Hi All,
I have a 40kD protein that make nice hexamers in solution (we have the crystal structure + secmalls data).
However, the SAXS data show the presence of additional component, which (we believe) could be a dodecamer.
We don't understand yet how the dodecamer could be formed as we only see hexamers in the crystal structure and the symmetry does not help.
Now, how can I model such a system ?
Can I calculate separate envelops for the 2 components ?
Thanks for your suggestions,
GIA
mixture with unknown component
Re: mixture with unknown component
if the structure of a hexamer is complete, I think you can try using SASREF MX.Now, how can I model such a system ?
You may try GASBOR MX, if the protein is not too large (40kDa should actually be ok).Can I calculate separate envelops for the 2 components ?
i would also consider separating it better, say using inline HPLC-SAXS.
Best, Alex
Re: mixture with unknown component
hi
thank for the reply
we are already using online hplc and we get only 1 pic
the problem is that the Rg and Dmax are much bigger than what we expect
for our hexamer (max dimension 110A) ... i post data and gnom
Best
GIAX
thank for the reply
we are already using online hplc and we get only 1 pic
the problem is that the Rg and Dmax are much bigger than what we expect
for our hexamer (max dimension 110A) ... i post data and gnom
Best
GIAX
- Attachments
-
- gnom.png (17.73 KiB) Viewed 3902 times
-
- curve.png (21.01 KiB) Viewed 3902 times
Re: mixture with unknown component
what does the MW estimation say?
Re: mixture with unknown component
if I compare it to another protein (170kDa, monomer) that
I have measured the same day, I get 440kDa for this one.
twice the MW of the hexamer (220kDa)
I have measured the same day, I get 440kDa for this one.
twice the MW of the hexamer (220kDa)
Re: mixture with unknown component
if you have a crystal structure, try to fit the data using just hexamer (CRYSOL) or a dimer of hexamers (program SASREF).
What fits better?
What fits better?
Re: mixture with unknown component
sorry for bothering with lots of questions.
i have problem to figure out the symmetries in the sasref server.
if my hexamer is symmetry P32, what should be the dodecamer ? (as i can't tell -a priori- if it is a real dimer of hexamers)
or should I take the problem the other way around: dodecamer that dissociates into hexamers ?
thank you
i have problem to figure out the symmetries in the sasref server.
if my hexamer is symmetry P32, what should be the dodecamer ? (as i can't tell -a priori- if it is a real dimer of hexamers)
or should I take the problem the other way around: dodecamer that dissociates into hexamers ?
thank you
Re: mixture with unknown component
I am not sure if SASREF MX is available as a server.sasref server.
given you have a crystal structure of hexamer - i think easiest is to considerdodecamer that dissociates into hexamers ?
it as a monomer and assume it associates into dimers (P2; dodecamers).
Best, Alex