[gmx-users] mutated structure

Ran Friedman ran at hemi.tau.ac.il
Fri Dec 16 17:14:42 CET 2005

Dear Hota,

I'd think that in order to observe structural transformations upon 
mutations, you should first get your system equilibrated (via EM, PR and 
at least 100ps unconstrained MD) and then run pretty long MD 
simulations. Later, you can compare relevant measures (e.g. contacts, 
hydrogen bonds, secondary structures) between simulations of mutant and 
wt proteins. Also, bear in mind that no matter how long your simulation 
is, the time scale for large structural changes (e.g. large domain 
motions) will be longer. Hopefully, you'll still be able to observe some 
changes under a reasonable simulation time (at least several nanoseconds).

As for the mutation itself, you can try to use programs that deal with 
it, e.g. jackal (available from Prof. Barry Honig) or swisspdb viewer 
rather than do it yourself.

Good luck,

Tamas Horvath wrote:

> Hi!
> I want to calculate with gromacs, how certain mutations affect the 
> structure of a protein.
> In order to do so, 1st I "mutate" the protein in the pdb file. I use a 
> very simple algorithm, which places the new aa in the same orientation 
> as the old aa was, but it does not ensure that there is no spatial 
> clashes (though in most cases there is no such problem).
> I run gromacs simulations on this new structure (based on the demo, 
> that comes with it)
> 1st a cg+steep energy minimasition
> 2nd a position restraining
> 3rd a 20ps periodic simulated annealing, with temperatures: 300 320 
> 320 300, and times: 0 2 4 6
> 4th simple 2ps md at 300K, and I get 10 structures from this run, 
> which then I compare to the wt structure
> What I'm asking is, that is it a reasonable approach? How may I modify 
> it to make it more reasonable?
> How may I detect if the protein is in it's favourable conformation? 
> (Mutations in the core may have extensive effects, which may need more 
> time to "settle")
> Any suggestions would be appreciated!
> Hota
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Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875

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