Dear Gretchen,

if it's subtle, it's always goos when possible to do some statistics. If you have different structure or if other structures are available on the PDB, you can compare them and discuss differents points. You suggest superposition. I will add studies of contact between DNA and proteins with nucplot for example. Only with the DNA, you have many approach, the curvature, le widness of minor and major groove, hydratation (Curves+ (Lavery  etal 2009). All this parameters mey vary in correlation with other events. Chimera has also interesting function and you can script them (probably pymol do that, but no idea of were are the function). I suggest that you do something very sistematics, it's in my opinion the best way to see something subtle and find evidence of what you have in mind. You van also use NACCESS (Hubbard and Thornton 1993), PISA (for the surface) Krissinel and Hendrick 2007.
If you use analysis for the parameters accessible with theses programms, you can see a tendency, or correlation between different effects and after try to propose a model or something.

I have no idea of what you expect to show, that's why i suggest a certain variety of progs.

Hope to help you.

Nicolas Foos


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De : CCP4 bulletin board [[log in to unmask]] de la part de Meinke, Gretchen [[log in to unmask]]
Envoyé : jeudi 8 octobre 2015 16:46
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Objet : [ccp4bb] Methods to analyze conformational changes in quaternary complexes

Hi.
I am wondering how people like to analyze a large group of complicated structures (in particular protein and DNA complexes),
for subtle conformational changes.  I wish to understand, and then describe these conformational changes, not just on the individual chain level, but also as a function of the quaternary structure in a comprehensive manner. Do people have favorite approaches/programs?  Is there a better way than what I am doing, which is almost one, by one? But this way, I worry that I will miss something.

For example, given many structures of identical (or nearly)  multi-chain protein, multi chain DNA complexes, in a variety of states .
I can align the entire complexes (usually easiest to align all the protein chains, and let the DNA follow), that gives one result.
I can align a particular protein chain, and that of course , gives a different result.
As far as I can tell, many of the web based analyses (eg. PDBe, while great, are usually chain by chain.

I typically use coot (SSM, LSQ), pymol (align).
Should I write some fancy script?


Thanks in advance! If I get lots of options, I will try to summarize.
Gretchen