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 09-04-2021, 10:34 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 22,724
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 TRACT revisited: an algebraic solution for determining overall rotational correlation times from cross-correlated relaxation rates

TRACT revisited: an algebraic solution for determining overall rotational correlation times from cross-correlated relaxation rates

Abstract

Accurate rotational correlation times ( \({\tau }_{\text{c}}\) ) are critical for quantitative analysis of fast timescale NMR dynamics. As molecular weights increase, the classic derivation of \({\tau }_{c}\) using transverse and longitudinal relaxation rates becomes increasingly unsuitable due to the non-trivial contribution of remote dipole‚??dipole interactions to longitudinal relaxation. Derivations using cross-correlated relaxation experiments, such as TRACT, overcome these limitations but are erroneously calculated in 65% of the citing literature. Herein, we developed an algebraic solutions to the Goldman relationship that facilitate rapid, point-by-point calculations for straightforward identification of appropriate spectral regions where global tumbling is likely to be dominant. The rigid-body approximation of the Goldman relationship has been previously shown to underestimate TRACT-based rotational correlation time estimates. This motivated us to develop a second algebraic solution that employs a simplified model-free spectral density function including an order parameter term that could, in principle, be set to an average backbone S2 ‚?? 0.9 to further improve the accuracy of \({\tau }_{\text{c}}\) estimation. These solutions enabled us to explore the boundaries of the Goldman relationship as a function of the H‚??N internuclear distance ( \(r\) ), difference of the two principal components of the axially-symmetric 15N CSA tensor ( \(\Delta {\delta }_{N}\) ), and angle of the CSA tensor relative to the N‚??H bond vector ( \(\theta\) ). We hope our algebraic solutions and analytical strategies will increase the accuracy and application of the TRACT experiment.



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
Cross-correlated relaxation rates between protein backbone H‚??X dipolar interactions
Cross-correlated relaxation rates between protein backbone H‚??X dipolar interactions Abstract The relaxation interference between dipole‚??dipole interactions of two separate spin pairs carries structural and dynamics information. In particular, when compared to individual dynamic behavior of those spin pairs, such cross-correlated relaxation (CCR) rates report on the correlation between the spin pairs. We have recently mapped out correlated motion along the backbone of the protein GB3, using CCR rates among and between consecutive HN‚??N and...
nmrlearner Journal club 0 03-13-2017 02:54 AM
[NMR paper] Anisotropy of Rotational Diffusion, Dipole-Dipole Cross-Correlated NMR Relaxation and Angles between Bond Vectors in Proteins.
Anisotropy of Rotational Diffusion, Dipole-Dipole Cross-Correlated NMR Relaxation and Angles between Bond Vectors in Proteins. Related Articles Anisotropy of Rotational Diffusion, Dipole-Dipole Cross-Correlated NMR Relaxation and Angles between Bond Vectors in Proteins. Chemphyschem. 2001 Sep 17;2(8-9):539-43 Authors: Deschamps M, Bodenhausen G Abstract Cross correlations between the fluctuations of dipolar (13) C(?) -(1) H(?) interactions yield information about the relative orientation of successive (13) C(?) -(1) H(?) bond vectors...
nmrlearner Journal club 0 05-22-2013 04:43 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 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 VŲgeli</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
NMR Cross-Correlated Relaxation Rates Reveal Ion Coordination Sites in DNA
NMR Cross-Correlated Relaxation Rates Reveal Ion Coordination Sites in DNA Radovan Fiala, Nad?a S?pac?kova?, Silvie Foldynova?-Tranti?rkova?, Jir?i? S?poner, Vladimi?r Sklena?r? and Luka?s? Tranti?rek http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja202397p/aop/images/medium/ja-2011-02397p_0003.gif Journal of the American Chemical Society DOI: 10.1021/ja202397p http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/vJtIag8UbVQ
nmrlearner Journal club 0 08-13-2011 02:47 AM
[NMR paper] Effective rotational correlation times of proteins from NMR relaxation interference.
Effective rotational correlation times of proteins from NMR relaxation interference. Related Articles Effective rotational correlation times of proteins from NMR relaxation interference. J Magn Reson. 2006 Jan;178(1):72-6 Authors: Lee D, Hilty C, Wider G, WŁthrich K Knowledge of the effective rotational correlation times, tauc, for the modulation of anisotropic spin-spin interactions in macromolecules subject to Brownian motion in solution is of key interest for the practice of NMR spectroscopy in structural biology. The value of tauc enables...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Polarization transfer by cross-correlated relaxation in solution NMR with very large
Polarization transfer by cross-correlated relaxation in solution NMR with very large molecules. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-pnas_full_free.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Polarization transfer by cross-correlated relaxation in solution NMR with very large molecules. Proc Natl Acad Sci U S A. 1999 Apr 27;96(9):4918-23 Authors: Riek R, Wider G, Pervushin K, W√ľthrich...
nmrlearner Journal club 0 08-21-2010 04:03 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 - 2023, 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 09:47 AM.


Map