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 Rate Thread Display Modes
  #1  
Unread 12-04-2016, 02:24 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,369
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 Spin Saturation Transfer Difference NMR (SSTD NMR): A New Tool to Obtain Kinetic Parameters of Chemical Exchange Processes.

Spin Saturation Transfer Difference NMR (SSTD NMR): A New Tool to Obtain Kinetic Parameters of Chemical Exchange Processes.

Spin Saturation Transfer Difference NMR (SSTD NMR): A New Tool to Obtain Kinetic Parameters of Chemical Exchange Processes.

J Vis Exp. 2016 Nov 12;(117):

Authors: Quirós MT, Macdonald C, Angulo J, Muñoz MP

Abstract
This detailed protocol describes the new Spin Saturation Transfer Difference Nuclear Magnetic Resonance protocol (SSTD NMR), recently developed in our group to study processes of mutual-site chemical exchange that are difficult to analyze by traditional methods. As the name suggests, this method combines the Spin Saturation Transfer method used for small molecules, with the Saturation Transfer Difference (STD) NMR method employed for the study of protein-ligand interactions, by measuring transient spin saturation transfer along increasing saturation times (build-up curves) in small organic and organometallic molecules undergoing chemical exchange. Advantages of this method over existing ones are: there is no need to reach coalescence of the exchanging signals; the method can be applied as long as one signal of the exchanging sites is isolated; there is no need to measure T1 or reach steady state saturation; rate constant values are measured directly, and T1 values are obtained in the same experiment, using only one set of experiments. To test the method, we have studied the dynamics of the hindered rotation of N,N-dimethylamides, for which much data is available for comparison. The thermodynamic parameters obtained using SSTD are very similar to the reported ones (spin-saturation transfer techniques and line-shape analysis). The method can be applied to more challenging substrates that cannot be studied by previous methods. We envisage that the simple experimental set up and the wide applicability of the method to a great variety of substrates will make this a common technique amongst organic and organometallic chemists without extensive expertise in NMR.


PMID: 27911361 [PubMed - in process]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[U. of Ottawa NMR Facility Blog] CEST - Chemical Exchange Saturation Transfer
CEST - Chemical Exchange Saturation Transfer Chemical Exchange Saturation Transfer (CEST) is a technique where one resonance, in slow exchange with a second resonance, is saturated with a selective low power pulse followed by a hard non-selective 90° pulse. The intensity of the second resonance is then diminished due to the transfer of saturation from the first resonance as the result of chemical exchange. The figure below demonstrates this for a 25 mM solution of salicylic acid in H2O/D2O buffered at pH 7. ...
nmrlearner News from NMR blogs 0 04-22-2016 08:45 PM
[NMR paper] Determination of pseudocontact shifts of low-populated excited states by NMR chemical exchange saturation transfer.
Determination of pseudocontact shifts of low-populated excited states by NMR chemical exchange saturation transfer. Determination of pseudocontact shifts of low-populated excited states by NMR chemical exchange saturation transfer. Phys Chem Chem Phys. 2016 Mar 22; Authors: Ma RS, Li QF, Wang AD, Zhang JH, Liu ZJ, Wu JH, Su XC, Ruan K Abstract Despite the critical roles of excited states in protein functions, they remain intractable for most structural studies because of their notably low populations. Chemical shifts for...
nmrlearner Journal club 0 03-24-2016 04:30 PM
[NMR paper] Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data.
Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data. Related Articles Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data. Angew Chem Int Ed Engl. 2016 Jan 28; Authors: Gu Y, Hansen AL, Peng Y, Brüschweiler R Abstract Functional motions of (15) N-labeled proteins can be monitored by solution NMR spin relaxation experiments over a broad range of timescales. These experiments however typically take of the order of several days to a week per...
nmrlearner Journal club 0 01-30-2016 09:13 PM
[NMR paper] Molecular Level Insights on Collagen-Polyphenols Interaction using Spin-Relaxation and Saturation Transfer Difference NMR.
Molecular Level Insights on Collagen-Polyphenols Interaction using Spin-Relaxation and Saturation Transfer Difference NMR. Related Articles Molecular Level Insights on Collagen-Polyphenols Interaction using Spin-Relaxation and Saturation Transfer Difference NMR. J Phys Chem B. 2015 Oct 8; Authors: Reddy RR, Phani Kumar BV, Shanmugam G, Madhan B, Mandal AB Abstract Interaction of small molecules with collagen has far reaching consequences in biological and industrial processes. The interaction between collagen and selected...
nmrlearner Journal club 0 10-09-2015 04:49 PM
[NMR paper] Observing and preventing rubidium runaway in a direct-infusion xenon-spin hyperpolarizer optimized for high-resolution hyper-CEST (chemical exchange saturation transfer using hyperpolarized nuclei) NMR.
Observing and preventing rubidium runaway in a direct-infusion xenon-spin hyperpolarizer optimized for high-resolution hyper-CEST (chemical exchange saturation transfer using hyperpolarized nuclei) NMR. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--link.aip.org-jhtml-linkto.gif Related Articles Observing and preventing rubidium runaway in a direct-infusion xenon-spin hyperpolarizer optimized for high-resolution hyper-CEST (chemical exchange saturation transfer using hyperpolarized nuclei) NMR. J Chem Phys. 2014 Feb 28;140(8):084203 ...
nmrlearner Journal club 0 03-05-2014 11:57 PM
[NMR paper] Synthesis of modified Trichinella spiralis disaccharide epitopes and a comparison of their recognition by chemical mapping and saturation transfer difference NMR.
Synthesis of modified Trichinella spiralis disaccharide epitopes and a comparison of their recognition by chemical mapping and saturation transfer difference NMR. Synthesis of modified Trichinella spiralis disaccharide epitopes and a comparison of their recognition by chemical mapping and saturation transfer difference NMR. Carbohydr Res. 2013 Nov 1;383C:1-13 Authors: Cui L, Ling CC, Sadowska J, Bundle DR Abstract A rat monoclonal antibody 9D4 raised against the cell surface N-glycan of the parasite Trichinella spirallis protects rats...
nmrlearner Journal club 0 11-20-2013 12:42 AM
[Question from NMRWiki Q&A forum] Saturation transfer difference TROSY
Saturation transfer difference TROSY Has anyone added a pulse scheme for cross saturation to their TROSY for Bruker platform? Could you share a pulse sequence if you have one? Thanks!
nmrlearner News from other NMR forums 0 05-18-2013 09:22 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


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 - 2017, 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 07:13 AM.


Map