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 08-14-2010, 04:19 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,586
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 Structural determination of biomolecular interfaces by nuclear magnetic resonance of

Abstract Protein interactions are important for understanding many molecular mechanisms underlying cellular processes. So far, interfaces between interacting proteins have been characterized by NMR spectroscopy mostly by using chemical shift perturbations and cross-saturation via intermolecular cross-relaxation. Although powerful, these techniques cannot provide unambiguous estimates of intermolecular distances between interacting proteins. Here, we present an alternative approach, called REDSPRINT (REDduced/Standard PRoton density INTerface identification), to map protein interfaces with greater accuracy by using multiple NMR probes. Our approach is based on monitoring the cross-relaxation from a source protein (or from an arbitrary ligand that need not be a protein) with high proton density to a target protein (or other biomolecule) with low proton density by using isotope-filtered nuclear Overhauser spectroscopy (NOESY). This methodology uses different isotropic labeling for the source and target proteins to identify the source-target interface and also determine the proton density of the source protein at the interface for protein-protein or protein-ligand docking. Simulation indicates significant gains in sensitivity because of the resultant relaxation properties, and the utility of this technique, including a method for direct determination of the protein interface, is demonstrated for two different proteinâ??protein complexes.
  • Content Type Journal Article
  • DOI 10.1007/s10858-010-9409-9
  • Authors
    • Fabien Ferrage, New York Structural Biology Center 89 Convent Avenue New York NY 10027 USA
    • Kaushik Dutta, New York Structural Biology Center 89 Convent Avenue New York NY 10027 USA
    • Alexander Shekhtman, New York Structural Biology Center 89 Convent Avenue New York NY 10027 USA
    • David Cowburn, New York Structural Biology Center 89 Convent Avenue New York NY 10027 USA

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
[NMR tweet] Gabriel Cornilescus Research interests are Protein and DNA Structure Determination using Nuclear Magnetic Resonance http://t.co/EXolKcUY
Gabriel Cornilescus Research interests are Protein and DNA Structure Determination using Nuclear Magnetic Resonance http://t.co/EXolKcUY Published by SomercoResearch (SOMERCO) on 2011-09-25T18:10:11Z Source: Twitter
nmrlearner Twitter NMR 0 09-25-2011 06:15 PM
[NMR tweet] RT @sciencedaily: Nuclear magnetic resonance with no magnets: Nuclear magnetic resonance (NMR) is a powerful tool for chemic... http://tinyurl.com/6lfyazv
RT @sciencedaily: Nuclear magnetic resonance with no magnets: Nuclear magnetic resonance (NMR) is a powerful tool for chemic... http://tinyurl.com/6lfyazv Published by Esceptiquisimo (EsceptiquísimoMéxico) on 2011-05-18T23:24:11Z Source: Twitter
nmrlearner Twitter NMR 0 05-18-2011 11:33 PM
[NMR tweet] RT @medical_tweets: Nuclear magnetic resonance with no magnets: Nuclear magnetic resonance (NMR) is a powerful tool for chemical analysis .. http://dld.bz/aa5dX
RT @medical_tweets: Nuclear magnetic resonance with no magnets: Nuclear magnetic resonance (NMR) is a powerful tool for chemical analysis .. http://dld.bz/aa5dX Published by CVO_ortopedia (C. Virtual Ortopedia) on 2011-05-18T21:49:27Z Source: Twitter
nmrlearner Twitter NMR 0 05-18-2011 10:30 PM
[NMR tweet] RT @sciencedaily: Nuclear magnetic resonance with no magnets: Nuclear magnetic resonance (NMR) is a powerful tool for chemic... http://tinyurl.com/6lfyazv
RT @sciencedaily: Nuclear magnetic resonance with no magnets: Nuclear magnetic resonance (NMR) is a powerful tool for chemic... http://tinyurl.com/6lfyazv Published by JEstebanTorres (JuliánEstebanTorres) on 2011-05-18T18:59:46Z Source: Twitter
nmrlearner Twitter NMR 0 05-18-2011 07:22 PM
[NMR tweet] RT @sciencedaily: Nuclear magnetic resonance with no magnets: Nuclear magnetic resonance (NMR) is a powerful tool for chemic... http://tinyurl.com/6lfyazv
RT @sciencedaily: Nuclear magnetic resonance with no magnets: Nuclear magnetic resonance (NMR) is a powerful tool for chemic... http://tinyurl.com/6lfyazv Published by yoghayalestio (yogha yalestio) on 2011-05-18T18:32:05Z Source: Twitter
nmrlearner Twitter NMR 0 05-18-2011 07:22 PM
[NMR tweet] RT @science_book: Comprehensive Biomolecular Nuclear Magnetic Resonance: Concepts and Protocols, Four-Volume Set - Elsevier Science. http://amzn.to/eauJFj
RT @science_book: Comprehensive Biomolecular Nuclear Magnetic Resonance: Concepts and Protocols, Four-Volume Set - Elsevier Science. http://amzn.to/eauJFj Published by j0rk (F.C.Jork) on 2011-02-27T02:02:18Z Source: Twitter
nmrlearner Twitter NMR 0 02-27-2011 02:33 AM
[NMR tweet] http://www.pulist.net/nuclear-magnetic-resonance-oxford-chemistry-primers-32.html #magnetic #resonance #spectroscopy #corpus Nuclear Mag
http://www.pulist.net/nuclear-magnetic-resonance-oxford-chemistry-primers-32.html #magnetic #resonance #spectroscopy #corpus Nuclear Mag Published by pulistbook (pulist books) on 2011-01-05T03:33:12Z Source: Twitter
nmrlearner Twitter NMR 0 01-05-2011 03:41 AM
[NMR paper] An NMR method for the determination of protein-binding interfaces using dioxygen-indu
An NMR method for the determination of protein-binding interfaces using dioxygen-induced spin-lattice relaxation enhancement. Related Articles An NMR method for the determination of protein-binding interfaces using dioxygen-induced spin-lattice relaxation enhancement. J Am Chem Soc. 2005 Apr 27;127(16):5826-32 Authors: Sakakura M, Noba S, Luchette PA, Shimada I, Prosser RS Using oxygen as a paramagnetic probe, researchers can routinely study topologies and protein-binding interfaces by NMR. The paramagnetic contribution to the amide (1)H...
nmrlearner Journal club 0 11-25-2010 08:21 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 03:37 AM.


Map