scholarly journals Ensemble description of the intrinsically disordered N-terminal domain of the Nipah virus P/V protein from combined NMR and SAXS

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marco Schiavina ◽  
Edoardo Salladini ◽  
Maria Grazia Murrali ◽  
Giancarlo Tria ◽  
Isabella C. Felli ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Shifts ◽  
Nipah Virus ◽  
Conformational Ensemble ◽  
Genome Replication ◽  
Nmr Studies ◽  
V Protein ◽  
Intrinsically Disordered ◽  
Terminal Domain ◽  
Starting Point

Abstract Using SAXS and NMR spectroscopy, we herein provide a high-resolution description of the intrinsically disordered N-terminal domain (PNT, aa 1–406) shared by the Nipah virus (NiV) phosphoprotein (P) and V protein, two key players in viral genome replication and in evasion of the host innate immune response, respectively. The use of multidimensional NMR spectroscopy allowed us to assign as much as 91% of the residues of this intrinsically disordered domain whose size constitutes a technical challenge for NMR studies. Chemical shifts and nuclear relaxation measurements provide the picture of a highly flexible protein. The combination of SAXS and NMR information enabled the description of the conformational ensemble of the protein in solution. The present results, beyond providing an overall description of the conformational behavior of this intrinsically disordered region, also constitute an asset for obtaining atomistic information in future interaction studies with viral and/or cellular partners. The present study can thus be regarded as the starting point towards the design of inhibitors that by targeting crucial protein–protein interactions involving PNT might be instrumental to combat this deadly virus.

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 ◽  
Vol 16 (2) ◽  
pp. 268-276 ◽  
Author(s):  
Lorenzo Baronti ◽  
Jenny Erales ◽  
Johnny Habchi ◽  
Isabella C. Felli ◽  
Roberta Pierattelli ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Nipah Virus ◽  
Intrinsically Disordered ◽  
Terminal Domain

27Al-MAS-NMR-Untersuchungen des thermischen Abbaus von NH4Al(SO4)2·12H2O / 27Al-MAS-NMR Studies on the Thermolysis of NH4Al(SO4)2· 12H2O

1991 ◽  
Vol 46 (11) ◽  
pp. 1515-1518 ◽  
Author(s):  
Gerhard Wegner ◽  
Gert Blumenthal ◽  
Dirk Müller ◽  
Dirk-Henning Menz ◽  
Antje Schmalstieg
Keyword(s):  
Nmr Spectroscopy ◽  
Structural Changes ◽  
Chemical Shifts ◽  
Mas Nmr ◽  
Nmr Studies ◽  
High Stage ◽  
27Al Mas Nmr ◽  
High Resolution Nmr ◽  
First Time

Products of the thermolysis of NH4Al-alum were prepared under dried air and characterized by X-ray powder diffraction, thermogravimetry, and for the first time by solid-state 27Al-MAS-NMR spectroscopy. It was found, that high resolution NMR spectroscopy is applicable to follow up the thermal decomposition and to indicate even minor structural changes. 27Al-MAS-NMR spectra show peaks with characteristic chemical shifts for octahedral Al-units up to a high stage of thermolysis. During the decomposition of Al2(SO4)3 to γ-Al2O3 we again observed three-peak spectra with the specific signal at ≈ 35 ppm for penta-coordinated Al ions as recently proved for the thermolysis of AlCl3 · 6 H2O.

scholarly journals The Interaction Mechanism of Intrinsically Disordered PP2A Inhibitor Proteins ARPP-16 and ARPP-19 With PP2A

2021 ◽  
Vol 8 ◽  
Author(s):  
Chandan Thapa ◽  
Pekka Roivas ◽  
Tatu Haataja ◽  
Perttu Permi ◽  
Ulla Pentikäinen
Keyword(s):  
Nmr Spectroscopy ◽  
Human Cancer ◽  
Interaction Mechanism ◽  
Inhibition Mechanism ◽  
Cellular Functions ◽  
Linear Motif ◽  
Intrinsically Disordered ◽  
Starting Point ◽  
Multiple Interaction ◽  
Pp2a Inhibitor

Protein phosphatase 2A (PP2A) activity is critical for maintaining normal physiological cellular functions. PP2A is inhibited by endogenous inhibitor proteins in several pathological conditions including cancer. A PP2A inhibitor protein, ARPP-19, has recently been connected to several human cancer types. Accordingly, the knowledge about ARPP-19—PP2A inhibition mechanism is crucial for the understanding the disease development and the therapeutic targeting of ARPP-19—PP2A. Here, we show the first structural characterization of ARPP-19, and its splice variant ARPP-16 using NMR spectroscopy, and SAXS. The results reveal that both ARPP proteins are intrinsically disordered but contain transient secondary structure elements. The interaction mechanism of ARPP-16/19 with PP2A was investigated using microscale thermophoresis and NMR spectroscopy. Our results suggest that ARPP—PP2A A-subunit interaction is mediated by linear motif and has modest affinity whereas, the interaction of ARPPs with B56-subunit is weak and transient. Like many IDPs, ARPPs are promiscuous binders that transiently interact with PP2A A- and B56 subunits using multiple interaction motifs. In summary, our results provide a good starting point for future studies and development of therapeutics that block ARPP-PP2A interactions.

