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: 2 votes, 5.00 average. Display Modes
  #1  
Unread 02-24-2016, 02:05 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,175
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 A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using q-NMR.

A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using q-NMR.

Related Articles A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using q-NMR.

Anal Biochem. 2016 Feb 17;

Authors: Goldoni L, Beringhelli T, Rocchia W, Realini N, Piomelli D

Abstract
Absolute analyte quantification by NMR spectroscopy is rarely pursued in metabolomics, even though this would allow researchers to compare results obtained using different techniques. Here we report on a new protocol that permits, after pH-controlled serum protein removal, the sensitive quantification (LOD 5-25 ?M) of hydrophilic nutrients and metabolites in the extracellular medium of cells in cultures. The method does not require the use of databases and utilizes PULCON (PUlse Length Based Concentration Determination) quantitative NMR to obtain results that are significantly more accurate and reproducible than those obtained by CPMG (Carr-Purcell-Meiboom-Gill) sequence or post processing filtering approaches. Three practical applications of the method highlight its flexibility under different cell culture conditions. We identified and quantified (i) metabolic differences, between genetically engineered human cell lines; (ii) alterations in cellular metabolism induced by differentiation of mouse myoblasts into myotubes; and (iii) metabolic changes caused by activation of neurotransmitter receptors in mouse myoblasts. Thus, the new protocol offers an easily implementable, efficient and versatile tool for the investigation of cellular metabolism and signal transduction.


PMID: 26898303 [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
A simple protocol for amino acid type selective isotope labeling in insect cells with improved yields and high reproducibility
A simple protocol for amino acid type selective isotope labeling in insect cells with improved yields and high reproducibility Abstract An easy to use and robust approach for amino acid type selective isotope labeling in insect cells is presented. It relies on inexpensive commercial media and can be implemented in laboratories without sophisticated infrastructure. In contrast to previous protocols, where either high protein amounts or high incorporation ratios were obtained, here we achieve both at the same time. By supplementing media with a well considered amount of yeast extract,...
nmrlearner Journal club 0 10-05-2011 08:57 PM
NMR-based metabolomics of mammalian cell and tissue cultures
NMR-based metabolomics of mammalian cell and tissue cultures Abstract NMR spectroscopy was used to evaluate growth media and the cellular metabolome in two systems of interest to biomedical research. The first of these was a Chinese hamster ovary cell line engineered to express a recombinant protein. Here, NMR spectroscopy and a quantum mechanical total line shape analysis were utilized to quantify 30 metabolites such as amino acids, Krebs cycle intermediates, activated sugars, cofactors, and others in both media and cell extracts. The impact of bioreactor scale and addition of...
nmrlearner Journal club 0 03-09-2011 04:19 AM
NMR-based metabolomics of mammalian cell and tissue cultures.
NMR-based metabolomics of mammalian cell and tissue cultures. NMR-based metabolomics of mammalian cell and tissue cultures. J Biomol NMR. 2011 Mar 4; Authors: Aranibar N, Borys M, Mackin NA, Ly V, Abu-Absi N, Abu-Absi S, Niemitz M, Schilling B, Li ZJ, Brock B, Russell RJ, Tymiak A, Reily MD NMR spectroscopy was used to evaluate growth media and the cellular metabolome in two systems of interest to biomedical research. The first of these was a Chinese hamster ovary cell line engineered to express a recombinant protein. Here, NMR spectroscopy and a...
nmrlearner Journal club 0 03-05-2011 01:02 PM
[NMR paper] Cell-free protein production and labeling protocol for NMR-based structural proteomic
Cell-free protein production and labeling protocol for NMR-based structural proteomics. Related Articles Cell-free protein production and labeling protocol for NMR-based structural proteomics. Nat Methods. 2004 Nov;1(2):149-53 Authors: Vinarov DA, Lytle BL, Peterson FC, Tyler EM, Volkman BF, Markley JL Structural proteomics requires robust, scalable methods. Here we describe a wheat germ cell-free platform for protein production that supports efficient NMR structural studies of eukaryotic proteins and offers advantages over cell-based methods....
nmrlearner Journal club 0 11-24-2010 10:01 PM
[NMR paper] A simple protocol to study blue copper proteins by NMR.
A simple protocol to study blue copper proteins by NMR. Related Articles A simple protocol to study blue copper proteins by NMR. Eur J Biochem. 2003 Feb;270(4):600-9 Authors: Gelis I, Katsaros N, Luchinat C, Piccioli M, Poggi L In the case of oxidized plastocyanin from Synechocystis sp. PCC6803, an NMR approach based on classical two and three dimensional experiments for sequential assignment leaves unobserved 14 out of 98 amino acids. A protocol which simply makes use of tailored versions of 2D HSQC and 3D CBCA(CO)NH and CBCANH leads to the...
nmrlearner Journal club 0 11-24-2010 09:01 PM
Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecu
Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecules. Rapid, Accurate and Simple Model to Predict NMR Chemical Shifts for Biological Molecules. J Phys Chem B. 2010 Nov 18; Authors: Atieh Z, Aubert-Fre?con M, Allouche AR We present a new model to predict chemical shifts for biological molecules. It is simple, fast, and involves a limited number of parameters. It is particularly adapted to be used in molecular dynamics studies with a molecular mechanic potential. We test the model for polyamines, which are rather...
nmrlearner Journal club 0 11-20-2010 06:01 PM
[NMR paper] Simple techniques for the quantification of protein secondary structure by 1H NMR spe
Simple techniques for the quantification of protein secondary structure by 1H NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Simple techniques for the quantification of protein secondary structure by 1H NMR spectroscopy. FEBS Lett. 1991 Nov 18;293(1-2):72-80 Authors: Wishart DS, Sykes BD, Richards FM Previous work by Wishart et al. (in press) and others has shown a strong tendency for protein secondary structure to be manifested in 1H NMR chemical...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] Simple techniques for the quantification of protein secondary structure by 1H NMR spe
Simple techniques for the quantification of protein secondary structure by 1H NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Simple techniques for the quantification of protein secondary structure by 1H NMR spectroscopy. FEBS Lett. 1991 Nov 18;293(1-2):72-80 Authors: Wishart DS, Sykes BD, Richards FM Previous work by Wishart et al. (in press) and others has shown a strong tendency for protein secondary structure to be manifested in 1H NMR chemical...
nmrlearner Journal club 0 08-21-2010 11:12 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 03:21 PM.


Map