIL. We do not, however, find evidence for the existence of canonical conformational selection or induced fit binding pathways. We observe four kinetically separated native-like bound states that interconvert on time scales of eighty to five hundred nanoseconds. These bound states share a core set of native intermolecular contacts and stable NTAIL helices and are differentiated by a sequential formation of native and non-native contacts and additional helical turns. Our analyses provide an atomic resolution structural description of intermediate states in a folding-upon-binding pathway and elucidate the nature of the kinetic barriers between metastable states in a dynamic and heterogenous, or "fuzzy", protein complex.
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Affiliation(s)
- Thomas Sisk
- Dartmouth College, Department of Chemistry, Hanover, NH, 03755
| | - Paul Robustelli
- Dartmouth College, Department of Chemistry, Hanover, NH, 03755
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3
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Abstract
Viruses infect all kingdoms of life; their genomes vary from DNA to RNA and in size from 2kB to 1 MB or more. Viruses frequently employ disordered proteins, that is, protein products of virus genes that do not themselves fold into independent three-dimensional structures, but rather, constitute a versatile molecular toolkit to accomplish a range of functions necessary for viral infection, assembly, and proliferation. Interestingly, disordered proteins have been discovered in almost all viruses so far studied, whether the viral genome consists of DNA or RNA, and whatever the configuration of the viral capsid or other outer covering. In this review, I present a wide-ranging set of stories illustrating the range of functions of IDPs in viruses. The field is rapidly expanding, and I have not tried to include everything. What is included is meant to be a survey of the variety of tasks that viruses accomplish using disordered proteins.
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Affiliation(s)
- H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Bignon C, Longhi S. In Vivo Protein-Protein Binding Competition Assay Based on Split-GFP Reassembly: Proof of Concept. Biomolecules 2023; 13:biom13020354. [PMID: 36830723 PMCID: PMC9952896 DOI: 10.3390/biom13020354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The split-green fluorescent protein (GFP) reassembly assay is a well-established approach to study protein-protein interactions (PPIs). In this assay, when two interacting proteins X and Y, respectively fused to residues 1-157 and to residues 158-237 of GFP, are co-expressed in E. coli, the two GFP halves are brought to sufficient proximity to reassociate and fold to recreate the functional GFP. At constant protein expression level, the intensity of fluorescence produced by the bacteria is proportional to the binding affinity of X to Y. We hypothesized that adding a third partner (Z) endowed with an affinity for either X or Y would lead to an in vivo competition assay. We report here the different steps of the set-up of this competition assay, and define the experimental conditions required to obtained reliable results. Results show that this competition assay is a potentially interesting tool for screening libraries of binding inhibitors, Z being either a protein or a chemical reagent.
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Wang H, Yang Z, Yang D. Approaches for the Identification of Intrinsically Disordered Protein Domains. Methods Mol Biol 2023; 2581:403-412. [PMID: 36413333 DOI: 10.1007/978-1-0716-2784-6_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Intrinsically disordered protein domains are those with high disorder proportion or a consecutive disordered region. They have no stable spatial structure but play an important role in the regulation of complex cellular functions and contribute to the increasing organism complexity during evolution. Here, we describe the approaches to predict intrinsic disorder values of residues in proteins and methods to identify the intrinsically disordered domains.
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Affiliation(s)
- Huqiang Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zhixiang Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Dong Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
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6
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Gondelaud F, Pesce G, Nilsson JF, Bignon C, Ptchelkine D, Gerlier D, Mathieu C, Longhi S. Functional benefit of structural disorder for the replication of measles, Nipah and Hendra viruses. Essays Biochem 2022; 66:915-34. [PMID: 36148633 DOI: 10.1042/EBC20220045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Bloyet LM. The Nucleocapsid of Paramyxoviruses: Structure and Function of an Encapsidated Template. Viruses 2021; 13:2465. [PMID: 34960734 DOI: 10.3390/v13122465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 01/28/2023] Open
Abstract
Viruses of the Paramyxoviridae family share a common and complex molecular machinery for transcribing and replicating their genomes. Their non-segmented, negative-strand RNA genome is encased in a tight homopolymer of viral nucleoproteins (N). This ribonucleoprotein complex, termed a nucleocapsid, is the template of the viral polymerase complex made of the large protein (L) and its co-factor, the phosphoprotein (P). This review summarizes the current knowledge on several aspects of paramyxovirus transcription and replication, including structural and functional data on (1) the architecture of the nucleocapsid (structure of the nucleoprotein, interprotomer contacts, interaction with RNA, and organization of the disordered C-terminal tail of N), (2) the encapsidation of the genomic RNAs (structure of the nucleoprotein in complex with its chaperon P and kinetics of RNA encapsidation in vitro), and (3) the use of the nucleocapsid as a template for the polymerase complex (release of the encased RNA and interaction network allowing the progress of the polymerase complex). Finally, this review presents models of paramyxovirus transcription and replication.
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Affiliation(s)
- Alireza Shahryari
- Institute of Diabetes and Regeneration Research Helmholtz Zentrum München 85764 Neuherberg Germany
- School of Medicine Department of Human Genetics Technical University of Munich Klinikum Rechts der Isar 81675 München Germany
- Institute of Stem Cell Research Helmholtz Zentrum München 85764 Neuherberg Germany
- Stem Cell Research Center Golestan University of Medical Sciences Gorgan 49341‐74515 Iran
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research Helmholtz Zentrum München 85764 Neuherberg Germany
- Institute of Stem Cell Research Helmholtz Zentrum München 85764 Neuherberg Germany
| | - Zahra Nazari
- Department of Biology School of Basic Sciences Golestan University Gorgan 49361‐79142 Iran
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research Helmholtz Zentrum München 85764 Neuherberg Germany
- School of Medicine Department of Human Genetics Technical University of Munich Klinikum Rechts der Isar 81675 München Germany
- Institute of Stem Cell Research Helmholtz Zentrum München 85764 Neuherberg Germany
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Gao C, Ma C, Wang H, Zhong H, Zang J, Zhong R, He F, Yang D. Intrinsic disorder in protein domains contributes to both organism complexity and clade-specific functions. Sci Rep 2021; 11:2985. [PMID: 33542394 PMCID: PMC7862400 DOI: 10.1038/s41598-021-82656-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/22/2021] [Indexed: 11/09/2022] Open
Abstract
Interestingly, some protein domains are intrinsically disordered (abbreviated as IDD), and the disorder degree of same domains may differ in different contexts. However, the evolutionary causes and biological significance of these phenomena are unclear. Here, we address these issues by genome-wide analyses of the evolutionary and functional features of IDDs in 1,870 species across the three superkingdoms. As the result, there is a significant positive correlation between the proportion of IDDs and organism complexity with some interesting exceptions. These phenomena may be due to the high disorder of clade-specific domains and the different disorder degrees of the domains shared in different clades. The functions of IDDs are clade-specific and the higher proportion of post-translational modification sites may contribute to their complex functions. Compared with metazoans, fungi have more IDDs with a consecutive disorder region but a low disorder ratio, which reflects their different functional requirements. As for disorder variation, it’s greater for domains among different proteins than those within the same proteins. Some clade-specific ‘no-variation’ or ‘high-variation’ domains are involved in clade-specific functions. In sum, intrinsic domain disorder is related to both the organism complexity and clade-specific functions. These results deepen the understanding of the evolution and function of IDDs.
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Affiliation(s)
- Chao Gao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing, 102206, China
| | - Chong Ma
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing, 102206, China.,Beijing Key Laboratory of Environmental and Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Huqiang Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing, 102206, China
| | - Haolin Zhong
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing, 102206, China
| | - Jiayin Zang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing, 102206, China
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, China
| | - Fuchu He
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing, 102206, China.
| | - Dong Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Proteome Research Center, Beijing Institute of Lifeomics, 38 Science Park Road, Changping District, Beijing, 102206, China.
