[RASMB] Sedimentation of rods

[Arthur Rowe]

Greetings Tom and all

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

Studies on the sedimentation behaviour of thymus deoxypentose nucleic acid with reference to its homogeneity, size and shape.
A R PEACOCKE, H K SCHACHMAN
Biochemistry and Virus Laboratory, University of California, Berkeley 4, Calif. U.S.A.
Biochimica et Biophysica Acta (Impact Factor: 4.66). 11/1954; 15(2):198-210. DOI:10.1016/0006-3002(54)90060-8

{fascinating to see an Impact Factor quoted for a 1954 paper !!!}

Somewhere I have their equation - did a factor of 2/9 come into it? I'll try and find out

Arthur


Professor Arthur J Rowe
NCMH/Food Sciences
University of Nottingham
Sutton Bonington
Leics LE12 5RD UK

Tel: +44 115 9516156
arthur.rowe at nottingham.ac.uk

On 8 May 2014, at 18:24, Laue, Thomas wrote:

> Thank you, Jeff- great paper and to the point. Tom
> From: Fagan, Jeffrey [jeffery.fagan at nist.gov]
> Sent: Thursday, May 08, 2014 1:01 PM
> To: Laue, Thomas; jphilo at mailway.com; rasmb at list.rasmb.org
> Subject: RE: [RASMB] Sedimentation of rods
> 
> Dear Tom, John et al.
>  
> I will shamelessly note that my group just published a paper on this in Langmuir
> “Rod Hydrodynamics and Length Distributions of Single-Wall Carbon Nanotubes Using Analytical Ultracentrifugation”
> http://pubs.acs.org/doi/abs/10.1021/la404892k
> 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).
>  
> Cheers,
> Jeff Fagan
>  
> From: rasmb-bounces at list.rasmb.org [mailto:rasmb-bounces at list.rasmb.org] On Behalf Of Laue, Thomas
> Sent: Thursday, May 08, 2014 12:21 PM
> To: jphilo at mailway.com; rasmb at list.rasmb.org
> Subject: Re: [RASMB] Sedimentation of rods
>  
> Hi John-
> I wouldn't count on my memory for anything, so any insights/recollections are welcome. I have no idea where I got that number... 
> 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. 
> I am assuming that the rods are stiff and have a uniform diameter (not a mixture of lateral association). Best wishes,
> Tom
> 
> 
> Biophys Chem. 1976 Jul;5(1-2):265-70.
> Anomalies in sedimentation. V. Chains at high fields, practical consequences.
> 
> Zimm BH, Schumaker VN, Zimm CB.
> Abstract
> 
> 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.
>  
> From: John Philo [jphilo at mailway.com]
> Sent: Thursday, May 08, 2014 12:03 PM
> To: rasmb at list.rasmb.org
> Cc: Laue, Thomas
> Subject: RE: [RASMB] Sedimentation of rods
> 
> 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.
>  
> I did once run velocity on some carbon nanotubes, but due to this very weak length dependence it provides very poor separation by length.
>  
> SEDNTERP will of course calculate length/diameter ratios for shorter rods (cylinders) out to ratios of about 10.
>  
> John
>  
> From: rasmb-bounces at list.rasmb.org [mailto:rasmb-bounces at list.rasmb.org] On Behalf Of Laue, Thomas
> Sent: Thursday, May 08, 2014 8:42 AM
> To: RASMB List ?[rasmb at list.rasmb.org]?
> Subject: [RASMB] Sedimentation of rods
> 
> Hi all-
> 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. 
> Any wisdom will be welcome.
> Best wishes,
> Tom
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