[RASMB] calculation of sedimentation coefficients of protein-rna complex

[Olwyn Byron]

Dear Pascal,

AtoB will read in the coordinates of nucelic acids as well as proteins, so
it will provide you with bead models of your complexes. However when using
HYDRO it is necessary to assign a buoyancy factor to the bead model. So you
will need to make an approximation at this point and give the entire bead
model a v-bar that corresponds to the weight average for the protein and
the nucelic acid. This means that your calculations will not be accurate
but to the best of my knowledge there is currently no way around this.

Best wishes,

Olwyn


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>Hi dear colleagues,
>
>I have the crystal structure of a RNA-protein complex and can generate
>atomic models of various RNA-protein complexes and would like to know if
>there is some programs that allow you to calculate the expected
>sedimentation coefficient to compare it with my experimental sedimentation
>velocity datas.
>I previously used AtoB from Byron HYDRO from Garcia de la Torre for protein
>structures but I would like to apply this to nucleic acid-protein complexes.
>
>Thanks in advance
>
>Pascal F. Egea
>
>PhD in Structural Biology and Biophysics
>University of California San Francisco
>Department of Biochemistry and Biophysics
>513  Parnassus Avenue Box 0448 Room S-1070
>CA 94143-0448 San Francisco
>tel (415)-476-3937
>fax (415)-476-1902
>email pascal at msg.ucsf.edu
>
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