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 06-24-2022, 11:45 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
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 DMSO-Quenched H/D-Exchange 2D NMR Spectroscopy and Its Applications in Protein Science

DMSO-Quenched H/D-Exchange 2D NMR Spectroscopy and Its Applications in Protein Science

Hydrogen/deuterium (H/D) exchange combined with two-dimensional (2D) NMR spectroscopy has been widely used for studying the structure, stability, and dynamics of proteins. When we apply the H/D-exchange method to investigate non-native states of proteins such as equilibrium and kinetic folding intermediates, H/D-exchange quenching techniques are indispensable, because the exchange reaction is usually too fast to follow by 2D NMR. In this article, we will describe the dimethylsulfoxide...

More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Quenched hydrogen-deuterium exchange NMR of a disease-relevant A?(1-42) amyloid polymorph.
Quenched hydrogen-deuterium exchange NMR of a disease-relevant A?(1-42) amyloid polymorph. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--journals.plos.org-plosone-resource-img-external-pone_120x30.png http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--www.ncbi.nlm.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Quenched hydrogen-deuterium exchange NMR of a disease-relevant A?(1-42) amyloid polymorph. PLoS One. 2017;12(3):e0172862 Authors: Wälti MA, Orts J, Riek R Abstract ...
nmrlearner Journal club 0 08-25-2017 04:11 AM
[NMR paper] Quenched Hydrogen Exchange NMR of Amyloid Fibrils.
Quenched Hydrogen Exchange NMR of Amyloid Fibrils. Related Articles Quenched Hydrogen Exchange NMR of Amyloid Fibrils. Methods Mol Biol. 2016;1345:211-22 Authors: Alexandrescu AT Abstract Amyloid fibrils are associated with a number of human diseases. These aggregatively misfolded intermolecular ?-sheet assemblies constitute some of the most challenging targets in structural biology because to their complexity, size, and insolubility. Here, protocols and controls are described for experiments designed to study hydrogen-bonding in...
nmrlearner Journal club 0 10-12-2015 01:04 AM
[NMR paper] Amide proton solvent protection in amylin fibrils probed by quenched hydrogen exchange NMR.
Amide proton solvent protection in amylin fibrils probed by quenched hydrogen exchange NMR. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.plosone.org-images-pone_120x30.png http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Amide proton solvent protection in amylin fibrils probed by quenched hydrogen exchange NMR. PLoS One. 2013;8(2):e56467 Authors: Alexandrescu AT Abstract Amylin is an endocrine hormone that...
nmrlearner Journal club 0 08-29-2013 01:53 PM
[NMR paper] The H/D-exchange Kinetics of the Escherichia coli Co-chaperonin GroES Studied by 2D-NMR and DMSO-Quenched Exchange Methods.
The H/D-exchange Kinetics of the Escherichia coli Co-chaperonin GroES Studied by 2D-NMR and DMSO-Quenched Exchange Methods. Related Articles The H/D-exchange Kinetics of the Escherichia coli Co-chaperonin GroES Studied by 2D-NMR and DMSO-Quenched Exchange Methods. J Mol Biol. 2013 Apr 11; Authors: Chandak MS, Nakamura T, Makabe K, Takenaka T, Mukaiyama A, Chaudhuri TK, Kato K, Kuwajima K Abstract We studied hydrogen/deuterium-exchange reactions of peptide amide protons of GroES using two different techniques: (1) two-dimensional (1)H-(15)N...
nmrlearner Journal club 0 04-16-2013 07:46 PM
The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments
The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments Abstract Dimethylsulfoxide (DMSO)-quenched hydrogen/deuterium (H/D)-exchange is a powerful method to characterize the H/D-exchange behaviors of proteins and protein assemblies, and it is potentially useful for investigating non-protected fast-exchanging amide protons in the unfolded state. However, the method has not been used for studies on fully unfolded proteins in a concentrated denaturant or protein solutions at high salt concentrations. In all of the current DMSO-quenched H/D-exchange studies of...
nmrlearner Journal club 0 02-11-2013 08:42 AM
[NMR paper] The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments.
The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary-Button_120x27px_FullText.gif Related Articles The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments. Protein Sci. 2013 Jan 22; Authors: Chandak MS, Nakamura T, Takenaka T, Chaudhuri TK, Yagi-Utsumi M, Chen J, Kato K, Kuwajima K Abstract DMSO-quenched H/D-exchange is a powerful method to characterize the H/D-exchange behaviors of...
nmrlearner Journal club 0 02-03-2013 10:19 AM
The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments
The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments Abstract DMSO-quenched H/D-exchange is a powerful method to characterize the H/D-exchange behaviors of proteins and protein assemblies, and it is potentially useful for investigating non-protected fast-exchanging amide protons in the unfolded state. However, the method has not been used for studies on fully unfolded proteins in a concentrated denaturant or protein solutions at high salt concentrations. In all of the current DMSO-quenched H/D-exchange studies of proteins so far reported, lyophilization was...
nmrlearner Journal club 0 02-03-2013 09:54 AM
[NMR paper] An NMR-based quenched hydrogen exchange investigation of model amyloid fibrils formed
An NMR-based quenched hydrogen exchange investigation of model amyloid fibrils formed by cold shock protein A. Related Articles An NMR-based quenched hydrogen exchange investigation of model amyloid fibrils formed by cold shock protein A. Pac Symp Biocomput. 2001;:67-78 Authors: Alexandrescu AT Acid-denatured cold shock protein A (CspA) self-assembles into polymers with properties typical of amyloid fibrils. In the present work, a quenched hydrogen exchange experiment was used to probe the interactions of CspA fibrils with solvent. Exchange...
nmrlearner Journal club 0 11-19-2010 08:32 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 02:06 PM.


Map