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Abstract
Negative strand RNA viruses (NSVs) include many important human pathogens, such as influenza virus, Ebola virus, and rabies virus. One of the unique characteristics that NSVs share is the assembly of the nucleocapsid and its role in viral RNA synthesis. In NSVs, the single strand RNA genome is encapsidated in the linear nucleocapsid throughout the viral replication cycle. Subunits of the nucleocapsid protein are parallelly aligned along the RNA genome that is sandwiched between two domains composed of conserved helix motifs. The viral RNA-dependent-RNA polymerase (vRdRp) must recognize the protein-RNA complex of the nucleocapsid and unveil the protected genomic RNA in order to initiate viral RNA synthesis. In addition, vRdRp must continuously translocate along the protein-RNA complex during elongation in viral RNA synthesis. This unique mechanism of viral RNA synthesis suggests that the nucleocapsid may play a regulatory role during NSV replication.
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Affiliation(s)
- Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA; (J.R.T.); (S.A.M.)
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Pfaller CK, Bloyet LM, Donohue RC, Huff AL, Bartemes WP, Yousaf I, Urzua E, Clavière M, Zachary M, de Masson d'Autume V, Carson S, Schieferecke AJ, Meyer AJ, Gerlier D, Cattaneo R. The C Protein Is Recruited to Measles Virus Ribonucleocapsids by the Phosphoprotein. J Virol 2020; 94:e01733-19. [PMID: 31748390 DOI: 10.1128/JVI.01733-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/08/2019] [Indexed: 11/20/2022] Open
Abstract
Measles virus (MeV), like all viruses of the order Mononegavirales, utilizes a complex consisting of genomic RNA, nucleoprotein, the RNA-dependent RNA polymerase, and a polymerase cofactor, the phosphoprotein (P), for transcription and replication. We previously showed that a recombinant MeV that does not express another viral protein, C, has severe transcription and replication deficiencies, including a steeper transcription gradient than the parental virus and generation of defective interfering RNA. This virus is attenuated in vitro and in vivo However, how the C protein operates and whether it is a component of the replication complex remained unclear. Here, we show that C associates with the ribonucleocapsid and forms a complex that can be purified by immunoprecipitation or ultracentrifugation. In the presence of detergent, the C protein is retained on purified ribonucleocapsids less efficiently than the P protein and the polymerase. The C protein is recruited to the ribonucleocapsid through its interaction with the P protein, as shown by immunofluorescence microscopy of cells expressing different combinations of viral proteins and by split luciferase complementation assays. Forty amino-terminal C protein residues are dispensable for the interaction with P, and the carboxyl-terminal half of P is sufficient for the interaction with C. Thus, the C protein, rather than being an "accessory" protein as qualified in textbooks so far, is a ribonucleocapsid-associated protein that interacts with P, thereby increasing replication accuracy and processivity of the polymerase complex.IMPORTANCE Replication of negative-strand RNA viruses relies on two components: a helical ribonucleocapsid and an RNA-dependent RNA polymerase composed of a catalytic subunit, the L protein, and a cofactor, the P protein. We show that the measles virus (MeV) C protein is an additional component of the replication complex. We provide evidence that the C protein is recruited to the ribonucleocapsid by the P protein and map the interacting segments of both C and P proteins. We conclude that the primary function of MeV C is to improve polymerase processivity and accuracy, rather than uniquely to antagonize the type I interferon response. Since most viruses of the Paramyxoviridae family express C proteins, their primary function may be conserved.
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Abstract
Measles virus is a negative strand virus and the genomic and antigenomic RNA binds to the nucleoprotein (N), assembling into a helical nucleocapsid. The polymerase complex comprises two proteins, the Large protein (L), that both polymerizes RNA and caps the mRNA, and the phosphoprotein (P) that co-localizes with L on the nucleocapsid. This review presents recent results about N and P, in particular concerning their intrinsically disordered domains. N is a protein of 525 residues with a 120 amino acid disordered C-terminal domain, Ntail. The first 50 residues of Ntail extricate the disordered chain from the nucleocapsid, thereby loosening the otherwise rigid structure, and the C-terminus contains a linear motif that binds P. Recent results show how the 5′ end of the viral RNA binds to N within the nucleocapsid and also show that the bases at the 3′ end of the RNA are rather accessible to the viral polymerase. P is a tetramer and most of the protein is disordered; comprising 507 residues of which around 380 are disordered. The first 37 residues of P bind N, chaperoning against non-specific interaction with cellular RNA, while a second interaction site, around residue 200 also binds N. In addition, there is another interaction between C-terminal domain of P (XD) and Ntail. These results allow us to propose a new model of how the polymerase binds to the nucleocapsid and suggests a mechanism for initiation of transcription.
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Affiliation(s)
- Serafima Guseva
- Université Grenoble Alpes, Le Centre National de la Recherche Scientifique, Commissariatá l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Grenoble, France
| | - Sigrid Milles
- Université Grenoble Alpes, Le Centre National de la Recherche Scientifique, Commissariatá l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Grenoble, France
| | - Martin Blackledge
- Université Grenoble Alpes, Le Centre National de la Recherche Scientifique, Commissariatá l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Grenoble, France
| | - Rob W H Ruigrok
- Université Grenoble Alpes, Le Centre National de la Recherche Scientifique, Commissariatá l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Grenoble, France
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Du Pont V, Jiang Y, Plemper RK. Bipartite interface of the measles virus phosphoprotein X domain with the large polymerase protein regulates viral polymerase dynamics. PLoS Pathog 2019; 15:e1007995. [PMID: 31381607 PMCID: PMC6695210 DOI: 10.1371/journal.ppat.1007995] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/15/2019] [Accepted: 07/22/2019] [Indexed: 11/18/2022] Open
Abstract
Measles virus (MeV) is a highly contagious, re-emerging, major human pathogen. Replication requires a viral RNA-dependent RNA polymerase (RdRP) consisting of the large (L) polymerase protein complexed with the homo-tetrameric phosphoprotein (P). In addition, P mediates interaction with the nucleoprotein (N)-encapsidated viral RNA genome. The nature of the P:L interface and RdRP negotiation of the ribonucleoprotein template are poorly understood. Based on biochemical interface mapping, swapping of the central P tetramerization domain (OD) for yeast GCN4, and functional assays, we demonstrate that the MeV P-to-L interface is bipartite, comprising a coiled-coil microdomain proximal to the OD and an unoccupied face of the triangular prism-shaped C-terminal P X-domain (P-XD), which is distinct from the known P-XD face that binds N-tail. Mixed null-mutant P tetramers regained L-binding competence in a ratio-dependent manner and fully reclaimed bioactivity in minireplicon assays and recombinant MeV, demonstrating that the individual L-binding interface elements are physically and mechanistically distinct. P-XD binding competence to L and N was likewise trans-complementable, which, combined with mathematical modeling, enabled the mechanistic characterization of P through two- and stoichiometrically-controlled three-way complementations. Only one each of the four XDs per P tetramer must be L or N binding-competent for bioactivity, but interaction of the same P-XD with L and N was mutually exclusive, and L binding superseded engaging N. Mixed P tetramers with a single, designated L binding-competent P-XD caused significant RdRP hyperactivity, outlining a model of iterative resolution and reformation of the P-XD:L interface regulating polymerase mobility. MeV belongs to the order of non-segmented negative polarity RNA viruses, which includes devastating human pathogens. While all feature encapsidated RNA genomes and P-L type polymerase complexes, insight into the intermolecular interactions within the polymerase hetero-oligomer and between the polymerase complex and the RNA-encapsidating N protein is rudimentary. Our mapping of the MeV P-to-L interaction revealed a bipartite interface with physically and mechanistically distinct contact zones, which provided a unique experimental platform to dissect the stoichiometry and dynamics of P interactions with L and N through functional trans-complementation assays in minireplicon settings and, ensuring physiological significance, recombinant virions. The identification and functional characterization of a novel L-binding face on the P-XD triangular prism, distinct from the side contacting N-tail, places P-XD at the center of a regulatory mechanism that controls the dynamics of polymerase advancement along the encapsidated genome through iterative separation and restoration of P-XD interaction with L. These observations and the high structural homology of polymerase components within the Paramyxoviridae recommend the P-XD:L protein-protein interface as premier target for directed drug discovery against emerging and re-emerging paramyxoviruses.
