[RASMB] Dissociation constants for protein/DNA complexes

Dmitry Veprintsev dmitry.veprintsev at psi.ch
Sat Jan 17 00:23:45 PST 2015


Hi Sarah,
Peter Schuck has published several papers using this approach,
and so did we

Specific recognition of p53 tetramers by peptides derived from p53
interacting proteins. <http://www.ncbi.nlm.nih.gov/pubmed/22693587>

Gabizon R, Brandt T, Sukenik S, Lahav N, Lebendiker M, Shalev DE,
*Veprintsev* D, Friedler A.

PLoS One. 2012;7(5):e38060. doi: 10.1371/journal.pone.0038060. Epub 2012
May 31.
PMID: 22693587 [PubMed - indexed for MEDLINE] Free PMC Article
<http://www.ncbi.nlm.nih.gov/pubmed/22693587>


Subunit-selective N-terminal domain associations organize the formation of
AMPA receptor heteromers. <http://www.ncbi.nlm.nih.gov/pubmed/21317873>

Rossmann M, Sukumaran M, Penn AC, *Veprintsev* DB, Babu MM, Greger IH.

EMBO J. 2011 Mar 2;30(5):959-71. doi: 10.1038/emboj.2011.16. Epub 2011 Feb
11.
PMID: 21317873 [PubMed - indexed for MEDLINE] Free PMC Article
<http://www.ncbi.nlm.nih.gov/pubmed/21317873>


22.

Conservation of DNA-binding specificity and oligomerisation properties
within the p53 family. <http://www.ncbi.nlm.nih.gov/pubmed/20030809>

Brandt T, Petrovich M, Joerger AC, *Veprintsev* DB.

BMC Genomics. 2009 Dec 23;10:628. doi: 10.1186/1471-2164-10-628.
PMID: 20030809 [PubMed - indexed for MEDLINE] Free PMC Article
<http://www.ncbi.nlm.nih.gov/pubmed/20030809>

Related citations
<http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed&from_uid=20030809>


best regards, Dmitry

On Thu, Jan 15, 2015 at 3:20 AM, Sarah Kessans <
sarah.kessans at canterbury.ac.nz> wrote:

>  Hi all,
>
>  We are trying a new (?) method of determining dissociation constants for
> protein/DNA complexes using velocity sedimentation and I am looking for
> feedback regarding the method.
>
>  Our method of determining Kds uses fluorescently-labeled oligos in
> complex with unlabeled protein.  By scanning at 488 nm, we can determine
> the size distribution of both unbound DNA and the protein/DNA complex.  We
> then calculate the area under each of the (baseline resolved) distribution
> curves, normalize these values to 100% total, and use the ratios (along
> with our known initial concentrations) to calculate the molar
> concentrations of bound/unbound protein/DNA.  From these data, we are able
> to get Kds that correspond well to Kds calculated from other experiments.
>
> We are looking to publish these results, and I was wondering if anyone
> knew of Kds calculated in this manner before (either in published
> literature or otherwise)?  Any suggestions/comments welcome, thanks!
>
>  Best,
> Sarah
>
>  ___________________________
> Sarah Kessans
> Post-doctoral Fellow
> Biomolecular Interaction Centre
> School of Biological Sciences
> University of Canterbury
>
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-- 
Dr. Dmitry Veprintsev
Group Leader
Conformational Dynamics of GPCRs
Laboratory of Biomolecular Research, OFLC/103
Paul Scherrer Institut
5232 Villigen PSI
Switzerland
dmitry.veprintsev at psi.ch
Tel +41 (0) 56 310 5246; Fax +41 (0)56 310 5288
Secretary Mrs. Stefanie Whale +41 (0)56 310 4252 stefanie.whale at psi.ch
http://www.psi.ch/~veprintsev_d
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