<html><head><base href="x-msg://99/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><font class="Apple-style-span" color="#950f0b">Greetings Tom and all</font><div><font class="Apple-style-span" color="#950f0b"><br></font></div><div><font class="Apple-style-span" color="#950f0b">The first description of the fact that s values for long rods relates to mass/unit length (rather than to mass) was given by Arthur Peacocke (Oxford biochemist) and Howard Schachman, and the sedimentation of calf thymus DNA described in those terms. Way back in history I recall using the relationship they derived to describe F-actin and its side-by-side dimer, among other things</font></div><div><font class="Apple-style-span" color="#950f0b"><br></font></div><div><span class="Apple-style-span" style="line-height: 18px; "><font class="Apple-style-span" color="#950f0b"><h1 class="pub-title" style="margin-top: 0px; margin-right: 0px; margin-bottom: 10px; margin-left: 0px; line-height: 24px; "><font class="Apple-style-span" face="'Helvetica Neue'" size="4">Studies on the sedimentation behaviour of thymus deoxypentose nucleic acid with reference to its homogeneity, size and shape.</font></h1><div id="rg-injektor-generated-rg_modules_publicliterature_actions_PublicationAuthorsProxy_10332766" class="pub-authors js-widgetContainer" style="font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; position: relative; font-size: 14px; line-height: 21px; margin-bottom: 10px; "><div class="js-expander-container js-expander-collapsed" style="overflow-x: hidden; overflow-y: hidden; position: relative; max-height: none; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; padding-right: 30px; "><a href="http://www.researchgate.net/publication/researcher/60418868_A_R_PEACOCKE" title="A R PEACOCKE" class="authors" style="text-decoration: none; cursor: pointer; ">A R PEACOCKE</a>, <a href="http://www.researchgate.net/publication/researcher/39956939_H_K_SCHACHMAN" title="H K SCHACHMAN" class="authors" style="text-decoration: none; cursor: pointer; ">H K SCHACHMAN</a></div></div></div><div class="pub-details" id="yui_3_14_1_1_1399623540405_494" style="font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 12px; "><div>Biochemistry and Virus Laboratory, University of California, Berkeley 4, Calif. U.S.A.</div><a href="http://www.researchgate.net/publication/journal/0006-3002_Biochimica_et_Biophysica_Acta" style="text-decoration: none; cursor: pointer; ">Biochimica et Biophysica Acta</a> (Impact Factor: 4.66). 11/1954; 15(2):198-210. DOI:10.1016/0006-3002(54)90060-8</div><div class="pub-details" id="yui_3_14_1_1_1399623540405_494" style="font-family: 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 12px; "><br></div></font></span></div><div><font class="Apple-style-span" color="#950f0b">{fascinating to see an Impact Factor quoted for a 1954 paper !!!}</font></div><div><font class="Apple-style-span" color="#950f0b"><br></font></div><div><font class="Apple-style-span" color="#950f0b">Somewhere I have their equation - did a factor of 2/9 come into it? I'll try and find out</font></div><div><font class="Apple-style-span" color="#950f0b"><br></font></div><div><font class="Apple-style-span" color="#950f0b">Arthur</font></div><div><font class="Apple-style-span" color="#950f0b"><br></font></div><div><font class="Apple-style-span" color="#950f0b"><br></font></div><div><font class="Apple-style-span" color="#950f0b">Professor Arthur J Rowe<br>NCMH/Food Sciences<br>University of Nottingham<br>Sutton Bonington<br>Leics LE12 5RD UK<br><br>Tel: +44 115 9516156<br><a href="mailto:arthur.rowe@nottingham.ac.uk">arthur.rowe@nottingham.ac.uk</a></font></div><div><br><div><div>On 8 May 2014, at 18:24, Laue, Thomas wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div ocsi="0" fpstyle="1" lang="EN-US" link="blue" vlink="purple"><div style="direction: ltr; font-family: 'Times New Roman'; color: rgb(0, 0, 0); font-size: 12pt; ">Thank you, Jeff- great paper and to the point. Tom<br><div style="font-family: 'Times New Roman'; color: rgb(0, 0, 0); font-size: 16px; "><hr tabindex="-1"><div id="divRpF819816" style="direction: ltr; "><font color="#000000" face="Tahoma" size="2"><b>From:</b><span class="Apple-converted-space"> </span>Fagan, Jeffrey [jeffery.fagan@nist.gov]<br><b>Sent:</b><span class="Apple-converted-space"> </span>Thursday, May 08, 2014 1:01 PM<br><b>To:</b><span class="Apple-converted-space"> </span>Laue, Thomas;<span class="Apple-converted-space"> </span><a href="mailto:jphilo@mailway.com" style="color: blue; text-decoration: underline; ">jphilo@mailway.com</a>;<span class="Apple-converted-space"> </span><a href="mailto:rasmb@list.rasmb.org" style="color: blue; text-decoration: underline; ">rasmb@list.rasmb.org</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>RE: [RASMB] Sedimentation of rods<br></font><br></div><div></div><div><div class="WordSection1"><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Dear Tom, John et al.</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">I will shamelessly note that my group just published a paper on this in Langmuir</span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">“Rod Hydrodynamics and Length Distributions of Single-Wall Carbon Nanotubes Using Analytical Ultracentrifugation”</span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "><a href="http://pubs.acs.org/doi/abs/10.1021/la404892k" target="_blank" style="color: blue; text-decoration: underline; ">http://pubs.acs.org/doi/abs/10.1021/la404892k</a></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">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></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Cheers,</span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); ">Jeff Fagan</span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125); "> </span></p><div><div style="border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; border-top-style: solid; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding-top: 3pt; padding-right: 0in; padding-bottom: 0in; padding-left: 0in; "><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; "><span class="Apple-converted-space"> </span><a href="mailto:rasmb-bounces@list.rasmb.org" style="color: blue; text-decoration: underline; ">rasmb-bounces@list.rasmb.org</a><span class="Apple-converted-space"> </span>[mailto:rasmb-bounces@list.rasmb.org]<span class="Apple-converted-space"> </span><b>On Behalf Of<span class="Apple-converted-space"> </span></b>Laue, Thomas<br><b>Sent:</b><span class="Apple-converted-space"> </span>Thursday, May 08, 2014 12:21 PM<br><b>To:</b><span class="Apple-converted-space"> </span><a href="mailto:jphilo@mailway.com" style="color: blue; text-decoration: underline; ">jphilo@mailway.com</a>;<span class="Apple-converted-space"> </span><a href="mailto:rasmb@list.rasmb.org" style="color: blue; text-decoration: underline; ">rasmb@list.rasmb.org</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [RASMB] Sedimentation of rods</span></div></div></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "> </p><div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 12pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><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...