scholarly journals Nuclear Localization of the Nipah Virus W Protein Allows for Inhibition of both Virus- and Toll-Like Receptor 3-Triggered Signaling Pathways

2005 ◽  
Vol 79 (10) ◽  
pp. 6078-6088 ◽  
Author(s):  
Megan L. Shaw ◽  
Washington B. Cardenas ◽  
Dmitriy Zamarin ◽  
Peter Palese ◽  
Christopher F. Basler
Keyword(s):  
Nuclear Localization ◽  
Nipah Virus ◽  
Toll Like Receptor ◽  
Promoter Activation ◽  
Double Stranded Rna ◽  
V Protein ◽  
Terminal Domain ◽  
P Gene ◽  
Localization Signal ◽  
Stimulation Of

ABSTRACT The Nipah virus V and W proteins, which are encoded by the P gene via RNA editing, have a common N-terminal domain but unique C-terminal domains. They localize to the cytoplasm and nucleus, respectively, and have both been shown to function as inhibitors of JAK/STAT signaling. Here we report that V and W proteins also block virus activation of the beta interferon (IFN-β) promoter and the IFN regulatory factor 3 (IRF3)-responsive IFN-stimulated gene 54 promoter. Surprisingly, only W protein shows strong inhibition of promoter activation in response to stimulation of Toll-like receptor 3 (TLR3) by extracellular double-stranded RNA. This activity is dependent on the nuclear localization of W protein. Within the unique C-terminal domain of W protein, we have identified a nuclear localization signal (NLS) that requires basic residues at positions 439, 440, and 442. This NLS is responsible for mediating the preferential interaction of W protein with karyopherin-α 3 and karyopherin-α 4. Nuclear localization of W protein therefore enables it to target both virus and TLR3 pathways, whereas the cytoplasmic V protein is restricted to inhibiting the virus pathway. We propose that this discrepancy is in part due to the V protein being less able to block signaling in response to the kinase, TBK-1, whereas both V and W can prevent promoter activation in response to IKKε. We demonstrate that, when the TLR3 pathway is stimulated, the levels of phosphorylated IRF3 are reduced in the presence of W protein but not V protein, confirming the differential effects of these proteins and illustrating that W protein-mediated inhibition is due to a loss of active IRF3.

Solid-State Carbon-13 NMR Studies of Vulcanized Elastomers. VII. Sulfur-Vulcanized Cis-1,4 Polybutadiene at 75.5 Mhz

1989 ◽  
Vol 62 (5) ◽  
pp. 908-927 ◽  
Author(s):  
R. S. Clough ◽  
J. L. Koenig
Keyword(s):  
Solid State ◽  
Nmr Spectroscopy ◽  
Chemical Shifts ◽  
Chemical Information ◽  
Chemical Probes ◽  
Nmr Studies ◽  
Nmr Characterization ◽  
The Individual ◽  
Insight Into

Abstract Solid-state C-13 NMR spectroscopy provides a wealth of chemical information concerning sulfur-vulcanized cis-l,4-polybutadiene. New resonances which appear upon curing have chemical shifts which are expected for crosslink and cyclic structures. The DEPT experiment with MAS worked well for the polybutadiene vulcanizate in the solid state. DEPT is very useful as an aid in the assignment of structures to resonances. The new resonances can be assigned to more than one type of structure given only chemical shift and DEPT information. Swelling measurements indicate the majority of the resonances are due to cyclics. Further work involving C-13 NMR characterization of polybutadiene vulcanizates treated with chemical probes and vulcanizates cured with organic accelerators should provide insight into the specific structures responsible for the individual resonances.

scholarly journals Dissociation of Paramyxovirus Interferon Evasion Activities: Universal and Virus-Specific Requirements for Conserved V Protein Amino Acids in MDA5 Interference

2010 ◽  
Vol 84 (21) ◽  
pp. 11152-11163 ◽  
Author(s):  
Aparna Ramachandran ◽  
Curt M. Horvath
Keyword(s):  
Measles Virus ◽  
Nipah Virus ◽  
Site Directed Mutagenesis ◽  
Helicase Domain ◽  
Protein Chain ◽  
Conserved Residues ◽  
V Protein ◽  
Protein Protein Interaction ◽  
Terminal Domain ◽  
Amino Acid Region

