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  
Old 10-29-2011, 12:15 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,776
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 The Effect of Viscosity on 1H NOESY Spectra

The Effect of Viscosity on 1H NOESY Spectra

For small molecules, 1H 2D NOESY spectra exhibit positive NOE's between protons close to one another in space and the off-diagonal correlations are opposite in phase to those of the diagonals. As molecules become larger and larger the motional correlation times become longer and longer. As the correlation times become longer and longer, the NOE's become less positive, cross zero and then become negative. For large molecules, like proteins, the NOE's are negative and the off-diagonal correlations between close protons are of the same phase as the diagonal peaks. When the correlation times are extremely long, for example in rigid macromolecules or solids, the dipolar coupling among all of the protons is inefficiently averaged by molecular motions and spin diffusion becomes efficient. Spin diffusion allows all of the protons in a dipolar coupled network to exhibit correlations with one another. The sign of the correlations is similar to that observed for chemical exchange or negative NOE's. This phenomenon is demonstrated in the figure below. In the figure, positive contours are represented in black and negative contours are represented in red. The NOESY spectrum on the left is that of a solution of menthol in CDCl3. The off-diagonal correlations between proximate protons is opposite in phase compared to the diagonal responses, typical of small molecules with short correlation times. The NOESY spectrum on the right is that of the same solution of menthol dissolved in a very viscous fluorinated oil. The extreme viscosity of the sample is sufficient to make the correlation time for the molecules very long such that the menthol behaves like a very large macromolecule where spin diffusion is efficient. As a result, off-diagonal responses are of the same phase as those of the diagonal and are observed between all protons in the molecule.This technique has been cleverly applied* to mixtures of molecules immersed in viscous oils where intra-molecular correlations are observed whereas inter-molecular correlations are not observed. The data allow for the observation of the constituent components of complex mixtures.


* Andre J. Simpson, Gwen Woods, and Omid Mehrzad, Anal. Chem, 80, 186-194 (2008).




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
[Question from NMRWiki Q&A forum] Folding vs. Aliasing (in NOESY spectra)
Folding vs. Aliasing (in NOESY spectra) Hi everyone Does anyone happen to know if/how I can tell whether peaks outside the spectral width were either folded or aliased into a (NOESY) spectrum, when all I have is the spectrum file (in .ucsf format, say), and I do not know how the spectrum was recorded? I am not aiming at finding out whether there were any such 'outside peaks', what I would like to know is, in case there were some, where I would have to look for them. Thanks a lot for your time!
nmrlearner News from other NMR forums 0 02-02-2012 09:43 PM
[Question from NMRWiki Q&A forum] Auto peak picking of N15Edit NOESY and C13 Edit NOESY spectrum
Auto peak picking of N15Edit NOESY and C13 Edit NOESY spectrum Dear friends, I am in process of doing structure calculation of a dimeric protein. The problem I faced is regarding the assignment of N15Edit NOESY and C13 Edit NOESY spectrum.I have already processed the fid data and converted to sparky ucsf format. Is there options available in sparky for auto peak picking, integration and assignment of my NOESY spectrum? And second query is regarding the generation of input files for structure calculation. In our Lab we are using ARIA 2.1 software for structure calculation? Is there any...
nmrlearner News from other NMR forums 0 12-14-2011 07:14 PM
Optimization of NMR spectroscopy of encapsulated proteins dissolved in low viscosity fluids
Optimization of NMR spectroscopy of encapsulated proteins dissolved in low viscosity fluids Abstract Comprehensive application of solution NMR spectroscopy to studies of macromolecules remains fundamentally limited by the molecular rotational correlation time. For proteins, molecules larger than 30 kDa require complex experimental methods, such as TROSY in conjunction with isotopic labeling schemes that are often expensive and generally reduce the potential information available. We have developed the reverse micelle encapsulation strategy as an alternative approach. Encapsulation of...
nmrlearner Journal club 0 07-15-2011 09:10 PM
[NMR paper] Simplification of protein NOESY spectra using bioorganic precursor synthesis and NMR
Simplification of protein NOESY spectra using bioorganic precursor synthesis and NMR spectral editing. Related Articles Simplification of protein NOESY spectra using bioorganic precursor synthesis and NMR spectral editing. J Am Chem Soc. 2004 May 5;126(17):5348-9 Authors: Lichtenecker R, Ludwiczek ML, Schmid W, Konrat R A novel method is proposed for the analysis of protein NOEs in solution. In this approach, chemically synthesized precursor compounds for the amino acids valine, leucine, and isoleucine are used for amino acid specific labeling...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).
Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). Related Articles Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE). J Biomol NMR. 2002 Aug;23(4):271-87 Authors: Gronwald W, Moussa S, Elsner R, Jung A, Ganslmeier B, Trenner J, Kremer W, Neidig KP, Kalbitzer HR Automated assignment of NOESY spectra is a prerequisite for automated structure determination of biological macromolecules. With the program KNOWNOE we present a novel, knowledge based approach to this problem. KNOWNOE...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Suppression of diagonal peaks in TROSY-type 1H NMR NOESY spectra of 15N-labeled prote
Suppression of diagonal peaks in TROSY-type 1H NMR NOESY spectra of 15N-labeled proteins. Related Articles Suppression of diagonal peaks in TROSY-type 1H NMR NOESY spectra of 15N-labeled proteins. J Magn Reson. 1999 Oct;140(2):499-503 Authors: Meissner A, Sørensen OW A novel method for suppression of diagonal peaks in the amide region of NOESY NMR spectra of 15N-labeled proteins is presented. The method is particularly useful for larger proteins at high magnetic fields where interference between dipolar and chemical shift anisotropy relaxation...
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] The effects of temperature, viscosity, and molecular size on the aluminum-27 QCT NMR
The effects of temperature, viscosity, and molecular size on the aluminum-27 QCT NMR of transferrins. Related Articles The effects of temperature, viscosity, and molecular size on the aluminum-27 QCT NMR of transferrins. J Magn Reson B. 1996 Feb;110(2):182-7 Authors: Aramini JM, Vogel HJ A number of reports in recent years have demonstrated the feasibility of detecting quadrupolar metal ions bound tightly to rather large proteins via the quadrupolar central transition (QCT) NMR approach. In this article, an in-depth investigation of several...
nmrlearner Journal club 0 08-22-2010 02:27 PM
Theoretical Noesy Spectra
Hello Does anybody know how can i obtain a theoretical Noesy Spectra? Thanks in advance J.I. MIranda
ji.miranda NMR structure calculation 0 02-19-2007 07:55 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 04:35 AM.


Map