Folks: I was wondering if I could get help with something. I have a peptide with a peptide with lysines and I would like to add acetyl groups to them. Is that possible? Thanks, Jesse
Hi Jesse, You can manually build onto your structure atom-by-atom using Build Structure (in menu under Tools… Structure Editing). It's not the most friendly builder, but once you play around with it for a while, you can see how the general process works. Basically to build outward you use the "Modify Structure" tab, with cycles of hydrogen addition and then changing a hydrogen to some other atom type. You would add hydrogens (could do with AddH the first time around… this tool is also in the Structure Editing section), then change one hydrogen to a carbon of the proper hybridization type, then add hydrogens again, then change one of the hydrogens on the carbon to an oxygen of the proper hybridization type. See the following (or click Help on the tool dialog) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html> Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 21, 2014, at 10:55 AM, JESSE JAYNES <jjsqrd@bellsouth.net> wrote:
Folks: I was wondering if I could get help with something. I have a peptide with a peptide with lysines and I would like to add acetyl groups to them. Is that possible? Thanks, Jesse
I should have added an "etc." … the steps I mentioned still wouldn't be the whole acetyl group! Elaine On Oct 21, 2014, at 11:06 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jesse, You can manually build onto your structure atom-by-atom using Build Structure (in menu under Tools… Structure Editing). It's not the most friendly builder, but once you play around with it for a while, you can see how the general process works. Basically to build outward you use the "Modify Structure" tab, with cycles of hydrogen addition and then changing a hydrogen to some other atom type. You would add hydrogens (could do with AddH the first time around… this tool is also in the Structure Editing section), then change one hydrogen to a carbon of the proper hybridization type, then add hydrogens again, then change one of the hydrogens on the carbon to an oxygen of the proper hybridization type.
See the following (or click Help on the tool dialog) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 21, 2014, at 10:55 AM, JESSE JAYNES <jjsqrd@bellsouth.net> wrote:
Folks: I was wondering if I could get help with something. I have a peptide with a peptide with lysines and I would like to add acetyl groups to them. Is that possible? Thanks, Jesse
Thank you Elaine. I appreciate it. I have been able to acetylate the lysine residues but now I am having difficulty in eliminating the charge. I noticed that each hydrogen on a normal epsilon amino group of lysine is assigned +0.34 charge. It would obviously be less than +1 and when I try and assign it +0 it basically is not capable of conducting the calculation. I will continue to read and work on it. Thanks, Jesse On Tuesday, October 21, 2014 1:18 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: I should have added an "etc." … the steps I mentioned still wouldn't be the whole acetyl group! Elaine On Oct 21, 2014, at 11:06 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jesse, You can manually build onto your structure atom-by-atom using Build Structure (in menu under Tools… Structure Editing). It's not the most friendly builder, but once you play around with it for a while, you can see how the general process works. Basically to build outward you use the "Modify Structure" tab, with cycles of hydrogen addition and then changing a hydrogen to some other atom type. You would add hydrogens (could do with AddH the first time around… this tool is also in the Structure Editing section), then change one hydrogen to a carbon of the proper hybridization type, then add hydrogens again, then change one of the hydrogens on the carbon to an oxygen of the proper hybridization type.
See the following (or click Help on the tool dialog) <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 21, 2014, at 10:55 AM, JESSE JAYNES <jjsqrd@bellsouth.net> wrote:
Folks: I was wondering if I could get help with something. I have a peptide with a peptide with lysines and I would like to add acetyl groups to them. Is that possible? Thanks, Jesse
Hi Jesse, I see I was wrong in previously suggesting you could add all the hydrogens first; sorry about that. Lysine nitrogens are automatically assigned a formal positive, tetrahedral atom type. So the first step of building should be to select that nitrogen and use the “modify structure” section of Build Structure tool to change it from 4 bonds tetrahedral to 3 bonds trigonal. In my testing just now, I specified a new name for the residue (via the options in Build Structure) because I thought it might not work to just leave it as LYS. Next select one of the two hydrogens on that nitrogen and change it to C with 3 bonds trigonal. Next select one of the two hydrogens on that carbon and change it to O with 1 bond, select the other hydrogen and change it to C with 4 bonds tetrahedral. Now the atom types will have been automatically adjusted as appropriate for an acetylated lysine. Now you can use addh on the whole structure, and any subsequent charge calculations should be fine. In my test the modified residue was named UNK and its net charge was 0. (You can see atom types by selecting the atom(s) and using menu: Actions… Label… IDATM type. The label won’t update automatically if the type is changed, you would have to re-label to see a difference. The types are documented here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html> ) Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Oct 22, 2014, at 5:00 AM, JESSE JAYNES <jjsqrd@bellsouth.net> wrote:
Thank you Elaine. I appreciate it.
I have been able to acetylate the lysine residues but now I am having difficulty in eliminating the charge. I noticed that each hydrogen on a normal epsilon amino group of lysine is assigned +0.34 charge. It would obviously be less than +1 and when I try and assign it +0 it basically is not capable of conducting the calculation. I will continue to read and work on it.
Thanks, Jesse
How wonderful. Thank you so much! I'll try it after my class. Best regards, Jesse Sent from my iPhone
On Oct 22, 2014, at 11:34 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Jesse, I see I was wrong in previously suggesting you could add all the hydrogens first; sorry about that. Lysine nitrogens are automatically assigned a formal positive, tetrahedral atom type. So the first step of building should be to select that nitrogen and use the “modify structure” section of Build Structure tool to change it from 4 bonds tetrahedral to 3 bonds trigonal. In my testing just now, I specified a new name for the residue (via the options in Build Structure) because I thought it might not work to just leave it as LYS. Next select one of the two hydrogens on that nitrogen and change it to C with 3 bonds trigonal. Next select one of the two hydrogens on that carbon and change it to O with 1 bond, select the other hydrogen and change it to C with 4 bonds tetrahedral.
Now the atom types will have been automatically adjusted as appropriate for an acetylated lysine. Now you can use addh on the whole structure, and any subsequent charge calculations should be fine. In my test the modified residue was named UNK and its net charge was 0.
(You can see atom types by selecting the atom(s) and using menu: Actions… Label… IDATM type. The label won’t update automatically if the type is changed, you would have to re-label to see a difference. The types are documented here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html> )
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 22, 2014, at 5:00 AM, JESSE JAYNES <jjsqrd@bellsouth.net> wrote:
Thank you Elaine. I appreciate it.
I have been able to acetylate the lysine residues but now I am having difficulty in eliminating the charge. I noticed that each hydrogen on a normal epsilon amino group of lysine is assigned +0.34 charge. It would obviously be less than +1 and when I try and assign it +0 it basically is not capable of conducting the calculation. I will continue to read and work on it.
Thanks, Jesse
participants (3)
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Elaine Meng -
JESSE JAYNES -
Jesse Jaynes