[RASMB] SV on membrane proteins

[Chad Brautigam]

Greetings, All, from the newbiest of membrane-protein newbies,

First, let me thank all of you experts who answered (both on- and off- 
board) my last question on the topic of membrane proteins.  'Preciate  
ya, as we say here in Texas.

I recently did some SV experiments on a membrane protein solubilized  
in the accursed floating detergent LDAO (DDAO to some of you).  I was  
able to fit the data nicely in SEDFIT using a discrete species model.   
By using the trick of setting the vbar to 0, I fitted for s and for  
the buoyant molar mass (Mb).  Hooray.

In a separate experiment, I used a combination of interference optics  
and absorbance optics to measure the amount of detergent bound to the  
protein.  This was very consistent from sample to sample (I tried 2  
different protein concentrations).  This method is à la le Maire et al  
(2008) Nat. Protocols, vol. 3, 1782.

OK, so I have Mb and I know the amount of detergent bound to the  
protein on a g/g basis (this quantity is deltasubD).

We have the justly famous formula:
Mp = Mb (1-phiprime*rho),
where (neglecting bound lipid)
(1 - phiprime*rho) = (1 - vbarp*rho) + deltasubD(1-vbarD*rho)

So, since I have Mb and deltasubD, and I know rho and the vbars, can I  
just plug the Mb that I get from SV into these equations and get a  
good estimate for Mp, or is there some SV subtlety here that my newbie  
brain hasn't apprehended?  I know this can be done for SE, but I've  
never seen anyone attempt it for SV.

Any and all responses will be 'preciated.

Chad

======================================
Chad A. Brautigam, Ph.D.
Assistant Professor
Department of Biochemistry
The University of Texas
Southwestern Medical Center at Dallas
Department of Biochemistry
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
Office:  214-645-6384
Fax:  214-645-6353
Email:  chad.brautigam at utsouthwestern.edu