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 10-22-2010, 06:02 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 Quantification of protein backbone hydrogen-deuterium exchange rates by solid state N

Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy.

Related Articles Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy.

J Biomol NMR. 2010 Oct 20;

Authors: Del Amo JM, Fink U, Reif B

We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline ?-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual (15)N-T (1) timescales). We observed chemical exchange for 6 residues with HDX exchange rates in the range from 0.2 to 5*s(-1). Backbone amide (15)N longitudinal relaxation times that we determined previously are not significantly affected for most residues, yielding no systematic artifacts upon quantification of backbone dynamics (Chevelkov et al. 2008b). Significant exchange was observed for the backbone amides of R21, S36 and K60, as well as for the sidechain amides of N38, N35 and for W41?. These residues could not be fit in our previous motional analysis, demonstrating that amide proton chemical exchange needs to be considered in the analysis of protein dynamics in the solid-state, in case D(2)O is employed as a solvent for sample preparation. Due to the intrinsically long (15)N relaxation times in the solid-state, the approach proposed here can expand the range of accessible HDX rates in the intermediate regime that is not accessible so far with exchange quench and MEXICO type experiments.

PMID: 20960033 [PubMed - as supplied by publisher]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Measurement of amide hydrogen exchange rates with the use of radiation damping
Measurement of amide hydrogen exchange rates with the use of radiation damping Abstract A simple method for measuring amide hydrogen exchange rates is presented, which is based on the selective inversion of water magnetization with the use of radiation damping. Simulations show that accurate exchange rates can be measured despite the complications of radiation damping and cross relaxation to the exchange process between amide and water protons. This method cannot eliminate the contributions of the exchange-relayed NOE and direct NOE to the measured exchange rates, but minimize the...
nmrlearner Journal club 0 09-30-2011 08:01 PM
Site-Specific Solid-State NMR Detection of Hydrogen-Deuterium Exchange Reveals Conformational Changes in a 7-Helical Transmembrane Protein.
Site-Specific Solid-State NMR Detection of Hydrogen-Deuterium Exchange Reveals Conformational Changes in a 7-Helical Transmembrane Protein. Site-Specific Solid-State NMR Detection of Hydrogen-Deuterium Exchange Reveals Conformational Changes in a 7-Helical Transmembrane Protein. Biophys J. 2011 Aug 3;101(3):L23-L25 Authors: Wang S, Shi L, Kawamura I, Brown LS, Ladizhansky V Solid-state NMR spectroscopy is an efficient tool for following conformational dynamics of membrane proteins at atomic resolution. We used this technique for the site-specific...
nmrlearner Journal club 0 08-03-2011 12:00 PM
[NMR paper] Water-protein hydrogen exchange in the micro-crystalline protein crh as observed by solid state NMR spectroscopy.
Water-protein hydrogen exchange in the micro-crystalline protein crh as observed by solid state NMR spectroscopy. Related Articles Water-protein hydrogen exchange in the micro-crystalline protein crh as observed by solid state NMR spectroscopy. J Biomol NMR. 2005 Jul;32(3):195-207 Authors: Böckmann A, Juy M, Bettler E, Emsley L, Galinier A, Penin F, Lesage A We report site-resolved observation of hydrogen exchange in the micro-crystalline protein Crh. Our approach is based on the use of proton T2' -selective 1H-13C-13C correlation spectra for...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Stopped-flow NMR measurement of hydrogen exchange rates in reduced horse cytochrome c
Stopped-flow NMR measurement of hydrogen exchange rates in reduced horse cytochrome c under strongly destabilizing conditions. Related Articles Stopped-flow NMR measurement of hydrogen exchange rates in reduced horse cytochrome c under strongly destabilizing conditions. Proteins. 1998 Aug 1;32(2):241-7 Authors: Bhuyan AK, Udgaonkar JB A procedure to measure exchange rates of fast exchanging protein amide hydrogens by time-resolved NMR spectroscopy following in situ initiation of the reaction by diluting a native protein solution into an...
nmrlearner Journal club 0 11-17-2010 11:15 PM
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state N
Quantification of protein backbone hydrogen-deuterium exchange rates by solid state NMR spectroscopy Abstract We present the quantification of backbone amide hydrogen-deuterium exchange rates (HDX) for immobilized proteins. The experiments make use of the deuterium isotope effect on the amide nitrogen chemical shift, as well as on proton dilution by deuteration. We find that backbone amides in the microcrystalline α-spectrin SH3 domain exchange rather slowly with the solvent (with exchange rates negligible within the individual 15Nâ??T 1 timescales). We observed chemical exchange for 6...
nmrlearner Journal club 0 10-27-2010 08:51 AM
[NMR paper] Human recombinant [C22A] FK506-binding protein amide hydrogen exchange rates from mas
Human recombinant FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Human recombinant FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR. Protein Sci. 1997 Oct;6(10):2203-17 ...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] Mechanism of hydrogen-deuterium exchange in trp repressor studied by 1H-15N NMR.
Mechanism of hydrogen-deuterium exchange in trp repressor studied by 1H-15N NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Mechanism of hydrogen-deuterium exchange in trp repressor studied by 1H-15N NMR. J Mol Biol. 1995 Nov 3;253(4):576-89 Authors: Finucane MD, Jardetzky O Amide proton exchange rates have been measured for fast-exchanging amides in trp aporepressor, and compared with the rates measured in the holorepressor. The results indicate that the presence...
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] Superslow backbone protein dynamics as studied by 1D solid-state MAS exchange NMR spe
Superslow backbone protein dynamics as studied by 1D solid-state MAS exchange NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Superslow backbone protein dynamics as studied by 1D solid-state MAS exchange NMR spectroscopy. J Magn Reson. 1999 Jun;138(2):244-55 Authors: Krushelnitsky A, Reichert D, Hempel G, Fedotov V, Schneider H, Yagodina L, Schulga A Superslow backbone dynamics of the protein barstar and the polypeptide polyglycine was studied by...
nmrlearner Journal club 0 08-21-2010 04:03 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 - 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 02:45 PM.


Map