Modeling Non-Interacting Species with MONSA?

Ab initio modelling: DAMMIF, DAMMIN, GASBOR, MONSA
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rrod9595
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Modeling Non-Interacting Species with MONSA?

#1 Post by rrod9595 » 2021.07.07 03:23

I am working with a system containing two phases: protein and RNA. I have experimental protein-RNA complexes I have been able to model well with MONSA using three inputs: protein, RNA, protein-RNA. These complexes also have a single peak and nicely fitting P(r) so I am confident in this setup.

If possible, though, I would like to validate some negative controls: scrambled RNA not supposed to interact with protein. Based on the P(r) fitting, I am confident that we have two separate populations (two distinct peaks). Is there a way to use MONSA to model this and show there are two distinct phases without connectivity? What settings would I use to do so? When I use default settings, I have difficulty showing there are two distinct species. I could try giving '0' connectivity in the .mst file but is there something else you would recommend?

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AL
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Re: Modeling Non-Interacting Species with MONSA?

#2 Post by AL » 2021.08.04 21:34

rrod9595 wrote:
2021.07.07 03:23
Based on the P(r) fitting, I am confident that we have two separate populations (two distinct peaks).
Please note, if the PDDF has two peaks it does not necessarily mean that it is a mixture of two non-interacting molecules, see e.g. SASDAG6 or SASDC56.

MONSA assumes that the input data are from monodisperse solutions (e.g. protein, RNA and a protein-RNA complex). If you have SAXS data from a mixture of protein and RNA and (atomistic) models of your protein and RNA, you can fit these models using OLIGOMER.

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