Proline Hydrogen Atom Numbers

Case number:845799-2008503
Topic:Biochem
Opened by:jeff101
Status:Open
Type:Bug
Opened on:Sunday, January 5, 2020 - 11:00
Last modified:Friday, April 17, 2020 - 15:41

In Foldit, how many hydrogen atoms are covalently bonded to a
proline residue's backbone nitrogen? What are these hydrogens'
atom numbers? How do these numbers change for prolines at each
end of a polypeptide chain?

Thanks!

(Sun, 01/05/2020 - 11:00  |  7 comments)


Susume's picture
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Here is Brow42's take on it:
"Prolines are strange; they loop around and bond to the backbone nitrogen. But rosetta can't support this bonding pattern. Instead, the last sidechain atom, 7, is bonded to a virtual atom 8, which is forced to be in the same spot as atom 1, the N. (however strong bands can overcome this constraint, breaking the proline). Also, the sidechain bond uses one of the bonds that would normally be a polar hydrogen. SInce there's usually only one polar hydrogen attached to the backbone N, proline's N is NOT a donor and cannot form an H-bond. The first hydrogen is 9, which is attached to C-alpha. There are no polar hydrogens."

He also discusses how atom numbers change in the N-terminal and C-terminal residues.

https://fold.it/portal/recipe/41664 is the link (scroll down to comment #6).

LociOiling's picture
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Some proline fun facts.

A N-terminal proline has 18 atoms, a C-terminal proline has 16, and mid-chain proline has 15.

From wikipedia, the formula for proline is C5H9NO2, a total of 17 atoms, with 8 heavy atoms.

In a protein, only the C terminal gets to keep the second oxygen, so the heavy atom count should be 7.

So the first proline hydrogen should be atom 8, except on the C terminal, where it's atom 9.

If you use Atom Explorer v1.0, atom 8 (or 9) appears to be in the same spot as atom 1, the nitrogen. Foldit doesn't show the hydrogen on its own, as described in the sidechain section of "protein backbone" on the wiki.

If you look at proline on its own in Jmol or the equivalent (open PDB "=pro"), it shows one hydrogen attached to the nitrogen. It also shows up in the online PDB viewer if you click the "hydrogens" button.

Back in Foldit, an N-terminal proline will show two hydrogens attached the black nub with the "Show all H" option. These hydrogens are the last two atoms, 17 and 18.

At least in the cartoon views, Foldit also doesn't show the hydrogen attached to the alpha carbon, opposite the sidechain. For proline, the "stick" view shows the alpha carbon hydrogen (with "show all H"). The alpha carbon hydrogen is atom 9 in a non-terminal proline. Each sidechain carbon has two hydrogens, so these are atoms 10 to 15.

LociOiling's picture
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Type: Question » Bug

I had managed to completely forget this discussion. The atom count of 18 for proline at the N terminal doesn't seem right to me, so I'm changing it from Question to Bug. My current thought is that the atom count should be 17 in this case, an increase of 2 instead of 3 from the mid-chain count of 15 atoms. That's how the other 19 amino acids work.

Nevertheless, proline is showing up at the N terminal in the coronavirus puzzles, so I've updated these recipes to deal with it:

Puzzle 1825 shows why the change is needed, with proline at the N terminal of chain B, Foldit segment 118.

Using Atom Explorer, the problem seems to happen at atom 9. For a mid-chain proline, atom 9 is the first hydrogen. For an N-terminal proline, the band drawn by Atom Explorer for atom 9 seems to come from the alpha carbon, which was already counted as atom 2.

brow42's picture
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I agree, this must be a bug. On 17 atoms are visible on the N-terminal proline, and I get this also by manual count (with 8 = virtual).

brow42's picture
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In this screen shot we see a second VIRTUAL atom added after #8. This extra atom is not present at the C terminal proline (not shown).

For some reason, the 2H(plus) are attached to VIRTUAL atom #8 instead of N atom #1.

https://fold.it/portal/files/chatimg/irc_269484_1587105538.png

brow42's picture
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It occurs to me that they needed to add a second VIRTUAL atom to orient atom 8 (which has the hydrogens) correctly, by specifying the 6-7-8 (Cdel-Ceps-V) and 7-8-9 (Ceps-V-V) dihedral angles.

rmoretti's picture
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Here's the atom ordering for a regular mid-chain proline:

1 N N
2 CA C
3 C C
4 O O
5 CB C
6 CG C
7 CD C
8 NV VIRTUAL
9 HA H
10 1HB H
11 2HB H
12 1HG H
13 2HG H
14 1HD H
15 2HD H

And for an N-terminal proline:

1 N N
2 CA C
3 C C
4 O O
5 CB C
6 CG C
7 CD C
8 NV VIRTUAL
9 CAV VIRTUAL
10 HA H
11 1HB H
12 2HB H
13 1HG H
14 2HG H
15 1HD H
16 2HD H
17 1H H
18 2H H

And for a C-terminal proline:

1 N N
2 CA C
3 C C
4 O O
5 OXT O
6 CB C
7 CG C
8 CD C
9 NV VIRTUAL
10 HA H
11 1HB H
12 2HB H
13 1HG H
14 2HG H
15 1HD H
16 2HD H

The reordering of the hydrogens and other atoms is because of an internal requirement that all the non-hydrogens come before all the hydrogens all the "backbone" atoms come before sidechain atoms, and the hydrogens are ordered in the same order as the atom they are attached to.

Regarding bonding for mid-chain and C-terminal prolines, it's as you would expect, except that the NV is attached to the CD atom. (The location of the NV "virtual nitrogen" atom is used to allow the proline sidechain to be flexible yet be able to close. Ideally, the NV and the N atoms are at the same location.) There are no hydrogens on the backbone nitrogen for a mid-chain proline.

For the N-terminal proline, NV is bonded to CD and CAV is bonded to NV, but the 1H and 2H atoms are bonded to the NV atom, not the N atom. This is to better allow the locations of the terminal amine hydrogens to follow the positioning of the sidechain. As before, the NV virtual nitrogen and the CAV virtual C-alpha atom are used for sidechain ring closure. (The addition of the CAV atom is needed to properly position the 1H and 2H atoms when they're attached to the NV atom.)

So, yeah, what Brow42 said.

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