<span class="Apple-converted-space"> </span><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.<span class="Apple-converted-space"> </span><br>I am assuming that the rods are stiff and have a uniform diameter (not a mixture of lateral association). Best wishes,<br>Tom<br><br></span></p><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "><a href="http://www.ncbi.nlm.nih.gov/pubmed/963220?dopt=Abstract" title="Biophysical chemistry." target="_blank" style="color: blue; text-decoration: underline; ">Biophys Chem.</a><span class="Apple-converted-space"> </span>1976 Jul;5(1-2):265-70.</span></div></div><h1 style="margin-right: 0in; margin-left: 0in; font-size: 24pt; font-family: 'Times New Roman', serif; font-weight: bold; "><span style="color: black; ">Anomalies in sedimentation. V. Chains at high fields, practical consequences.</span></h1><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><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" style="color: blue; text-decoration: underline; ">Zimm BH</a>,<span class="Apple-converted-space"> </span><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Schumaker%20VN%5BAuthor%5D&cauthor=true&cauthor_uid=963220" target="_blank" style="color: blue; text-decoration: underline; ">Schumaker VN</a>,<span class="Apple-converted-space"> </span><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Zimm%20CB%5BAuthor%5D&cauthor=true&cauthor_uid=963220" target="_blank" style="color: blue; text-decoration: underline; ">Zimm CB</a>.</span></div></div><div><h3 style="margin-right: 0in; margin-left: 0in; font-size: 13.5pt; font-family: 'Times New Roman', serif; font-weight: bold; "><span style="color: black; ">Abstract</span></h3><div><div style="margin-top: 0px; margin-right: 0in; margin-left: 0in; margin-bottom: 0px; font-size: 12pt; font-family: 'Times New Roman', serif; "><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.</span></div></div></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> </span></p><div><div class="MsoNormal" align="center" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; text-align: center; "><span style="color: black; "><hr align="center" size="2" width="100%"></span></div><div id="divRpF502793"><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 12pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; color: black; ">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; color: black; "><span class="Apple-converted-space"> </span>John Philo [jphilo@mailway.com]<br><b>Sent:</b><span class="Apple-converted-space"> </span>Thursday, May 08, 2014 12:03 PM<br><b>To:</b><span class="Apple-converted-space"> </span><a href="mailto:rasmb@list.rasmb.org" target="_blank" style="color: blue; text-decoration: underline; ">rasmb@list.rasmb.org</a><br><b>Cc:</b><span class="Apple-converted-space"> </span>Laue, Thomas<br><b>Subject:</b><span class="Apple-converted-space"> </span>RE: [RASMB] Sedimentation of rods</span><span style="color: black; "></span></p></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10pt; 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; "></span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10pt; 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; "></span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10pt; 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; "></span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> </span></p><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 10pt; font-family: Arial, sans-serif; color: blue; ">John</span><span style="color: black; "></span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> </span></p><div class="MsoNormal" align="center" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; text-align: center; "><span style="color: black; "><hr align="center" size="2" width="100%"></span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 12pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; color: black; ">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; color: black; "><span class="Apple-converted-space"> </span><a href="mailto:rasmb-bounces@list.rasmb.org" target="_blank" style="color: blue; text-decoration: underline; ">rasmb-bounces@list.rasmb.org</a><span class="Apple-converted-space"> </span>[<a href="mailto:rasmb-bounces@list.rasmb.org" target="_blank" style="color: blue; text-decoration: underline; ">mailto:rasmb-bounces@list.rasmb.org</a>]<span class="Apple-converted-space"> </span><b>On Behalf Of<span class="Apple-converted-space"> </span></b>Laue, Thomas<br><b>Sent:</b><span class="Apple-converted-space"> </span>Thursday, May 08, 2014 8:42 AM<br><b>To:</b><span class="Apple-converted-space"> </span>RASMB List ?[rasmb@list.rasmb.org]?<br><b>Subject:</b><span class="Apple-converted-space"> </span>[RASMB] Sedimentation of rods</span><span style="color: black; "></span></p><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><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.<span class="Apple-converted-space"> </span><br>Any wisdom will be welcome.<br>Best wishes,<br>Tom</span></div></div></div></div></div></div></div></div></div>_______________________________________________<br>RASMB mailing list<br><a href="mailto:RASMB@list.rasmb.org" style="color: blue; text-decoration: underline; ">RASMB@list.rasmb.org</a><br><a href="http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org" style="color: blue; text-decoration: underline; ">http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org</a><br></div></span></blockquote></div><br><div>
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