ABSTRACT The V protein of the paramyxovirus subfamily Paramyxovirinae is an important virulence factor that can interfere with host innate immunity by inactivating the cytosolic pathogen recognition receptor MDA5. This interference is a result of a protein-protein interaction between the highly conserved carboxyl-terminal domain of the V protein and the helicase domain of MDA5. The V protein C-terminal domain (CTD) is an evolutionarily conserved 49- to 68-amino-acid region that coordinates two zinc atoms per protein chain. Site-directed mutagenesis of conserved residues in the V protein CTD has revealed both universal and virus-specific requirements for zinc coordination in MDA5 engagement and has also identified other conserved residues as critical for MDA5 interaction and interference. Mutation of these residues produces V proteins that are specifically defective for MDA5 interference and not impaired in targeting STAT1 for proteasomal degradation via the VDC ubiquitin ligase complex. Results demonstrate that mutation of conserved charged residues in the V proteins of Nipah virus, measles virus, and mumps virus also abolishes MDA5 interaction. These findings clearly define molecular determinants for MDA5 inhibition by the paramyxovirus V proteins.

scholarly journals Identification of a Region in the Common Amino-Terminal Domain of Hendra Virus P, V, and W Proteins Responsible for Phase Transition and Amyloid Formation

Biomolecules ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1324
Author(s):  
Edoardo Salladini ◽  
Frank Gondelaud ◽  
Juliet F. Nilsson ◽  
Giulia Pesce ◽  
Christophe Bignon ◽  
...  
Keyword(s):  
Phase Transition ◽  
Congo Red ◽  
Cellular Protein ◽  
Hendra Virus ◽  
Amyloid Formation ◽  
V Protein ◽  
Amino Terminal ◽  
Intrinsically Disordered ◽  
Terminal Domain

Henipaviruses are BSL-4 zoonotic pathogens responsible in humans for severe encephalitis. Their V protein is a key player in the evasion of the host innate immune response. We previously showed that the Henipavirus V proteins consist of a long intrinsically disordered N-terminal domain (NTD) and a β-enriched C-terminal domain (CTD). These terminals are critical for V binding to DDB1, which is a cellular protein that is a component of the ubiquitin ligase E3 complex, as well as binding to MDA5 and LGP2, which are two host sensors of viral RNA. Here, we serendipitously discovered that the Hendra virus V protein undergoes a liquid-to-hydrogel phase transition and identified the V region responsible for this phenomenon. This region, referred to as PNT3 and encompassing residues 200–310, was further investigated using a combination of biophysical and structural approaches. Congo red binding assays, together with negative-staining transmisison electron microscopy (TEM) studies, show that PNT3 forms amyloid-like fibrils. Fibrillation abilities are dramatically reduced in a rationally designed PNT3 variant in which a stretch of three contiguous tyrosines, falling within an amyloidogenic motif, were replaced by three alanines. Worthy to note, Congo red staining experiments provided hints that these amyloid-like fibrils form not only in vitro but also in cellula after transfection or infection. The present results set the stage for further investigations aimed at assessing the functional role of phase separation and fibrillation by the Henipavirus V proteins.

10B-, 11B-, 13C-NMR-Untersuchungen von closo-Pentaalkyl-1.5-dicarbapentaboranen(5) / 10B-, 11B-, 13C NMR Studies of closo-Pentaalkyl-1,5-dicarbapentaboranes(5)

1981 ◽  
Vol 36 (6) ◽  
pp. 704-707 ◽  
Author(s):  
Roland Köster ◽  
Bernd Wrackmeyer
Keyword(s):  
Nmr Spectroscopy ◽  
13C Nmr ◽  
Chemical Shifts ◽  
Parent Compound ◽  
Coupling Constants ◽  
Mo Calculations ◽  
Nmr Studies ◽  
Nmr Parameters ◽  
Alkyl Substitution ◽  
C Nmr

AbstractNMR parameters [chemical] shifts (δ11B, δ13C) and coupling constants (1J(13C1H), 1J(13C11B), 1J(13C13C), 1J(11B11B) of closo-pentaalkyl-1,5-dicarbapentaboranes(5) were determinated by 10B, 11B, and 13C NMR spectroscopy. The magnitudes of 1J(13C11B) and 1J(13C13C) correspond to 1J(11B1H), 1J(13C11B) and 1J(13C1H) in the parent compound 1,5-C2B3H5 . According to predictions from MO calculations 1J(11B11B) was found to be < 10 Hz. Together with these data the δ11B and δ13C values show that neither the structure nor the bonding situation in the polyhedron are significantly affected by alkyl substitution.

NMR spectroscopy in the conformational analysis of peptides: an overview

2020 ◽  
Vol 27 ◽  
Author(s):  
Marian Vincenzi ◽  
Flavia Anna Mercurio ◽  
Marilisa Leone
Keyword(s):  
Nmr Spectroscopy ◽  
Protein Interactions ◽  
3D Structure ◽  
Theoretical Background ◽  
Triple Resonance ◽  
Protein Protein Interactions ◽  
Nmr Studies ◽  
Conformational Preferences ◽  
Dynamic Perspective ◽  
Nmr Methods

Background: NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. Objective: This review provides a toolkit to investigate peptide conformational properties by NMR. Methods: Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through Pubmed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. Results: The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. Conclusion: NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.

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