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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 11-24-2010, 10:01 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,732
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 The NMR solution structure of a mutant of the Max b/HLH/LZ free of DNA: insights into

The NMR solution structure of a mutant of the Max b/HLH/LZ free of DNA: insights into the specific and reversible DNA binding mechanism of dimeric transcription factors.

Related Articles The NMR solution structure of a mutant of the Max b/HLH/LZ free of DNA: insights into the specific and reversible DNA binding mechanism of dimeric transcription factors.

J Mol Biol. 2004 Sep 17;342(3):813-32

Authors: Sauvé S, Tremblay L, Lavigne P

Basic region-helix1-loop-helix2-leucine zipper (b/H(1)LH(2)/LZ) transcription factors bind specific DNA sequence in their target gene promoters as dimers. Max, a b/H(1)LH(2)/LZ transcription factor, is the obligate heterodimeric partner of the related b/H(1)LH(2)/LZ proteins of the Myc and Mad families. These heterodimers specifically bind E-box DNA sequence (CACGTG) to activate (e.g. c-Myc/Max) and repress (e.g. Mad1/Max) transcription. Max can also homodimerize and bind E-box sequences in c-Myc target gene promoters. While the X-ray structure of the Max b/H(1)LH(2)/LZ/DNA complex and that of others have been reported, the precise sequence of events leading to the reversible and specific binding of these important transcription factors is still largely unknown. In order to provide insights into the DNA binding mechanism, we have solved the NMR solution structure of a covalently homodimerized version of a Max b/H(1)LH(2)/LZ protein with two stabilizing mutations in the LZ, and characterized its backbone dynamics from (15)N spin-relaxation measurements in the absence of DNA. Apart from minor differences in the pitch of the LZ, possibly resulting from the mutations in the construct, we observe that the packing of the helices in the H(1)LH(2) domain is almost identical to that of the two crystal structures, indicating that no important conformational change in these helices occurs upon DNA binding. Conversely to the crystal structures of the DNA complexes, the first 14 residues of the basic region are found to be mostly unfolded while the loop is observed to be flexible. This indicates that these domains undergo conformational changes upon DNA binding. On the other hand, we find the last four residues of the basic region form a persistent helical turn contiguous to H(1). In addition, we provide evidence of the existence of internal motions in the backbone of H(1) that are of larger amplitude and longer time-scale (nanoseconds) than the ones in the H(2) and LZ domain. Most interestingly, we note that conformers in the ensemble of calculated structures have highly conserved basic residues (located in the persistent helical turn of the basic region and in the loop) known to be important for specific binding in a conformation that matches that of the DNA-bound state. These partially prefolded conformers can directly fit into the major groove of DNA and as such are proposed to lie on the pathway leading to the reversible and specific DNA binding. In these conformers, the conserved basic side-chains form a cluster that elevates the local electrostatic potential and could provide the necessary driving force for the generation of the internal motions localized in the H(1) and therefore link structural determinants with the DNA binding function. Overall, our results suggests that the Max homodimeric b/H(1)LH(2)/LZ can rapidly and preferentially bind DNA sequence through transient and partially prefolded states and subsequently, adopt the fully helical bound state in a DNA-assisted mechanism or induced-fit.

PMID: 15342239 [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
Solution NMR Insights into Docking Interactions Involving Inactive ERK2
Solution NMR Insights into Docking Interactions Involving Inactive ERK2 http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi2000559/aop/images/medium/bi-2011-000559_0008.gif Biochemistry DOI: 10.1021/bi2000559 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/6siUjjajeQA More...
nmrlearner Journal club 0 04-20-2011 02:51 AM
[NMR paper] NMR studies on the solution structure of a deletion mutant of the transcarboxylase bi
NMR studies on the solution structure of a deletion mutant of the transcarboxylase biotin carrier subunit. Related Articles NMR studies on the solution structure of a deletion mutant of the transcarboxylase biotin carrier subunit. Int J Biol Macromol. 2002 Oct 1;30(5):233-42 Authors: Jank MM, Sadowsky JD, Peikert C, Berger S A deletion mutant of the transcarboxylase biotin carrier protein was completely labeled with 13C and 15N. A multitude of 2D and 3D NMR spectra were recorded and assigned. An NMR solution structure was derived from the data...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Fluctuations in free or substrate-complexed lysozyme and a mutant of it detected on x
Fluctuations in free or substrate-complexed lysozyme and a mutant of it detected on x-ray crystallography and comparison with those detected on NMR. Related Articles Fluctuations in free or substrate-complexed lysozyme and a mutant of it detected on x-ray crystallography and comparison with those detected on NMR. J Biochem. 2002 May;131(5):701-4 Authors: Ohmura T, Motoshima H, Ueda T, Imoto T A mutant lysozyme in which Arg14 and His15 were deleted together exhibited higher activity toward glycol chitin than the wild-type lysozyme. Moreover,...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[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] High-resolution solution structure of the inhibitor-free catalytic fragment of human
High-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast collagenase determined by multidimensional NMR. Related Articles High-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast collagenase determined by multidimensional NMR. Biochemistry. 1998 Feb 10;37(6):1495-504 Authors: Moy FJ, Chanda PK, Cosmi S, Pisano MR, Urbano C, Wilhelm J, Powers R The high-resolution solution structure of the inhibitor-free catalytic fragment of human fibroblast collagenase (MMP-1), a...
nmrlearner Journal club 0 11-17-2010 11:06 PM
Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel.
Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel. Biochem Biophys Res Commun. 2010 Sep 9; Authors: Pielak RM, Chou JJ The M2 protein of influenza A virus forms a proton-selective channel that is required for viral replication; it is also the target of the anti-influenza drugs, amantadine and rimantadine. Widespread drug-resistant mutants, however, has greatly compromised the effectiveness of these drugs. Here, we report the...
nmrlearner Journal club 0 09-14-2010 02:03 PM
[NMR paper] NMR study on solution structure of the site-specific mutant Leu48----Ala transforming
NMR study on solution structure of the site-specific mutant Leu48----Ala transforming growth factor alpha. Related Articles NMR study on solution structure of the site-specific mutant Leu48----Ala transforming growth factor alpha. Int J Pept Protein Res. 1992 Feb;39(2):111-6 Authors: Kline TP, Mueller L The NMR spectra of the Leu48----Ala mutant of human transforming growth factor alpha were compared to that of the wild-type. All chemical shift changes are less than or equal to 0.02 ppm with the exception of resonances associated with residues...
nmrlearner Journal club 0 08-21-2010 11:41 PM



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 09:13 PM.


Map