Re: [ccp4bb] Characterization of Protein Conformational Changes

- Protein crystallography

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

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From: "Spiller, Benjamin" benjamin {- dot -} spiller {- at -} VANDERBILT {- dot -} EDU
Date: 2009-01-07

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Subject: Re: Characterization of Protein Conformational Changes
From: Nathaniel Echols nathaniel {- dot -} echols {- at -} GMAIL {- dot -} COM
Date: 2009-01-07

On Wed, Jan 7, 2009 at 1:54 PM, Jacob Keller
wrote:
> I am sure that most here have dealt with the issue, when making
superpositions of conformationally-different structures,> of which regions
to align as references and which to call "mobile." Conformational changes
can range from very local (e.g.,
> unwinding of a helix) to very diffuse (e.g., subtle but significant rigid
body shifts between two domains.) In the first case,
> it would probably make sense to do a global least-squares fitting, but in
the latter, one would do better to fix one of the
> domains, and show the shift in the other domain. These cases, however,
presuppose that one knows which type of case
> one is dealing with. This could be done by guesswork and trial-and-error,
but does anybody know of an approach (e.g., a
> program) to define the most reasonable way to think about a given
conformational change? Variable-size sliding-window
> least-squares superpositions with comparisons of local versus global
rmsd's come to mind, but I do not know whether
> this has been implemented anywhere, and would not know readily how to set
the parameters thereof either.

DynDom may do this, but I'm not familiar with the program. (It's in CCP4
now, I think)

If you're just trying to get a reasonable superposition and don't care very
much about the resulting statistics, you can usually use a much simpler
method called a "sieve-fit", described in these references:

http://www.ncbi.nlm.nih.gov/pubmed/2067013
http://www.ncbi.nlm.nih.gov/pubmed/10734184

In practice, the procedure described in the second paper generally worked
very well for the intended purpose of visualizing any arbitrary
conformational change in the PDB clearly. The code that actually performs
this isn't distributed as far as I know; however, it should be relatively
trivial to re-implement using CCTBX or something equivalent.

PyMOL's "align" command also does some kind of iterative optimization by
throwing away outliers, but it's much less aggressive and appears to try for
the best global fit, excluding loops etc.

-Nat

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

Previous message:
Subject: position available
From: "Spiller, Benjamin" benjamin {- dot -} spiller {- at -} VANDERBILT {- dot -} EDU
Date: 2009-01-07

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From: Matthew Chu linghonmatthew {- at -} GMAIL {- dot -} COM
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