[RASMB] Sedimentation of rods

Laue, Thomas Tom.Laue at unh.edu
Thu May 8 13:45:13 PDT 2014


Thank you, Jack

________________________________
From: John J. Correia [jcorreia at umc.edu]
Sent: Thursday, May 08, 2014 3:09 PM
To: Laue, Thomas; Fagan, Jeffrey; jphilo at mailway.com; rasmb at list.rasmb.org
Subject: RE: [RASMB] Sedimentation of rods

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..

I’ve attached the pdf.

From: rasmb-bounces at list.rasmb.org [mailto:rasmb-bounces at list.rasmb.org] On Behalf Of Laue, Thomas
Sent: Thursday, May 08, 2014 12:24 PM
To: Fagan, Jeffrey; jphilo at mailway.com; rasmb at list.rasmb.org
Subject: Re: [RASMB] Sedimentation of rods

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<mailto:jphilo at mailway.com>; rasmb at list.rasmb.org<mailto: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> [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<mailto:jphilo at mailway.com>; rasmb at list.rasmb.org<mailto: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.<http://www.ncbi.nlm.nih.gov/pubmed/963220?dopt=Abstract> 1976 Jul;5(1-2):265-70.
Anomalies in sedimentation. V. Chains at high fields, practical consequences.
Zimm BH<http://www.ncbi.nlm.nih.gov/pubmed?term=Zimm%20BH%5BAuthor%5D&cauthor=true&cauthor_uid=963220>, Schumaker VN<http://www.ncbi.nlm.nih.gov/pubmed?term=Schumaker%20VN%5BAuthor%5D&cauthor=true&cauthor_uid=963220>, Zimm CB<http://www.ncbi.nlm.nih.gov/pubmed?term=Zimm%20CB%5BAuthor%5D&cauthor=true&cauthor_uid=963220>.
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<mailto: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> [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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