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, 10:03 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 Characterization of protein-ligand interactions by high-resolution solid-state NMR sp

Characterization of protein-ligand interactions by high-resolution solid-state NMR spectroscopy.

Related Articles Characterization of protein-ligand interactions by high-resolution solid-state NMR spectroscopy.

J Am Chem Soc. 2004 Nov 3;126(43):13948-53

Authors: Zech SG, Olejniczak E, Hajduk P, Mack J, McDermott AE

A novel approach for detection of ligand binding to a protein in solid samples is described. Hydrated precipitates of the anti-apoptotic protein Bcl-xL show well-resolved (13)C-(13)C 2D solid-state NMR spectra that allow site-specific assignment of resonances for many residues in uniformly (13)C-enriched samples. Binding of a small peptide or drug-like organic molecule leads to changes in the chemical shift of resonances from multiple residues in the protein that can be monitored to characterize binding. Differential chemical shifts can be used to distinguish between direct protein-ligand contacts and small conformational changes of the protein induced by ligand binding. The agreement with prior solution-state NMR results indicates that the binding pocket in solid and liquid samples is similar for this protein. Advantages of different labeling schemes involving selective (13)C enrichment of methyl groups of Ala, Val, Leu, and Ile (Cdelta1) for characterizing protein-ligand interactions are also discussed. It is demonstrated that high-resolution solid-state NMR spectroscopy on uniformly or extensively (13)C-enriched samples has the potential to screen proteins of moderate size ( approximately 20 kDa) for ligand binding as hydrated solids. The results presented here suggest the possibility of using solid-state NMR to study ligand binding in proteins not amenable to solution NMR.

PMID: 15506755 [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
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. J Biomol NMR. 2011 Sep 22; Authors: Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular...
nmrlearner Journal club 0 09-23-2011 05:30 PM
[NMR paper] Protein structure determination by high-resolution solid-state NMR spectroscopy: appl
Protein structure determination by high-resolution solid-state NMR spectroscopy: application to microcrystalline ubiquitin. Related Articles Protein structure determination by high-resolution solid-state NMR spectroscopy: application to microcrystalline ubiquitin. J Am Chem Soc. 2005 Jun 22;127(24):8618-26 Authors: Zech SG, Wand AJ, McDermott AE High-resolution solid-state NMR spectroscopy has become a promising method for the determination of three-dimensional protein structures for systems which are difficult to crystallize or exhibit low...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Investigation of ligand-receptor systems by high-resolution solid-state NMR: recent p
Investigation of ligand-receptor systems by high-resolution solid-state NMR: recent progress and perspectives. Related Articles Investigation of ligand-receptor systems by high-resolution solid-state NMR: recent progress and perspectives. Arch Pharm (Weinheim). 2005 Jun;338(5-6):217-28 Authors: Luca S, Heise H, Lange A, Baldus M Solid-state Nuclear Magnetic Resonance (NMR) provides a general method to study molecular structure and dynamics in a non-crystalline and insoluble environment. We discuss the latest methodological progress to...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] High-resolution solid-state NMR spectroscopy of the prion protein HET-s in its amyloi
High-resolution solid-state NMR spectroscopy of the prion protein HET-s in its amyloid conformation. Related Articles High-resolution solid-state NMR spectroscopy of the prion protein HET-s in its amyloid conformation. Angew Chem Int Ed Engl. 2005 Apr 15;44(16):2441-4 Authors: Siemer AB, Ritter C, Ernst M, Riek R, Meier BH
nmrlearner Journal club 0 11-25-2010 08:21 PM
High Resolution (1)H-Detected Solid-State NMR Spectroscopy of Protein Aliphatic Reson
High Resolution (1)H-Detected Solid-State NMR Spectroscopy of Protein Aliphatic Resonances: Access to Tertiary Structure Information. Related Articles High Resolution (1)H-Detected Solid-State NMR Spectroscopy of Protein Aliphatic Resonances: Access to Tertiary Structure Information. J Am Chem Soc. 2010 Oct 12; Authors: Asami S, Schmieder P, Reif B Biological magic angle spinning (MAS) solid-state nuclear magnetic resonance spectroscopy has developed rapidly over the past two decades. For the structure determination of a protein by solid-state NMR,...
nmrlearner Journal club 0 10-15-2010 02:01 AM
High Resolution 1H-Detected Solid-State NMR Spectroscopy of Protein Aliphatic Resonan
High Resolution 1H-Detected Solid-State NMR Spectroscopy of Protein Aliphatic Resonances: Access to Tertiary Structure Information Sam Asami, Peter Schmieder and Bernd Reif http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja106170h/aop/images/medium/ja-2010-06170h_0003.gif Journal of the American Chemical Society DOI: 10.1021/ja106170h http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/FuDz8jUhWPE
nmrlearner Journal club 0 10-13-2010 04:10 AM
High resolution 13C-detected solid-state NMR spectroscopy of a deuterated protein
High resolution 13C-detected solid-state NMR spectroscopy of a deuterated protein Abstract High resolution 13C-detected solid-state NMR spectra of the deuterated beta-1 immunoglobulin binding domain of the protein G (GB1) have been collected to show that all 15N, 13Cā?², 13CĪ± and 13CĪ² sites are resolved in 13Cā??13C and 15Nā??13C spectra, with significant improvement in T 2 relaxation times and resolution at high magnetic field (750 MHz). The comparison of echo T 2 values between deuterated and protonated GB1 at various spinning rates and under different decoupling schemes indicates...
nmrlearner Journal club 0 09-01-2010 10:56 AM
High resolution (13)C-detected solid-state NMR spectroscopy of a deuterated protein.
High resolution (13)C-detected solid-state NMR spectroscopy of a deuterated protein. Related Articles High resolution (13)C-detected solid-state NMR spectroscopy of a deuterated protein. J Biomol NMR. 2010 Aug 29; Authors: Tang M, Comellas G, Mueller LJ, Rienstra CM High resolution (13)C-detected solid-state NMR spectra of the deuterated beta-1 immunoglobulin binding domain of the protein G (GB1) have been collected to show that all (15)N, (13)C', (13)Calpha and (13)Cbeta sites are resolved in (13)C-(13)C and (15)N-(13)C spectra, with significant...
nmrlearner Journal club 0 08-31-2010 09:42 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 09:50 AM.


Map