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, 09:51 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,227
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 Binding ability of a HHP-tagged protein towards Ni2+ studied by paramagnetic NMR rela

Binding ability of a HHP-tagged protein towards Ni2+ studied by paramagnetic NMR relaxation: the possibility of obtaining long-range structure information.

Related Articles Binding ability of a HHP-tagged protein towards Ni2+ studied by paramagnetic NMR relaxation: the possibility of obtaining long-range structure information.

J Biomol NMR. 2004 Jun;29(2):175-85

Authors: Jensen MR, Lauritzen C, Dahl SW, Pedersen J, Led JJ

The binding ability of a protein with a metal binding tag towards Ni(2+) was investigated by longitudinal paramagnetic NMR relaxation, and the possibility of obtaining long-range structure information from the paramagnetic relaxation was explored. A protein with a well-defined solution structure (Escherichia coli thioredoxin) was used as the model system, and the peptide His-His-Pro (HHP) fused to the N-terminus of the protein was used as the metal binding tag. It was found that the tag forms a stable dimer complex with the paramagnetic Ni(2+) ion, where each metal ion binds two HHP-tagged protein molecules. However, it was also found that additional sites in the protein compete with the HHP-tag for the binding of the metal ion. These binding sites were identified as the side chain carboxylate groups of the aspartic and glutamic acid residues. Yet, the carboxylate groups bind the Ni(2+) ions considerably weaker than the HHP-tag, and only protons spatially close to the carboxylate sites are affected by the Ni(2+) ions bound to these groups. As for the protons that are unaffected by the carboxylate-bound Ni(2+) ions, it was found that the long-range distances derived from the paramagnetic relaxation enhancements are in good agreement with the solution structure of thioredoxin. Specifically, the obtained long-range paramagnetic distance constraints revealed that the dimer complex is asymmetric with different orientations of the two protein molecules relative to the Ni(2+) ion.

PMID: 15014231 [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
Engineering of a bis-chelator motif into a protein ?-helix for rigid lanthanide binding and paramagnetic NMR spectroscopy.
Engineering of a bis-chelator motif into a protein ?-helix for rigid lanthanide binding and paramagnetic NMR spectroscopy. Engineering of a bis-chelator motif into a protein ?-helix for rigid lanthanide binding and paramagnetic NMR spectroscopy. Chem Commun (Camb). 2011 May 27; Authors: Swarbrick JD, Ung P, Su XC, Maleckis A, Chhabra S, Huber T, Otting G, Graham B Attachment of two nitrilotriacetic acid-based ligands to a protein ?-helix in an i, i + 4 configuration produces an octadentate chelating motif that is able to bind paramagnetic...
nmrlearner Journal club 0 05-28-2011 06:50 PM
[NMR paper] Metal binding sites in proteins: identification and characterization by paramagnetic NMR relaxation.
Metal binding sites in proteins: identification and characterization by paramagnetic NMR relaxation. Related Articles Metal binding sites in proteins: identification and characterization by paramagnetic NMR relaxation. Biochemistry. 2005 Aug 23;44(33):11014-23 Authors: Jensen MR, Petersen G, Lauritzen C, Pedersen J, Led JJ A method is presented that allows the identification and quantitative characterization of metal binding sites in proteins using paramagnetic nuclear magnetic resonance spectroscopy. The method relies on the nonselective...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] The energetic cost of domain reorientation in maltose-binding protein as studied by N
The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy. Related Articles The energetic cost of domain reorientation in maltose-binding protein as studied by NMR and fluorescence spectroscopy. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12700-5 Authors: Millet O, Hudson RP, Kay LE Maltose-binding protein (MBP) is a two-domain protein that undergoes a ligand-mediated conformational rearrangement from an "open" to a "closed" structure on binding to maltooligosaccharides. To...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Protein dynamics using frequency-dependent order parameters from analysis of NMR rela
Protein dynamics using frequency-dependent order parameters from analysis of NMR relaxation data. Related Articles Protein dynamics using frequency-dependent order parameters from analysis of NMR relaxation data. J Magn Reson. 2003 Mar;161(1):118-25 Authors: Idiyatullin D, Daragan VA, Mayo KH A novel approach is described to analyze NMR relaxation data on proteins. This method introduces the frequency-dependent order parameter, S(2)(omega), in order to estimate contributions to the generalized order parameter S(2) from different motional...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] Ligand-induced structural changes to maltodextrin-binding protein as studied by solut
Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy. Related Articles Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy. J Mol Biol. 2001 Jun 15;309(4):961-74 Authors: Evenäs J, Tugarinov V, Skrynnikov NR, Goto NK, Muhandiram R, Kay LE Solution NMR studies on the physiologically relevant ligand-free and maltotriose-bound states of maltodextrin-binding protein (MBP) are presented. Together with existing data on MBP in complex with...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] An investigation of the dynamics of ribosomal protein L9 using heteronuclear NMR rela
An investigation of the dynamics of ribosomal protein L9 using heteronuclear NMR relaxation measurements. Related Articles An investigation of the dynamics of ribosomal protein L9 using heteronuclear NMR relaxation measurements. J Mol Biol. 1998 Aug 21;281(3):539-51 Authors: Lillemoen J, Hoffman DW The dynamic properties of ribosomal protein L9 from Bacillus stearothermophilus were investigated in solution using an analysis of nitrogen-15 longitudinal and transverse relaxation rates and amide nitrogen-proton nuclear Overhauser effects. The...
nmrlearner Journal club 0 11-17-2010 11:15 PM
[NMR paper] Effect of antibody binding on protein motions studied by hydrogen-exchange labeling a
Effect of antibody binding on protein motions studied by hydrogen-exchange labeling and two-dimensional NMR. Related Articles Effect of antibody binding on protein motions studied by hydrogen-exchange labeling and two-dimensional NMR. Biochemistry. 1992 Nov 10;31(44):10678-85 Authors: Mayne L, Paterson Y, Cerasoli D, Englander SW We have used hydrogen-exchange labeling detected by 2D NMR to study antibody-protein interactions for two monoclonal antibodies raised against horse cytochrome c. The data show that these antibodies bind mainly to the...
nmrlearner Journal club 0 08-21-2010 11:45 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 - 2019, 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 01:47 PM.


Map