[RASMB] Peptide sedimentation

[Walter Stafford]

I would like to add that one should always run any sample at a series of concentrations - not only to test for self-association but also for non-ideality. Small peptides can often have a very high charge-to-mass ratio and will exhibit significant non-ideality even at 150 mM ionic strength. This is true in some cases for larger proteins as well. Always a good idea to either rule it out ... or in.

Also if you have no suitable chromophore, you can use interference optics if you have an XL-I. But be very careful with the dialysis so that you are assured of getting a good optical match between sample and buffer.

And as pointed out already, run at the highest speed possible.

You will have to use whole boundary fitting methods since you will not see a well defined boundary. Resolution will not be optimum (because of diffusion) , and you will definitely need to globally fit over a range of concentrations, both to demonstrate concentration dependence (or lack thereof) and to extract any other parameters (like equilibrium constants and non-ideality) if there is concentration dependence.
_________________________
Walter Stafford
wstafford3 at walterstafford.com



On Jul 9, 2013, at 05:51, Fasolini, Marina [Nervianoms] wrote:

> Dear All
> I need to follow the aggregation of some peptides of about 4 KDa . I would like to estimate the dimension of these aggregates.
> Since my experience is mostly in protein sedimentation, I was wondering if you have some tips for me. Which wavelength do you use for absorbance optic? Which is the best concentration to run?
> At which speed do you suggest me to run the experiment?
> Any help will be appreciated.
> Thanks in advance
> Marina
>  
>  
>  
> MARINA FASOLINI
> Structural Chemistry
> 
> Nerviano Medical Sciences http://www.nervianoms.com
> Viale Pasteur 10
> 20014 Nerviano - Milano
> marina.fasolini at nervianoms.com 
> Tel. +390331581462
> Fax. +390331581360
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