AMBER: simulating part of a molecule with homology modeling

From: Dave, Sonya <>
Date: Sat, 10 Feb 2007 18:00:11 -0600


I have a protein with unknown structure (clh3a), and a evolutionarily related homolog(clc0). They share a good deal of sequence homology in one domain that I am interested in (the second cbs domain). However, I only need the model of the last alpha helix of the cbs domain of clh3a. This last alpha helix shows no sequence homology with it's corresponding part of clc 0. In any case, I "aligned" the alpha and found a homologous structure in InsightII.

Then, i ran the simulation of them in amber. I did as similar to the tutorial, first in vacuum, then add explicit water molecules. The vacuum simulation looks basically like the original alpha helix of clc0. However, the model using conjugate, and then the explicit solvents, do not show a alpha helix form. they just show an unstructured segment of amino acids. I am using the force field ff99, which, as I understand, emphasizes alpha helixes.

Any suggestions? Is this the right way of approaching the problem? Also, does anyone know how I can find a homolog with more sequence homology, preferably something that is also part of a cbs domain. I tried the compartive mo deling linked through pubmed. However, my alpha helix is too short a segment for it to find a homolog (it is 7 a.a.'s)

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Received on Sun Feb 11 2007 - 06:07:50 PST
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