NMR paper Novel NMR Assignment Strategy Reveals Structural Heterogeneity in Solution of the nsP3 HVD Domain of Venezuelan Equine Encephalitis Virus.

		BioNMR > Educational resources > Journal club
[NMR paper] Novel NMR Assignment Strategy Reveals Structural Heterogeneity in Solution of the nsP3 HVD Domain of Venezuelan Equine Encephalitis Virus.

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

12-29-2020, 04:50 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Novel NMR Assignment Strategy Reveals Structural Heterogeneity in Solution of the nsP3 HVD Domain of Venezuelan Equine Encephalitis Virus.

Related Articles Novel NMR Assignment Strategy Reveals Structural Heterogeneity in Solution of the nsP3 HVD Domain of Venezuelan Equine Encephalitis Virus.

Molecules. 2020 Dec 10;25(24):

Authors: Agback P, Shernyukov A, Dominguez F, Agback T, Frolova EI

Abstract
In recent years, intrinsically disordered proteins (IDPs) and disordered domains have attracted great attention. Many of them contain linear motifs that mediate interactions with other factors during formation of multicomponent protein complexes. NMR spectrometry is a valuable tool for characterizing this type of interactions on both amino acid (aa) and atomic levels. Alphaviruses encode a nonstructural protein nsP3, which drives viral replication complex assembly. nsP3 proteins contain over 200-aa-long hypervariable domains (HVDs), which exhibits no homology between different alphavirus species, are predicted to be intrinsically disordered and appear to be critical for alphavirus adaptation to different cells. Previously, we have shown that nsP3 HVD of chikungunya virus (CHIKV) is completely disordered with low tendency to form secondary structures in free form. In this new study, we used novel NMR approaches to assign the spectra for the nsP3 HVD of Venezuelan equine encephalitis virus (VEEV). The HVDs of CHIKV and VEEV have no homology but are both involved in replication complex assembly and function. We have found that VEEV nsP3 HVD is also mostly disordered but contains a short stable ?-helix in its C-terminal fragment, which mediates interaction with the members of cellular Fragile X syndrome protein family. Our NMR data also suggest that VEEV HVD has several regions with tendency to form secondary structures.

PMID: 33321815 [PubMed - in process]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] NMR study of non-structural proteins-part III: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV). NMR study of non-structural proteins-part III: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV). http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles NMR study of non-structural proteins-part III: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV). Biomol NMR Assign. 2017 Sep 05;: Authors: Lykouras MV, Tsika AC, Lichière J,...	nmrlearner	Journal club	0	09-07-2017 10:42 PM
Kinetic, Mutational, and Structural Studies of theVenezuelan Equine Encephalitis Virus Nonstructural Protein 2 CysteineProtease Kinetic, Mutational, and Structural Studies of theVenezuelan Equine Encephalitis Virus Nonstructural Protein 2 CysteineProtease http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.5b00992/20160519/images/medium/bi-2015-00992a_0007.gif Biochemistry DOI: 10.1021/acs.biochem.5b00992 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/4quzBrsbNVA More...	nmrlearner	Journal club	0	05-20-2016 12:05 AM
Equine ordure: NMR reveals fungal antibiotic Equine ordure: NMR reveals fungal antibiotic http://www.spectroscopynow.com/common/images/thumbnails/149f056366a.jpgNMR spectroscopy reveals the structure of an antibiotic protein, copsin, from a surprising source: the grey shag fungus that grows on horse dung. The antibiotic has the same ultiamte effect on bacteria as small molecule compounds but offers an entirely different biochemistry that might be exploited in drugs to defeat antibiotic resistance. Read the rest at Spectroscopynow.com	nmrlearner	General	0	12-01-2014 12:17 PM
[NMR paper] NMR study of non-structural proteins-part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV). NMR study of non-structural proteins-part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV). Related Articles NMR study of non-structural proteins-part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV). Biomol NMR Assign. 2014 Oct 8; Authors: Makrynitsa GI, Ntonti D, Marousis KD, Tsika AC, Lichière J, Papageorgiou N, Coutard B, Bentrop D, Spyroulias GA Abstract Macro...	nmrlearner	Journal club	0	10-09-2014 07:31 PM
[NMR paper] NMR study of non-structural proteins-part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV). NMR study of non-structural proteins-part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV). Related Articles NMR study of non-structural proteins-part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV). Biomol NMR Assign. 2014 Sep 13; Authors: Melekis E, Tsika AC, Lichière J, Chasapis CT, Margiolaki I, Papageorgiou N, Coutard B, Bentrop D, Spyroulias GA Abstract Macro domains are ADP-ribose-binding modules present...	nmrlearner	Journal club	0	09-14-2014 02:26 PM
[NMR paper] (19)F NMR Reveals Multiple Conformations at the Dimer Interface of the Nonstructural Protein 1 Effector Domain from Influenza A Virus. (19)F NMR Reveals Multiple Conformations at the Dimer Interface of the Nonstructural Protein 1 Effector Domain from Influenza A Virus. Related Articles (19)F NMR Reveals Multiple Conformations at the Dimer Interface of the Nonstructural Protein 1 Effector Domain from Influenza A Virus. Structure. 2014 Feb 25; Authors: Aramini JM, Hamilton K, Ma LC, Swapna GV, Leonard PG, Ladbury JE, Krug RM, Montelione GT Abstract Nonstructural protein 1 of influenza A virus (NS1A) is a*conserved virulence factor comprised of an N-terminal double-stranded...	nmrlearner	Journal club	0	03-04-2014 06:37 PM
19F NMR Reveals Multiple Conformations at the Dimer Interface of the Nonstructural Protein 1 Effector Domain from Influenza A Virus 19F NMR Reveals Multiple Conformations at the Dimer Interface of the Nonstructural Protein 1 Effector Domain from Influenza A Virus Publication date: Available online 27 February 2014 Source:Structure</br> Author(s): JamesM. Aramini , Keith Hamilton , Li-Chung Ma , G.V.T. Swapna , PaulG. Leonard , JohnE. Ladbury , RobertM. Krug , GaetanoT. Montelione</br> Nonstructural protein 1 of influenza A virus (NS1A) is aconserved virulence factor comprised of an N-terminal double-stranded RNA (dsRNA)-binding domain and a multifunctional C-terminal effector domain...	nmrlearner	Journal club	0	02-28-2014 06:08 AM
[NMR paper] Solution NMR structure of CD1104B from pathogenic Clostridium difficile reveals a distinct ?-helical architecture and provides first structural representative of protein domain family PF14203. Solution NMR structure of CD1104B from pathogenic Clostridium difficile reveals a distinct ?-helical architecture and provides first structural representative of protein domain family PF14203. Related Articles Solution NMR structure of CD1104B from pathogenic Clostridium difficile reveals a distinct ?-helical architecture and provides first structural representative of protein domain family PF14203. J Struct Funct Genomics. 2013 Sep 19; Authors: Pulavarti SV, Eletsky A, Lee HW, Acton TB, Xiao R, Everett JK, Prestegard JH, Montelione GT, Szyperski T ...	nmrlearner	Journal club	0	09-21-2013 06:50 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off