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, 09:25 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,906
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 Solution NMR study of DNA recognition mechanism of IRF4 protein.

Solution NMR study of DNA recognition mechanism of IRF4 protein.

Related Articles Solution NMR study of DNA recognition mechanism of IRF4 protein.

Nucleic Acids Symp Ser (Oxf). 2004;(48):105-6

Authors: Ishizaki I, Nomura M, Yamamoto K, Matsuyama T, Mishima M, Kojima C

Transcription factor IRF-4 prefers the DNA sequence including CCGAAA. The consensus sequence of the IRF family proteins is NNGAAA, and all crystal structures indicate the NN region does not interact with IRF proteins directly. Here the sequence preference of IRF-4 was investigated by NMR and fluorescence antisotropy as an example of the indirect sequence recognition. The 1H-15N HSQC spectra of the IRF-4/DNA complex containing the CCGAAA sequence indicated that the 1:1 complex was formed. The dissociation constants (Kd) for two DNA oligomers containing CCGAAA and GGGAAA were determined by fluorescence antistropy, but their difference was very small.

PMID: 17150500 [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
Systematic Study of Protein Detection Mechanism of Self-Assembling 19F NMR/MRI Nanoprobes toward Rational Design and Improved Sensitivity
Systematic Study of Protein Detection Mechanism of Self-Assembling 19F NMR/MRI Nanoprobes toward Rational Design and Improved Sensitivity Yousuke Takaoka, Keishi Kiminami, Keigo Mizusawa, Kazuya Matsuo, Michiko Narazaki, Tetsuya Matsuda and Itaru Hamachi http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja203996c/aop/images/medium/ja-2011-03996c_0004.gif Journal of the American Chemical Society DOI: 10.1021/ja203996c http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/fqTSjFalrGg
nmrlearner Journal club 0 07-12-2011 08:16 AM
[NMR paper] Insights into the mechanism of heterodimerization from the 1H-NMR solution structure
Insights into the mechanism of heterodimerization from the 1H-NMR solution structure of the c-Myc-Max heterodimeric leucine zipper. Related Articles Insights into the mechanism of heterodimerization from the 1H-NMR solution structure of the c-Myc-Max heterodimeric leucine zipper. J Mol Biol. 1998 Aug 7;281(1):165-81 Authors: Lavigne P, Crump MP, Gagné SM, Hodges RS, Kay CM, Sykes BD The oncoprotein c-Myc (a member of the helix-loop-helix-leucine zipper (b-HLH-LZ) family of transcription factors) must heterodimerize with the b-HLH-LZ Max...
nmrlearner Journal club 0 11-17-2010 11:15 PM
[NMR paper] Recognition of DNA by GAL4 in solution: use of a monomeric protein-DNA complex for st
Recognition of DNA by GAL4 in solution: use of a monomeric protein-DNA complex for study by NMR. Related Articles Recognition of DNA by GAL4 in solution: use of a monomeric protein-DNA complex for study by NMR. Biochemistry. 1994 Mar 15;33(10):3071-8 Authors: Baleja JD, Mau T, Wagner G The complex of a monomer of GAL4 with DNA has been investigated by two-dimensional 1H nuclear magnetic resonance (NMR) spectroscopy. Previous X-ray analysis has revealed a structure in which a dimer of the N-terminal 65-residue fragment of GAL4 forms a complex,...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Recognition of DNA by GAL4 in solution: use of a monomeric protein-DNA complex for st
Recognition of DNA by GAL4 in solution: use of a monomeric protein-DNA complex for study by NMR. Related Articles Recognition of DNA by GAL4 in solution: use of a monomeric protein-DNA complex for study by NMR. Biochemistry. 1994 Mar 15;33(10):3071-8 Authors: Baleja JD, Mau T, Wagner G The complex of a monomer of GAL4 with DNA has been investigated by two-dimensional 1H nuclear magnetic resonance (NMR) spectroscopy. Previous X-ray analysis has revealed a structure in which a dimer of the N-terminal 65-residue fragment of GAL4 forms a complex,...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Electrostatic recognition in redox copper proteins: a 1H NMR study of the protonation
Electrostatic recognition in redox copper proteins: a 1H NMR study of the protonation behavior of His 19 in oxidized and reduced Cu,Zn superoxide dismutase. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Electrostatic recognition in redox copper proteins: a 1H NMR study of the protonation behavior of His 19 in oxidized and reduced Cu,Zn superoxide dismutase. Arch Biochem Biophys. 1993 Mar;301(2):244-50 Authors: Desideri A, Polticelli F, Falconi M, Sette M, Ciriolo MR, Paci M,...
nmrlearner Journal club 0 08-21-2010 11:53 PM
[NMR paper] 1H-NMR study of the mechanism of assembly and equilibrium heme orientation of sperm w
1H-NMR study of the mechanism of assembly and equilibrium heme orientation of sperm whale myoglobin reconstituted with protohemin type-isomers. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles 1H-NMR study of the mechanism of assembly and equilibrium heme orientation of sperm whale myoglobin reconstituted with protohemin type-isomers. Biochim Biophys Acta. 1990 Nov 15;1041(2):186-94 Authors: Hauksson JB, La Mar GN, Pande U, Pandey RK, Parish DW, Singh JP, Smith KM The...
nmrlearner Journal club 0 08-21-2010 11:04 PM
Postdoctoral position to study Protein-Protein Interactions and their role in Mechanisms of Signal Transduction using protein solution NMR/x-ray crystallography
Spincore.com are advertising a postdoc NMR position. It sounds pretty interesting. """ Postdoctoral position to study Protein-Protein Interactions and their role in Mechanisms of Signal Transduction using protein solution NMR /x-ray crystallography Case Medical School, Cleveland, Ohio, USA How are signaling events transmitted from one protein to another? To answer this question we are looking to add a postdoctoral co-workers to our interdisciplinary team. Our interest is to understand protein-protein interactions, protein structure and dynamics in the context of cell signaling...
steveUK Job marketplace 0 08-10-2008 02:37 PM
NMR post-doc position: NMR-based dynamics study of enzyme mechanism
The following post-doc position in NMR is available in University of Missouri: Ad text: """ We have an opening for a postdoctoral fellow to use NMR to study dynamics of an enzyme while it is carrying on reversible catalysis. The prospects are promising and can be compared with thorough enzymology and crystallography of its ligand-dependent conformational changes (done in our dept.). The enzyme is sizeable enough to be challenging, but we have a battery of excellent 800 MHz spectra of deuterated samples for launching the project. The postdoctoral fellow will be housed in a new...
administrator Job marketplace 0 07-14-2007 03:55 AM


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 - 2020, 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 10:21 AM.


Map