ab initio model volume vs POROD volume

Ab initio modelling: DAMMIF, DAMMIN, GASBOR, MONSA
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tomas
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ab initio model volume vs POROD volume

#1 Post by tomas » 2013.11.15 11:49

Hi,
trying to confirm protein complex formation with this results:
protein1: Vporod=75000
complex protein1+2: Vporod=121000
from these numbers you can say, yes the complex have been formed,

but DAMMIN (and GASBOR similarly) ab initio model of protein 1 is BIGGER than complex of protein 1+2.
filtered models volume of map contoured at 10A is:
protein1 V=113000
complex protein1+2=68000

What is the explanation of this effect?
Thank you Tomas
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Alex
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Re: ab initio model volume vs POROD volume

#2 Post by Alex » 2013.11.15 12:45

From Kratky plots - your proteins look completely unfolded.
Alex

tomas
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Re: ab initio model volume vs POROD volume

#3 Post by tomas » 2013.11.15 13:06

Hi Alex,
Protein 1 have big (30%) flexible/unfolded portion. We have crystal structure of protein1 with 456AMK and whole construct in solution have 644AMK.
About protein 2 we don't know anything....

Question: In case of my kind of unfolded proteins you should not trust Vporod and ab initio models?
Thank you, Tomas

Alex
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Re: ab initio model volume vs POROD volume

#4 Post by Alex » 2013.11.15 13:13

Hi Tomas
Kratky plot of your proteins resemble the ones from unfolded proteins (not partially unfolded but rather completely unfolded).
In case of my kind of unfolded proteins you should not trust Vporod and ab initio models
From my experience with unfolded proteins - one gets much higher estimation of MW from volume than expected (like 1.5 or 2 times higher)

HTH,
Alex

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