AMBER Archive (2004)

Subject: RE: AMBER: Molecular dynamic

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Tue Jul 13 2004 - 10:21:09 CDT

>
> > The template for the modeling contains 3
> > 'MSE' and 1 'TAR'. MSE refers Selenomethionine, and TAR refers to
> > tartaric acid. I don't know how these molecules got into the crystal
> structure. And the
> > auther did not mention anything about these unuausl molecules
> > with their crystal structure.

Selenomehionines are methionines with a selenium atom replacing the
sulfur. This modified amino acid is used in order to introduce heavy atoms
into the
protein structure, as a method of solving the crystal structure - the
method is called "heavy atom isomosrphous replacement". It does NOT affect
the rest of the structure, because the methionines are already there - it
just replaces the sulfur with the heavier selenium. Before starting the
simulation, just replace the Se-Met with Met.

The tartaric acid comes probably from the crystallization solution. Check
the structure and see what sort of contacts it forms with the protein -
especially if it forms any salt bridges. This may be siginififcant if
these contacts are in aregion of particular functional interest (active
site, binding site, etc.). If this not the case, you can probably ignore
it.

Hope this helps,

Joseph 

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Joseph Nachman				Department of Biochemistry
nachman_at_hera.med.utoronto.ca		University of Toronto
					Medical Sciences Building
tel: +1 416 978-5510			Toronto, Ontario M5S 1A8
fax: +1 416 978-8548			Canada
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