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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 06-29-2014, 02:00 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,732
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 Heteronuclear Transverse and Longitudinal Relaxation in AX4 Spin Systems: Application to 15N Relaxations in 15NH4+

Heteronuclear Transverse and Longitudinal Relaxation in AX4 Spin Systems: Application to 15N Relaxations in 15NH4+

Publication date: Available online 28 June 2014
Source:Journal of Magnetic Resonance

Author(s): Nicolas D. Werbeck , D. Flemming Hansen

The equations that describe the time-evolution of transverse and longitudinal 15N magnetisations in tetrahedral ammonium ions, 15NH4 +, are derived from the Bloch-Wangsness-Redfield density operator relaxation theory. It is assumed that the relaxation of the spin-states is dominated by (1) the intra-molecular 15N-1H and 1H-1H dipole-dipole interactions and (2) interactions of the ammonium protons with remote spins, which also include the contribution to the relaxations that arise from the exchange of the ammonium protons with the bulk solvent. The dipole-dipole cross-correlated relaxation mechanisms between each of the 15N-1H and 1H-1H interactions are explicitly taken into account in the derivations. An application to 15N-ammonium bound to a 41 kDa domain of the protein DnaK is presented, where a comparison between experiments and simulations show that the ammonium ion rotates rapidly within its binding site with a local correlation time shorter than approximately 1 ns. The theoretical framework provided here forms the basis for further investigations of dynamics of AX4 spin systems, with ammonium ions in solution and bound to proteins of particular interest.
Graphical abstract

Highlights








More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Full relaxation matrix analysis of apparent cross-correlated relaxation rates in four-spin systems
Full relaxation matrix analysis of apparent cross-correlated relaxation rates in four-spin systems January 2013 Publication year: 2013 Source:Journal of Magnetic Resonance, Volume 226</br> </br> Cross-correlated relaxation (CCR) rates are an established tool for the extraction of relative bond orientations in biomolecules in solution. CCR between dipolar interactions in four-spin systems is a particularly well-suited mechanism. In this paper, a simple approach to analyze systematic experimental errors is formulated in a subspace of the complete four-spin Hilbert space....
nmrlearner Journal club 0 12-15-2012 09:51 AM
Full relaxation matrix analysis of apparent cross-correlated relaxation rates in four-spin systems
Full relaxation matrix analysis of apparent cross-correlated relaxation rates in four-spin systems Available online 12 November 2012 Publication year: 2012 Source:Journal of Magnetic Resonance</br> </br> Cross-correlated relaxation (CCR) rates are an established tool for the extraction of relative bond orientations in biomolecules in solution. CCR between dipolar interactions in four-spin systems is a particularly well-suited mechanism. In this paper, a simple approach to analyze systematic experimental errors is formulated in a subspace of the complete four-spin...
nmrlearner Journal club 0 12-01-2012 06:10 PM
Full relaxation matrix analysis of apparent cross-correlated relaxation rates in four-spin systems
Full relaxation matrix analysis of apparent cross-correlated relaxation rates in four-spin systems Publication year: 2012 Source:Journal of Magnetic Resonance</br> Beat Vögeli</br> Cross-correlated relaxation (CCR) rates are an established tool for the extraction of relative bond orientations in biomolecules in solution. CCR between dipolar interactions in four-spin systems is a particularly well-suited mechanism. In this paper, a simple approach to analyze systematic experimental errors is formulated in a subspace of the complete four-spin Hilbert space. It is shown...
nmrlearner Journal club 0 11-13-2012 07:30 AM
13C relaxation experiments for aromatic side chains employing longitudinal- and transverse-relaxation optimized NMR spectroscopy
13C relaxation experiments for aromatic side chains employing longitudinal- and transverse-relaxation optimized NMR spectroscopy Abstract Aromatic side chains are prevalent in protein binding sites, perform functional roles in enzymatic catalysis, and form an integral part of the hydrophobic core of proteins. Thus, it is of great interest to probe the conformational dynamics of aromatic side chains and its response to biologically relevant events. Indeed, measurements of 13C relaxation rates in aromatic moieties have a long history in biomolecular NMR, primarily in the context of...
nmrlearner Journal club 0 07-05-2012 04:13 AM
Relaxation theory of nuclear singlet states in two spin-1/2 systems
Relaxation theory of nuclear singlet states in two spin-1/2 systems Publication year: 2010 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 56, Issue 3, April 2010, Pages 217-231</br> Giuseppe*Pileio</br> More...
nmrlearner Journal club 0 09-13-2011 09:15 PM
Continuous-wave EPR at 275 GHz: Application to high-spin Fe3+ systems
Continuous-wave EPR at 275 GHz: Application to high-spin Fe3+ systems Publication year: 2011 Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 11 March 2011</br> G., Mathies , H., Blok , J.A.J.M., Disselhorst , P., Gast , H., van der Meer , ...</br> The 275 GHz electron-paramagnetic-resonance spectrometer we reported on in 2004 has been equipped with a new probe head, which contains a cavity especially designed for operation in continuous-wave mode. The sensitivity and signal stability that is achieved with this new probe head is illustrated...
nmrlearner Journal club 0 03-12-2011 05:21 PM
[NMR paper] An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation
An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates. Related Articles An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates. J Am Chem Soc. 2002 Sep 11;124(36):10743-53 Authors: Korzhnev DM, Skrynnikov NR, Millet O, Torchia DA, Kay LE Rotating-frame relaxation rates, R(1)(rho), are often measured in NMR studies of protein dynamics. We show here that large systematic errors can be introduced into measured values of heteronuclear R(1)(rho) rates using schemes which are...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Application of cross-correlated NMR spin relaxation to the zinc-finger protein CRP2(L
Application of cross-correlated NMR spin relaxation to the zinc-finger protein CRP2(LIM2): evidence for collective motions in LIM domains. Related Articles Application of cross-correlated NMR spin relaxation to the zinc-finger protein CRP2(LIM2): evidence for collective motions in LIM domains. Biochemistry. 2001 Aug 14;40(32):9596-604 Authors: Schüler W, Kloiber K, Matt T, Bister K, Konrat R The solution structure of quail CRP2(LIM2) was significantly improved by using an increased number of NOE constraints obtained from a 13C,15N-labeled...
nmrlearner Journal club 0 11-19-2010 08:44 PM



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 05:45 AM.


Map