[gmx-users] loop simulation

David spoel at xray.bmc.uu.se
Mon Apr 12 11:08:01 CEST 2004

On Mon, 2004-04-12 at 10:50, egorov wrote:
> Dear gmx-users,
> please, help me in the next question.
> System:
> Protein with bound cofactor. Both structures - with bound
> cofactor and without it are known cristallographically. There is a
> loop without organized second structure in the bining pocket. This
> loop is situated very close to protein core when without cofactor and sligtly
> away the core when cofactor is bound. By its outer side this loop take
> part in ligand binding, but by inner - close cavity between itself and
> protein core.
> Question : could I and if so, then how to use MD to produce
> relatively well-grounded structure with bound cofactor and opened cavity.
If I understand you correctly you want to simulate the complex with the
loop not covering the binding pocket. That means you would have to
extrapolate to a structure you do not know much about. A possible way
would be to perform simulations of the open and closed form of the
protein alone and then use essential dynamics sampling. See papers by De
Groot et al.

> Best regards,
> D.Egorov
> Department of Clinical Laboratory and Microbiological Diagnostics,
> Ural State Meical Academy mailto:egorov at newhospital.ru
> 12.04.2004.
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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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