[Chimera-users] PDB file of D-amino acids

[Mohsen Asadbegi]

Thank you for the precise clarification,

Regarding Force field, does it possible to use the existing force fields of
L-amino acids (For instance CHARMM36) for D-amino acids?

Regards,
Mohsen.

On Wed, 3 Apr 2019 at 22:49, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Yes, D- and L- refer to the configuration at the alpha-carbon of an amino
> acid. For further explanation see any biochemistry textbook, or:
> <https://en.wikipedia.org/wiki/Amino_acid#Isomerism>
>
> I wrote that previous answer and I still agree with it (and using this
> “invert” command was same as suggestion #1 in my reply today).  However,
> the example commands should contain “@“ instead of “ at “ which is shown in
> the page because it was automatically substituted in by the mail system.
>
> Elaine
>
>
> > On Apr 3, 2019, at 12:05 PM, Mohsen Asadbegi <mohsenasad.7091 at gmail.com>
> wrote:
> >
> > Dear Dr. Elaine
> >
> > Thanks for your comprehensive answer,
> >
> > Regarding construction of d-peptide, I have found another answer, that
> is provided below:
> >
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-October/010366.html
> >
> >  In above web page, it is suggested to invert only alpha-carbon of each
> residue to convert a L-amino acid to D-amino acid.
> > Do you confirm this method? Which atoms of a L-amino acid should be
> inverted by invert command in CHIMERA?
> >
> > Reagrds,
> > Mohsen Asadbegi.
> >
> >
> > On Wed, 3 Apr 2019 at 22:12, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Mohsen,
> > For entirely D-amino acids, I like Mark’s suggestion of inverting the
> coordinates.  However, I think it would work to just invert the sign of X,
> Y, or Z coordinates (rather than all 3) since any of those would reflect
> the molecule across a plane.  There is some python code to flip the sign of
> all X-coordinates in this previous post:
> > <
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-September/005490.html
> >
> >
> > For mixtures of D- and L-amino acids,
> >
> > (1) there is a Chimera “invert” command to swap two substituents of an
> atom, which could be used to change chirality.
> > <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/invert.html>
> >
> > (2) for a variety of nonstandard or nonnatural amino acid sidechains,
> there is a Chimera plugin available from the SwissSidechain folks for
> adding the sidechains to make D-amino acids, see:
> > <https://www.swisssidechain.ch/visualization/chimera.php>
> > You could build the residues you want to make into D-amino acids as Gly
> in Chimera and then use this plugin to mutate them.
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On Apr 3, 2019, at 3:05 AM, Mark J van Raaij <mjvanraaij at cnb.csic.es>
> wrote:
> > >
> > > may not the smartest way, but you could generate a peptide of L-amino
> acids and then make the mirror image by inverting the sign of all the x, y,
> z coordinates.
> > > Either by hand in a text editor or with a program (I know of PDBSET
> from CCP4, but there are probably other options). The program may complain
> that you are doing something that is "not allowed" in protein structure,
> but you can probably override that.
> > > In protein crystallography this is sometimes needed when heavy atom
> positions have been determined, sometimes we don't know if the given
> coordinates are correct or if the mirror image is it.
> > >
> > > Mark J van Raaij
> > > Dpto de Estructura de Macromoleculas
> > > Centro Nacional de Biotecnologia - CSIC
> > > calle Darwin 3
> > > E-28049 Madrid, Spain
> > > tel. (+34) 91 585 4616
> > > http://wwwuser.cnb.csic.es/~mjvanraaij
> > > Section Editor of Acta Crystallographica F, Structural Biology
> Communications
> > > http://journals.iucr.org/f/
> > >
> > >
> > >> On 3 Apr 2019, at 12:47, Mohsen Asadbegi <mohsenasad.7091 at gmail.com>
> wrote:
> > >>
> > >> Hello every one!
> > >> I want to convert a sequence of d-amino acids or a sequence of
> d-amino acids and L-amino acids to a PDB file.
> > >>  How can I construct such PDB file? I know that this is possible to
> enter the sequence of L-amino acids in CHIMERA (uppercase characters of the
> amino acids for example: LFVVA), But regarding d-peptides and retro-inverso
> peptides I don't know the exact way of building PDB files.
> > >>
> > >>
> > >> Regards,
> > >> Mohsen Asadbegi
> >
> > _______________________________________________
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