AMBER Archive (2009)

Subject: Re: [AMBER] Creating conditions for biased MD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Apr 20 2009 - 13:46:41 CDT

I think it might be easier with dihedral angle restraints. it depends
on the rest of the system- if it's just the one helix, you could use
the impose command in leap to make a continuous helix as a reference
for SMD.

On Mon, Apr 20, 2009 at 1:31 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> 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_at_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_at_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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