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 Rating: Thread Rating: 1 votes, 5.00 average. Display Modes
  #1  
Unread 07-06-2016, 03:13 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
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 In-Cell Protein Structures from 2D NMR Experiments.

In-Cell Protein Structures from 2D NMR Experiments.

In-Cell Protein Structures from 2D NMR Experiments.

J Phys Chem Lett. 2016 Jul 5;

Authors: Müntener T, Häussinger D, Selenko P, Theillet FX

Abstract
In-cell NMR spectroscopy provides atomic resolution insights into the structural properties of proteins in cells. However, it is rarely used to solve entire protein structures de novo. Here, we introduce a paramagnetic lanthanide-tag to simultaneously measure protein pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) to be used as input for structure calculation routines within the Rosetta program. We employ this approach to determine the structure of the protein G B1 domain (GB1) in intact Xenopus laevis oocytes from 1H-15N 2D in-cell NMR experiments. Specifically, we derive well-defined GB1 ensembles from low concentration in-cell NMR samples (~50 ?M) measured at moderate magnetic field strengths (600 MHz), thus offering novel routes for intracellular structure determination with data from 2D in-cell NMR experiments.


PMID: 27379949 [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
Peering into cell structures - UD Daily
http://www.bionmr.com//t0.gstatic.com/images?q=tbn:ANd9GcSCwT2cWE7tmsRZUKzKKIVOxl2OLMvleQvZJs4RDMPQCLWmqbLR3x7aYhw8hniT7-hqXgl8UJF- UD Daily <img alt="" height="1" width="1"> Peering into cell structures UD Daily The research team used magic-angle-spinning nuclear magnetic resonance spectrometry (NMR) in the Department of Chemistry and Biochemistry at UD to unveil the structure of the CAP-Gly protein assembled on polymerized microtubules. The CAP-Gly ... and more &raquo; Peering into cell structures - UD Daily
nmrlearner Online News 0 11-25-2015 11:51 AM
[NMR paper] Spectral snapshots of bacterial cell-wall composition and the influence of antibiotics by whole-cell NMR.
Spectral snapshots of bacterial cell-wall composition and the influence of antibiotics by whole-cell NMR. Spectral snapshots of bacterial cell-wall composition and the influence of antibiotics by whole-cell NMR. Biophys J. 2015 Mar 24;108(6):1380-9 Authors: Nygaard R, Romaniuk JA, Rice DM, Cegelski L Abstract Gram-positive bacteria surround themselves with a thick cell wall that is essential to cell survival and is a major target of antibiotics. Quantifying alterations in cell-wall composition are crucial to evaluating drug...
nmrlearner Journal club 0 03-27-2015 11:59 PM
[NMR paper] Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures.
Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures. Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures. J Am Chem Soc. 2014 Jan 6; Authors: Mao B, Tejero R, Baker D, Montelione GT Abstract We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement...
nmrlearner Journal club 0 01-08-2014 11:23 AM
[NMR paper] Investigation of proteins in living bacteria with in-cell NMR experiments.
Investigation of proteins in living bacteria with in-cell NMR experiments. Related Articles Investigation of proteins in living bacteria with in-cell NMR experiments. Top Curr Chem. 2008;273:203-14 Authors: Dötsch V Abstract In recent years NMR methods have been developed that enable the observation of proteins insideliving bacterial cells. Because of the sensitivity of the chemical shift to environmental changesthese in-cell NMR experiments can be used to study protein conformation, molecular interaction ordynamics in a*protein's natural...
nmrlearner Journal club 0 04-24-2013 09:48 PM
[NMR paper] Cell-free protein synthesis in an autoinduction system for NMR studies of protein-protein interactions.
Cell-free protein synthesis in an autoinduction system for NMR studies of protein-protein interactions. Related Articles Cell-free protein synthesis in an autoinduction system for NMR studies of protein-protein interactions. J Biomol NMR. 2005 Jul;32(3):235-41 Authors: Ozawa K, Jergic S, Crowther JA, Thompson PR, Wijffels G, Otting G, Dixon NA Cell-free protein synthesis systems provide facile access to proteins in a nascent state that enables formation of soluble, native protein-protein complexes even if one of the protein components is prone...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures?
Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures? Related Articles Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures? Proteins. 2005 Jul 1;60(1):139-47 Authors: Garbuzynskiy SO, Melnik BS, Lobanov MY, Finkelstein AV, Galzitskaya OV We have compared structures of 78 proteins determined by both NMR and X-ray methods. It is shown that X-ray and NMR structures...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Methyl groups as probes for proteins and complexes in in-cell NMR experiments.
Methyl groups as probes for proteins and complexes in in-cell NMR experiments. Related Articles Methyl groups as probes for proteins and complexes in in-cell NMR experiments. J Am Chem Soc. 2004 Jun 9;126(22):7119-25 Authors: Serber Z, Straub W, Corsini L, Nomura AM, Shimba N, Craik CS, Ortiz de Montellano P, Dötsch V Studying protein components of large intracellular complexes by in-cell NMR has so far been impossible because the backbone resonances are unobservable due to their slow tumbling rates. We describe a methodology that overcomes...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[BMNRC community] In-cell NMR: three-dimensional protein structures
In-cell NMR: three-dimensional protein structures http://www.nature.com/nature/journal/v458/n7234/edsumm/e090305-13.html Go to BMNRC community to find more info about this topic.
nmrlearner News from other NMR forums 0 08-27-2010 07:58 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 01:45 PM.


Map