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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 05-20-2016, 03:04 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,777
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 Characterization of proteins by in-cell NMR spectroscopy in cultured mammalian cells.

Characterization of proteins by in-cell NMR spectroscopy in cultured mammalian cells.

Characterization of proteins by in-cell NMR spectroscopy in cultured mammalian cells.

Nat Protoc. 2016 Jun;11(6):1101-1111

Authors: Barbieri L, Luchinat E, Banci L


Abstract
In-cell NMR spectroscopy is a unique tool for characterizing biological macromolecules in their physiological environment at atomic resolution. Recent progress in NMR instruments and sample preparation methods allows functional processes, such as metal uptake, disulfide-bond formation and protein folding, to be analyzed by NMR in living, cultured human cells. This protocol describes the necessary steps to overexpress one or more proteins of interest inside human embryonic kidney 293T (HEK293T) cells, and it explains how to set up in-cell NMR experiments. The cDNA is transiently transfected as a complex with a cationic polymer (DNA:PEI (polyethylenimine)), and protein expression is carried on for 2-3 d, after which the NMR sample is prepared. (1)H and (1)H-(15)N correlation NMR experiments (for example, using band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence (SOFAST-HMQC)) can be carried out in
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Algal autolysate medium to label proteins for NMR in mammalian cells.
Algal autolysate medium to label proteins for NMR in mammalian cells. Related Articles Algal autolysate medium to label proteins for NMR in mammalian cells. J Biomol NMR. 2016 Apr 22; Authors: Fuccio C, Luchinat E, Barbieri L, Neri S, Fragai M Abstract In-cell NMR provides structural and functional information on proteins directly inside living cells. At present, the high costs of the labeled media for mammalian cells represent a limiting factor for the development of this methodology. Here we report a protocol to prepare a...
nmrlearner Journal club 0 04-24-2016 10:29 PM
Algal autolysate medium to label proteins for NMR in mammalian cells
Algal autolysate medium to label proteins for NMR in mammalian cells Abstract In-cell NMR provides structural and functional information on proteins directly inside living cells. At present, the high costs of the labeled media for mammalian cells represent a limiting factor for the development of this methodology. Here we report a protocol to prepare a homemade growth medium from Spirulina platensis autolysate, suitable to express uniformly labeled proteins inside mammalian cells at a reduced cost-per-sample. The human proteins SOD1 and Mia40 were...
nmrlearner Journal club 0 04-22-2016 08:45 PM
[NMR paper] Fluorine NMR-based assay in living mammalian cells.
Fluorine NMR-based assay in living mammalian cells. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Fluorine NMR-based assay in living mammalian cells. Anal Biochem. 2015 Dec 11; Authors: Veronesi M, Giacomina F, Romeo E, Castellani B, Ottonello G, Lambruschini C, Garau G, Scarpelli R, Bandiera T, Piomelli D, Dalvit C Abstract Nuclear Magnetic Resonance (NMR)-based screening has been recognized as a powerful approach for the identification...
nmrlearner Journal club 0 12-28-2015 12:26 AM
[NMR paper] In-Cell NMR Characterization of the Secondary Structure Populations of a Disordered Conformation of ?-Synuclein within E. coli Cells.
In-Cell NMR Characterization of the Secondary Structure Populations of a Disordered Conformation of ?-Synuclein within E. coli Cells. In-Cell NMR Characterization of the Secondary Structure Populations of a Disordered Conformation of ?-Synuclein within E. coli Cells. PLoS One. 2013;8(8):e72286 Authors: Waudby CA, Camilloni C, Fitzpatrick AW, Cabrita LD, Dobson CM, Vendruscolo M, Christodoulou J Abstract ?-Synuclein is a small protein strongly implicated in the pathogenesis of Parkinson's disease and related neurodegenerative disorders. We...
nmrlearner Journal club 0 08-31-2013 06:56 PM
[NMR paper] Protein dynamics in living cells studied by in-cell NMR spectroscopy.
Protein dynamics in living cells studied by in-cell NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Protein dynamics in living cells studied by in-cell NMR spectroscopy. FEBS Lett. 2013 Jan 11; Authors: Li C, Liu M Abstract Most proteins function in cells where protein concentrations can reach 400g/l. However, most quantitative studies of protein properties are performed in idealized, dilute conditions. Recently developed in-cell NMR techniques...
nmrlearner Journal club 0 02-03-2013 10:22 AM
Protein dynamics in living cells studied by in-cell NMR spectroscopy
Protein dynamics in living cells studied by in-cell NMR spectroscopy Available online 11 January 2013 Publication year: 2013 Source:FEBS Letters</br> </br> Most proteins function in cells where protein concentrations can reach 400g/l. However, most quantitative studies of protein properties are performed in idealized, dilute conditions. Recently developed in-cell NMR techniques can provide protein structure and other biophysical properties inside living cells at atomic resolution. Here we review how protein dynamics, including global and internal motions have been...
nmrlearner Journal club 0 02-03-2013 10:13 AM



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 11:12 AM.


Map