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 09-26-2014, 01:03 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,208
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 Probing the rate limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by 15Nz-exchange NMR spectroscopy.

Probing the rate limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by 15Nz-exchange NMR spectroscopy.

Related Articles Probing the rate limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by 15Nz-exchange NMR spectroscopy.

J Am Chem Soc. 2014 Sep 25;

Authors: Ryu KS, Tugarinov V, Clore GM

Abstract
The kinetics of translocation of the homeodomain transcription factor HoxD9 between specific sites of the same or opposite polarities on the same DNA molecule have been studied by 15Nz-exchange NMR spectroscopy. We show that exchange occurs by two facilitated diffusion mech-anisms: a second-order intermolecular exchange reaction between specific sites located on different DNA molecules without the protein dissociating into free solution that pre-dominates at high concentrations of free DNA, and a first-order intramolecular process involving direct transfer be-tween specific sites located on the same DNA molecule. Control experiments using a mixture of two DNA molecules, each possessing only a single specific site, indicate that trans-fer between specific sites by full dissociation of HoxD9 into solution followed by reassociation is too slow to measure by z-exchange spectroscopy. Intramolecular transfer with com-parable rate constants occurs between sites of the same and opposing polarity indicating that both rotation-coupled slid-ing and hopping/flipping (analogous to geminate recombi-nation) occur. The half-life for intramolecular transfer (0.5 -1 s) is many orders of magnitude larger than the calculated transfer time (1-100 ?s) by sliding, leading us to conclude that the intramolecular transfer rates measured by z-exchange spectroscopy represent the rate-limiting step for a one base pair shift from the specific site to the immediately adjacent non-specific site. At zero concentration of added salt, the intramolecular transfer rate constants between sites of opposing polarity are smaller than those between sites of the same polarity, suggesting that hopping/flipping may be-come rate limiting at very low salt concentrations.


PMID: 25253516 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Small-Molecule Binding Sites on Proteins Establishedby Paramagnetic NMR Spectroscopy
Small-Molecule Binding Sites on Proteins Establishedby Paramagnetic NMR Spectroscopy Jia-Ying Guan, Peter H. J. Keizers, Wei-Min Liu, Frank Lo?hr, Simon P. Skinner, Edwin A. Heeneman, Harald Schwalbe, Marcellus Ubbink and Gregg Siegal http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja401323m/aop/images/medium/ja-2013-01323m_0009.gif Journal of the American Chemical Society DOI: 10.1021/ja401323m http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/ZukfjIRmQq8
nmrlearner Journal club 0 04-05-2013 11:03 PM
[NMR paper] Small molecule binding sites on proteins established by paramagnetic NMR spectroscopy.
Small molecule binding sites on proteins established by paramagnetic NMR spectroscopy. Related Articles Small molecule binding sites on proteins established by paramagnetic NMR spectroscopy. J Am Chem Soc. 2013 Mar 20; Authors: Guan JY, Keizers PH, Liu WM, Loehr F, Skinner SP, Heeneman EA, Schwalbe H, Ubbink M, Siegal GD Abstract Determining the three dimensional structure of a small molecule-protein complex with weak affinity can be a significant challenge. We present a paramagnetic NMR method to determine intermolecular structure...
nmrlearner Journal club 0 03-21-2013 02:58 PM
[NMR paper] Probing Slow Chemical Exchange at Carbonyl Sites in Proteins by Chemical Exchange Saturation Transfer NMR Spectroscopy.
Probing Slow Chemical Exchange at Carbonyl Sites in Proteins by Chemical Exchange Saturation Transfer NMR Spectroscopy. Probing Slow Chemical Exchange at Carbonyl Sites in Proteins by Chemical Exchange Saturation Transfer NMR Spectroscopy. Angew Chem Int Ed Engl. 2013 Feb 28; Authors: Vallurupalli P, Kay LE Abstract Seeing the invisible: A 13 CO NMR chemical exchange saturation transfer (CEST) experiment for the study of "invisible" excited protein states with lifetimes on the order of 5-50 ms has been developed. The 13 CO chemical...
nmrlearner Journal club 0 03-02-2013 11:45 AM
[NMR paper] Probing specific lipid-protein interaction by saturation transfer difference NMR spectroscopy.
Probing specific lipid-protein interaction by saturation transfer difference NMR spectroscopy. Related Articles Probing specific lipid-protein interaction by saturation transfer difference NMR spectroscopy. J Am Chem Soc. 2005 Sep 28;127(38):13110-1 Authors: Soubias O, Gawrisch K We studied the interaction of mono- and polyunsaturated phosphatidylcholines with rhodopsin by 1H NMR saturation transfer difference spectroscopy with magic angle spinning (STD-MAS NMR). The results indicate a strong preference for interaction of rhodopsin with the...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Mechanisms for the enhanced thermal stability of a mutant of transcription factor 1 a
Mechanisms for the enhanced thermal stability of a mutant of transcription factor 1 as explained by (1)H, (15)N and (13)C NMR chemical shifts and secondary structure analysis. Related Articles Mechanisms for the enhanced thermal stability of a mutant of transcription factor 1 as explained by (1)H, (15)N and (13)C NMR chemical shifts and secondary structure analysis. Biochim Biophys Acta. 2000 Mar 16;1478(1):113-24 Authors: Vu HM, Liu W, Grove A, Geiduschek EP, Kearns DR A variant of the bacteriophage SPO1-encoded transcription factor 1 (TF1)...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] New perceptions of transcription factor properties from NMR.
New perceptions of transcription factor properties from NMR. Related Articles New perceptions of transcription factor properties from NMR. Biochem Cell Biol. 1998;76(2-3):368-78 Authors: Bagby S, Arrowsmith CH, Ikura M The complementarity of NMR and X-ray crystallography for biomacromolecular studies has been particularly evident in analysis of transcription factor structures and interactions. While X-ray crystallography can be used to tackle relatively complicated structural problems including multicomponent (three and higher) complexes, NMR...
nmrlearner Journal club 0 11-17-2010 11:06 PM
[NMR paper] A 1H-NMR study of the transcription factor 1 from Bacillus subtilis phage SPO1 by sel
A 1H-NMR study of the transcription factor 1 from Bacillus subtilis phage SPO1 by selective 2H-labeling. Complete assignment and structural analysis of the aromatic resonances for a 22-kDa homodimer. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles A 1H-NMR study of the transcription factor 1 from Bacillus subtilis phage SPO1 by selective 2H-labeling. Complete assignment and structural analysis of the aromatic resonances for a 22-kDa homodimer. Eur J...
nmrlearner Journal club 0 08-21-2010 11:53 PM
[Ryan's blog] From FID to Structure in 30 Minutes? Investigating the CASE Limiting Step
Source: Ryan's blog From FID to Structure in 30 Minutes? Investigating the CASE Limiting Step In yesterday's post I pointed you to an article that has become the most accessed article of all time in the Journal of Cheminformatics, co-authored by representatives of ACD/Labs. This article is a very comprehensive outline of the different approaches,...
nmrlearner News from NMR blogs 0 08-21-2010 08:57 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 - 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 04:03 AM.


Map