Hello Hari,
The general rule is to truncate/delete residues that are
predicted to be disordered, for example, by secondary structure
prediction or homology modeling. You do have to be careful as there
may be functionally important, conserved, structured loops that you
want to retain. However, as Artem noted, the results can be
unpredictable, especially with regard to expression. You may have to
go with a brute force approach. For a case like yours, I might try
deleting every 3-4 residues, which only leaves you half a dozen or so
constructs to test. Definitely test both sequence clusters you
describe.
Good luck!
ho
UC Berkeley
---------------------------------------------------------------------------------------------
Date: Mon, 30 Mar 2009 14:11:02 +0100
From: Haridasan Namboodiri <vnambood...@locuspharma.com>
Subject: Design Constructs
Hello
I am designing a protein construct for structural biology. It is a protei=
n kinase=20
which has not been crystallized earlier. I was comparing the kinase domai=
ns of=20
other closely related family members characterized biochemically vs=20
crystallization constructs. For crystallography constructs, there are dif=
ferent=20
stretches of amino acid residues particularly at the N-terminus (some con=
tain=20
extra 2-5 residues while others have 15-20 residues.
My question: Is there a rational way of designing exact constructs one=20=
would propose to make, eg., by a sequence alignment showing nearest=20
homology neighbors that guided construct design etc..
Sincerely
Hari
Haridasan V. M. Namboodiri, PhD
Scientist-Structural Biology
Locus Pharmaceuticals, Inc.
Four Valley Square
512 Township Line Road
Blue Bell, PA 19422
email: vnambood...@locuspharma.com
Ph: 215-358-2012
Fax: 215-358-2020
