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Protein-Protein Docking Problem.

Protein-Protein Docking Problem. - Protein Forum

Protein-Protein Docking Problem. - Protein Forum


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  #1  
Old 01-11-2008, 08:07 AM
Bell
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Default Protein-Protein Docking Problem.



I am looking for a solution to the following problem. Any insight will
be greatly appreciated.

A membrane receptor (A) has an extracellular domain (AE),
transmembrane domain (AT) and intracellular domain (AI).

A bacteria (B) binds to (AE) leading to dimerization of (A) at (AT)
and subsequent downstream signaling through (AI).

(A) has no known natural ligands.

(A) has one known inhibitor (I) binding to (AE)

The structure of (AE) bound to (I) is available from PDB.

How do we identify which protein in (B) binds to (AE).

The obvious solution is to dock all proteins with known structures in
(B) to all known pockets in AE. Any better solutions?

Thanks

Bell Eapen
GulfDoctor.net
Dermatologist.co.in
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  #2  
Old 01-11-2008, 03:52 PM
DK
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Default Protein-Protein Docking Problem.

In article <[Only registered users see links. ]>, Bell <[Only registered users see links. ]> wrote:

Not going to work. Without extra biochemical info on
the interaction interface, protein docking does not work.
And even if it did, what you are proposing woul take forever.

A better solution is to approach this as what it is - purely
experimental problem. Use zero length cross-linker to
link A to B, pull down A, digest and identify bacterial
peptides. This will likely result in a short list of potential
candidates, which can be expressed and their binding
to the receptor measured.

DK
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