[Chimera-users] Intersurf, protein interface display

[Thomas Goddard]

Miguel suggests another coloring for protein interface surfaces based
on surface complementarity judged by looking at surface normals.

   Tom


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Date: Sat, 12 Mar 2005 17:25:29 +0000
From: =?ISO-8859-15?Q?Miguel_Ortiz_Lombard=EDa?= <mol1 at york.ac.uk>
To: Thomas Goddard <goddard at cgl.ucsf.edu>
Subject: Re: [Chimera-users] Intersurf, protein interface display

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Hi Tom,

With regard to your very interesting message, I would like to add
another useful way of studying the surfaces of protein-protein (or
protein-whatever) interactions. This way involves the concept of
"surface complementarity", where the buried surfaces are scanned to see
how parallel are the normals to them at every point (in a grid). It is
shown that specific or high-affinity interactions have usually higher
complementarity. There is a paper by Lawrence and Colman
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=8263940)
and a program by the same authors in the CCP4 suite called "sc" that
performs such calculation. The "sc" program is also able to add the
"surface complementarity value" to the vertexes of the interacting
surfaces calculated in GRASP. I currently have a little program
(modified by me from a Raster3D jiffy) to colour such a modified surface
according to those values and render it with the render program from
Raster3D. But I don't like GRASP and would like to have this analysis as
a possibility in chimera.

Such analysis have been very useful for me in the past, especially to
study protein-protein interactions. If this is also interesting for you
I would be glad to be of help.


Cheers,



Miguel

Thomas Goddard wrote:
> Hi Conrad,
>
>   I read the paper
>
>     Intersurf: dynamic interface between proteins
>     Nicolas Ray, Xavier Cavin, Jean-Claude Paul, Bernard Maigret
>     Journal of Molecular Graphics and Modelling, 23 (205) 347-354
>
> It addresses 3 problems: how to find a surface interface between 2 proteins,
> ways to color such a surface, and how to flatten that surface into two
> dimensions.
>
> The surface calculation was a neat algorithm -- take the
> Delauney tetrahedralization of all atom positions from both proteins,
> then find tetrehedra with vertices from both proteins and cut those
> tetrahedra in half.  The tetrahedra are cut in half with one or 2
> triangles using vertices on tetrahedron edges that connect an atom
> in one protein to an atom in the other protein.  The vertices are
> placed midway between the atoms moved in by their vdw radii.
>
> They proposed 2 ways of coloring the surface.  One colored vertices
> by how far apart the atoms were in the two proteins that were used to
> create that vertex.  Red to blue shows short to long distances.  The
> other coloring shows types of possible interactions between the two
> residues associated with the two atoms for the tetrahedron edge that
> the surface vertex splits.  They gave different colors for predicted
> hydrogen bonding, hydrophobic packing, pi ... X, pi ... pi, same charges,
> opposite charges.  Not sure what the pi bonding notation means.
>
> They also described how to flatten the 3-dimensional to a 2-dimensional
> surface with one to one correspondence between vertices and edges.
> Their method tried to come as close as possible to a conformal map.
> Conformal means the angles of the triangles stay the same to the extent
> possible.
>
> These calculations took a few seconds on 2000-5000 atom proteins.
>
> Here's my assessment.  I think the concept of showing a protein interaction
> interface and coloring it to show interactions sounds useful for protein-
> protein interaction people.  I think the flattening into 2 dimensions
> is probably not useful.  Conformal maps greatly distort the area of
> the surface if it has curvature (you've seen the maps where Greenland
> is bigger than Africa, Americas, Asia and Europe combined).  So the flattened
> surface is going to be hard to recognize as the interface, unless it
> is already pretty flat.  If it is already pretty flat you might as
> weill just look at the 3-d surface.
>
> If we wanted to do something with interface surfaces I would suggest
> talking to Tanya Korteme.  We already have all the infra-structure to
> create the surfaces.  I would not use the Delauney surfaces, instead
> just use MSMS surfaces on both proteins showing only the parts associated
> with atoms in one protein that are within 5 angstroms of atoms in the
> other protein.  The zone calculation code I wrote for multiscale could
> do that fast.  We could offer a range of atom colorings that map onto
> the surface (hydrogen bonds, distance to nearest atom in other protein,
> charge complementarity, etc...).
>
> I don't have time or enough interest to work on this project.  But
> perhaps someone else will.  We have talked about collaborating with
> Tanya Korteme in the past and this would be a good opportunity.
>
>       Tom
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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correo-e: mol1 at york.ac.uk
http://www.ysbl.york.ac.uk/~mol
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