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Affiliation(s)
- Venice Du Pont
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, United States of America
| | - Yi Jiang
- Department of Mathematics and Statistics, Georgia State University, Atlanta, Georgia, United States of America
| | - Richard K. Plemper
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, United States of America
- * E-mail:
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15
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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: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Abstract
The interaction between NTAIL and XD from the measles virus represents a paradigmatic example of molecular recognition between an intrinsically disordered protein and a folded partner. By binding to XD, a small portion of NTAIL (classically denoted as MoRE) undergoes a disorder-to-order transition, populating an α-helical structure, while the reminder of the protein remains disordered. Here, we demonstrate an unexpected crosstalk between such a disordered region and the adjacent molecular recognition element (MoRE). This result was obtained by producing a series of truncation and site-directed variants of NTAIL while measuring the effects on the kinetics of folding and binding. We show that the disordered region of NTAIL exerts its inhibitory role by slowing the folding step of the MoRE, thereby tuning the affinity of the interaction.
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Affiliation(s)
- Francesca Troilo
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Daniela Bonetti
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Christophe Bignon
- Aix-Marseille Univ, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Sonia Longhi
- Aix-Marseille Univ, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille, France
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
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17
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Zhou D, Yang Y, Zhao B, Yu J, Cao Y, Yan H, Zhao W, Chen L, Chen F, Li X, Zhang E, Yang J, Zhong M, Chen M, Hu Q, Deng L, Yan H. 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; 161:144-53. [DOI: 10.1016/j.antiviral.2018.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [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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18
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Le Breton N, Longhi S, Rockenbauer A, Guigliarelli B, Marque SRA, Belle V, Martinho M. Probing the dynamic properties of two sites simultaneously in a protein–protein interaction process: a SDSL-EPR study. Phys Chem Chem Phys 2019; 21:22584-22588. [DOI: 10.1039/c9cp04660g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Probing two sites simultaneously in a protein–protein interaction process combining spin labels of different EPR signatures.
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Affiliation(s)
| | - S. Longhi
- Aix Marseille Univ
- CNRS
- AFMB
- Marseille
- France
| | - A. Rockenbauer
- Research Center of Natural Sciences
- Budapest University of Technology and Economics
- Budapest
- Hungary
| | | | | | - V. Belle
- Aix Marseille Univ., CNRS, BIP
- Marseille
- France
| | - M. Martinho
- Aix Marseille Univ., CNRS, BIP
- Marseille
- France
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19
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Bignon C, Troilo F, Gianni S, Longhi S. Modulation of Measles Virus N TAIL Interactions through Fuzziness and Sequence Features of Disordered Binding Sites. Biomolecules 2018; 9:biom9010008. [PMID: 30591682 PMCID: PMC6359293 DOI: 10.3390/biom9010008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/10/2018] [Accepted: 12/18/2018] [Indexed: 12/27/2022] Open
Abstract
In this paper we review our recent findings on the different interaction mechanisms of the C-terminal domain of the nucleoprotein (N) of measles virus (MeV) NTAIL, a model viral intrinsically disordered protein (IDP), with two of its known binding partners, i.e., the C-terminal X domain of the phosphoprotein of MeV XD (a globular viral protein) and the heat-shock protein 70 hsp70 (a globular cellular protein). The NTAIL binds both XD and hsp70 via a molecular recognition element (MoRE) that is flanked by two fuzzy regions. The long (85 residues) N-terminal fuzzy region is a natural dampener of the interaction with both XD and hsp70. In the case of binding to XD, the N-terminal fuzzy appendage of NTAIL reduces the rate of α-helical folding of the MoRE. The dampening effect of the fuzzy appendage on XD and hsp70 binding depends on the length and fuzziness of the N-terminal region. Despite this similarity, NTAIL binding to XD and hsp70 appears to rely on completely different requirements. Almost any mutation within the MoRE decreases XD binding, whereas many of them increase the binding to hsp70. In addition, XD binding is very sensitive to the α-helical state of the MoRE, whereas hsp70 is not. Thus, contrary to hsp70, XD binding appears to be strictly dependent on the wild-type primary and secondary structure of the MoRE.
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Affiliation(s)
- Christophe Bignon
- CNRS and Aix-Marseille Univ Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257 Marseille, France.
| | - Francesca Troilo
- CNRS and Aix-Marseille Univ Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257 Marseille, France.
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli' and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli' and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Sapienza Università di Roma, 00185 Rome, Italy.
| | - Sonia Longhi
- CNRS and Aix-Marseille Univ Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257 Marseille, France.
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20
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Bignon C, Troilo F, Gianni S, Longhi S. Partner-Mediated Polymorphism of an Intrinsically Disordered Protein. J Mol Biol 2018; 430:2493-2507. [DOI: 10.1016/j.jmb.2017.11.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/16/2017] [Accepted: 11/19/2017] [Indexed: 10/18/2022]
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21
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Abstract
Measles is a highly transmissible disease caused by measles virus and remains a major cause of child mortality in developing countries. Measles virus nucleoprotein (N) encapsidates the RNA genome of the virus for providing protection from host cell endonucleases and for specific recognition of viral RNA as template for transcription and replication. This protein is over-expressed at the time of viral replication. The C-terminal of N protein is intrinsically disordered, which enables this protein to interact with several host cell proteins. It was previously proved in our laboratory that N expressing human cancerous cells undergo programmed cell death because of reactive oxygen species (ROS) generation as well as Caspase 3 activation. The phosphoprotein (P) along with N protein enclosed viral genomic RNA forming a ribonucleoprotein complex (RNP). It also establishes interaction with the large protein (L) i.e. viral RNA dependent RNA polymerase to ensure viral replication within host cells. The host cell receptors of this virus are CD46, SLAM/CD150 and PVRL4. Measles virus is latently oncotropic in nature and possesses oncolytic property by syncytia formation. We try to highlight the application of this property in developing a virotherapeutic vehicle.
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Affiliation(s)
| | - Pramod Kumar Yadava
- Applied Molecular Biology Laboratory, School of life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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22
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Abstract
The proposal that coupled folding to binding is not an obligatory mechanism for intrinsically disordered (ID) proteins was put forward 10 years ago. The notion of fuzziness implies that conformational heterogeneity can be maintained upon interactions of ID proteins, which has a functional impact either on regulated assembly or activity of the corresponding complexes. Here I review how the concept has evolved in the past decade, via increasing experimental data providing insights into the mechanisms, pathways and regulatory modes. The effects of structural diversity and transient contacts on protein assemblies have been collected and systematically analyzed (Fuzzy Complexes Database, http://protdyn-database.org). Fuzziness has also been exploited as a framework to decipher molecular organization of higher-order protein structures. Quantification of conformational heterogeneity opens exciting future perspectives for drug discovery from small molecule-ID protein interactions to supramolecular assemblies.
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Affiliation(s)
- Monika Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary.
