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 01-15-2014, 05:16 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 Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding.

Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding.

Related Articles Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding.

Prog Nucl Magn Reson Spectrosc. 2014 Feb;77:49-68

Authors: Tugarinov V

Abstract
A description of the utility of deuteration in protein NMR is provided with an emphasis on quantitative evaluation of the effects of deuteration on a number of NMR parameters of proteins: (1) chemical shifts, (2) scalar coupling constants, (3) relaxation properties (R1 and R2 rates) of nuclei directly attached to one or more deuterons as well as protons of methyl groups in a highly deuterated environment, (4) scalar relaxation of (15)N and (13)C nuclei in (15)N-D and (13)C-D spin systems as a measure of hydrogen bonding strength, and (5) NOE-based applications of deuteration in NMR studies of protein structure. The discussion is restricted to the 'indirect' use of deuterium in the sense that the description of NMR parameters and properties of the nuclei affected by nearby deuterons ((15)N, (13)C, (1)H) is provided rather than those of deuterium itself.


PMID: 24411830 [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
[NMR paper] Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates
Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates Publication date: Available online 11 October 2013 Source:Journal of Magnetic Resonance</br> Author(s): Mitsuhiro Takeda , Yohei Miyanoiri , Tsutomu Terauchi , Chin-Jiun Yang , Masatsune Kainosho</br> Polar side-chains in proteins play important roles in formingand maintaining three-dimensional structures, and thus participate invarious biological functions. Until recently, most protein NMR studieshave focused onthe non-exchangeable protons of amino acid...
nmrlearner Journal club 0 10-11-2013 10:43 AM
Indirect Use of Deuterium in Solution NMR Studies of Protein Structure and Hydrogen Bonding
Indirect Use of Deuterium in Solution NMR Studies of Protein Structure and Hydrogen Bonding Publication date: Available online 28 August 2013 Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br> Author(s): Vitali Tugarinov</br> A description of the utility of deuteration in protein NMR is provided with an emphasis on quantitative evaluation of the effects of deuteration on a number of NMR parameters of proteins: (1) chemical shifts, (2) scalar coupling constants, (3) relaxation properties (R 1 and R 2 rates) of nuclei directly attached to one or more...
nmrlearner Journal club 0 08-29-2013 01:27 AM
Molecular Hydrogen Tweezers: Structure and Mechanisms by Neutron Diffraction, NMR, and Deuterium Labeling Studies in Solid and Solution
Molecular Hydrogen Tweezers: Structure and Mechanisms by Neutron Diffraction, NMR, and Deuterium Labeling Studies in Solid and Solution Felix Schulz, Victor Sumerin, Sami Heikkinen, Bjo?rn Pedersen, Cong Wang, Michiko Atsumi, Markku Leskela?, Timo Repo, Pekka Pyykko?, Winfried Petry and Bernhard Rieger http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja206394w/aop/images/medium/ja-2011-06394w_0015.gif Journal of the American Chemical Society DOI: 10.1021/ja206394w http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
nmrlearner Journal club 0 11-30-2011 09:37 AM
[NMR paper] NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of c
NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths. Related Articles NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths. Protein Sci. 2001 Sep;10(9):1856-68 Authors: Alexandrescu AT, Snyder DR, Abildgaard F Hydrogen bonding in cold-shock protein A of Escherichia coli has been investigated using long-range HNCO spectroscopy. Nearly half of the...
nmrlearner Journal club 0 11-19-2010 08:44 PM
[NMR paper] Solution (1)H NMR study of the influence of distal hydrogen bonding and N terminus ac
Solution (1)H NMR study of the influence of distal hydrogen bonding and N terminus acetylation on the active site electronic and molecular structure of Aplysia limacina cyanomet myoglobin. Related Articles Solution (1)H NMR study of the influence of distal hydrogen bonding and N terminus acetylation on the active site electronic and molecular structure of Aplysia limacina cyanomet myoglobin. J Biol Chem. 2000 Jan 14;275(2):742-51 Authors: Nguyen BD, Xia Z, Cutruzzolá F, Allocatelli CT, Brunori M, La Mar GN The sea hare Aplysia limacina...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] Solution NMR characterization of hydrogen bonds in a protein by indirect measurement
Solution NMR characterization of hydrogen bonds in a protein by indirect measurement of deuterium quadrupole couplings. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Solution NMR characterization of hydrogen bonds in a protein by indirect measurement of deuterium quadrupole couplings. J Magn Reson. 1997 Jul;127(1):54-64 Authors: Liwang AC, Bax A Hydrogen bonds stabilize protein and nucleic acid structure, but little direct spectroscopic data have been available for...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Solution NMR characterization of hydrogen bonds in a protein by indirect measurement
Solution NMR characterization of hydrogen bonds in a protein by indirect measurement of deuterium quadrupole couplings. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Solution NMR characterization of hydrogen bonds in a protein by indirect measurement of deuterium quadrupole couplings. J Magn Reson. 1997 Jul;127(1):54-64 Authors: Liwang AC, Bax A Hydrogen bonds stabilize protein and nucleic acid structure, but little direct spectroscopic data have been available for...
nmrlearner Journal club 0 08-22-2010 03:03 PM
Hydrogen-bonding potential to refine NMR structure
An Empirical Backbone-Backbone Hydrogen-Bonding Potential in Proteins and Its Applications to NMR Structure Refinement and Validation Alexander Grishaev and Ad Bax J. Am. Chem. Soc.; 2004; 126(23) pp 7281 - 7292 http://pubs.acs.org./isubscribe/journals/jacsat/126/i23/figures/ja0319994n00001.gif Abstract: A new multidimensional potential is described that encodes for the relative spatial arrangement of the peptidyl backbone units as observed within a large database of high-resolution X-ray structures. The detailed description afforded by such an analysis provides an opportunity to study...
nmrlearner Journal club 0 06-29-2005 04:16 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 02:04 PM.


Map