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

[Elaine Meng]

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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