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23
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Atkinson SC, Audsley MD, Lieu KG, Marsh GA, Thomas DR, Heaton SM, Paxman JJ, Wagstaff KM, Buckle AM, Moseley GW, Jans DA, Borg NA. Recognition by host nuclear transport proteins drives disorder-to-order transition in Hendra virus V. Sci Rep 2018; 8:358. [PMID: 29321677 PMCID: PMC5762688 DOI: 10.1038/s41598-017-18742-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/15/2017] [Indexed: 01/04/2023] Open
Abstract
Hendra virus (HeV) is a paramyxovirus that causes lethal disease in humans, for which no vaccine or antiviral agent is available. HeV V protein is central to pathogenesis through its ability to interact with cytoplasmic host proteins, playing key antiviral roles. Here we use immunoprecipitation, siRNA knockdown and confocal laser scanning microscopy to show that HeV V shuttles to and from the nucleus through specific host nuclear transporters. Spectroscopic and small angle X-ray scattering studies reveal HeV V undergoes a disorder-to-order transition upon binding to either importin α/β1 or exportin-1/Ran-GTP, dependent on the V N-terminus. Importantly, we show that specific inhibitors of nuclear transport prevent interaction with host transporters, and reduce HeV infection. These findings emphasize the critical role of host-virus interactions in HeV infection, and potential use of compounds targeting nuclear transport, such as the FDA-approved agent ivermectin, as anti-HeV agents.
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Affiliation(s)
- Sarah C Atkinson
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Michelle D Audsley
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Kim G Lieu
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Glenn A Marsh
- CSIRO Livestock Industries, Australian Animal Health Laboratory, Victoria, Australia
| | - David R Thomas
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Steven M Heaton
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Jason J Paxman
- La Trobe Institute for Molecular Sciences and Department of Biochemistry and Genetics, La Trobe University, Melbourne, Victoria, Australia
| | - Kylie M Wagstaff
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Ashley M Buckle
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Gregory W Moseley
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - David A Jans
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
| | - Natalie A Borg
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
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24
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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25
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Sugai A, Sato H, Takayama I, Yoneda M, Kai C. Nipah and Hendra Virus Nucleoproteins Inhibit Nuclear Accumulation of Signal Transducer and Activator of Transcription 1 (STAT1) and STAT2 by Interfering with Their Complex Formation. J Virol 2017; 91:e01136-17. [PMID: 28835499 DOI: 10.1128/JVI.01136-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/16/2017] [Indexed: 12/25/2022] Open
Abstract
Henipaviruses, such as Nipah (NiV) and Hendra (HeV) viruses, are highly pathogenic zoonotic agents within the Paramyxoviridae family. The phosphoprotein (P) gene products of the paramyxoviruses have been well characterized for their interferon (IFN) antagonist activity and their contribution to viral pathogenicity. In this study, we demonstrated that the nucleoprotein (N) of henipaviruses also prevents the host IFN signaling response. Reporter assays demonstrated that the NiV and HeV N proteins (NiV-N and HeV-N, respectively) dose-dependently suppressed both type I and type II IFN responses and that the inhibitory effect was mediated by their core domains. Additionally, NiV-N prevented the nuclear transport of signal transducer and activator of transcription 1 (STAT1) and STAT2. However, NiV-N did not associate with Impα5, Impβ1, or Ran, which are members of the nuclear transport system for STATs. Although P protein is known as a binding partner of N protein and actively retains N protein in the cytoplasm, the IFN antagonist activity of N protein was not abolished by the coexpression of P protein. This suggests that the IFN inhibition by N protein occurs in the cytoplasm. Furthermore, we demonstrated that the complex formation of STATs was hampered in the N protein-expressing cells. As a result, STAT nuclear accumulation was reduced, causing a subsequent downregulation of interferon-stimulated genes (ISGs) due to low promoter occupancy by STAT complexes. This novel route for preventing host IFN responses by henipavirus N proteins provides new insight into the pathogenesis of these viruses.IMPORTANCE Paramyxoviruses are well known for suppressing interferon (IFN)-mediated innate immunity with their phosphoprotein (P) gene products, and the henipaviruses also possess P, V, W, and C proteins for evading host antiviral responses. There are numerous studies providing evidence for the relationship between viral pathogenicity and antagonistic activities against IFN responses by P gene products. Meanwhile, little attention has been paid to the influence of nucleoprotein (N) on host innate immune responses. In this study, we demonstrated that both the NiV and HeV N proteins have antagonistic activity against the JAK/STAT signaling pathway by preventing the nucleocytoplasmic trafficking of STAT1 and STAT2. This inhibitory effect is due to an impairment of the ability of STATs to form complexes. These results provide new insight into the involvement of N protein in viral pathogenicity via its IFN antagonism.
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26
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Whelan JN, Reddy KD, Uversky VN, Teng MN. Functional correlations of respiratory syncytial virus proteins to intrinsic disorder. Mol Biosyst 2017; 12:1507-26. [PMID: 27062995 DOI: 10.1039/c6mb00122j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein intrinsic disorder is an important characteristic demonstrated by the absence of higher order structure, and is commonly detected in multifunctional proteins encoded by RNA viruses. Intrinsically disordered regions (IDRs) of proteins exhibit high flexibility and solvent accessibility, which permit several distinct protein functions, including but not limited to binding of multiple partners and accessibility for post-translational modifications. IDR-containing viral proteins can therefore execute various functional roles to enable productive viral replication. Respiratory syncytial virus (RSV) is a globally circulating, non-segmented, negative sense (NNS) RNA virus that causes severe lower respiratory infections. In this study, we performed a comprehensive evaluation of predicted intrinsic disorder of the RSV proteome to better understand the functional role of RSV protein IDRs. We included 27 RSV strains to sample major RSV subtypes and genotypes, as well as geographic and temporal isolate differences. Several types of disorder predictions were applied to the RSV proteome, including per-residue (PONDR®-FIT and PONDR® VL-XT), binary (CH, CDF, CH-CDF), and disorder-based interactions (ANCHOR and MoRFpred). We classified RSV IDRs by size, frequency and function. Finally, we determined the functional implications of RSV IDRs by mapping predicted IDRs to known functional domains of each protein. Identification of RSV IDRs within functional domains improves our understanding of RSV pathogenesis in addition to providing potential therapeutic targets. Furthermore, this approach can be applied to other NNS viruses that encode essential multifunctional proteins for the elucidation of viral protein regions that can be manipulated for attenuation of viral replication.
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Affiliation(s)
- Jillian N Whelan
- Division of Allergy and Immunology, Department of Internal Medicine, and the Joy McCann Culverhouse Airway Diseases Research Center, University of South Florida Morsani College of Medicine, Tampa, FL, USA.
| | - Krishna D Reddy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA and Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia
| | - Michael N Teng
- Division of Allergy and Immunology, Department of Internal Medicine, and the Joy McCann Culverhouse Airway Diseases Research Center, University of South Florida Morsani College of Medicine, Tampa, FL, USA.
