Hi everybody
I have a question about soluble structures analysis.
I've been working on a heme protein who presents two isomers. These isomers
can only be detected by NMR and its ratio varies among organisms. My goal is to
explain how the isomer ratio is modulated and why one isomer is more stable
than the other.
Someone think that the isomer ratio is modulated by steric interaction between
the side chain of two non-conserved residues and heme subtituents. We suppose
that the ratio is an effect of the heme cavity in the protein core. In order to
prove this, we have analyzed the NMR structure of four organism (they are the
only structures determined). Their rmsd is <= 1.8. We calculated the heme
cavity using CASTp, but we didn't find any correlation between volume cavity
and isomer ratio of the soluble structures. We also calculated distances
between residue side-chain atoms and heme substituents atoms. We found a great
correlation between some distances and isomer ratios; nevertheless, residues
side-chain position in soluble structures varies even among the family of the
best structures. So, I am not sure that the results that I obtained could be
meaningful. Does anybody have an idea to prove that they could be???
For the moment I don't have any other idea to explain the isomer ratios. Do
you think that the analysis of soluble structure could let me to go forward in
this explanation or should I stop here and use my results as a simple
description??.
Thanks in advance
Marcela Núñez
Tél: + 33 (0)6.12.67.38.80
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