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 05-13-2014, 03:11 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 (19) F NMR as a Probe of Ligand Interactions with the iNOS Binding site of SPRY-Domain Containing SOCS Box Protein 2.

(19) F NMR as a Probe of Ligand Interactions with the iNOS Binding site of SPRY-Domain Containing SOCS Box Protein 2.

(19) F NMR as a Probe of Ligand Interactions with the iNOS Binding site of SPRY-Domain Containing SOCS Box Protein 2.

Chem Biol Drug Des. 2014 May 9;

Authors: Leung EW, Yagi H, Harjani JR, Mulcair MD, Scanlon MJ, Baell JB, Norton RS

Abstract
SPRY domain-containing SOCS box protein 2 (SPSB2) regulates inducible nitric oxide synthase (iNOS) by targeting it for proteasomal degradation. Inhibiting this interaction prolongs the intracellular lifetime of iNOS, leading in turn to enhanced killing of infectious pathogens such as bacteria and parasites. SPSB2 recognizes a linear motif (DINNN) in the disordered N-terminus of iNOS, and ligands that target the DINNN binding site on SPSB2 are potentially novel anti-infective agents. We have explored (19) F NMR as a means of probing ligand binding to SPSB2. All six Trp residues in SPSB2 were replaced with 5-F-Trp by utilizing a Trp auxotroph strain of Escherichia coli. The labelled protein was well folded and bound a DINNN-containing peptide with similar affinity to native SPSB2. Six well-resolved 5-F-Trp resonances were observed in the (19) F NMR spectrum and were assigned using site-directed mutagenesis. The (19) F resonance of W207 was significantly perturbed upon binding to DINNN-containing peptides. Other resonances were perturbed to a lesser extent although in a way that was sensitive to the composition of the peptide. Analogues of compounds identified in a fragment screen also perturbed the W207 resonance, confirming their binding to the iNOS peptide binding site on SPSB2. (19) F NMR promises to be a valuable approach in developing inhibitors that bind to the DINNN binding site. This article is protected by copyright. All rights reserved.


PMID: 24813479 [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
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. Methods Enzymol. 2011;493:241-75 Authors: Ziarek JJ, Peterson FC, Lytle BL, Volkman BF Over the last 15years, the role of NMR spectroscopy in the lead identification and optimization stages of pharmaceutical drug discovery has steadily increased. NMR occupies a unique niche in the biophysical analysis of drug-like...
nmrlearner Journal club 0 03-05-2011 01:02 PM
Searching the protein structure database for ligand-binding site similarities ... - 7thSpace Interactive (press release)
Searching the protein structure database for ligand-binding site similarities ... - 7thSpace Interactive (press release) <img alt="" height="1" width="1" /> Searching the protein structure database for ligand-binding site similarities ... 7thSpace Interactive (press release) CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR) protocol and has been successfully applied to aid the ... Read here
nmrlearner Online News 0 01-27-2011 04:31 AM
Site-specific free energy changes in proteins upon ligand binding by NMR: Ca(2+) -displacement by Ln(3+) in a Ca(2+) -binding protein from Entamoeba histolytica.
Site-specific free energy changes in proteins upon ligand binding by NMR: Ca(2+) -displacement by Ln(3+) in a Ca(2+) -binding protein from Entamoeba histolytica. Site-specific free energy changes in proteins upon ligand binding by NMR: Ca(2+) -displacement by Ln(3+) in a Ca(2+) -binding protein from Entamoeba histolytica. Chem Biol Drug Des. 2011 Jan 14; Authors: Chandra K, Mustafi SM, Muthukumar S, Chary KV The study of protein-ligand interaction has been of a great interest in contemporary structural biology. The understanding of the nature...
nmrlearner Journal club 0 01-18-2011 10:22 PM
An NMR-Based Structural Rationale for Contrasting Stoichiometry and Ligand Binding Site(s) in Fatty Acid-binding Proteins.
An NMR-Based Structural Rationale for Contrasting Stoichiometry and Ligand Binding Site(s) in Fatty Acid-binding Proteins. An NMR-Based Structural Rationale for Contrasting Stoichiometry and Ligand Binding Site(s) in Fatty Acid-binding Proteins. Biochemistry. 2011 Jan 12; Authors: He Y, Estephan R, Yang X, Vela A, Wang H, Bernard C, Stark RE Liver fatty acid-binding protein (LFABP) is a 14-kDa cytosolic polypeptide, differing from other family members in number of ligand binding sites, diversity of bound ligands, and transfer of fatty acid(s) to...
nmrlearner Journal club 0 01-14-2011 12:05 PM
[NMR paper] Probing the binding entropy of ligand-protein interactions by NMR.
Probing the binding entropy of ligand-protein interactions by NMR. Related Articles Probing the binding entropy of ligand-protein interactions by NMR. Chembiochem. 2005 Sep;6(9):1585-91 Authors: Homans SW
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Docking multiple conformations of a flexible ligand into a protein binding site using
Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints. Related Articles Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints. Proteins. 2002 Feb 15;46(3):295-307 Authors: Zabell AP, Post CB A method is described for docking a large, flexible ligand using intra-ligand conformational restraints from exchange-transferred NOE (etNOE) data. Numerous conformations of the ligand are generated in isolation, and a subset of representative conformations is...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] An investigation of the ligand-binding site of the glutamine-binding protein of Esche
An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR. Related Articles An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR. Biochemistry. 1994 Jul 26;33(29):8651-61 Authors: Hing AW, Tjandra N, Cottam PF, Schaefer J, Ho C Glutamine-binding protein (GlnBP) is an essential component of the glutamine transport system in Escherichia coli. Rotational-echo double-resonance...
nmrlearner Journal club 0 08-22-2010 03:29 AM
[NMR paper] On the ligand-protein and ligand-flavin interactions in NADPH-adrenodoxin reductase a
On the ligand-protein and ligand-flavin interactions in NADPH-adrenodoxin reductase as studied by 31P- and 13C-NMR. Use of 13C-enriched FAD as a probe. Related Articles On the ligand-protein and ligand-flavin interactions in NADPH-adrenodoxin reductase as studied by 31P- and 13C-NMR. Use of 13C-enriched FAD as a probe. J Biochem. 1991 Jan;109(1):144-9 Authors: Fujii S, Nonaka Y, Okamoto M, Miura R The interaction between 2',5'-ADP and NADPH-adrenodoxin reductase from bovine adrenocortical mitochondria was examined by titrating the enzyme with...
nmrlearner Journal club 0 08-21-2010 11:16 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 01:58 AM.


Map