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27
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Bonetti D, Troilo F, Toto A, Brunori M, Longhi S, Gianni S. Analyzing the Folding and Binding Steps of an Intrinsically Disordered Protein by Protein Engineering. Biochemistry 2017; 56:3780-3786. [DOI: 10.1021/acs.biochem.7b00350] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniela Bonetti
- Istituto
Pasteur Italia-Fondazione Cenci Bolognetti, Istituto di Biologia e
Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Francesca Troilo
- Istituto
Pasteur Italia-Fondazione Cenci Bolognetti, Istituto di Biologia e
Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
- Aix-Marseille Univ, CNRS, Architecture et Fonction des
Macromolécules Biologiques (AFMB), UMR 7257, 13288 Marseille, France
| | - Angelo Toto
- Aix-Marseille Univ, CNRS, Architecture et Fonction des
Macromolécules Biologiques (AFMB), UMR 7257, 13288 Marseille, France
| | - Maurizio Brunori
- Istituto
Pasteur Italia-Fondazione Cenci Bolognetti, Istituto di Biologia e
Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
| | - Sonia Longhi
- Aix-Marseille Univ, CNRS, Architecture et Fonction des
Macromolécules Biologiques (AFMB), UMR 7257, 13288 Marseille, France
| | - Stefano Gianni
- Istituto
Pasteur Italia-Fondazione Cenci Bolognetti, Istituto di Biologia e
Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli”, Sapienza Università di Roma, 00185 Rome, Italy
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28
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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 DOI: 10.1007/s00018-017-2556-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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29
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Natalello A, Santambrogio C, Grandori R. Are Charge-State Distributions a Reliable Tool Describing Molecular Ensembles of Intrinsically Disordered Proteins by Native MS? J Am Soc Mass Spectrom 2017; 28:21-28. [PMID: 27730522 DOI: 10.1007/s13361-016-1490-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/13/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution. However, structural rearrangements during electrospray-ionization (ESI) or after the transfer to the gas phase could affect data obtained by native ESI-MS. In particular, charge-state distributions (CSDs) are affected by protein conformation inside ESI droplets, while ion mobility (IM) reflects protein conformation in the gas phase. This review focuses on the available evidence relating IDP solution ensembles with CSDs, trying to summarize cases of apparent consistency or discrepancy. The protein-specificity of ionization patterns and their responses to ligands and buffer conditions suggests that CSDs are imprinted to protein structural features also in the case of IDPs. Nevertheless, it seems that these proteins are more easily affected by electrospray conditions, leading in some cases to rearrangements of the conformational ensembles. Graphical Abstract ᅟ.
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Affiliation(s)
- Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
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30
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Bloyet LM, Brunel J, Dosnon M, Hamon V, Erales J, Gruet A, Lazert C, Bignon C, Roche P, Longhi S, Gerlier D. Modulation of Re-initiation of Measles Virus Transcription at Intergenic Regions by PXD to NTAIL Binding Strength. PLoS Pathog 2016; 12:e1006058. [PMID: 27936158 PMCID: PMC5148173 DOI: 10.1371/journal.ppat.1006058] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/12/2016] [Indexed: 12/22/2022] Open
Abstract
Measles virus (MeV) and all Paramyxoviridae members rely on a complex polymerase machinery to ensure viral transcription and replication. Their polymerase associates the phosphoprotein (P) and the L protein that is endowed with all necessary enzymatic activities. To be processive, the polymerase uses as template a nucleocapsid made of genomic RNA entirely wrapped into a continuous oligomer of the nucleoprotein (N). The polymerase enters the nucleocapsid at the 3'end of the genome where are located the promoters for transcription and replication. Transcription of the six genes occurs sequentially. This implies ending and re-initiating mRNA synthesis at each intergenic region (IGR). We explored here to which extent the binding of the X domain of P (XD) to the C-terminal region of the N protein (NTAIL) is involved in maintaining the P/L complex anchored to the nucleocapsid template during the sequential transcription. Amino acid substitutions introduced in the XD-binding site on NTAIL resulted in a wide range of binding affinities as determined by combining protein complementation assays in E. coli and human cells and isothermal titration calorimetry. Molecular dynamics simulations revealed that XD binding to NTAIL involves a complex network of hydrogen bonds, the disruption of which by two individual amino acid substitutions markedly reduced the binding affinity. Using a newly designed, highly sensitive dual-luciferase reporter minigenome assay, the efficiency of re-initiation through the five measles virus IGRs was found to correlate with NTAIL/XD KD. Correlatively, P transcript accumulation rate and F/N transcript ratios from recombinant viruses expressing N variants were also found to correlate with the NTAIL to XD binding strength. Altogether, our data support a key role for XD binding to NTAIL in maintaining proper anchor of the P/L complex thereby ensuring transcription re-initiation at each intergenic region.
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Affiliation(s)
- 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
| | - Joanna Brunel
- 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
| | - Marion Dosnon
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, Marseille, France
- CNRS, AFMB UMR 7257, Marseille, France
| | - Véronique Hamon
- Aix Marseille University, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France
- CNRS, CRCM UMR 7258, Marseille, France
- INSERM, CRCM U1068, Marseille, France
| | - Jenny Erales
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, Marseille, France
- CNRS, AFMB UMR 7257, Marseille, France
| | - Antoine Gruet
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, Marseille, France
- CNRS, AFMB UMR 7257, Marseille, France
| | - Carine Lazert
- 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
| | - Christophe Bignon
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, Marseille, France
- CNRS, AFMB UMR 7257, Marseille, France
| | - Philippe Roche
- Aix Marseille University, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France
- CNRS, CRCM UMR 7258, Marseille, France
- INSERM, CRCM U1068, Marseille, France
| | - Sonia Longhi
- Aix-Marseille University, Architecture et Fonction des Macromolécules Biologiques (AFMB) UMR 7257, Marseille, France
- CNRS, AFMB UMR 7257, Marseille, France
| | - 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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31
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Jiang Y, Qin Y, Chen M. Host-Pathogen Interactions in Measles Virus Replication and Anti-Viral Immunity. Viruses 2016; 8:v8110308. [PMID: 27854326 PMCID: PMC5127022 DOI: 10.3390/v8110308] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/06/2016] [Accepted: 11/07/2016] [Indexed: 12/12/2022] Open
Abstract
The measles virus (MeV) is a contagious pathogenic RNA virus of the family Paramyxoviridae, genus Morbillivirus, that can cause serious symptoms and even fetal complications. Here, we summarize current molecular advances in MeV research, and emphasize the connection between host cells and MeV replication. Although measles has reemerged recently, the potential for its eradication is promising with significant progress in our understanding of the molecular mechanisms of its replication and host-pathogen interactions.
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Affiliation(s)
- Yanliang Jiang
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Yali Qin
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Mingzhou Chen
- State Key Laboratory of Virology and Modern Virology Research Center, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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32
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Miskei M, Antal C, Fuxreiter M. FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies. Nucleic Acids Res 2016; 45:D228-D235. [PMID: 27794553 PMCID: PMC5210525 DOI: 10.1093/nar/gkw1019] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/07/2016] [Accepted: 10/20/2016] [Indexed: 12/17/2022] Open
Abstract
FuzDB (http://protdyn-database.org) compiles experimentally observed fuzzy protein complexes, where intrinsic disorder (ID) is maintained upon interacting with a partner (protein, nucleic acid or small molecule) and directly impacts biological function. Entries in the database have both (i) structural evidence demonstrating the structural multiplicity or dynamic disorder of the ID region(s) in the partner bound form of the protein and (ii) in vitro or in vivo biological evidence that indicates the significance of the fuzzy region(s) in the formation, function or regulation of the assembly. Unlike the other intrinsically disordered or unfolded protein databases, FuzDB focuses on ID regions within a biological context, including higher-order assemblies and presents a detailed analysis of the structural and functional data. FuzDB also provides interpretation of experimental results to elucidate the molecular mechanisms by which fuzzy regions-classified on the basis of topology and mechanism-interfere with the structural ensembles and activity of protein assemblies. Regulatory sites generated by alternative splicing (AS) or post-translational modifications (PTMs) are also collected. By assembling all this information, FuzDB could be utilized to develop stochastic structure-function relationships for proteins and could contribute to the emergence of a new paradigm.
