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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Tom we published a paper where we constructed s vs n models for different topologies of tubulin polymers. We made higher order hydro models from a tubulin monomer
and dimer bead model that spanned rods through spirals of various kinds of rise over runs. These s vs n data were used to fit velocity data to an isodesmic model of self-association. The rods gave an s vs n that was flat above n = 20..
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I’ve attached the pdf.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> rasmb-bounces@list.rasmb.org [mailto:rasmb-bounces@list.rasmb.org]
<b>On Behalf Of </b>Laue, Thomas<br>
<b>Sent:</b> Thursday, May 08, 2014 12:24 PM<br>
<b>To:</b> Fagan, Jeffrey; jphilo@mailway.com; rasmb@list.rasmb.org<br>
<b>Subject:</b> Re: [RASMB] Sedimentation of rods<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="color:black">Thank you, Jeff- great paper and to the point. Tom<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> Fagan, Jeffrey [jeffery.fagan@nist.gov]<br>
<b>Sent:</b> Thursday, May 08, 2014 1:01 PM<br>
<b>To:</b> Laue, Thomas; <a href="mailto:jphilo@mailway.com">jphilo@mailway.com</a>;
<a href="mailto:rasmb@list.rasmb.org">rasmb@list.rasmb.org</a><br>
<b>Subject:</b> RE: [RASMB] Sedimentation of rods</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear Tom, John et al.</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I will shamelessly note that my group just published a paper on this in Langmuir</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">“Rod Hydrodynamics and Length Distributions of Single-Wall Carbon Nanotubes Using Analytical Ultracentrifugation”</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><a href="http://pubs.acs.org/doi/abs/10.1021/la404892k" target="_blank">http://pubs.acs.org/doi/abs/10.1021/la404892k</a>
</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The biggest caveats for using rod hydrodynamic theories are how stiff the rods are and having them be actually straight; both factors (i.e. having flexible
or bent/kinked rods) can cause the effective friction to be significantly reduced from the rod prediction (although this is only mentioned in passing in the paper).</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Cheers,</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Jeff Fagan</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">
<a href="mailto:rasmb-bounces@list.rasmb.org">rasmb-bounces@list.rasmb.org</a> [<a href="mailto:rasmb-bounces@list.rasmb.org">mailto:rasmb-bounces@list.rasmb.org</a>]
<b>On Behalf Of </b>Laue, Thomas<br>
<b>Sent:</b> Thursday, May 08, 2014 12:21 PM<br>
<b>To:</b> <a href="mailto:jphilo@mailway.com">jphilo@mailway.com</a>; <a href="mailto:rasmb@list.rasmb.org">
rasmb@list.rasmb.org</a><br>
<b>Subject:</b> Re: [RASMB] Sedimentation of rods</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:black">Hi John-<br>
I wouldn't count on my memory for anything, so any insights/recollections are welcome. I have no idea where I got that number...
<br>
Vern Schumaker and Bruno Zimm did a fair amount of work with large DNA molecules, but it is better represented as a flexible polymer than as a rod. Also, it is important to note that at very large sizes, asymmetric particles will show a speed-dependent sedimentation.
Below is the abstract from their paper. <br>
I am assuming that the rods are stiff and have a uniform diameter (not a mixture of lateral association). Best wishes,<br>
Tom<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><a href="http://www.ncbi.nlm.nih.gov/pubmed/963220?dopt=Abstract" target="_blank" title="Biophysical chemistry.">Biophys Chem.</a> 1976 Jul;5(1-2):265-70.<o:p></o:p></span></p>
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<h1><span style="color:black">Anomalies in sedimentation. V. Chains at high fields, practical consequences.<o:p></o:p></span></h1>
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<p class="MsoNormal"><span style="color:black"><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Zimm%20BH%5BAuthor%5D&cauthor=true&cauthor_uid=963220" target="_blank">Zimm BH</a>,
<a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Schumaker%20VN%5BAuthor%5D&cauthor=true&cauthor_uid=963220" target="_blank">
Schumaker VN</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Zimm%20CB%5BAuthor%5D&cauthor=true&cauthor_uid=963220" target="_blank">
Zimm CB</a>.<o:p></o:p></span></p>
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<h3><span style="color:black">Abstract<o:p></o:p></span></h3>
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<p><span style="color:black">The theory of a preceding paper [B.H. Zimm, Biophys, Chem. 1 (1974) 279] is used to calculate a numerical table for the change of sedimentation coefficient with centrifugal field for chain molecules. A simple formula is found to
fit the results within 1.3% up to the centrifugal field at which S/So = 0.377; this formula is S/So=(1+0.1155y2)-1/4, where y is proportional to M2/So times the centripetal acceleration, M being the molecular weight and So the sedimentation coefficient at
zero acceleration. Applying this formula to DNA, we conclude that at a given centrifuge speed the sedimentation coefficient must reach a maximum at a particular molecular weight and be smaller at higher molecular weights. The value of the maximum depends on
the conditions, but can come at less than 150 S for DNA under typical conditions. When a maximum is present, the profile of a sedimenting non-homogeneous band is also severely distorted.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"> John Philo [jphilo@mailway.com]<br>
<b>Sent:</b> Thursday, May 08, 2014 12:03 PM<br>
<b>To:</b> <a href="mailto:rasmb@list.rasmb.org" target="_blank">rasmb@list.rasmb.org</a><br>
<b>Cc:</b> Laue, Thomas<br>
<b>Subject:</b> RE: [RASMB] Sedimentation of rods</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:blue">Tom, I don't think your recollection of a constant value of ~2.7 S is correct in general for protein rods. For very long rods (high length to diameter ratios) the
sedimentation coefficient does become independent of length, but the sedimentation coefficient value will be determined by the buoyant mass per unit length, which of course depends strongly on the rod diameter.
</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:blue">I did once run velocity on some carbon nanotubes, but due to this very weak length dependence it provides very poor separation by length.
</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:blue">SEDNTERP will of course calculate length/diameter ratios for shorter rods (cylinders) out to ratios of about 10.
</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:blue">John</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">
<a href="mailto:rasmb-bounces@list.rasmb.org" target="_blank">rasmb-bounces@list.rasmb.org</a> [<a href="mailto:rasmb-bounces@list.rasmb.org" target="_blank">mailto:rasmb-bounces@list.rasmb.org</a>]
<b>On Behalf Of </b>Laue, Thomas<br>
<b>Sent:</b> Thursday, May 08, 2014 8:42 AM<br>
<b>To:</b> RASMB List ?[rasmb@list.rasmb.org]?<br>
<b>Subject:</b> [RASMB] Sedimentation of rods</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Hi all-<br>
We are looking at a protein that forms rods. I have little background on systems like this, and am looking for some guidance. In particular, my recollection is that for long rods, as the rod length increases, the s collapses back to a constant ~2.7 s.
<br>
Any wisdom will be welcome.<br>
Best wishes,<br>
Tom<o:p></o:p></span></p>
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