Subject: Dock, two substrates in one binding site

From: JianHui Wu <[email-masked]>
Date: Wed, 13 Jun 2001 16:09:52 -0400

Dear All,

I work on a protein which catalyzes substrates A and B into a peptide
AB. Obviously, these two substrates have to bind with the protein before
the catalytic reaction can take place. I like to dock these two
substates into the putative binding site and wonder how to dock two
substrates into one binding site at the same time. To dock them one by
one is probably not a good way. One way I like to try is to dock the
peptide AB instead and split AB into A and B followed by some MM/MD
refinement. The purpose of this study is to build a model for the
catalytic reaction. After substrates A and B in the reasonable binding
mode, QM perhaps can be applied to the binding site to search for
tansition state (?). Any comment or suggestion will be greatly
appreciated.

Yours sincerely,

Jian Hui Wu
McGill Translational Research in Cancer
Lady Davis Institute
Jewish General Hospital
Montreal, QC