Re: [ccp4bb] coiled coil question

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: coiled coil question
From: Sergei Strelkov sergei {- dot -} strelkov {- at -} PHARM {- dot -} KULEUVEN {- dot -} BE
Date: 2009-10-04

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Subject: Re: coiled coil question
From: Sergei Strelkov sergei {- dot -} strelkov {- at -} PHARM {- dot -} KULEUVEN {- dot -} BE
Date: 2009-10-04

Subject: Re: coiled coil question
From: James Holton JMHolton {- at -} LBL {- dot -} GOV
Date: 2009-10-04

I think the definition of a "coiled coil" is that the helices are
symmetric (Crick 1953). That is, every coiled coil is a helical bundle,
but not every helical bundle is a coiled coil. It is a matter of
semantics as to HOW MUCH a coiled coil can deviate from perfect internal
symmetry before it can no longer be called a "coiled coil", and as is
usually the case the people who study them tend to have tighter
restrictions than those who do not.

A few crystallographically symmetric CCs have been mentioned already,
and couple of the designed coiled coils are also in this category: 1rh4,
2o6n, and were it not for a slight tilt in the superhelical axis
relative to the c axis 1tgg would probably have been
crystallographically symmetric. We actually had a little trouble
figuring out if the 3-fold in 1tgg was a rotation axis with a
pseudo-screw or a screw axis with a pseudo rotation. The latter turned
out to be the case, and I think this structure is an instructive example
of how NCS can approach CS in a continuous way.

The standard way to evaluate the "internal symmetry" of a coiled coil is
to evaluate the Crick parameters of it (Crick, 1953). I think there are
several programs out there now such as TWISTER that can do this fit. If
you can't find one, I wrote a little jiffy for generating idealized
coiled coils, given the Crick parameters here:
http://bl831.als.lbl.gov/~jamesh/pickup/supertwist.awk

Should be a simple matter to generate a series of idealized coiled coils
and lsqkab them to a model of interest to find the Crick parameters that
give the lowest rmsd. Then it is up to you to decide if the rmsd is low
enough to call the molecule "symmetric".

-James Holton
MAD Scientist

Xie Jiabao wrote:
> Dear all,
>
> Is anyone aware of a structure where the individual alpha helical
> chains of a coiled coil are related by a crystallographic axis? Or
> does anyone know of a coiled coil structure (dimer or higher order
> oligomer) that is perfectly symmetric at least in terms of the protein
> backbone or alpha carbon atoms?
>
> Thanks and best regards,
> Xie
>
>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: coiled coil question
From: Sergei Strelkov sergei {- dot -} strelkov {- at -} PHARM {- dot -} KULEUVEN {- dot -} BE
Date: 2009-10-04

Next message:
Subject: Re: coiled coil question
From: Sergei Strelkov sergei {- dot -} strelkov {- at -} PHARM {- dot -} KULEUVEN {- dot -} BE
Date: 2009-10-04