EOM Defining Contacts within a Monomeric protein

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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nmeri
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Joined: 2018.04.06 01:10

EOM Defining Contacts within a Monomeric protein

#1 Post by nmeri » 2018.04.06 01:58

Hi,
I am very new to SAXS data analysis and EOM (and to this forum). I am currently working on a 280 aa fully disordered protein with a central domain that folds upon binding its partner (so in absence of the partner, it still has some exchange between unfolded and partially folded). I am analyzing the data collected by someone else on this protein. log I(q) vs q (attached) you can see 3 different concentrations and 2 different exposure of each concentration, which in my opinion looks quite reasonable.

I have used each curve to generate EOM models with Native or Random chain properties. We have several lines of evidence that this protein forms an intramolecular long range contact, so I would like to reweigh my ensembles accordingly. In EOM manual, it is quite clear how to define these contacts, I am just trying to make sure if I understand it correctly. Even for a single monomeric protein, do I need to define a core symmetry (p2) for modeling such contacts? or the contacts option is only exclusively tailored for oligomeric proteins?

Another follow up question: How reliable is it for me to infer distances between residue x and y from given ensemble pdbs? I envision it as calculating end to end distance from residue x to residue y, is that correct?

Thank you!
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nmeri
Member
Posts: 3
Joined: 2018.04.06 01:10

Re: EOM Defining Contacts within a Monomeric protein

#2 Post by nmeri » 2018.05.21 23:49

Still wondering how this would work.. Any help is appreciated!
Cheers

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