BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > NMR community > News from NMR blogs
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  
Unread 03-12-2014, 01:10 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,174
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 Chemical Exchange Agents to Simplify NMR Spectra

Chemical Exchange Agents to Simplify NMR Spectra

One can simplify 1H NMR spectra by eliminating exchangeable proton signals. This is most commonly done by adding a drop or two of D2O to the NMR sample. An example of this can be seen in a previous post. The deuterium from the D2O replaces the exchangeable protons (-OH, -NH, -NH2, -COOH) of the sample and their 1H signals disappear. The disadvantage of this technique is the introduction of a strong HDO signal which may overlap with other signals in the spectrum and thereby hinder the interpretation.

An alternative of the "D2O shake" is to add a drop or two of concentrated trifluoroacetic acid (TFA) to the sample. TFA has a single exchangeable proton at ~ 14 - 16 ppm. The -COOH proton of the TFA exchanges with the exchangeable protons in the sample. The exchange rate is usually fast enough on the NMR time scale such that the resultant spectrum has a single broad resonance representing all of the exchangeable protons at a chemical shift between the chemical shift of the pure TFA and that of the exchangeable protons in the sample (usually >10 ppm depending on the sample and the amount of TFA added). The broad peak at a shift > 10 ppm is not likely to overlap with other resonances in the spectrum and therefore will not hinder the interpretation of the data. An example of the use of TFA is shown in the figure below.


The bottom spectrum is that of sucrose dissolved in DMSO-d6. One can observe all of the -OH protons in addition to all of the other sugar protons. The middle spectrum is that of pure TFA in DMSO-d6. The -COOH resonance appears at ~ 15.6 ppm. The top spectrum is that of sucrose in DMSO-d6 with a drop of TFA added. One can see that all of the -OH protons of the sugar (highlighted in yellow) have combined with the -COOH resonance of the TFA yielding a single broad resonance at ~ 13 ppm as a result of the exchange. In addition to moving the -OH resonances out of the way, one can see simplifications to the other sugar protons as the result of loosing the J coupling between the -OH protons and the remaining sugar protons.

A comparison of the use of TFA compared to D2O as an exchange agent is shown in the figure below.


Both methods produce similar results except that the spectrum with added D2O has a large HDO peak (off-scale in the figure) which overlaps with other signals.



Source: University of Ottawa NMR Facility Blog
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Nutation frequency modulation on NMR signal of nuclear spins in chemical exchange with solvent water under the BEST conditions.
Nutation frequency modulation on NMR signal of nuclear spins in chemical exchange with solvent water under the BEST conditions. Related Articles Nutation frequency modulation on NMR signal of nuclear spins in chemical exchange with solvent water under the BEST conditions. Magn Reson Chem. 2014 Jan 24; Authors: Yao S, Keizer DW Abstract Solvent exchange properties of protein backbone amide protons provide valuable residue-specific information on protein solvent accessibility, structure stability and flexibility and hence are of significant...
nmrlearner Journal club 0 01-25-2014 02:07 PM
[Question from NMRWiki Q&A forum] Software to calculate chemical exchange lineshape
Software to calculate chemical exchange lineshape Are there any modern programs (preferably freeware) that will simulate line broadening in the presence of exchange. Somewhere I have a copy of "DNMR3" (on a 5 1/4 " floppy) and I feel it will be a nightmare trying to get this to work (particularly the graphics output). Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 04-10-2013 07:05 AM
[NMR paper] Probing Slow Chemical Exchange at Carbonyl Sites in Proteins by Chemical Exchange Saturation Transfer NMR Spectroscopy.
Probing Slow Chemical Exchange at Carbonyl Sites in Proteins by Chemical Exchange Saturation Transfer NMR Spectroscopy. Probing Slow Chemical Exchange at Carbonyl Sites in Proteins by Chemical Exchange Saturation Transfer NMR Spectroscopy. Angew Chem Int Ed Engl. 2013 Feb 28; Authors: Vallurupalli P, Kay LE Abstract Seeing the invisible: A 13 CO NMR chemical exchange saturation transfer (CEST) experiment for the study of "invisible" excited protein states with lifetimes on the order of 5-50 ms has been developed. The 13 CO chemical...
nmrlearner Journal club 0 03-02-2013 11:45 AM
[NMR thesis] I. Quantum-mechanical chemical exchange. II. NMR of semiconductors
I. Quantum-mechanical chemical exchange. II. NMR of semiconductors Kurur, Narayanan Damodaran (1992) I. Quantum-mechanical chemical exchange. II. NMR of semiconductors. Dissertation (Ph.D.), California Institute of Technology. http://resolver.caltech.edu/CaltechTHESIS:09022011-090934651 More...
nmrlearner NMR theses 0 09-02-2011 07:31 PM
[Question from NMRWiki Q&A forum] Chemical exchange of Tyr residues - what information can be found about dynamics?
Chemical exchange of Tyr residues - what information can be found about dynamics? I have an aromatic spectrum of Tyr residues in p53 DNA binding domain. No peaks are seen for Tyr-205 at high temp, but as temp decreases 4 peaks are shown. Tyr-163 and Tyr-236 show two peak each at high temps. How come there aren't 4 peaks? The dynamic processes are said to occur on different time scales. What is the interpretation of this information? How is the core domain of p53 influenced by this? Thanks for your help! Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 04-11-2011 12:48 AM
TROSY-selected ZZ-exchange experiment for characterizing slow chemical exchange in large proteins
TROSY-selected ZZ-exchange experiment for characterizing slow chemical exchange in large proteins Abstract A TROSY-selected ZZ-exchange experiment is described for measuring slow chemical exchange rates by monitoring the TROSY component of 15N longitudinal magnetization. Application of the proposed pulse sequence to the cadherin 8 N-terminal extracelluar domain demonstrates that enhanced sensitivity is obtained, compared to a previously described TROSY-detected ZZ-exchange sequence (Sahu et al. J Am Chem Soc 129: 13232â??13237, 2007), by preserving the TROSY effect during the mixing...
nmrlearner Journal club 0 01-09-2011 12:46 PM
[NMR paper] Editing of chemical exchange-relayed NOEs in NMR experiments for the observation of p
Editing of chemical exchange-relayed NOEs in NMR experiments for the observation of protein-water interactions. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Editing of chemical exchange-relayed NOEs in NMR experiments for the observation of protein-water interactions. J Magn Reson. 1999 Feb;136(2):214-8 Authors: Melacini G, Kaptein R, Boelens R An experimental approach for the editing of exchange-relayed NOEs in water-selective NOE experiments is presented. The...
nmrlearner Journal club 0 08-21-2010 04:03 PM
Programs for simulation of lineshape change due to chemical exchange
http://www.shokhirev.com/nikolai/abc/nmrtut/ik1.gif 1) A simple web server for prediction of effect of chemical exchange on NMR lineshapes can be found here. 2) TwoLineNMR and TwoSiteExchange 3) MEXICO from Alex Bain group.
nmrlearner NMR software 1 06-04-2009 05:54 PM



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 Off
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 07:25 AM.


Map