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 05-24-2016, 11:36 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics.

NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics.

Related Articles NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics.

PLoS One. 2015;10(8):e0134823

Authors: Gupta G, Lim L, Song J

Abstract
Dengue genome encodes a two component protease complex (NS2B-NS3pro) essential for the viral maturation/infectivity, thus representing a key drug target. Previously, due to its "complete insolubility", the isolated NS3pro could not be experimentally studied and it remains elusive what structure it adopts without NS2B and why NS2B is indispensable. Here as facilitated by our previous discovery, the isolated NS3pro has been surprisingly deciphered by NMR to be the first intrinsically-disordered chymotrypsin-like fold, which exists in a loosely-packed state with non-native long-range interactions as revealed by paramagnetic relaxation enhancement (PRE). The disordered NS3pro appears to be needed for binding a human host factor to trigger the membrane remodeling. Moreover, we have in vitro refolded the NS3pro in complex with either NS2B (48-100) or the full-length NS2B (1-130) anchored into the LMPC micelle, and the two complexes have similar activities but different dynamics. We also performed molecular dynamics (MD) simulations and the results revealed that NS2B shows the highest structural fluctuations in the complex, thus providing the dynamic basis for the observation on its conformational exchange between open and closed states. Remarkably, the NS2B cofactor plays a central role in maintaining the correlated motion network required for the catalysis as we previously decoded for the SARS 3CL protease. Indeed, a truncated NS2B (48-100;?77-84) with the flexible loop deleted is able to trap the NS2B-NS3pro complex in a highly dynamic and catalytically-impotent state. Taken together, our study implies potential strategies to perturb the NS2B-NS3pro interface for design of inhibitors for treating dengue infection.


PMID: 26258523 [PubMed - indexed for MEDLINE]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Conformational change study of dengue virus NS2B-NS3 protease using 19F NMR spectroscopy.
Conformational change study of dengue virus NS2B-NS3 protease using 19F NMR spectroscopy. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Conformational change study of dengue virus NS2B-NS3 protease using 19F NMR spectroscopy. Biochem Biophys Res Commun. 2015 Jun 12;461(4):677-80 Authors: Zhu L, Yang J, Li H, Sun H, Liu J, Wang J Abstract The dengue virus NS2B-NS3 protease (NS2B-NS3p), an important antiviral target for drug development,...
nmrlearner Journal club 0 08-02-2015 07:10 AM
[NMR paper] Membrane topology of NS2B of dengue virus revealed by NMR spectroscopy.
Membrane topology of NS2B of dengue virus revealed by NMR spectroscopy. Related Articles Membrane topology of NS2B of dengue virus revealed by NMR spectroscopy. Biochim Biophys Acta. 2015 Jun 11; Authors: Li Y, Li Q, Wong YL, Liew LS, Kang C Abstract Non-structural (NS) proteins of dengue virus (DENV) are important for viral replication. There are four membrane proteins that are coded by viral genome. NS2B was shown to be one of the membrane proteins and its main function was confirmed to regulate viral protease activity. Its...
nmrlearner Journal club 0 06-15-2015 02:45 PM
[NMR paper] Urea Dependent 15N NMR-Relaxation Studies on PfP2 Multimers Reveal that the C-Terminal Behaves like an Independent Intrinsically Disordered Peptide.
Urea Dependent 15N NMR-Relaxation Studies on PfP2 Multimers Reveal that the C-Terminal Behaves like an Independent Intrinsically Disordered Peptide. Related Articles Urea Dependent 15N NMR-Relaxation Studies on PfP2 Multimers Reveal that the C-Terminal Behaves like an Independent Intrinsically Disordered Peptide. Protein Pept Lett. 2015 Mar 6; Authors: Hosur RV Abstract Intrinsically disordered proteins or such domains in globular proteins are believed to be playing important roles in protein functions by virtue of their ability...
nmrlearner Journal club 0 03-10-2015 07:22 PM
[NMR paper] NMR contributions to structural dynamics studies of intrinsically disordered proteins.
NMR contributions to structural dynamics studies of intrinsically disordered proteins. Related Articles NMR contributions to structural dynamics studies of intrinsically disordered proteins. J Magn Reson. 2014 Apr;241:74-85 Authors: Konrat R Abstract Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic...
nmrlearner Journal club 0 03-25-2014 11:49 AM
NMR contributions to structural dynamics studies of intrinsically disordered proteins
NMR contributions to structural dynamics studies of intrinsically disordered proteins Publication date: April 2014 Source:Journal of Magnetic Resonance, Volume 241</br> Author(s): Robert Konrat</br> Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development...
nmrlearner Journal club 0 03-21-2014 12:52 AM
[NMR paper] NMR analysis of a novel enzymatically-active unlinked Dengue NS2B-NS3 protease complex.
NMR analysis of a novel enzymatically-active unlinked Dengue NS2B-NS3 protease complex. Related Articles NMR analysis of a novel enzymatically-active unlinked Dengue NS2B-NS3 protease complex. J Biol Chem. 2013 Mar 19; Authors: Kim YM, Gayen S, Kang C, Joy J, Huang Q, Chen AS, Wee JL, Ang MJ, Lim HA, Hung AW, Li R, Noble CG, Lee LT, Yip A, Wang QY, Chia CS, Hill J, Shi PY, Keller TH Abstract The dengue virus (DENV) is a mosquito-borne pathogen responsible for an estimated 100 million human infections annually. The viral genome encodes a...
nmrlearner Journal club 0 03-21-2013 02:58 PM
[NMR paper] NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyas
NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system. Related Articles NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system. Biochemistry. 2004 Jul 6;43(26):8322-32 Authors: Di Lello P, Benison GC, Valafar H, Pitts KE, Summers AO, Legault P, Omichinski JG Mercury resistant bacteria have developed a system of two enzymes (MerA and MerB), which allows them to efficiently...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Real-time NMR studies on folding of mutants of barnase and chymotrypsin inhibitor 2.
Real-time NMR studies on folding of mutants of barnase and chymotrypsin inhibitor 2. Related Articles Real-time NMR studies on folding of mutants of barnase and chymotrypsin inhibitor 2. FEBS Lett. 1998 Feb 13;423(1):110-2 Authors: Killick TR, Freund SM, Fersht AR The folding and unfolding of proteins is generally assumed to be so co-operative that the overall process may be followed by a single probe, such as tryptophan fluorescence. Folding kinetics of three mutants of barnase and chymotrypsin inhibitor 2 (CI2) were studied by real-time NMR....
nmrlearner Journal club 0 11-17-2010 11:06 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 03:01 PM.


Map