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 09-09-2017, 06:59 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,704
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 Label-free quantitative 1H NMR spectroscopy to study low-affinity ligand-protein interactions in solution: A contribution to the mechanism of polyphenol-mediated astringency.

Label-free quantitative 1H NMR spectroscopy to study low-affinity ligand-protein interactions in solution: A contribution to the mechanism of polyphenol-mediated astringency.

Label-free quantitative 1H NMR spectroscopy to study low-affinity ligand-protein interactions in solution: A contribution to the mechanism of polyphenol-mediated astringency.

PLoS One. 2017;12(9):e0184487

Authors: Delius J, Frank O, Hofmann T

Abstract
Nuclear magnetic resonance (NMR) spectroscopy is well-established in assessing the binding affinity between low molecular weight ligands and proteins. However, conventional NMR-based binding assays are often limited to small proteins of high purity and may require elaborate isotopic labeling of one of the potential binding partners. As protein-polyphenol complexation is assumed to be a key event in polyphenol-mediated oral astringency, here we introduce a label-free, ligand-focused 1H NMR titration assay to estimate binding affinities and characterize soluble complex formation between proteins and low molecular weight polyphenols. The method makes use of the effects of NMR line broadening due to protein-ligand interactions and quantitation of the non-bound ligand at varying protein concentrations by quantitative 1H NMR spectroscopy (qHNMR) using electronic reference to access in vivo concentration (ERETIC 2). This technique is applied to assess the interaction kinetics of selected astringent tasting polyphenols and purified mucin, a major lubricating glycoprotein of human saliva, as well as human whole saliva. The protein affinity values (BC50) obtained are subsequently correlated with the intrinsic mouth-puckering, astringent oral sensation imparted by these compounds. The quantitative NMR method is further exploited to study the effect of carboxymethyl cellulose, a candidate "anti-astringent" protein binding antagonist, on the polyphenol-protein interaction. Consequently, the NMR approach presented here proves to be a versatile tool to study the interactions between proteins and low-affinity ligands in solution and may find promising applications in the discovery of bioactives.


PMID: 28886151 [PubMed - in process]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Quantitative analysis of protein-ligand interactions by NMR.
Quantitative analysis of protein-ligand interactions by NMR. Quantitative analysis of protein-ligand interactions by NMR. Prog Nucl Magn Reson Spectrosc. 2016 Aug;96:47-57 Authors: Furukawa A, Konuma T, Yanaka S, Sugase K Abstract Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug...
nmrlearner Journal club 0 08-31-2016 02:34 PM
Quantitative analysis of protein–ligand interactions by NMR
Quantitative analysis of protein–ligand interactions by NMR Publication date: Available online 3 March 2016 Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br> Author(s): Ayako Furukawa, Tsuyoshi Konuma, Saeko Yanaka, Kenji Sugase</br> Protein–ligand interactions have been commonly studied through static structures of the protein–ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein–ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development....
nmrlearner Journal club 0 03-03-2016 08:32 PM
Hyperpolarized Water to Study Protein–Ligand Interactions
From The DNP-NMR Blog: Hyperpolarized Water to Study Protein–Ligand Interactions Chappuis, Q., et al., Hyperpolarized Water to Study Protein–Ligand Interactions. The Journal of Physical Chemistry Letters, 2015. 6(9): p. 1674-1678. http://dx.doi.org/10.1021/acs.jpclett.5b00403
nmrlearner News from NMR blogs 0 06-06-2015 12:01 PM
[NMR paper] The study of transient protein-nanoparticle interactions by solution NMR spectroscopy.
The study of transient protein-nanoparticle interactions by solution NMR spectroscopy. Related Articles The study of transient protein-nanoparticle interactions by solution NMR spectroscopy. Biochim Biophys Acta. 2015 Apr 30; Authors: Assfalg M, Ragona L, Pagano K, D'Onofrio M, Zanzoni S, Tomaselli S, Molinari H Abstract The rapid development of novel nanoscale materials for applications in biomedicine urges an improved characterization of the nano-bio interfaces. Nanoparticles exhibit unique structures and properties, often...
nmrlearner Journal club 0 05-06-2015 11:59 AM
The study of transient protein-nanoparticle interactions by solution NMR spectroscopy
The study of transient protein-nanoparticle interactions by solution NMR spectroscopy Publication date: Available online 30 April 2015 Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics</br> Author(s): Michael Assfalg , Laura Ragona , Katiuscia Pagano , Mariapina D’Onofrio , Serena Zanzoni , Simona Tomaselli , Henriette Molinari</br> The rapid development of novel nanoscale materials for applications in biomedicine urges an improved characterization of the nano-bio interfaces. Nanoparticles exhibit unique structures and properties, often...
nmrlearner Journal club 0 04-30-2015 09:13 PM
[NMR paper] Analyzing protein-ligand interactions by dynamic NMR spectroscopy.
Analyzing protein-ligand interactions by dynamic NMR spectroscopy. Related Articles Analyzing protein-ligand interactions by dynamic NMR spectroscopy. Methods Mol Biol. 2013;1008:243-66 Authors: Mittermaier A, Meneses E Abstract Nuclear magnetic resonance (NMR) spectroscopy can provide detailed information on protein-ligand interactions that is inaccessible using other biophysical techniques. This chapter focuses on NMR-based approaches for extracting affinity and rate constants for weakly binding transient protein complexes with lifetimes...
nmrlearner Journal club 0 06-05-2013 06:53 PM
[NMR paper] NMR study of a membrane protein in detergent-free aqueous solution.
NMR study of a membrane protein in detergent-free aqueous solution. Related Articles NMR study of a membrane protein in detergent-free aqueous solution. Proc Natl Acad Sci U S A. 2005 Jun 21;102(25):8893-8 Authors: Zoonens M, Catoire LJ, Giusti F, Popot JL One of the major obstacles to membrane protein (MP) structural studies is the destabilizing effect of detergents. Amphipols (APols) are short amphipathic polymers that can substitute for detergents to keep MPs water-soluble under mild conditions. In the present work, we have explored the...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Solution NMR study of DNA recognition mechanism of IRF4 protein.
Solution NMR study of DNA recognition mechanism of IRF4 protein. Related Articles Solution NMR study of DNA recognition mechanism of IRF4 protein. Nucleic Acids Symp Ser (Oxf). 2004;(48):105-6 Authors: Ishizaki I, Nomura M, Yamamoto K, Matsuyama T, Mishima M, Kojima C Transcription factor IRF-4 prefers the DNA sequence including CCGAAA. The consensus sequence of the IRF family proteins is NNGAAA, and all crystal structures indicate the NN region does not interact with IRF proteins directly. Here the sequence preference of IRF-4 was...
nmrlearner Journal club 0 11-24-2010 09:25 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 - 2017, 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 05:35 AM.


Map