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Re: [ccp4bb]: Protein Dimensions



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I have been watching with interest the responses to Michael DiDonato recent
question as I have been looking a similar program.  Ways for determining a
protein's dimensions from a three-dimensional structure have been written for
analytical ultracentrifugation work (peruse
http://www.ucc.uconn.edu/~wwwbiotc/UAF.html and associated links) in order to
predict Stokes radii.  Unfortunately, most don't run when downloaded and those
that do have arrays sizes that are too small (they seem to think that proteins are
all the size of lysozyme).  We have a problem where a protein seems to be a
hexamer in gel filtration but the X-ray structure shows an enlongated tetramer.
While the enzyme's long axis is in the range of the observed Stokes radius, a
better prediction would be nice.  I heard that Janet Thornton had such a program
which calculated the ellipsoidal axes of a protein from X-ray coordinates, but I
have not been able to track down the source code.  I know that I should contact
Janet, but someone must have made a little jiffy program to do this.

Cheers,

Michael Garavito

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>
> On Wed, 20 Feb 2002, Luca Jovine wrote:
>
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> >
> > >What is the best way to determine a proteins dimensions from the three
> > >dimensional structure?  I could just measure from end to end at the
> > >widest point (between CA's) in Xfit, but is there a better method that
> > >would take into account a Van der Waals surface or something similar.
> >
> > There might be better ways, but:
> >
> > 1) within CNS, you can use the input file molecule_extent.inp, which
> > "Determines the extent of a molecule in orthogonal Angstroms"
> >
> > 2) in WHATIF, you can use the command MINMAX which determines the
> > extreme values for the coordinates within a user-specified range
> >
> > Hope this helps, Luca
>

--
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R. Michael Garavito, Ph.D.                   Email:  garavito@msu.edu
Dept. of Biochemistry & Molecular Biology   Office:  (517) 355-9724
Michigan State University                      Lab:  (517) 353-9125
East Lansing, MI 48824-1319                    FAX:  (517) 353-9334
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