Re: protein folding

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Fri Jul 10 2009 - 08:51:56 CDT

Dear Dong, Dear Doty,

As Axel said it, the martini force field treats the secondary structure
as input parameter. therefore you CANNOT simulate folding/unfolding ...
Different versions of MARTINI and other heavy-atom based coarse grain
force fields employ an elastic network model to keep the secondary
structure stable. Otherwise the secondary structure is not stable in
coarse grain simulations. Therefore, I would say any attempt to simulate
folding/unfolding events with a force field that artificially keeps
secondary structure fixed is useless .

Now, I've seen some attempts to derive coarse grain force fields that
are able to maintain secondary structure without artificially forcing it
to be stable. But I don't think these efforts are published yet ... At
least not to my knowledge.

Your best choice for folding/unfolding is an all-atom force field
without secondary structure-biasing ... of course you'll be limited to
peptides and very small proteins ... but if you have big computers you
can go to microseconds simulations and maybe you'll be able to see
folding events for such small structures ....

Cheers
Vlad

Dong Luo wrote:
> Basically all atom simulation is not suitable for conformational
> sampling yet especially for folding process IMO. Based on my
> experience, it's only possible for a peptide less than 30 residues and
> may only work for alpha helix as expected secondary structure in case
> of Charmm force field. I'm not sure of martini force field.
> Alternatively, I started with full folded helix structure and observe
> it unfolds, it is faster than the folding process. And heat annealing
> (by controlling the temperature) is employed to accelerate it.
>
> Dong
>
> ------------------------------------------------------------------------
> *From:* doty alexiou <doty_alexiou_at_hotmail.com>
> *To:* namd-list <namd-l_at_ks.uiuc.edu>
> *Sent:* Friday, July 10, 2009 4:00:37 AM
> *Subject:* namd-l: protein folding
>
>
>
>
> Hi.I am running an NAMD simulation of a protein(folding process) using
> the extended martini foce field.The simulation has run about 70-80
> ns(323 k,timestep 10,PBC,in water,RMSD is about 18 till now).Up until
> now,there is no sign of the expected secondary structure of the
> protein.Is there any suggestion about what could be wrong or if i
> should expect it longer?Thank u.
>
>
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-- 
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Dr. Vlad Cojocaru
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