[ccp4bb] question about structure analysis

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CCP4bb <-- 2007 <-- April 2007 <-- 04 April 2007

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Subject: truncate error on x86 64
From: Daniele de Sanctis de {- dot -} sanctisd {- at -} GMAIL {- dot -} COM
Date: 2007-04-04

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Subject: Re: truncate error on x86 64
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-04

Subject: question about structure analysis
From: Marcela NUNEZ marcela {- dot -} nunezq {- at -} YAHOO {- dot -} FR
Date: 2007-04-04

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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CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 04 April 2007

Previous message:
Subject: truncate error on x86 64
From: Daniele de Sanctis de {- dot -} sanctisd {- at -} GMAIL {- dot -} COM
Date: 2007-04-04

Next message:
Subject: Re: truncate error on x86 64
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-04