<div dir="ltr">Hi Sarah, <div>Peter Schuck has published several papers using this approach, </div><div>and so did we</div><div><p class=""><a href="http://www.ncbi.nlm.nih.gov/pubmed/22693587">Specific recognition of p53 tetramers by peptides derived from p53 interacting proteins.</a></p><div class=""><p class="">Gabizon R, Brandt T, Sukenik S, Lahav N, Lebendiker M, Shalev DE, <b>Veprintsev</b> D, Friedler A.</p><p class=""><span class="" title="PloS one">PLoS One</span>. 2012;7(5):e38060. doi: 10.1371/journal.pone.0038060. Epub 2012 May 31.</p></div><div class=""><div class=""><dl class=""><dt>PMID:</dt> <dd>22693587</dd> <dd>[PubMed - indexed for MEDLINE] </dd></dl><a class="" href="http://www.ncbi.nlm.nih.gov/pubmed/22693587">Free PMC Article</a></div><div class=""><br></div><div class=""><br></div><div class=""><p class=""><a href="http://www.ncbi.nlm.nih.gov/pubmed/21317873">Subunit-selective N-terminal domain associations organize the formation of AMPA receptor heteromers.</a></p><div class=""><p class="">Rossmann M, Sukumaran M, Penn AC, <b>Veprintsev</b> DB, Babu MM, Greger IH.</p><p class=""><span class="" title="The EMBO journal">EMBO J</span>. 2011 Mar 2;30(5):959-71. doi: 10.1038/emboj.2011.16. Epub 2011 Feb 11.</p></div><div class=""><div class=""><dl class=""><dt>PMID:</dt> <dd>21317873</dd> <dd>[PubMed - indexed for MEDLINE] </dd></dl><a class="" href="http://www.ncbi.nlm.nih.gov/pubmed/21317873">Free PMC Article</a></div><div class=""><br></div><div class=""><br></div><div class=""><div class="">22.</div><div class=""><p class=""><a href="http://www.ncbi.nlm.nih.gov/pubmed/20030809">Conservation of DNA-binding specificity and oligomerisation properties within the p53 family.</a></p><div class=""><p class="">Brandt T, Petrovich M, Joerger AC, <b>Veprintsev</b> DB.</p><p class=""><span class="" title="BMC genomics">BMC Genomics</span>. 2009 Dec 23;10:628. doi: 10.1186/1471-2164-10-628.</p></div><div class=""><div class=""><dl class=""><dt>PMID:</dt> <dd>20030809</dd> <dd>[PubMed - indexed for MEDLINE] </dd></dl><a class="" href="http://www.ncbi.nlm.nih.gov/pubmed/20030809">Free PMC Article</a></div><p class=""><a href="http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed&from_uid=20030809">Related citations</a></p><p class=""><br></p><p class="">best regards, Dmitry</p></div></div></div></div></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jan 15, 2015 at 3:20 AM, Sarah Kessans <span dir="ltr"><<a href="mailto:sarah.kessans@canterbury.ac.nz" target="_blank">sarah.kessans@canterbury.ac.nz</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>Hi all,</div>
<div><br>
</div>
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.
<div><br>
</div>
<div>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. </div>
<div><br>
<div>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!</div>
<div><br>
</div>
<div>Best,</div>
<div>Sarah<br>
<div><br>
<div style="font-family:Tahoma;font-size:13px">
<div style="font-family:Tahoma;font-size:13px">___________________________
<div>Sarah Kessans</div>
<div>Post-doctoral Fellow</div>
<div>Biomolecular Interaction Centre</div>
<div>School of Biological Sciences</div>
<div>University of Canterbury</div>
</div>
</div>
</div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature">Dr. Dmitry Veprintsev<br>Group Leader<br>Conformational Dynamics of GPCRs<br>Laboratory of Biomolecular Research, OFLC/103<br>Paul Scherrer Institut<br>5232 Villigen PSI<br>Switzerland<br><a href="mailto:dmitry.veprintsev@psi.ch" target="_blank">dmitry.veprintsev@psi.ch</a><br>Tel +41 (0) 56 310 5246; Fax +41 (0)56 310 5288<br>Secretary Mrs. Stefanie Whale +41 (0)56 310 4252 <a href="mailto:stefanie.whale@psi.ch" target="_blank">stefanie.whale@psi.ch</a><br><a href="http://www.psi.ch/~veprintsev_d" target="_blank">http://www.psi.ch/~veprintsev_d</a></div>
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