Re: [ccp4bb]: Protein Dimensions

["Gerard \"DVD\" Kleywegt" <gerard@xray.bmc.uu.se>]

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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.
> 
> I'm not sure what the standard way of doing this is.

not sure if there *is* a standard way. if the molecule is roughly spherical,
you could quote the radius of gyration (which you get, e.g., from the STats
command in MOLEMAN2).

otherwise, you could align the inertia axes with the X, Y and Z axes (XYz
ALign command in MOLEMAN2; if you only want to use the CA atoms, first do:
SElect ANd NAme " CA "). you can then use the STats command again to see the
min and max values of the X, Y and Z coords after the transformation which
gives you the dimensions. including the vdw surface seems unnecessary - it
just means adding 3-4 A to all dimensions

aligning your molecule thusly also means that the X-Y plane (after the
transformation) becomes the 'least-squares plane' of your entire molecule, so
that looking at it along the Z-axis should give you something of a
'least-cluttered view'

for example (using 1CBS):

1 - read your molecule:

 MOLEMAN2 > read pdb1cbs.ent
 [...]
 Nr of selected atoms : (       1213) 
 
2 - only select protein atoms (in this case there is only one
    protein chain; otherwise you would have to select which one(s)
    you want to use as well):

 MOLEMAN2 > select and type prot
 [...]
 Nr of selected atoms : (       1091) 

3 - align the inertia axes with X, Y and Z:

 MOLEMAN2 > xyz align
 Moving CofG of selected atoms to (0,0,0)
 Nr of selected atoms : (       1091) 
 Centre-of-Gravity : (  17.683   20.809   27.605) 
 CofG now at (0,0,0)
 Eigen value 1 =     109122.3 Vector :   0.005613 -0.225587  0.974207
 Eigen value 2 =      77836.4 Vector :   0.967170 -0.246298 -0.062605
 Eigen value 3 =      43595.5 Vector :   0.254068  0.942575  0.216799
 Determinant : (   1.000) 
 [...]
 Rotation angle                             120.793

4 - list statistics:

 MOLEMAN2 > stats
 [...]
       Item    Average     St.Dev        Min        Max        RMS  Harm.ave.
       ----    -------     ------        ---        ---        ---  ---------
    X-coord      0.000     10.001    -26.023     20.321
    Y-coord      0.000      8.447    -19.027     17.482
    Z-coord      0.000      6.321    -16.355     14.927
   B-factor     15.480      8.207      3.920     53.120     17.521     12.568
    Occpncy      1.000      0.000      1.000      1.000      1.000      1.000

 Radius of gyration (A) : (  14.537) 

so in this case, one could cite the dimensions as (roughly) 45 A * 35 A * 30
A. alternatively, the radius of gyration could be quoted (being ~15 A), but
the ratio between the longest and shortest dimension is 1.5 so the molecule
is more of an ellipsoid than a sphere

--dvd

******************************************************************
                        Gerard J.  Kleywegt
    [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                Biomedical Centre  Box 596
                SE-751 24 Uppsala  SWEDEN

    http://xray.bmc.uu.se/gerard/  mailto:gerard@xray.bmc.uu.se
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