how to build N-linked glycans
Hi there, How would you recommend I go about building an N-linked glycan chain off of an ASN in an existing model using ChimeraX or ISOLDE? Is there documentation on this somewhere? Cheers, Alexis
Hi Alexis, Thought the easiest way might be to record a quick video demo of this (can't do a voiceover right now - sitting in meetings). Short story is that it's still a little clunky and expects you to know a few things about general glycan structure, but it's pretty straightforward once you get the hang of it. Video: https://drive.google.com/file/d/1U60eIAAwlDcOu4ajgkQ10p-bQ9qzIeE3/view?usp=s... Key points: - the Asn amide should be in *trans*, and the sugar's H1 should also be *trans* to the amide hydrogen - the "stem" is (Asn)-NAG-NAG-BMA, and (except in extremely rare cases) the sugars are arranged such that the ring oxygen alternates sides from one sugar to the next Best, Tristaan On Thu, Nov 9, 2023 at 6:21 AM Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi there,
How would you recommend I go about building an N-linked glycan chain off of an ASN in an existing model using ChimeraX or ISOLDE? Is there documentation on this somewhere?
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Hi Tristan, Thank you! That video was just perfect. For future reference and better searchability, I have transcribed this as a step-by-step guide which others may find useful: Steps 1. Add the first sugar 1. Select the H atom which is in trans in the Asn amide; if it doesn’t point in the direction of the glycans as suggested by the map, first change to an Asn rotamer with suitable orientation) 1. Delete it (del sel) 2. Place the center of view (colored axial vectors cross) approximately where you want the first sugar to be placed 3. Add the first sugar: isolde add ligand NAG 4. Show all atoms in the ligand: show sel 5. Add a label to the C1 atom: label sel&@C1 atom 6. Change right-mouse mode to move atoms (can use the ChimeraX ribbon for this) 7. Right click (shift) and shift-right click (rotate) to orient the sugar so that the C1 atom is in approximately the correct position to form a N-C bond with the Asn; the plane of the sugar ring should be approximately normal to the amide plane of the Asn 1. Note: when I shift-right click, I get a zoom action, not a rotate; this looks like it’s a Mac thing because it works for Tristan in his video. Also, setting the shift-right click to rotate selected atoms does not work (it shifts them) 2. My workaround: 1. ui mousemode right "translate selected atoms" 2. ui mousemode alt right "rotate selected atoms" 1. Clear the selection (Ctrl-click somewhere or ~sel) 2. Select the C1 atom from NAG (Ctrl-click) and the N from Asn (Shift-Ctrl-click) 3. Create a covalent bond between the two selected atoms: bond sel 4. Run a short simulation to let the sugar find a suitable local minimum (press the play button in the ISOLDE ribbon; when done, press the green stop sign button) 1. Add the second sugar 1. Select the hydroxyl H atom that’s “diametrically” opposed to the C1 atom (HO4, which is attached to O4) 2. Delete it: del sel 3. Move your cursor to where you want the next sugar, add another ligand (isolde add ligand NAG) 4. Label the C1 atom 5. Move/rotate the atoms for the new ligand such that C1 is positioned to bond with the O4 atom of the previous sugar residue. Rotate the new sugar such that the ring oxygen alternates sides from one sugar to the next. 6. Select the C1 atom from the new sugar residue and the O4 atom from the previous sugar residue and bond them (bond sel) 7. Relax the chain by running a short simulation (isolde play button) 2. Repeat the steps above to add more sugar residues. The "stem" is (Asn)-NAG-NAG-BMA. On Thu, Nov 9, 2023 at 5:00 AM Tristan Croll <tcroll@altoslabs.com> wrote:
Hi Alexis,
Thought the easiest way might be to record a quick video demo of this (can't do a voiceover right now - sitting in meetings). Short story is that it's still a little clunky and expects you to know a few things about general glycan structure, but it's pretty straightforward once you get the hang of it.
Video: https://drive.google.com/file/d/1U60eIAAwlDcOu4ajgkQ10p-bQ9qzIeE3/view?usp=s...
