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 02-18-2016, 08:10 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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 Residence Times of Molecular Complexes in Solution from NMR Data of Intermolecular Hydrogen-bond Scalar Coupling.

Residence Times of Molecular Complexes in Solution from NMR Data of Intermolecular Hydrogen-bond Scalar Coupling.

Related Articles Residence Times of Molecular Complexes in Solution from NMR Data of Intermolecular Hydrogen-bond Scalar Coupling.

J Phys Chem Lett. 2016 Feb 16;

Authors: Zandarashvili L, Esadze A, Kemme CA, Chattopadhyay A, Nguyen D, Iwahara J

Abstract
The residence times of molecular complexes in solution are important for understanding biomolecular functions and drug actions. Here we show that NMR data of intermolecular hydrogen-bond scalar couplings can yield information on the residence times of molecular complexes in solution. The molecular exchange of binding partners via the breakage and reformation of a complex causes self-decoupling of intermolecular hydrogen-bond scalar couplings, and this self-decoupling effect depends on the residence time of the complex. For protein-DNA complexes, we investigated the salt-concentration dependence of intermolecular hydrogen-bond scalar couplings between the protein side-chain (15)N and DNA phosphate (31)P nuclei, from which the residence times were analyzed. The results were consistent with those obtained by (15)Nz-exchange spectroscopy. This self-decoupling-based kinetic analysis is unique in that it does not require any different signatures for the states involved in the exchange, whereas such conditions are crucial for kinetic analyses by typical NMR and other methods.


PMID: 26881297 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Improved validation of IDP ensembles by one-bond Cαâ??Hα scalar couplings
Improved validation of IDP ensembles by one-bond Cαâ??Hα scalar couplings Abstract Intrinsically disordered proteins (IDPs) are best described by ensembles of conformations and a variety of approaches have been developed to determine IDP ensembles. Because of the large number of conformations, however, cross-validation of the determined ensembles by independent experimental data is crucial. The 1JCαHα coupling constant is particularly suited for cross-validation, because it has a large magnitude and mostly depends on the often less accessible...
nmrlearner Journal club 0 10-04-2015 02:58 PM
[NMR paper] Observation of scalar nuclear spin-spin coupling in van der Waals complexes.
From Mendeley Biomolecular NMR group: Observation of scalar nuclear spin-spin coupling in van der Waals complexes. Proceedings of the National Academy of Sciences of the United States of America (2012). Volume: 109, Issue: 31. Pages: 12393-7. Micah P Ledbetter, Giacomo Saielli, Alessandro Bagno, Nhan Tran, Michael V Romalis et al. Scalar couplings between covalently bound nuclear spins are a ubiquitous feature in nuclear magnetic resonance (NMR) experiments, imparting valuable information to NMR spectra regarding molecular structure and conformation. Such couplings arise due to a...
nmrlearner Journal club 0 09-09-2014 03:44 PM
[NMR paper] Detection of a transient intramolecular hydrogen bond using 1JNH scalar couplings
Detection of a transient intramolecular hydrogen bond using 1JNH scalar couplings Publication date: Available online 18 April 2014 Source:Journal of Magnetic Resonance</br> Author(s): ShengQi Xiang , Markus Zweckstetter</br> Hydrogen bonds are essential for the structure, stability and folding of proteins. The identification of intramolecular hydrogen bonds, however, is challenging, in particular in transiently folded states. Here we studied the presence of intramolecular hydrogen bonds in the folding nucleus of the coiled-coil structure of the GCN4 leucine zipper....
nmrlearner Journal club 0 04-18-2014 01:35 PM
[NMR paper] Observation of scalar nuclear spin-spin coupling in van der Waals complexes.
From Mendeley Biomolecular NMR group: Observation of scalar nuclear spin-spin coupling in van der Waals complexes. Proceedings of the National Academy of Sciences of the United States of America (2012). Volume: 109, Issue: 31. Pages: 12393-7. Micah P Ledbetter, Giacomo Saielli, Alessandro Bagno, Nhan Tran, Michael V Romalis et al. Scalar couplings between covalently bound nuclear spins are a ubiquitous feature in nuclear magnetic resonance (NMR) experiments, imparting valuable information to NMR spectra regarding molecular structure and conformation. Such couplings arise due to a...
nmrlearner Journal club 0 10-17-2013 12:49 PM
[NMR paper] Observation of scalar nuclear spin-spin coupling in van der Waals complexes.
From Mendeley Biomolecular NMR group: Observation of scalar nuclear spin-spin coupling in van der Waals complexes. Proceedings of the National Academy of Sciences of the United States of America (2012). Volume: 109, Issue: 31. Pages: 12393-7. Micah P Ledbetter, Giacomo Saielli, Alessandro Bagno, Nhan Tran, Michael V Romalis et al. Scalar couplings between covalently bound nuclear spins are a ubiquitous feature in nuclear magnetic resonance (NMR) experiments, imparting valuable information to NMR spectra regarding molecular structure and conformation. Such couplings arise due to a...
nmrlearner Journal club 0 11-22-2012 11:49 AM
[NMR paper] Observation of scalar nuclear spin-spin coupling in van der Waals complexes.
From Mendeley Biomolecular NMR group: Observation of scalar nuclear spin-spin coupling in van der Waals complexes. Proceedings of the National Academy of Sciences of the United States of America (2012). Volume: 109, Issue: 31. Pages: 12393-7. Micah P Ledbetter, Giacomo Saielli, Alessandro Bagno, Nhan Tran, Michael V Romalis et al. Scalar couplings between covalently bound nuclear spins are a ubiquitous feature in nuclear magnetic resonance (NMR) experiments, imparting valuable information to NMR spectra regarding molecular structure and conformation. Such couplings arise due to a...
nmrlearner Journal club 0 10-29-2012 12:57 AM
Improved accuracy in measuring one-bond and two-bond 15N,13Cα coupling constants in proteins by double-inphase/antiphase (DIPAP) spectroscopy
Improved accuracy in measuring one-bond and two-bond 15N,13Cα coupling constants in proteins by double-inphase/antiphase (DIPAP) spectroscopy Abstract An extension to HN(CO-α/β-N,Cα-J)-TROSY (Permi and Annila in J Biomol NMR 16:221â??227, 2000) is proposed that permits the simultaneous determination of the four coupling constants 1 J Nâ?²(i)Cα(i), 2 J HN(i)Cα(i), 2 J Cα(iâ??1)Nâ?²(i), and 3 J Cα(iâ??1)HN(i) in 15N,13C-labeled proteins. Contrasting the original scheme, in which two separate subspectra exhibit the 2 J CαNâ?² coupling as inphase and antiphase splitting (IPAP), we...
nmrlearner Journal club 0 06-10-2011 01:41 AM
[NMR paper] Refinement of the NMR structures for acyl carrier protein with scalar coupling data.
Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Related Articles Refinement of the NMR structures for acyl carrier protein with scalar coupling data. Proteins. 1990;8(4):377-85 Authors: Kim Y, Prestegard JH Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observations, not just distance constraints. Here, coupling...
nmrlearner Journal club 0 08-21-2010 10:48 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 - 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 08:12 PM.


Map