Carlos: late in thanking you. I had to fix hardware and software problems.
Complex:
phi Gly227C Gly228N Gly228CA Gly228C ca 78 degrees (positive)
psi Gly228N Gly228CA Gly228C Gln229N -19 degrees
In a cartoon view, two cylinders make an angle of ca 40 degrees,
interconnected by 227 228. I would like to approximately straighten
that, to get a continuous cylinder. In a helix view, phi should be
turned anticlockwise to reach at least the value -80 degrees (the
value of corresponding nearby dihedral is just -80 degrees, while
farther away it takes normal values, -57 degrees). psi, at least, has
the correct sign.
The bent helix is capped on both sides, but there are other similar,
capped helices around, so that I guess the work should be carried out
on the whole model. If I could restrain the capping groups alone of
the bent helix (while finding a way that helicity, where correct, is
conserved) I could imagine that straightening could occur. Otherwise,
if all amino acids, except 227 228 of the bent helix, are restrained,
how could the helix get straightened? Is that a task for SMD at all?
thanks
francesco
On Mon, Mar 30, 2009 at 1:56 PM, Carlos Simmerling
<carlos.simmerling.gmail.com> wrote:
> francesco, I think dihedral restraints may be the only way to go without a
> helical ref structure. you'd definitely want to also restrain all other
> residues in this helix to maintain it, or else you might just move the bend.
> when changing the restraints over time, give thought to which direction to
> rotate, which depends on the initial conformation of the Gly residues, if
> they are currently adopting positive phi values then it's more complex than
> just going from pp2 to alpha, for example, where you can just reduce psi.
>
> On Mon, Mar 30, 2009 at 6:16 AM, Francesco Pietra <chiendarret.gmail.com>wrote:
>
>> Hi:
>> I would like to modify the conformation of a protein at one helix,
>> which is bent at a region of three amino acids, Ile, Gly, Gly. Viewed
>> in cartoon representation, it is constituted of two straight portions
>> interconnected through a largely non helical set of the three amino
>> acids.
>>
>> I would appreciate suggestions how to get the three aa taking part to
>> the well ordered helical conformation, so that what is now (in
>> cartoon) two straight portions interconnected by something like a loop
>> becomes a wholly straitened motif. Rotation about dihedrals? Make the
>> process with the isolated helix or in the whole context of the
>> protein?
>>
>> I guess that steered MD (on which I have no experience) is the
>> approach in Amber, though I wonder how to provide the target.
>> Possibly, any biased MD should be carried out in explicit medium. In
>> my hands, continuum models were unsuccessful with this protein.
>>
>> If these are not such naive questions to merit attention, thanks
>>
>> francesco pietra
>>
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Received on Wed May 20 2009 - 11:53:08 PDT
