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 05-03-2020, 02:46 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 21,400
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 Deleterious effects of carbon‚??carbon dipolar coupling on RNA NMR dynamics

Deleterious effects of carbon‚??carbon dipolar coupling on RNA NMR dynamics

Abstract

Many regulatory RNAs undergo dynamic exchanges that are crucial for their biological functions and NMR spectroscopy is a versatile tool for monitoring dynamic motions of biomolecules. Meaningful information on biomolecular dynamics requires an accurate measurement of relaxation parameters such as longitudinal (R1) rates, transverse (R2) rates and heteronuclear Overhauser effect (hNOE). However, earlier studies have shown that the large 13C‚??13C interactions complicate analysis of the carbon relaxation parameters. To investigate the effect of 13C‚??13C interactions on RNA dynamic studies, we performed relaxation measurements on various RNA samples with different labeling patterns and compared these measurements with the computational simulations. For uniformly labeled samples, contributions of the neighboring carbon to R1 measurements were observed. These contributions increased with increasing magnetic field and overall correlation time (\({\tau }_{\text{C}}\)) for R1 rates, necessitating more careful analysis for uniformly labeled large RNAs. In addition, the hNOE measurements were also affected by the adjacent carbon nuclei. Unlike R1 rates, R1Ō? rates showed relatively good agreement between uniformly- and site-selectively labeled samples, suggesting no dramatic effect from their attached carbon, in agreement with previous observations. Overall, having more accurate rate measurements avoids complex analysis and will be a key for interpreting 13C relaxation rates for molecular motion that can provide valuable insights into cellular molecular recognition events.



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
Carbon-carbon spin-spin coupling constants: Practical applications of theoretical calculations
Carbon-carbon spin-spin coupling constants: Practical applications of theoretical calculations Publication date: April 2018 Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 105</br> Author(s): Leonid B. Krivdin</br> Practical applications of theoretical calculations of carbon-carbon spin-spin coupling constants in particular classes of organic and bioorganic molecules are reviewed, concentrating mainly on saturated, unsaturated, aromatic and heteroaromatic compounds and their functional derivatives as well as on carbohydrates and natural...
nmrlearner Journal club 0 04-14-2018 01:49 PM
[NMR paper] Cross-Correlated Relaxation of Dipolar Coupling and Chemical-Shift Anisotropy in Magic-Angle Spinning R1? NMR Measurements: Application to Protein Backbone Dynamics Measurements.
Cross-Correlated Relaxation of Dipolar Coupling and Chemical-Shift Anisotropy in Magic-Angle Spinning R1? NMR Measurements: Application to Protein Backbone Dynamics Measurements. Cross-Correlated Relaxation of Dipolar Coupling and Chemical-Shift Anisotropy in Magic-Angle Spinning R1? NMR Measurements: Application to Protein Backbone Dynamics Measurements. J Phys Chem B. 2016 Aug 8; Authors: Kurauskas V, Weber E, Hessel A, Ayala I, Marion D, Schanda P Abstract Transverse relaxation rate measurements in MAS solid-state NMR...
nmrlearner Journal club 0 08-09-2016 02:42 PM
Asynchronous through-bond homonuclear isotropic mixing: application to carbon‚??carbon transfer in perdeuterated proteins under MAS
Asynchronous through-bond homonuclear isotropic mixing: application to carbon‚??carbon transfer in perdeuterated proteins under MAS Abstract Multiple-bond carbon‚??carbon homonuclear mixing is a hurdle in extensively deuterated proteins and under fast MAS due to the absence of an effective proton dipolar-coupling network. Such conditions are now commonly employed in solid-state NMR spectroscopy. Here, we introduce an isotropic homonuclear 13C‚??13C through-bond mixing sequence, MOCCA, for the solid state. Even though applied under MAS, this scheme...
nmrlearner Journal club 0 08-29-2015 09:18 PM
Protein resonance assignment at MAS frequencies approaching 100¬*kHz: a quantitative comparison of J-coupling and dipolar-coupling-based transfer methods
Protein resonance assignment at MAS frequencies approaching 100¬*kHz: a quantitative comparison of J-coupling and dipolar-coupling-based transfer methods Abstract We discuss the optimum experimental conditions to obtain assignment spectra for solid proteins at magic-angle spinning (MAS) frequencies around 100¬*kHz. We present a systematic examination of the MAS dependence of the amide proton T 2‚?≤ times and a site-specific comparison of T 2‚?≤ at 93¬*kHz versus 60¬*kHz MAS frequency. A...
nmrlearner Journal club 0 08-13-2015 02:00 PM
Long-Range Proton-Carbon Coupling Constants: NMR methods and applications
Long-Range Proton-Carbon Coupling Constants: NMR methods and applications Publication date: Available online 20 July 2013 Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br> Author(s): Teodor Parella , Juan Fťlix Espinosa</br> A general review of novel NMR methods to measure heteronuclear long-range proton-carbon coupling constants ( n J CH ; n>1) in small molecules is made. NMR experiments are classified in terms of NMR pulse scheme and cross-peak nature. A discussion about simplicity, general applicability and accuracy for each...
nmrlearner Journal club 0 07-20-2013 11:27 AM
The Use of Residual Dipolar Coupling in Studying Proteins by NMR.
The Use of Residual Dipolar Coupling in Studying Proteins by NMR. The Use of Residual Dipolar Coupling in Studying Proteins by NMR. Top Curr Chem. 2011 Sep 28; Authors: Chen K, Tjandra N Abstract The development of residual dipolar coupling (RDC) in protein NMR spectroscopy, over a decade ago, has become a useful and almost routine tool for accurate protein solution structure determination. RDCs provide orientation information of magnetic dipole-dipole interaction vectors within a common reference frame. Its measurement requires a...
nmrlearner Journal club 0 09-30-2011 06:00 AM
The Use of Residual Dipolar Coupling in Studying Proteins by NMR.
The Use of Residual Dipolar Coupling in Studying Proteins by NMR. The Use of Residual Dipolar Coupling in Studying Proteins by NMR. Top Curr Chem. 2011 Sep 28; Authors: Chen K, Tjandra N Abstract The development of residual dipolar coupling (RDC) in protein NMR spectroscopy, over a decade ago, has become a useful and almost routine tool for accurate protein solution structure determination. RDCs provide orientation information of magnetic dipole-dipole interaction vectors within a common reference frame. Its measurement requires a...
nmrlearner Journal club 0 09-30-2011 05:59 AM
[Question from NMRWiki Q&A forum] How can I calculate a carbon-proton coupling constant for a molecule?
How can I calculate a carbon-proton coupling constant for a molecule? I'm trying to explain a missing HMBC peak, and having a coupling constant less than 10 Hz would do that nicely. It's a formamidine derivative with a 3 bond correlation N=CHNC The C is a quaternary carbon in a benzene ring. Any help would be appreciated. Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 02-04-2011 07:12 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 - 2021, 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 01:17 PM.


Map