Key points: - the Asn amide should be in *trans*, and the sugar's H1 should also be *trans* to the amide hydrogen - the "stem" is (Asn)-NAG-NAG-BMA, and (except in extremely rare cases) the sugars are arranged such that the ring oxygen alternates sides from one sugar to the next
Best, Tristaan
On Thu, Nov 9, 2023 at 6:21 AM Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi there,
How would you recommend I go about building an N-linked glycan chain off of an ASN in an existing model using ChimeraX or ISOLDE? Is there documentation on this somewhere?
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Hi Alexis, Thanks very much for adding the annotated guide!! A tip regarding the right-click translate-rotate: the trick is to right-click and hold first, *then* hold shift to rotate the selection. Best, Tristan On Thu, 9 Nov 2023 at 21:08, Alexis Rohou <a.rohou@gmail.com> wrote:
Hi Tristan,
Thank you! That video was just perfect.
For future reference and better searchability, I have transcribed this as a step-by-step guide which others may find useful:
Steps
1.
Add the first sugar 1.
Select the H atom which is in trans in the Asn amide; if it doesn’t point in the direction of the glycans as suggested by the map, first change to an Asn rotamer with suitable orientation)
1.
Delete it (del sel) 2.
Place the center of view (colored axial vectors cross) approximately where you want the first sugar to be placed 3.
Add the first sugar: isolde add ligand NAG 4.
Show all atoms in the ligand: show sel 5.
Add a label to the C1 atom: label sel&@C1 atom 6.
Change right-mouse mode to move atoms (can use the ChimeraX ribbon for this) 7.
Right click (shift) and shift-right click (rotate) to orient the sugar so that the C1 atom is in approximately the correct position to form a N-C bond with the Asn; the plane of the sugar ring should be approximately normal to the amide plane of the Asn 1.
Note: when I shift-right click, I get a zoom action, not a rotate; this looks like it’s a Mac thing because it works for Tristan in his video. Also, setting the shift-right click to rotate selected atoms does not work (it shifts them) 2.
My workaround: 1.
ui mousemode right "translate selected atoms" 2.
ui mousemode alt right "rotate selected atoms"
1.
Clear the selection (Ctrl-click somewhere or ~sel) 2.
Select the C1 atom from NAG (Ctrl-click) and the N from Asn (Shift-Ctrl-click) 3.
Create a covalent bond between the two selected atoms: bond sel 4.
Run a short simulation to let the sugar find a suitable local minimum (press the play button in the ISOLDE ribbon; when done, press the green stop sign button)
1.
Add the second sugar 1.
Select the hydroxyl H atom that’s “diametrically” opposed to the C1 atom (HO4, which is attached to O4) 2.
Delete it: del sel 3.
Move your cursor to where you want the next sugar, add another ligand (isolde add ligand NAG) 4.
Label the C1 atom 5.
Move/rotate the atoms for the new ligand such that C1 is positioned to bond with the O4 atom of the previous sugar residue. Rotate the new sugar such that the ring oxygen alternates sides from one sugar to the next. 6.
Select the C1 atom from the new sugar residue and the O4 atom from the previous sugar residue and bond them (bond sel) 7.
Relax the chain by running a short simulation (isolde play button) 2.
Repeat the steps above to add more sugar residues. The "stem" is (Asn)-NAG-NAG-BMA.
On Thu, Nov 9, 2023 at 5:00 AM Tristan Croll <tcroll@altoslabs.com> wrote:
Hi Alexis,
Thought the easiest way might be to record a quick video demo of this (can't do a voiceover right now - sitting in meetings). Short story is that it's still a little clunky and expects you to know a few things about general glycan structure, but it's pretty straightforward once you get the hang of it.
Video: https://drive.google.com/file/d/1U60eIAAwlDcOu4ajgkQ10p-bQ9qzIeE3/view?usp=s...
Key points: - the Asn amide should be in *trans*, and the sugar's H1 should also be *trans* to the amide hydrogen - the "stem" is (Asn)-NAG-NAG-BMA, and (except in extremely rare cases) the sugars are arranged such that the ring oxygen alternates sides from one sugar to the next
Best, Tristaan
On Thu, Nov 9, 2023 at 6:21 AM Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi there,
How would you recommend I go about building an N-linked glycan chain off of an ASN in an existing model using ChimeraX or ISOLDE? Is there documentation on this somewhere?
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT <https://www.google.com/maps/search/1+Ashley+Road,+Altrincham,+Cheshire,+Unit...>
-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
participants (2)
-
Alexis Rohou -
Tristan Croll