[RASMB] Sedimentation equilibrium query

[Nikola Wenta]

Dear Kanchan,
It should be possible to centrifuge both proteins in one run. Their molecular weights seem to be similar enough to run them at the same speeds until equilibrium. You can use the sedimentation equilibrium times simulator from UltraScan II that you can download from http://ultrascan.uthscsa.edu/ for free for Windows, Linux and MAC. In this software which is very easy to learn, you can enter protein MW, vbar, buffer composition and even protein shapes (if known) to make the simulation as precise as possible. Take a look here: http://ultrascan.uthscsa.edu/manual/calc_equiltime.html to see what kind of advices the software can give you regarding best speeds and estimated run times. I have used the simulator on my own, and it gave me very reliable hints on how to set the runs up for my proteins. To be on the safe side, you can add some maybe 10-20% time to the suggested run times. Keep in mind that once the protein is in equilibrium, it will still be in equilibrium hours later :) , so it's ok to let them centrifuge a little bit longer. By the way, when you are using the suggestions for run times at different speed steps that UltraScan gives you, you can set the run up on Friday and program the speed profile into the centrifuge control software; when you arrive back on Monday, it will all already be done, and you can pick up your data and directly analyze them with UltraScan very conveniently.
Best regards
Niko
 
Dr. Nikola Wenta
Research Fellow
D82
School of Biomedical Sciences
University of Nottingham
Queen's Medical Centre
Nottingham NG7 2UH
Tel: +44-(0)115-8230298
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