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 08-22-2010, 03:33 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,565
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 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, 27 kDa in molecular mass, with a 19 base pair full-binding-site DNA [Marmorstein, R., Carey, M., Ptashne, M., & Harrison, S. C. (1992) Nature 356, 408-414]. We have developed a smaller system, half in molecular mass, which is amenable for detailed analysis using NMR. Titration of a 10 base pair half-binding-site DNA with GAL4-(65) shows 1:1 binding, illustrating that one monomer of the protein binds in a specific manner to half-site DNA. The components of the protein-DNA complex are mainly in fast exchange on the NMR chemical shift time scale, with an equilibrium dissociation constant of 161 +/- 12 microM. With a basis of chemical shift data for free GAL4 protein and for the free half-site DNA, the fast exchange facilitates 1H resonance assignments in the complex since cross-peak positions can be examined at different protein:DNA ratios. Chemical shift changes in the DNA reveal the base pairs that are important for recognition by GAL4. Intermolecular NOE cross-peaks are also observed in spectra of the protein-DNA complex. Their identification places the C-terminal end of the first alpha-helix (residues 12-17) in a position such that the amino acids are able to read the DNA sequence in a manner entirely consistent with the X-ray structure of the related complex.(ABSTRACT TRUNCATED AT 250 WORDS)

PMID: 8130221 [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
[NMR paper] NMR solution structure of the monomeric form of the bacteriophage lambda capsid stabi
NMR solution structure of the monomeric form of the bacteriophage lambda capsid stabilizing protein gpD. Related Articles NMR solution structure of the monomeric form of the bacteriophage lambda capsid stabilizing protein gpD. J Biomol NMR. 2005 Apr;31(4):351-6 Authors: Iwai H, Forrer P, Plückthun A, Güntert P
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] 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...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] NMR solution structure and topological orientation of monomeric phospholamban in dode
NMR solution structure and topological orientation of monomeric phospholamban in dodecylphosphocholine micelles. Related Articles NMR solution structure and topological orientation of monomeric phospholamban in dodecylphosphocholine micelles. Biophys J. 2003 Oct;85(4):2589-98 Authors: Zamoon J, Mascioni A, Thomas DD, Veglia G Phospholamban is an integral membrane protein that regulates the contractility of cardiac muscle by maintaining cardiomyocyte calcium homeostasis. Abnormalities in association of protein kinase A with PLB have recently...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Solution NMR study of the monomeric form of p13suc1 protein sheds light on the hinge
Solution NMR study of the monomeric form of p13suc1 protein sheds light on the hinge region determining the affinity for a phosphorylated substrate. Related Articles Solution NMR study of the monomeric form of p13suc1 protein sheds light on the hinge region determining the affinity for a phosphorylated substrate. J Biol Chem. 2002 Apr 5;277(14):12375-81 Authors: Odaert B, Landrieu I, Dijkstra K, Schuurman-Wolters G, Casteels P, Wieruszeski JM, Inze D, Scheek R, Lippens G Cyclin-dependent kinase subunit (CKS) proteins bind to cyclin-dependent...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of
NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Related Articles NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell. 1998 Apr 17;93(2):289-99 Authors: Legault P, Li J, Mogridge J, Kay LE, Greenblatt J The structure of the complex formed by the arginine-rich motif of the transcriptional antitermination protein N of phage lambda and boxB RNA was determined by heteronuclear magnetic resonance...
nmrlearner Journal club 0 11-17-2010 11:06 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] 1H NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA
1H NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA binding domain with a half-site response element. Related Articles 1H NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA binding domain with a half-site response element. Biochemistry. 1991 Dec 17;30(50):11620-4 Authors: Remerowski ML, Kellenbach E, Boelens R, van der Marel GA, van Boom JH, Maler BA, Yamamoto KR, Kaptein R The complex of the rat glucocorticoid receptor (GR) DNA binding domain (DBD) and half-site sequence of the...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] 1H NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA
1H NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA binding domain with a half-site response element. Related Articles 1H NMR studies of DNA recognition by the glucocorticoid receptor: complex of the DNA binding domain with a half-site response element. Biochemistry. 1991 Dec 17;30(50):11620-4 Authors: Remerowski ML, Kellenbach E, Boelens R, van der Marel GA, van Boom JH, Maler BA, Yamamoto KR, Kaptein R The complex of the rat glucocorticoid receptor (GR) DNA binding domain (DBD) and half-site sequence of the...
nmrlearner Journal club 0 08-21-2010 11:12 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 03:19 PM.


Map