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 03-14-2013, 10:05 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 NMR mapping of RANTES surfaces interacting with CCR5 using linked extracellular domains.

NMR mapping of RANTES surfaces interacting with CCR5 using linked extracellular domains.

Related Articles NMR mapping of RANTES surfaces interacting with CCR5 using linked extracellular domains.

FEBS J. 2013 Mar 8;

Authors: Schnur E, Kessler N, Zherdev Y, Noah E, Scherf T, Ding FX, Rabinovich S, Arshava B, Kurbatska V, Leonciks A, Tsimanis A, Rosen O, Naider F, Anglister J

Abstract
Chemokines constitute a large family of small proteins that regulate leukocyte trafficking to the site of inflammation by binding to specific cell-surface receptors belonging to the GPCR superfamily. The interactions between N-terminal (Nt-) peptides of these GPCRs and chemokines have been studied extensively using NMR spectroscopy. However, due to lower affinities of peptides representing the three extracellular loops (ECLs) of chemokine receptors to their respective chemokine ligands, information concerning these interactions is scarce. To overcome the low affinity of ECL peptides to chemokines, we linked two or three CCR5 extracellular domains by either biosynthesis in Escherichia coli or by chemical synthesis. Using such chimeras, CCR5 binding to RANTES was followed using (1) H-(15) N-HSQC spectra to monitor titration of the chemokine with peptides corresponding to the extracellular surface of the receptor. Nt-CCR5 and ECL2 were found to be the major contributors to CCR5 binding to RANTES, creating a nearly closed ring around this protein by interacting with opposing faces of the chemokine. A RANTES positively charged surface involved in Nt-CCR5 binding resembles the positively charged surface in HIV-1 gp120 formed by the C4 and the base of the V3. The opposing surface on RANTES, composed primarily of ?2-?3 hairpin residues, binds ECL2 and was found to be analogous to a surface in the crown of the gp120 V3. The chemical and biosynthetic approaches for linking GPCR surface regions discussed herein should be widely applicable to investigation of interactions of extracellular segments of chemokine receptors with their respective ligands. © 2013 The Authors Journal compilation © 2013 FEBS.


PMID: 23480650 [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
NMR analysis of Lys63-linked polyubiquitin recognition by the tandem ubiquitin-interacting motifs of Rap80
NMR analysis of Lys63-linked polyubiquitin recognition by the tandem ubiquitin-interacting motifs of Rap80 Abstract Ubiquitin is a post-translational modifier that is involved in cellular functions through its covalent attachment to target proteins. Ubiquitin can also be conjugated to itself at seven lysine residues and at its amino terminus to form eight linkage-specific polyubiquitin chains for individual cellular processes. The Lys63-linked polyubiquitin chain is recognized by tandem ubiquitin-interacting motifs (tUIMs) of Rap80 for the regulation of DNA repair. To understand the...
nmrlearner Journal club 0 02-25-2012 12:16 AM
[NMR paper] Identification of protein surfaces by NMR measurements with a pramagnetic Gd(III) che
Identification of protein surfaces by NMR measurements with a pramagnetic Gd(III) chelate. Related Articles Identification of protein surfaces by NMR measurements with a pramagnetic Gd(III) chelate. J Am Chem Soc. 2002 Jan 23;124(3):372-3 Authors: Pintacuda G, Otting G Gd-diethylenetriamine pentaacetic acid-bismethylamide, Gd(DTPA-BMA), is shown to be a reagent suitable for the identification of protein surfaces. Compared to the conventionally used spin-label TEMPOL, Gd(DTPA-BMA) is a stronger relaxation agent, requiring lesser concentrations...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Mapping the interacting regions between troponins T and C. Binding of TnT and TnI pep
Mapping the interacting regions between troponins T and C. Binding of TnT and TnI peptides to TnC and NMR mapping of the TnT-binding site on TnC. Related Articles Mapping the interacting regions between troponins T and C. Binding of TnT and TnI peptides to TnC and NMR mapping of the TnT-binding site on TnC. J Biol Chem. 2001 Sep 28;276(39):36606-12 Authors: Blumenschein TM, Tripet BP, Hodges RS, Sykes BD Muscular contraction is triggered by an increase in calcium concentration, which is transmitted to the contractile proteins by the troponin...
nmrlearner Journal club 0 11-19-2010 08:44 PM
[NMR paper] Mapping the cytochrome c553 interacting site using 1H and 15N NMR.
Mapping the cytochrome c553 interacting site using 1H and 15N NMR. Related Articles Mapping the cytochrome c553 interacting site using 1H and 15N NMR. FEBS Lett. 1999 Oct 22;460(1):77-80 Authors: Morelli X, Guerlesquin F Cytochrome c553 is the electron transfer partner of formate dehydrogenase and of
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] Design of an expression system for detecting folded protein domains and mapping macro
Design of an expression system for detecting folded protein domains and mapping macromolecular interactions by NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Design of an expression system for detecting folded protein domains and mapping macromolecular interactions by NMR. Protein Sci. 1997 Nov;6(11):2359-64 Authors: ...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] Proton NMR assignments and solution conformation of RANTES, a chemokine of the C-C ty
Proton NMR assignments and solution conformation of RANTES, a chemokine of the C-C type. Related Articles Proton NMR assignments and solution conformation of RANTES, a chemokine of the C-C type. Biochemistry. 1995 Apr 25;34(16):5329-42 Authors: Skelton NJ, Aspiras F, Ogez J, Schall TJ 1H NMR has been used to investigate the structural properties of RANTES, a protein from the C-C branch of the chemotactic cytokine family that has a strong chemoattractive effect on monocytes, lymphocytes, and eosinophils. Titration of pH from 5.0 to 2.5...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] NMR identification of protein surfaces using paramagnetic probes.
NMR identification of protein surfaces using paramagnetic probes. Related Articles NMR identification of protein surfaces using paramagnetic probes. Biochemistry. 1990 Oct 30;29(43):10041-8 Authors: Petros AM, Mueller L, Kopple KD Paramagnetic agents produce line broadening and thus cancellation of anti phase cross-peak components in two-dimensional correlated nuclear magnetic resonance spectra. The specificity of this effect was examined to determine its utility for identifying surface residues of proteins. Ubiquitin and hen egg white...
nmrlearner Journal club 0 08-21-2010 11:04 PM
[NMR paper] NMR studies of protein surfaces. The interaction of lysozyme with tri-N-acetylglucosa
NMR studies of protein surfaces. The interaction of lysozyme with tri-N-acetylglucosamine. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles NMR studies of protein surfaces. The interaction of lysozyme with tri-N-acetylglucosamine. Biochem Pharmacol. 1990 Jul 1;40(1):65-8 Authors: Petros AM, Kopple KD
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 07:21 PM.


Map