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 05-01-2012, 07:06 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 18,814
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 Increased precision for analysis of proteinâ??ligand dissociation constants determined from chemical shift titrations

Increased precision for analysis of proteinâ??ligand dissociation constants determined from chemical shift titrations


Abstract NMR is ideally suited for the analysis of proteinâ??protein and protein ligand interactions with dissociation constants ranging from ~2 ÎĽM to ~1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K D ) of 1:1 proteinâ??protein or proteinâ??ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K D , and nonlinear least squares analysis of chemical shift changes as a function of ligand concentration is employed to determine estimates for the parameters K D and the maximum chemical shift change (Î?δmax). During a typical NMR titration, the initial protein concentration, [P 0], is held nearly constant. For this condition, to determine the most accurate parameters for K D and Î?δmax from nonlinear least squares analyses requires initial protein concentrations that are ~0.5 Ă? K D , and a maximum concentration for the ligand, or titrant, of ~10 Ă? [P 0]. From a practical standpoint, these requirements are often difficult to achieve. Using Monte Carlo simulations, we demonstrate that co-variation of the ligand and protein concentrations during a titration leads to an increase in the precision of the fitted K D and Î?δmax values when [P 0] > K D . Importantly, judicious choice of protein and ligand concentrations for a given NMR titration, combined with nonlinear least squares analyses using two independent variables (ligand and protein concentrations) and two parameters (K D and Î?δmax) is a straightforward approach to increasing the accuracy of measured dissociation constants for 1:1 proteinâ??ligand interactions.
  • Content Type Journal Article
  • Category Article
  • Pages 1-14
  • DOI 10.1007/s10858-012-9630-9
  • Authors
    • Craig J. Markin, Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
    • Leo Spyracopoulos, Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada

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
Electrostatically-driven fast association and perdeuteration allow detection of transferred cross-relaxation for G protein-coupled receptor ligands with equilibrium dissociation constants in the high-to-low nanomolar range
Electrostatically-driven fast association and perdeuteration allow detection of transferred cross-relaxation for G protein-coupled receptor ligands with equilibrium dissociation constants in the high-to-low nanomolar range Abstract The mechanism of signal transduction mediated by G protein-coupled receptors is a subject of intense research in pharmacological and structural biology. Ligand association to the receptor constitutes a critical event in the activation process. Solution-state NMR can be amenable to high-resolution structure determination of agonist molecules in their...
nmrlearner Journal club 0 06-25-2011 04:12 AM
[NMR paper] Signal assignments and chemical-shift structural analysis of uniformly 13C, 15N-label
Signal assignments and chemical-shift structural analysis of uniformly 13C, 15N-labeled peptide, mastoparan-X, by multidimensional solid-state NMR under magic-angle spinning. Related Articles Signal assignments and chemical-shift structural analysis of uniformly 13C, 15N-labeled peptide, mastoparan-X, by multidimensional solid-state NMR under magic-angle spinning. J Biomol NMR. 2004 Apr;28(4):311-25 Authors: Fujiwara T, Todokoro Y, Yanagishita H, Tawarayama M, Kohno T, Wakamatsu K, Akutsu H Carbon-13 and nitrogen-15 signals of fully...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] NMR methods for the determination of protein-ligand dissociation constants.
NMR methods for the determination of protein-ligand dissociation constants. Related Articles NMR methods for the determination of protein-ligand dissociation constants. Curr Top Med Chem. 2003;3(1):39-53 Authors: Fielding L This article is a review with 83 references of the application of NMR to the measurement of the dissociation constants of protein-ligand complexes. After briefly discussing some general concepts of molecular stability, the text turns to consider which NMR parameters are reporters of complex formation. The available data...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis
Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis. Biochemistry. 1997 May 27;36(21):6326-35 Authors: Ubbink M, Bendall DS The complexes of horse ferrous and ferric cytochrome c with Cd-substituted pea plastocyanin have been characterized by nuclear magnetic resonance, in order to determine the binding sites and to study...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis
Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis. Biochemistry. 1997 May 27;36(21):6326-35 Authors: Ubbink M, Bendall DS The complexes of horse ferrous and ferric cytochrome c with Cd-substituted pea plastocyanin have been characterized by nuclear magnetic resonance, in order to determine the binding sites and to study...
nmrlearner Journal club 0 08-22-2010 03:03 PM
[NMR paper] Defining the precision with which a protein structure is determined by NMR. Applicati
Defining the precision with which a protein structure is determined by NMR. Application to motilin. Related Articles Defining the precision with which a protein structure is determined by NMR. Application to motilin. Biochemistry. 1993 Feb 16;32(6):1610-7 Authors: Shriver J, Edmondson S A simple procedure is introduced for accurately defining the precision with which the Cartesian coordinates of any macromolecular structure are determined by nuclear Overhauser data. The method utilizes an ensemble of structures obtained from an array of...
nmrlearner Journal club 0 08-21-2010 11:53 PM
[NMR paper] 15N NMR assignments and chemical shift analysis of uniformly labeled 15N calbindin D9
15N NMR assignments and chemical shift analysis of uniformly labeled 15N calbindin D9k in the apo, (Cd2+)1 and (Ca2+)2 states. Related Articles 15N NMR assignments and chemical shift analysis of uniformly labeled 15N calbindin D9k in the apo, (Cd2+)1 and (Ca2+)2 states. FEBS Lett. 1992 Jun 1;303(2-3):136-40 Authors: Skelton NJ, Akke M, Kördel J, Thulin E, Forsén S, Chazin WJ 15N has been uniformly incorporated into the EF-hand Ca(2+)-binding protein calbindin D9k so that heteronuclear experiments can be used to further characterize the...
nmrlearner Journal club 0 08-21-2010 11:41 PM
[NMR paper] Structural analysis of silk with 13C NMR chemical shift contour plots.
Structural analysis of silk with 13C NMR chemical shift contour plots. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Structural analysis of silk with 13C NMR chemical shift contour plots. Int J Biol Macromol. 1999 Mar-Apr;24(2-3):167-71 Authors: Asakura T, Iwadate M, Demura M, Williamson MP The polymorphic structures of silk fibroins in the solid state were examined on the basis of a quantitative relationship between the 13C chemical shift and local structure in...
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 - 2018, 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 11:44 PM.


Map