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Affiliation(s)
- Marton Miskei
- MTA-DE Momentum, Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Csaba Antal
- MTA-DE Momentum, Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, H-4032 Debrecen, Hungary
| | - Monika Fuxreiter
- MTA-DE Momentum, Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, H-4032 Debrecen, Hungary
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33
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Song D, Wang W, Ye W, Ji D, Luo R, Chen HF. ff14IDPs force field improving the conformation sampling of intrinsically disordered proteins. Chem Biol Drug Des 2016; 89:5-15. [PMID: 27484738 DOI: 10.1111/cbdd.12832] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 12/13/2022]
Abstract
Intrinsically disordered proteins are proteins which lack of specific tertiary structure and unable to fold spontaneously without the partner binding. These intrinsically disordered proteins are found to associate with various diseases, such as diabetes, cancer, and neurodegenerative diseases. However, current widely used force fields, such as ff99SB, ff14SB, OPLS/AA, and Charmm27, are insufficient in sampling the conformational characters of intrinsically disordered proteins. In this study, the CMAP method was used to correct the φ/ψ distributions of disorder-promoting amino acids. The simulation results show that the force filed parameters (ff14IDPs) can improve the φ/ψ distributions of the disorder-promoting amino acids, with RMSD less than 0.10% relative to the benchmark data of intrinsically disordered proteins. Further test suggests that the calculated secondary chemical shifts under ff14IDPs are in quantitative agreement with the data of NMR experiment for five tested systems. In addition, the simulation results show that ff14IDPs can still be used to model structural proteins, such as tested lysozyme and ubiquitin, with better performance in coil regions than the original general Amber force field ff14SB. These findings confirm that the newly developed Amber ff14IDPs is a robust model for improving the conformation sampling of intrinsically disordered proteins.
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Affiliation(s)
- Dong Song
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Wei Ye
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Dingjue Ji
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical Engineering and Materials Science, and Biomedical Engineering, University of California, Irvine, CA, 92697-3900, USA
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China.,Shanghai Center for Bioinformation Technology, Shanghai, 200235, China
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34
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Han M, Xu J, Ren Y, Li J. Simulation of coupled folding and binding of an intrinsically disordered protein in explicit solvent with metadynamics. J Mol Graph Model 2016; 68:114-27. [PMID: 27423742 DOI: 10.1016/j.jmgm.2016.06.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 06/22/2016] [Accepted: 06/29/2016] [Indexed: 11/22/2022]
Abstract
The C-terminal domain of measles virus nucleoprotein is an intrinsically disordered protein that could bind to the X domain (XD) of phosphoprotein P to exert its physiological function. Experiments reveal that the minimal binding unit is a 21-residue α-helical molecular recognition element (α-MoRE-MeV), which adopts a fully helical conformation upon binding to XD. Due to currently limited computing power, direct simulation of this coupled folding and binding process with atomic force field in explicit solvent cannot be achieved. In this work, two advanced sampling methods, metadynamics and parallel tempering, are combined to characterize the free energy surface of this process and investigate the underlying mechanism. Starting from an unbound and partially folded state of α-MoRE-MeV, multiple folding and binding events are observed during the simulation and the energy landscape was well estimated. The results demonstrate that the isolated α-MoRE-MeV resembles a molten globule and rapidly interconverts between random coil and multiple partially helical states in solution. The coupled folding and binding process occurs through the induced fit mechanism, with the residual helical conformations providing the initial binding sites. Upon binding, α-MoRE-MeV can easily fold into helical conformation without obvious energy barriers. Two mechanisms, namely, the system tending to adopt the structure in which the free energy of isolated α-MoRE-MeV is the minimum, and the binding energy of α-MoRE-MeV to its partner protein XD tending to the minimum, jointly dominate the coupled folding and binding process. With the advanced sampling approach, more IDP systems could be simulated and common mechanisms concerning the coupled folding and binding process could be investigated in the future.
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35
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Dorival J, Annaval T, Risser F, Collin S, Roblin P, Jacob C, Gruez A, Chagot B, Weissman KJ. Characterization of Intersubunit Communication in the Virginiamycin trans-Acyl Transferase Polyketide Synthase. J Am Chem Soc 2016; 138:4155-67. [DOI: 10.1021/jacs.5b13372] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jonathan Dorival
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Thibault Annaval
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Fanny Risser
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Sabrina Collin
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Pierre Roblin
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, 91192 Gif-sur-Yvette CEDEX, France
- UR1268 Biopolymères, Interactions Assemblages (BIA), INRA, Rue de la Géraudière
BP 71627, 44316 Nantes CEDEX 3, France
| | - Christophe Jacob
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Arnaud Gruez
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Benjamin Chagot
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
| | - Kira J. Weissman
- UMR
7365, Ingénierie Moléculaire et Physiopathologie Articulaire
(IMoPA), CNRS-Université de Lorraine, Biopôle de l’Université de Lorraine, Campus Biologie Santé, 9
Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy CEDEX, France
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36
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Gruet A, Dosnon M, Blocquel D, Brunel J, Gerlier D, Das RK, Bonetti D, Gianni S, Fuxreiter M, Longhi S, Bignon C. Fuzzy regions in an intrinsically disordered protein impair protein-protein interactions. FEBS J 2016; 283:576-94. [PMID: 26684000 DOI: 10.1111/febs.13631] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 11/22/2015] [Accepted: 12/15/2015] [Indexed: 12/13/2022]
Abstract
Despite the partial disorder-to-order transition that intrinsically disordered proteins often undergo upon binding to their partners, a considerable amount of residual disorder may be retained in the bound form, resulting in a fuzzy complex. Fuzzy regions flanking molecular recognition elements may enable partner fishing through non-specific, transient contacts, thereby facilitating binding, but may also disfavor binding through various mechanisms. So far, few computational or experimental studies have addressed the effect of fuzzy appendages on partner recognition by intrinsically disordered proteins. In order to shed light onto this issue, we used the interaction between the intrinsically disordered C-terminal domain of the measles virus (MeV) nucleoprotein (NTAIL ) and the X domain (XD) of the viral phosphoprotein as model system. After binding to XD, the N-terminal region of NTAIL remains conspicuously disordered, with α-helical folding taking place only within a short molecular recognition element. To study the effect of the N-terminal fuzzy region on NTAIL /XD binding, we generated N-terminal truncation variants of NTAIL , and assessed their binding abilities towards XD. The results revealed that binding increases with shortening of the N-terminal fuzzy region, with this also being observed with hsp70 (another MeV NTAIL binding partner), and for the homologous NTAIL /XD pairs from the Nipah and Hendra viruses. Finally, similar results were obtained when the MeV NTAIL fuzzy region was replaced with a highly dissimilar artificial disordered sequence, supporting a sequence-independent inhibitory effect of the fuzzy region.
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Affiliation(s)
- Antoine Gruet
- Aix-Marseille Université, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France.,Centre National de la Recherche Scientifique, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
| | - Marion Dosnon
- Aix-Marseille Université, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France.,Centre National de la Recherche Scientifique, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
| | - David Blocquel
- Aix-Marseille Université, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France.,Centre National de la Recherche Scientifique, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
| | - Joanna Brunel
- Centre International de Recherche en Infectiologie, INSERM U1111, Centre National de la Recherche Scientifique, UMR 5308, Université Lyon 1, Lyon, France
| | - Denis Gerlier
- Centre International de Recherche en Infectiologie, INSERM U1111, Centre National de la Recherche Scientifique, UMR 5308, Université Lyon 1, Lyon, France
| | - Rahul K Das
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St Louis, MO, USA
| | - Daniela Bonetti
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli' and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Sapienza Università di Roma, Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche 'A. Rossi Fanelli' and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Sapienza Università di Roma, Rome, Italy.,Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Monika Fuxreiter
- Hungarian Academy of Sciences, Momentum Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Hungary
| | - Sonia Longhi
- Aix-Marseille Université, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France.,Centre National de la Recherche Scientifique, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
| | - Christophe Bignon
- Aix-Marseille Université, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France.,Centre National de la Recherche Scientifique, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, Marseille, France
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37
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Sharma R, Raduly Z, Miskei M, Fuxreiter M. Fuzzy complexes: Specific binding without complete folding. FEBS Lett 2015; 589:2533-42. [PMID: 26226339 DOI: 10.1016/j.febslet.2015.07.022] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/20/2015] [Accepted: 07/21/2015] [Indexed: 12/17/2022]
Abstract
Specific molecular recognition is assumed to require a well-defined set of contacts and devoid of conformational and interaction ambiguities. Growing experimental evidence demonstrates however, that structural multiplicity or dynamic disorder can be retained in protein complexes, termed as fuzziness. Fuzzy regions establish alternative contacts between specific partners usually via transient interactions. Nature often tailors the dynamic properties of these segments via post-translational modifications or alternative splicing to fine-tune affinity. Most experimentally characterized fuzzy complexes are involved in regulation of gene-expression, signal transduction and cell-cycle regulation. Fuzziness is also characteristic to viral protein complexes, cytoskeleton structure, and surprisingly in a few metabolic enzymes. A plausible role of fuzzy complexes in increasing half-life of intrinsically disordered proteins is also discussed.
