Re: [ccp4bb] Design Constructs

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: James Foadi james_foadi {- at -} YAHOO {- dot -} CO {- dot -} UK
Date: 2009-03-31

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Subject: Re: Design Constructs
From: Jayashankar s {- dot -} jayashankar {- at -} GMAIL {- dot -} COM
Date: 2009-03-31

Hi Hari,
Right terminal residues for constructs.

some time back there was some discussion with this subject.
you can check that threads also.

S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.

On Tue, Mar 31, 2009 at 5:10 AM, Ho-Leung Ng wrote:

> 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
> 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: vnamboodiri@locuspharma.com
> Ph: 215-358-2012
> Fax: 215-358-2020
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: failed compilation for Pointless
From: James Foadi james_foadi {- at -} YAHOO {- dot -} CO {- dot -} UK
Date: 2009-03-31

Next message:
Subject: how to present the electron density map
From: xu zhen xu7610 {- at -} HOTMAIL {- dot -} COM
Date: 2009-03-31