I think you miss the point. its not folded. there is a braod ensemble
of structures, dominated by *local* pp2 conformations. there is not a
single structure, as indicated by many experiments and simulations. so
'folded' has little meaning. in fact, ala5 is a decent model for
*unfolded* proteins. using a single structure for your reference is
conceptually incorrect. you might look into J coupling calculations-
see recent work in biophys by Lauren Wickstrom in my lab for examples
on ala peptides- but be careful with pH. there is also good related
work from Best and Hummer, but make sure to read the erratum as much
of the Amber data is very wrong in the original article.
On 3/19/10, Dongshan Wei <dswei0523.gmail.com> wrote:
> Thanks a lot to Adrian and Bud.
>
> Another question, is there any published papers pointing out the folded
> structure of Ala_5 is Polyproline II instead of alpha-helix?
>
> Dongshan
>
> On Thu, Mar 18, 2010 at 8:49 PM, M. L. Dodson <
> activesitedynamics.comcast.net> wrote:
>
>> On Thu, Mar 18, 2010 at 05:36:06PM -0400, Adrian Roitberg wrote:
>> > To do what you want, you need to impose phi/psi ideal helical angles for
>> > each alanine. You can do this by using the 'impose' command in leap.
>> >
>> > However, and I cannot emphasize strongly enough: Ala_5 is NOT an alpha
>> > helix !
>> >
>> > It is a polyproline II structure, but highly flexible.
>> >
>> > It is time people stop referring to alanine peptides as 'alpha helical'
>> >
>> > Adrian
>> >
>> >
>> > On 3/18/10 5:28 PM, Dongshan Wei wrote:
>> > >Hi All,
>> > >
>> > >I need to calculate the RMSD of Ala5 (ACE-Ala5-NME) peptide in water
>> > > and
>> > >want to choose an ideal alpha-helix structure as my reference
>> > > structure.
>> > >Does anyone know how or where to obtain the ideal alpha-helix structure
>> of
>> > >peptides? I looked through the PDB data bank and there is no such a
>> short
>> > >peptide crystal structure.
>> > >
>> > >Thanks!
>> > >
>> > >Dongshan
>>
>> In the ambertools distribution, one of the nab example programs,
>> peptide, can be used to build oligopeptides of a single secondary
>> structure. At one time, the available structure data base for peptide
>> was patched to include the parameters for polyproline II. An
>> ambertools distribution is not readily available to me right now, but
>> it should be easy to check. You will have to compile the nab program.
>>
>> Bud Dodson
>> --
>> M. L. Dodson
>> Business Email: activesitedynamics-at-comcast-dot-net
>> Personal Email: mldodson-at-comcast-dot-net
>> Phone: eight_three_two-56_three-386_one
>>
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>>
>
>
>
> --
> -----------------------------------------------------------------------------------
> Dr. Dongshan Wei
> Department of Chemistry
> Boston University
> Boston, MA, 02215
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Mar 19 2010 - 10:30:03 PDT
