Structural disorder within paramyxoviral nucleoproteins

Longhi, Sonia

doi:10.1016/j.febslet.2015.05.055

Cited by 20 publications

(15 citation statements)

References 106 publications

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“…They are also in accordance with previous results obtained with MeV variants bearing an internal N TAIL deletion (residues 440‐482), which were found to support increased reporter activity in mini‐replicon studies . The finding that N TAIL is intrinsically able to modulate the interaction with XD is also consistent with the hypothesis that the N TAIL /XD interaction needs to be dynamically formed and broken to enable the polymerase complex to be dynamically tethered onto the nucleocapsid template in order to allow transcription and replication to take place .…”

Section: Resultssupporting

confidence: 91%

Fuzzy regions in an intrinsically disordered protein impair protein–protein interactions

et al. 2016

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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 (N TAIL ) and the X domain (XD) of the viral phosphoprotein as model system. After binding to XD, the N-terminal region of N TAIL remains conspicuously disordered, with a-helical folding taking place only within a short molecular recognition element. To study the effect of the N-terminal fuzzy region on N TAIL /XD binding, we generated N-terminal truncation variants of N TAIL , 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 N TAIL binding partner), and for the homologous N TAIL /XD pairs from the Nipah and Hendra viruses. Finally, similar results were obtained when the MeV N TAIL 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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Section: Resultssupporting

confidence: 91%

Fuzzy regions in an intrinsically disordered protein impair protein–protein interactions

et al. 2016

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“…3E). Transient sampling of a folded region does not facilitate a conformational selection mechanism in any case, as is seen for other IDPs, such as NTAIL (52,53). Assuming this to be the case, Prp2 might be able to select and further stabilize already transiently populated helical conformations of the N-terminal parts, and the C-terminal parts could subsequently bind to Prp2 as well.…”

Section: Discussionmentioning

confidence: 95%

Structural analysis of the intrinsically disordered splicing factor Spp2 and its binding to the DEAH-box ATPase Prp2

Hamann

Schmitt

Favretto

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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The spliceosome consists of five small RNAs and more than 100 proteins. Almost 50% of the human spliceosomal proteins were predicted to be intrinsically disordered or to contain disordered regions, among them the G-patch protein Spp2. The G-patch region of Spp2 binds to the DEAH-box ATPase Prp2, and both proteins together are essential for promoting the transition from the Bact to the catalytically active B* spliceosome. Here we show by circular dichroism and nuclear magnetic resonance (NMR) spectroscopy that Spp2 is intrinsically disordered in solution. Crystal structures of a complex consisting of Prp2-ADP and the G-patch domain of Spp2 demonstrate that the G-patch gains a defined fold when bound to Prp2. While the N-terminal region of the G-patch always folds into an α-helix in five different crystal structures, the C-terminal part is able to adopt two alternative conformations. NMR studies further revealed that the N-terminal part of the Spp2 G-patch, which is the most conserved region in different G-patch proteins, transiently samples helical conformations, possibly facilitating a conformational selection binding mechanism. The structural analysis unveils the role of conserved residues of the G-patch in the dynamic interaction mode of Spp2 with Prp2, which is vital to maintain the binding during the Prp2 domain movements needed for RNA translocation.

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“…In the case of NiV [42], Hendra virus [88], SeV [38,89] and MeV [27,30,44,89] the C-terminal domain of P (XD) is structurally conserved and consists of a bundle of 3 α-helices that are structurally analogous, and that dynamically binds to a α-MoRE located near the C-terminus of N TAIL ([90,91], see [92] for reviews). This N TAIL -XD interaction is commonly characterized by a rather low affinity (K D within the 3–50 μM range, [39,46,89] and this work).…”

Section: Discussionmentioning

confidence: 99%

Modulation of Re-initiation of Measles Virus Transcription at Intergenic Regions by PXD to NTAIL Binding Strength

et al. 2016

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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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Structural disorder within paramyxoviral nucleoproteins

Cited by 20 publications

References 106 publications

Fuzzy regions in an intrinsically disordered protein impair protein–protein interactions

Fuzzy regions in an intrinsically disordered protein impair protein–protein interactions

Structural analysis of the intrinsically disordered splicing factor Spp2 and its binding to the DEAH-box ATPase Prp2

Modulation of Re-initiation of Measles Virus Transcription at Intergenic Regions by PXD to NTAIL Binding Strength

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