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 08-22-2010, 02:27 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,587
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 Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium

Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR.

Related Articles Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR.

Protein Sci. 1996 Jun;5(6):1060-6

Authors: Yi Q, Baker D

We use mass spectrometry in conjunction with hydrogen-deuterium exchange and NMR to characterize the conformational dynamics of the 62-residue IgG binding domain of protein L under conditions in which the native state is marginally stable. Mass spectra of protein L after short incubations in D2O reveal the presence of two distinct populations containing different numbers of protected protons. NMR experiments indicate that protons in the hydrophobic core are protected in one population, whereas all protons are exchanged for deuterons in the other. As the exchange period is increased, molecules are transferred from the former population to the latter. The absence of molecules with a subset of the core protons protected suggests that exchange occurs in part via a highly concerted transition to an excited state in which all protons exchange rapidly with deuterons. A steady increase in the molecular weight of the population with protected protons, and variation in the exchange rates of the individual protected protons indicates the presence of an additional exchange mechanism. A simple model in which exchange results from rapid (> 10(5)/s) local fluctuations around the native state superimposed upon transitions to an unfolded excited state at approximately 0.06/s is supported by qualitative agreement between the observed mass spectra and the mass spectra simulated according to the model using NMR-derived estimates of the proton exchange rates.

PMID: 8762137 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
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] Measuring pK(a) values in protein folding transition state ensembles by NMR spectrosc
Measuring pK(a) values in protein folding transition state ensembles by NMR spectroscopy. Related Articles Measuring pK(a) values in protein folding transition state ensembles by NMR spectroscopy. J Am Chem Soc. 2005 Jun 29;127(25):8904-5 Authors: Tollinger M, Kay LE, Forman-Kay JD Protein folding kinetic data have been obtained for the marginally stable N-terminal SH3 domain of the Drosophila protein drk as a function of pH in order to investigate the electrostatic properties of Asp8 in the folding transition state ensemble. The slow exchange...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Evidence for a strong hydrogen bond in the catalytic dyad of transition-state analogu
Evidence for a strong hydrogen bond in the catalytic dyad of transition-state analogue inhibitor complexes of chymotrypsin from proton-triton NMR isotope shifts. Related Articles Evidence for a strong hydrogen bond in the catalytic dyad of transition-state analogue inhibitor complexes of chymotrypsin from proton-triton NMR isotope shifts. J Am Chem Soc. 2002 Apr 24;124(16):4196-7 Authors: Westler WM, Frey PA, Lin J, Wemmer DE, Morimoto H, Williams PG, Markley JL We present here the first accurate measurements of 1H (H) versus 3H (T) isotope...
nmrlearner Journal club 0 11-24-2010 08:49 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 15N??T 1 timescales). We observed chemical exchange for 6...
nmrlearner Journal club 0 10-27-2010 08:51 AM
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...
nmrlearner Journal club 0 10-22-2010 06:02 AM
NMR study of hydrogen exchange during the B-Z transition of a DNA duplex induced by t
NMR study of hydrogen exchange during the B-Z transition of a DNA duplex induced by the Z? domains of yatapoxvirus E3L. Related Articles NMR study of hydrogen exchange during the B-Z transition of a DNA duplex induced by the Z? domains of yatapoxvirus E3L. FEBS Lett. 2010 Oct 8; Authors: Lee EH, Seo YJ, Ahn HC, Kang YM, Kim HE, Lee YM, Choi BS, Lee JH The Yaba-like disease viruses (YLDV) are members of the Yatapoxvirus family and have double-stranded DNA genomes. The E3L protein, which is essential for pathogenesis in the vaccinia virus,...
nmrlearner Journal club 0 10-13-2010 02:18 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
[Question from NMRWiki Q&A forum] What has been done with direct detection of Deuterium?
What has been done with direct detection of Deuterium? Hello, I am trying to investigate what has been done in NMR using direct detection of deuterium in liquids. - Could you suggest any citations? What kind of sensitivity gain there is in using broadband probe vs. lock channel? Has anything been done/can be done to detect scalar couplings with protons like in COSY or TOCSY? Are HD couplings other than geminal detectable? Thanks.
nmrlearner News from other NMR forums 0 08-22-2010 02:30 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 02:45 AM.


Map