BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 12-29-2020, 04:50 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Novel NMR Assignment Strategy Reveals Structural Heterogeneity in Solution of the nsP3 HVD Domain of Venezuelan Equine Encephalitis Virus.

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...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
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): James*M. Aramini , Keith Hamilton , Li-Chung Ma , G.V.T. Swapna , Paul*G. Leonard , John*E. Ladbury , Robert*M. Krug , Gaetano*T. Montelione</br> Nonstructural protein 1 of influenza A virus (NS1A) is a*conserved 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


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 01:29 AM.


Map