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38
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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39
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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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40
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Dosnon M, Bonetti D, Morrone A, Erales J, di Silvio E, Longhi S, Gianni S. Demonstration of a folding after binding mechanism in the recognition between the measles virus NTAIL and X domains. ACS Chem Biol 2015; 10:795-802. [PMID: 25511246 DOI: 10.1021/cb5008579] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In the past decade, a wealth of experimental data has demonstrated that a large fraction of proteins, while functional, are intrinsically disordered at physiological conditions. Many intrinsically disordered proteins (IDPs) undergo a disorder-to-order transition upon binding to their biological targets, a phenomenon known as induced folding. Induced folding may occur through two extreme mechanisms, namely conformational selection and folding after binding. Although the pre-existence of ordered structures in IDPs is a prerequisite for conformational selection, it does not necessarily commit to this latter mechanism, and kinetic studies are needed to discriminate between the two possible scenarios. So far, relatively few studies have addressed this issue from an experimental perspective. Here, we analyze the interaction kinetics between the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) and the X domain (XD) of the viral phosphoprotein. Data reveal that NTAIL recognizes XD by first forming a weak encounter complex in a disordered conformation, which is subsequently locked-in by a folding step; i.e., binding precedes folding. The implications of our kinetic results, in the context of previously reported equilibrium data, are discussed. These results contribute to enhancing our understanding of the molecular mechanisms by which IDPs recognize their partners and represent a paradigmatic example of the need of kinetic methods to discriminate between reaction mechanisms.
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Affiliation(s)
- Marion Dosnon
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 13288, Marseille, France
- CNRS, AFMB UMR 7257, 13288, Marseille, France
| | - Daniela Bonetti
- Istituto
Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli” and Istituto di Biologia e Patologia
Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Angela Morrone
- Istituto
Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli” and Istituto di Biologia e Patologia
Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Jenny Erales
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 13288, Marseille, France
- CNRS, AFMB UMR 7257, 13288, Marseille, France
| | - Eva di Silvio
- Istituto
Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli” and Istituto di Biologia e Patologia
Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
| | - Sonia Longhi
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 13288, Marseille, France
- CNRS, AFMB UMR 7257, 13288, Marseille, France
| | - Stefano Gianni
- Istituto
Pasteur - Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche
“A. Rossi Fanelli” and Istituto di Biologia e Patologia
Molecolari del CNR, Sapienza Università di Roma, 00185, Rome, Italy
- Department
of Chemistry, University of Cambridge, Cambridge CB21EW, United Kingdom
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41
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D'Urzo A, Konijnenberg A, Rossetti G, Habchi J, Li J, Carloni P, Sobott F, Longhi S, Grandori R. Molecular basis for structural heterogeneity of an intrinsically disordered protein bound to a partner by combined ESI-IM-MS and modeling. J Am Soc Mass Spectrom 2015; 26:472-481. [PMID: 25510932 DOI: 10.1007/s13361-014-1048-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 11/04/2014] [Accepted: 11/08/2014] [Indexed: 06/04/2023]
Abstract
Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered N(TAIL) domain and the phosphoprotein X domain (P(XD)) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire N(TAIL) domain bound to P(XD) at atomic resolution.
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Affiliation(s)
- Annalisa D'Urzo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy
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Schneider R, Maurin D, Communie G, Kragelj J, Hansen DF, Ruigrok RWH, Jensen MR, Blackledge M. Visualizing the molecular recognition trajectory of an intrinsically disordered protein using multinuclear relaxation dispersion NMR. J Am Chem Soc 2015; 137:1220-9. [PMID: 25551399 DOI: 10.1021/ja511066q] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite playing important roles throughout biology, molecular recognition mechanisms in intrinsically disordered proteins remain poorly understood. We present a combination of (1)H(N), (13)C', and (15)N relaxation dispersion NMR, measured at multiple titration points, to map the interaction between the disordered domain of Sendai virus nucleoprotein (NT) and the C-terminal domain of the phosphoprotein (PX). Interaction with PX funnels the free-state equilibrium of NT by stabilizing one of the previously identified helical substates present in the prerecognition ensemble in a nonspecific and dynamic encounter complex on the surface of PX. This helix then locates into the binding site at a rate coincident with intrinsic breathing motions of the helical groove on the surface of PX. The binding kinetics of complex formation are thus regulated by the intrinsic free-state conformational dynamics of both proteins. This approach, providing high-resolution structural and kinetic information about a complex folding and binding interaction trajectory, can be applied to a number of experimental systems to provide a general framework for understanding conformational disorder in biomolecular function.
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Erales J, Blocquel D, Habchi J, Beltrandi M, Gruet A, Dosnon M, Bignon C, Longhi S. Order and Disorder in the Replicative Complex of Paramyxoviruses. Adv Exp Med Biol 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] [What about the content of this article? (0)] [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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Dolan PT, Roth AP, Xue B, Sun R, Dunker AK, Uversky VN, LaCount DJ. Intrinsic disorder mediates hepatitis C virus core-host cell protein interactions. Protein Sci 2014; 24:221-35. [PMID: 25424537 DOI: 10.1002/pro.2608] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 11/19/2014] [Indexed: 12/18/2022]
Abstract
Viral proteins bind to numerous cellular and viral proteins throughout the infection cycle. However, the mechanisms by which viral proteins interact with such large numbers of factors remain unknown. Cellular proteins that interact with multiple, distinct partners often do so through short sequences known as molecular recognition features (MoRFs) embedded within intrinsically disordered regions (IDRs). In this study, we report the first evidence that MoRFs in viral proteins play a similar role in targeting the host cell. Using a combination of evolutionary modeling, protein-protein interaction analyses and forward genetic screening, we systematically investigated two computationally predicted MoRFs within the N-terminal IDR of the hepatitis C virus (HCV) Core protein. Sequence analysis of the MoRFs showed their conservation across all HCV genotypes and the canine and equine Hepaciviruses. Phylogenetic modeling indicated that the Core MoRFs are under stronger purifying selection than the surrounding sequence, suggesting that these modules have a biological function. Using the yeast two-hybrid assay, we identified three cellular binding partners for each HCV Core MoRF, including two previously characterized cellular targets of HCV Core (DDX3X and NPM1). Random and site-directed mutagenesis demonstrated that the predicted MoRF regions were required for binding to the cellular proteins, but that different residues within each MoRF were critical for binding to different partners. This study demonstrated that viruses may use intrinsic disorder to target multiple cellular proteins with the same amino acid sequence and provides a framework for characterizing the binding partners of other disordered regions in viral and cellular proteomes.
