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 11-24-2010, 09:01 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
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 Use of selective Trp side chain labeling to characterize protein-protein and protein-

Use of selective Trp side chain labeling to characterize protein-protein and protein-ligand interactions by NMR spectroscopy.

Related Articles Use of selective Trp side chain labeling to characterize protein-protein and protein-ligand interactions by NMR spectroscopy.

J Am Chem Soc. 2003 Mar 12;125(10):2892-3

Authors: Rodriguez-Mias RA, Pellecchia M

Recent studies on amino acid occurrence in protein binding sites suggest that only a reduced number of residues are responsible for most interaction energy in protein-protein and protein-ligand interactions. Above all, tryptophan (Trp) seems to be the most frequent residue in protein's hot spots. Here we report a novel, efficient, and cost-effective method to selectively incorporate specific isotope labels into the side chains of Trp residues in recombinant proteins. We show that the method proposed allows selective NMR observation of Trp side chains that enables studies of ligand binding, protein-protein interactions, hydrogen binding, protein folding, and side chain dynamics. Examples with the protein BIR3 will be given.

PMID: 12617653 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment
Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment Abstract Obtaining NMR assignments for slowly tumbling molecules such as detergent-solubilized membrane proteins is often compromised by low sensitivity as well as spectral overlap. Both problems can be addressed by amino-acid specific isotope labeling in conjunction with 15Nā??1H correlation experiments. In this work an extended combinatorial selective in vitro labeling scheme is proposed that seeks to reduce the number of samples required for assignment. Including three...
nmrlearner Journal club 0 01-21-2012 06:26 PM
Probing Protein Side Chain Dynamics via (13)C NMR Relaxation.
Probing Protein Side Chain Dynamics via (13)C NMR Relaxation. Probing Protein Side Chain Dynamics via (13)C NMR Relaxation. Protein Pept Lett. 2011 Jan 11; Authors: Yang D Protein side chain dynamics is associated with protein stability, folding, and intermolecular interactions. Detailed dynamics information is crucial for the understanding of protein function and biochemical and biophysical properties, which can be obtained using NMR relaxation techniques. In this review, (13)C relaxation of methine, methylene and methyl groups with and without...
nmrlearner Journal club 0 01-13-2011 12:00 PM
[NMR paper] NMR assignment of protein side chains using residue-correlated labeling and NOE spect
NMR assignment of protein side chains using residue-correlated labeling and NOE spectra. Related Articles NMR assignment of protein side chains using residue-correlated labeling and NOE spectra. J Magn Reson. 2003 Dec;165(2):237-47 Authors: Mueller GA, Kirby TW, DeRose EF, London RE A new approach for the isotopic labeling of proteins is proposed that aims to facilitate side chain resonance assignments. Residue-correlated (RC) labeling is achieved by the expression of a protein on a medium containing a mixture of labeled, e.g., amino acids,...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studi
Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2. Related Articles Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2. Biochemistry. 2001 Jun 5;40(22):6559-69 Authors: Flynn PF, Bieber Urbauer RJ, Zhang H, Lee AL, Wand AJ A detailed characterization of the main chain and side chain dynamics in R. capsulatus ferrocytochrome c(2) derived from (2)H NMR relaxation of methyl group resonances is...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] Protein expression, selective isotopic labeling, and analysis of hyperfine-shifted NM
Protein expression, selective isotopic labeling, and analysis of hyperfine-shifted NMR signals of Anabaena 7120 vegetative ferredoxin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Protein expression, selective isotopic labeling, and analysis of hyperfine-shifted NMR signals of Anabaena 7120 vegetative ferredoxin. Arch Biochem Biophys. 1995 Jan 10;316(1):619-34 Authors: Cheng H, Westler WM, Xia B, Oh BH, Markley JL Two alternative T7 RNA promoter/polymerase systems...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] URPI: a utility program for planning selective protein double-labeling with 13C and 1
URPI: a utility program for planning selective protein double-labeling with 13C and 15N in NMR analyses. Related Articles URPI: a utility program for planning selective protein double-labeling with 13C and 15N in NMR analyses. J Magn Reson B. 1994 Jan;103(1):89-90 Authors: Shinagawa K, Ohya M, Wakamatsu K
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] URPI: a utility program for planning selective protein double-labeling with 13C and 1
URPI: a utility program for planning selective protein double-labeling with 13C and 15N in NMR analyses. Related Articles URPI: a utility program for planning selective protein double-labeling with 13C and 15N in NMR analyses. J Magn Reson B. 1994 Jan;103(1):89-90 Authors: Shinagawa K, Ohya M, Wakamatsu K
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Selective and extensive 13C labeling of a membrane protein for solid-state NMR invest
Selective and extensive 13C labeling of a membrane protein for solid-state NMR investigations. Related Articles Selective and extensive 13C labeling of a membrane protein for solid-state NMR investigations. J Biomol NMR. 1999 May;14(1):71-4 Authors: Hong M, Jakes K The selective and extensive 13C labeling of mostly hydrophobic amino acid residues in a 25 kDa membrane protein, the colicin Ia channel domain, is reported. The novel 13C labeling approach takes advantage of the amino acid biosynthetic pathways in bacteria and suppresses the...
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 - 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 11:03 AM.


Map