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 07-06-2020, 10:08 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,040
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 pseudocontact shifts in a symmetric protein homotrimer.

NMR pseudocontact shifts in a symmetric protein homotrimer.

Related Articles NMR pseudocontact shifts in a symmetric protein homotrimer.

J Biomol NMR. 2020 Jul 03;:

Authors: Müntener T, Böhm R, Atz K, Häussinger D, Hiller S

Abstract
NMR pseudocontact shifts are a valuable tool for structural and functional studies of proteins. Protein multimers mediate key functional roles in biology, but methods for their study by pseudocontact shifts are so far not available. Paramagnetic tags attached to identical subunits in multimeric proteins cause a combined pseudocontact shift that cannot be described by the standard single-point model. Here, we report pseudocontact shifts generated simultaneously by three paramagnetic Tm-M7PyThiazole-DOTA tags to the trimeric molecular chaperone Skp and provide an approach for the analysis of this and related symmetric systems. The pseudocontact shifts were described by a "three-point" model, in which positions and parameters of the three paramagnetic tags were fitted. A good correlation between experimental data and predicted values was found, validating the approach. The study establishes that pseudocontact shifts can readily be applied to multimeric proteins, offering new perspectives for studies of large protein complexes by paramagnetic NMR spectroscopy.


PMID: 32621004 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
NMR pseudocontact shifts in a symmetric protein homotrimer
NMR pseudocontact shifts in a symmetric protein homotrimer Abstract NMR pseudocontact shifts are a valuable tool for structural and functional studies of proteins. Protein multimers mediate key functional roles in biology, but methods for their study by pseudocontact shifts are so far not available. Paramagnetic tags attached to identical subunits in multimeric proteins cause a combined pseudocontact shift that cannot be described by the standard single-point model. Here, we report pseudocontact shifts generated simultaneously by three paramagnetic...
nmrlearner Journal club 0 07-04-2020 03:45 AM
Integral membrane protein structure determination using pseudocontact shifts
Integral membrane protein structure determination using pseudocontact shifts Abstract Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary...
nmrlearner Journal club 0 01-21-2015 08:39 PM
[NMR paper] Erratum to: PARAssign-paramagnetic NMR assignments of protein nuclei on the basis of pseudocontact shifts.
Erratum to: PARAssign-paramagnetic NMR assignments of protein nuclei on the basis of pseudocontact shifts. Related Articles Erratum to: PARAssign-paramagnetic NMR assignments of protein nuclei on the basis of pseudocontact shifts. J Biomol NMR. 2013 Jun 23; Authors: Skinner SP, Moshev M, Hass MA, Keizers PH, Ubbink M Abstract
nmrlearner Journal club 0 06-26-2013 09:39 AM
[NMR paper] PARAssign-paramagnetic NMR assignments of protein nuclei on the basis of pseudocontact shifts.
PARAssign-paramagnetic NMR assignments of protein nuclei on the basis of pseudocontact shifts. Related Articles PARAssign-paramagnetic NMR assignments of protein nuclei on the basis of pseudocontact shifts. J Biomol NMR. 2013 Mar 23; Authors: Skinner SP, Moshev M, Hass MA, Ubbink M Abstract The use of paramagnetic NMR data for the refinement of structures of proteins and protein complexes is widespread. However, the power of paramagnetism for protein assignment has not yet been fully exploited. PARAssign is software that uses...
nmrlearner Journal club 0 03-26-2013 01:30 PM
Proteinâ??protein HADDocking using exclusively pseudocontact shifts
Proteinâ??protein HADDocking using exclusively pseudocontact shifts <div class="Abstract" lang="en">Abstract <div class="normal">In order to enhance the structure determination process of macromolecular assemblies by NMR, we have implemented long-range pseudocontact shift (PCS) restraints into the data-driven protein docking package HADDOCK. We demonstrate the efficiency of the method on a synthetic, yet realistic case based on the lanthanide-labeled N-terminal ε domain of the E. coli DNA polymerase III (ε186) in complex with the HOT domain. Docking from the bound form of the two...
nmrlearner Journal club 0 06-06-2011 12:53 AM
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings.
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings. Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings. J Am Chem Soc. 2011 Apr 5; Authors: Sgourakis NG, Lange OF, Dimaio F, Andre? I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D Symmetric protein dimers, trimers, and higher-order cyclic oligomers play key roles in many biological processes. However, structural studies of oligomeric systems by solution NMR...
nmrlearner Journal club 0 04-07-2011 09:54 PM
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings Nikolaos G. Sgourakis, Oliver F. Lange, Frank DiMaio, Ingemar Andre?, Nicholas C. Fitzkee, Paolo Rossi, Gaetano T. Montelione, Ad Bax and David Baker http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja111318m/aop/images/medium/ja-2010-11318m_0008.gif Journal of the American Chemical Society DOI: 10.1021/ja111318m http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
nmrlearner Journal club 0 04-06-2011 10:54 AM
Generation of Pseudocontact Shifts in Protein NMR Spectra with a Genetically Encoded
Generation of Pseudocontact Shifts in Protein NMR Spectra with a Genetically Encoded Cobalt(II)-Binding Amino Acid. Related Articles Generation of Pseudocontact Shifts in Protein NMR Spectra with a Genetically Encoded Cobalt(II)-Binding Amino Acid. Angew Chem Int Ed Engl. 2010 Nov 25; Authors: Nguyen TH, Ozawa K, Stanton-Cook M, Barrow R, Huber T, Otting G
nmrlearner Journal club 0 11-27-2010 02:45 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 - 2020, 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 10:02 AM.


Map