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Affiliation(s)
- Patrick T Dolan
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, 47907
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Ono YI, Miyashita M, Ono Y, Okazaki H, Watanabe S, Tochio N, Kigawa T, Nishimura C. Comparison of residual alpha- and beta-structures between two intrinsically disordered proteins by using NMR. Biochim Biophys Acta 2014; 1854:229-38. [PMID: 25523747 DOI: 10.1016/j.bbapap.2014.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 11/20/2014] [Accepted: 12/10/2014] [Indexed: 11/24/2022]
Abstract
Intrinsically disordered proteins contain some residual structures, which may fold further upon binding to the partner protein for function. The residual structures observed in two intrinsically disordered proteins, including the C-terminal segment of peripherin-2 (63 residues) and measles virus nucleocapsid protein Ntail (125 residues), were compared using NMR. Differences in the chemical shifts of alpha-, beta- and carbonyl carbons between the observed structure and calculated random coil revealed the existence of a helix and some possible beta-structures in both proteins. The intensity of signals in the C-terminal segment of peripherin-2 in NMR spectra was informative and locally low, particularly in the middle and N-terminal parts: this suggested the broadening of the signals caused by the formation of residual structures in those areas. Furthermore, the protection of exchange of amide protons was significantly observed at the N-terminus. Conversely, the intensities of signals for Ntail were random beyond the overall areas of protein, and indicated no characteristic pattern. Only a faint protection of amide-proton exchange in Ntail was observed in the C-terminus. It was concluded that Ntail was more intrinsically disordered than the C-terminal segment of peripherin-2. The combination of chemical shifts with the amide-proton exchanges and signal intensities was useful for the analyses of the remaining secondary structures. The beta-structure might be more detectable by the protection of amide-proton exchange than the helical structure, although the changes in chemical shifts were sensitive for the detection of elements of both secondary structures.
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Affiliation(s)
- Yu-ichi Ono
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan
| | - Manami Miyashita
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan
| | - Yumi Ono
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan
| | - Honoka Okazaki
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan
| | - Satoru Watanabe
- NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan
| | - Naoya Tochio
- NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan
| | - Takanori Kigawa
- NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan
| | - Chiaki Nishimura
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan.
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Baronti L, Erales J, Habchi J, Felli IC, Pierattelli R, Longhi S. Dynamics of the Intrinsically Disordered C-Terminal Domain of the Nipah Virus Nucleoprotein and Interaction with the X Domain of the Phosphoprotein as Unveiled by NMR Spectroscopy. Chembiochem 2014; 16:268-76. [DOI: 10.1002/cbic.201402534] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Indexed: 12/12/2022]
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Sigalov AB. Unusual biophysics of immune signaling-related intrinsically disordered proteins. Self Nonself 2014; 1:271-281. [PMID: 21487502 DOI: 10.4161/self.1.4.13641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 09/15/2010] [Accepted: 09/15/2010] [Indexed: 11/19/2022]
Abstract
Intrinsically disordered (ID) regions, the regions that lack a well-defined three-dimensional structure under physiological conditions, are preferentially located in the cytoplasmic segments of plasma membrane proteins, many of which are known to be involved in cell signaling. This is in line with our studies that demonstrated that cytoplasmic domains of signaling subunits of immune receptors, including those of ζ, CD3ε, CD3δ and CD3γ chains of T cell receptor, Igα and Igβ chains of B cell receptor as well as the Fc receptor γ chain represent a novel class of ID proteins (IDPs). The domains all have one or more copies of an immunoreceptor tyrosine-based activation motif, tyrosine residues of which are phosphorylated upon receptor engagement in an early and obligatory event in the signaling cascade. Our studies of these IDPs revealed several unusual biophysical phenomena, including (1) the specific dimerization of disordered protein molecules, (2) the fast and slow dimerization equilibrium, depending on the protein, (3) no disorder-to-order transition and the lack of significant chemical shift and peak intensity changes upon dimerization or interaction with a well-folded partner protein and (4) the dual mode of binding to model membranes (with and without folding), depending on the lipid bilayer stability. Here, I highlight several of these studies that not only facilitate a rethinking process of the fundamental paradigms in protein biophysics but also open new perspectives on the molecular mechanisms involved in receptor signaling.
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Wang W, Ye W, Jiang C, Luo R, Chen H. New Force Field on Modeling Intrinsically Disordered Proteins. Chem Biol Drug Des 2014; 84:253-69. [DOI: 10.1111/cbdd.12314] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 02/15/2014] [Accepted: 02/24/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Wang
- State Key Laboratory of Microbial metabolism Department of Bioinformatics and Biostatistics College of Life Sciences and Biotechnology Shanghai Jiaotong University 800 Dongchuan Road Shanghai 200240 China
| | - Wei Ye
- State Key Laboratory of Microbial metabolism Department of Bioinformatics and Biostatistics College of Life Sciences and Biotechnology Shanghai Jiaotong University 800 Dongchuan Road Shanghai 200240 China
| | - Cheng Jiang
- State Key Laboratory of Microbial metabolism Department of Bioinformatics and Biostatistics College of Life Sciences and Biotechnology Shanghai Jiaotong University 800 Dongchuan Road Shanghai 200240 China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry and Biomedical Engineering University of California Irvine CA 92697‐3900 USA
| | - Hai‐Feng Chen
- State Key Laboratory of Microbial metabolism Department of Bioinformatics and Biostatistics College of Life Sciences and Biotechnology Shanghai Jiaotong University 800 Dongchuan Road Shanghai 200240 China
- Shanghai Center for Bioinformation Technology 1275 Keyuan Road Shanghai 200235 China
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Persson L, Longhi S, Enarsson J, Andersen O, Haghigi S, Nilsson S, Lagging M, Johansson M, Bergström T. Elevated antibody reactivity to measles virus NCORE protein among patients with multiple sclerosis and their healthy siblings with intrathecal oligoclonal immunoglobulin G production. J Clin Virol 2014; 61:107-12. [PMID: 25022622 DOI: 10.1016/j.jcv.2014.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/07/2014] [Accepted: 06/11/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Patients with multiple sclerosis (MS) and their healthy siblings with the MS oligoclonal bands (OCB) trait, (a hyperimmune condition in form of two or more CSF enriched OCBs) harbor in cerebrospinal fluid (CSF) and serum elevated immunoglobulin G (IgG) titers against measles crude whole-cell antigen. The underlying mechanism resulting in the increased IgG antibody reactivity to measles remains unclear. The response may represent specific IgG reactivity to measles antigens or unspecific auto-antibodies targeting cellular components in the crude whole virus antigens commonly used in detection assays. OBJECTIVE To determine the specificity of the measles IgG antibody reactivity by using a purified single nucleoprotein as antigen, thereby minimizing the contribution from auto-antibodies. STUDY DESIGN The conserved N-terminal portion of the measles nucleocapsid protein (NCORE) was expressed as a specific antigen devoid of human or primate components. Serological analyses were performed on CSF and sera from MS patients, their clinically healthy siblings and healthy unrelated controls. RESULTS MS patients demonstrated higher IgG reactivity compared to healthy controls in both CSF (P<0.001) and serum (P<0.001), and compared to siblings in CSF (P<0.001) and serum (P=0.2). Siblings with MS OCB trait showed higher IgG reactivity than healthy controls in CSF (P=0.002) and serum (P=0.01). Comparison between siblings with MS OCB trait and siblings without MS OCB trait showed (P=0.04) for CSF and (P=0.08) for serum. CONCLUSION These findings suggest a measles-specific component in the antibody reactivity demonstrated by MS patients and their siblings with the MS OCB trait.
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Affiliation(s)
- Linn Persson
- Section for Clinical Virology, Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10 B, 41264 Gothenburg, Sweden
| | - Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, CNRS et Université Aix-Marseille, 13288 Marseille, France
| | - Johanna Enarsson
- Section for Clinical Virology, Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10 B, 41264 Gothenburg, Sweden
| | - Oluf Andersen
- Section of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Sara Haghigi
- Section of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Staffan Nilsson
- Department of Mathematical Statistics, Chalmers University of Technology, Gothenburg, Sweden
| | - Martin Lagging
- Section for Clinical Virology, Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10 B, 41264 Gothenburg, Sweden
| | - Maria Johansson
- Section for Clinical Virology, Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10 B, 41264 Gothenburg, Sweden
| | - Tomas Bergström
- Section for Clinical Virology, Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10 B, 41264 Gothenburg, Sweden.
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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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