PDB file of D-amino acids
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
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@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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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
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@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@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@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
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@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@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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@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@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Mohsen, If you are asking in general, it may be beyond the scope of this mailing list. You would have to investigate further into CHARMM or whatever software/forcefield combination you are using for molecular mechanics/dynamics. I would guess the answer is “not necessarily” because some force fields or programs may apply chirality restraints — you might have to use different residue names and different parameter files for D-amino acids than for their L- counterparts. If you mean in Chimera, doing minimization/MD using MMTK (which does not have any CHARMM forcefield options), I don’t know how well it would work, but you could try. If you do, would need to check results carefully for any strange distortions. Regards, Elaine
On Apr 4, 2019, at 5:32 AM, Mohsen Asadbegi <mohsenasad.7091@gmail.com> wrote:
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.
participants (3)
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Elaine Meng -
Mark J van Raaij -
Mohsen Asadbegi