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 02-29-2020, 09:52 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 Sensitivity-enhanced three-dimensional and carbon-detected two-dimensional NMR of proteins using hyperpolarized water

Sensitivity-enhanced three-dimensional and carbon-detected two-dimensional NMR of proteins using hyperpolarized water

Abstract

Signal enhancements of up to two orders of magnitude in protein NMR can be achieved by employing HDO as a vector to introduce hyperpolarization into folded or intrinsically disordered proteins. In this approach, hyperpolarized HDO produced by dissolution-dynamic nuclear polarization (D-DNP) is mixed with a protein solution waiting in a high-field NMR spectrometer, whereupon amide proton exchange and nuclear Overhauser effects (NOE) transfer hyperpolarization to the protein and enable acquisition of a signal-enhanced high-resolution spectrum. To date, the use of this strategy has been limited to 1D and 1H-15N 2D correlation experiments. Here we introduce 2D 13C-detected D-DNP, to reduce exchange-induced broadening and other relaxation penalties that can adversely affect proton-detected D-DNP experiments. We also introduce hyperpolarized 3D spectroscopy, opening the possibility of D-DNP studies of larger proteins and IDPs, where assignment and residue-specific investigation may be impeded by spectral crowding. The signal enhancements obtained depend in particular on the rates of chemical and magnetic exchange of the observed residues, thus resulting in non-uniform â??hyperpolarization-selectiveâ?? signal enhancements. The resulting spectral sparsity, however, makes it possible to resolve and monitor individual amino acids in IDPs of over 200 residues at acquisition times of just over a minute. We apply the proposed experiments to two model systems: the compactly folded protein ubiquitin, and the intrinsically disordered protein (IDP) osteopontin (OPN).



Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] High-resolution 2D NMR of disordered proteins enhanced by hyperpolarized water.
High-resolution 2D NMR of disordered proteins enhanced by hyperpolarized water. High-resolution 2D NMR of disordered proteins enhanced by hyperpolarized water. Anal Chem. 2018 Mar 12;: Authors: Szekely O, Olsen GL, Felli IC, Frydman L Abstract This study demonstrates the usefulness derived from relying on hyperpolarized water obtained by dissolution DNP, for site-resolved biophysical NMR studies of intrinsically disordered proteins. Thanks to the facile amide-solvent exchange experienced by protons in these proteins, 2D NMR...
nmrlearner Journal club 0 03-13-2018 07:39 PM
[NMR paper] Sensitivity-enhanced Four-dimensional Amide-amide Correlation NMR Experiments for Sequential Assignment of Proline-rich Disordered Proteins.
Sensitivity-enhanced Four-dimensional Amide-amide Correlation NMR Experiments for Sequential Assignment of Proline-rich Disordered Proteins. Sensitivity-enhanced Four-dimensional Amide-amide Correlation NMR Experiments for Sequential Assignment of Proline-rich Disordered Proteins. J Am Chem Soc. 2018 Feb 28;: Authors: Wong LE, Maier J, Wienands J, Becker S, Griesinger C Abstract Proline is prevalent in intrinsically disordered proteins (IDPs). NMR assignment of proline-rich IDPs is a challenge due to low dispersion of chemical...
nmrlearner Journal club 0 03-01-2018 09:20 PM
Sensitivity-enhanced detection of non-labile proton and carbon NMR spectra on water resonances #DNPNMR
From The DNP-NMR Blog: Sensitivity-enhanced detection of non-labile proton and carbon NMR spectra on water resonances #DNPNMR Novakovic, M., et al., Sensitivity-enhanced detection of non-labile proton and carbon NMR spectra on water resonances. Phys. Chem. Chem. Phys., 2017. 20(1): p. 56-62. https://www.ncbi.nlm.nih.gov/pubmed/29171604
nmrlearner News from NMR blogs 0 02-19-2018 08:46 PM
[NMR paper] A Novel High-Resolution and Sensitivity-Enhanced Three-Dimensional Solid-State NMR Experiment Under Ultrafast Magic Angle Spinning Conditions.
A Novel High-Resolution and Sensitivity-Enhanced Three-Dimensional Solid-State NMR Experiment Under Ultrafast Magic Angle Spinning Conditions. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.nature.com-images-lo_npg.gif http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.ncbi.nlm.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles A Novel High-Resolution and Sensitivity-Enhanced Three-Dimensional Solid-State NMR Experiment Under Ultrafast Magic Angle Spinning Conditions. Sci Rep. 2015;5:11810 ...
nmrlearner Journal club 0 08-03-2016 04:58 AM
Closed-cycle cold helium magic-angle spinning for sensitivity-enhanced multi-dimensional solid-state NMR
From The DNP-NMR Blog: Closed-cycle cold helium magic-angle spinning for sensitivity-enhanced multi-dimensional solid-state NMR Matsuki, Y., et al., Closed-cycle cold helium magic-angle spinning for sensitivity-enhanced multi-dimensional solid-state NMR. J Magn Reson, 2015. 259: p. 76-81. http://www.ncbi.nlm.nih.gov/pubmed/26302269
nmrlearner News from NMR blogs 0 01-22-2016 04:20 PM
[NMR paper] Closed-cycle cold helium magic-angle spinning for sensitivity-enhanced multi-dimensional solid-state NMR.
Closed-cycle cold helium magic-angle spinning for sensitivity-enhanced multi-dimensional solid-state NMR. Related Articles Closed-cycle cold helium magic-angle spinning for sensitivity-enhanced multi-dimensional solid-state NMR. J Magn Reson. 2015 Aug 12;259:76-81 Authors: Matsuki Y, Nakamura S, Fukui S, Suematsu H, Fujiwara T Abstract Magic-angle spinning (MAS) NMR is a powerful tool for studying molecular structure and dynamics, but suffers from its low sensitivity. Here, we developed a novel helium-cooling MAS NMR probe system...
nmrlearner Journal club 0 08-25-2015 08:30 PM
Closed-cycle cold helium magic-angle spinning for sensitivity-enhanced multi-dimensional solid-state NMR
Closed-cycle cold helium magic-angle spinning for sensitivity-enhanced multi-dimensional solid-state NMR Publication date: Available online 12 August 2015 Source:Journal of Magnetic Resonance</br> Author(s): Yoh Matsuki, Shinji Nakamura, Shigeo Fukui, Hiroto Suematsu, Toshimichi Fujiwara</br> Magic-angle spinning (MAS) NMR is a powerful tool for studying molecular structure and dynamics, but suffers from its low sensitivity. Here, we developed a novel helium-cooling MAS NMR probe system adopting a closed-loop gas recirculation mechanism. In addition to...
nmrlearner Journal club 0 08-13-2015 02:00 PM
Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins
Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins Abstract Well-resolved 2Hâ??13C correlation spectra, reminiscent of 1Hâ??13C correlations, are obtained for perdeuterated ubiquitin and for perdeuterated outer-membrane protein G (OmpG) from E. coli by exploiting the favorable lifetime of 2H double-quantum (DQ) states. Sufficient signal-to-noise was achieved due to the short deuterium T 1, allowing for high repetition rates and enabling 3D experiments with a 2Hâ??13C transfer step in a reasonable time....
nmrlearner Journal club 0 11-01-2011 01:52 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 - 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 12:27 PM.


Map