[gmx-users] mutated structure

[Tamas Horvath]

Well, I thought that this is not a very simple matter, but for superficial
aa-s it works nice, and even for more problematic aas there are visible
changes.
The main problem is, that I have to deal with 1000s of mutations, so I have
to do it in a high throughput manner... (as high-thorughput as it is
reasonably possible)

On 12/16/05, Ran Friedman <ran at hemi.tau.ac.il> wrote:
>
> 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,
> Ran.
>
> 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
> http://bioinfo.tau.ac.il/~ran <http://bioinfo.tau.ac.il/%7Eran>
> 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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