pro_closure energy scoring function

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pro_closure energy scoring function
#1

Hi,

I know that this is ring closure energy of proline. however could someone provide me some more details about this energy term? What is a physical meaning of this function?

Ewa

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Sat, 2013-11-16 13:22
peony

In most of Rosetta protocols which move atoms, that movement is done on an internal coordinate representation - that is bond lengths, angles, and dihedrals. As a consequence of this, to uniquely specify an atom position Rosetta represents atoms as an "atom tree", with each atom being built based on the lengths, angles and dihedrals from atoms prior to it in the tree. That representation runs into problems with rings. In that case, you could either go around the ring one way to build the atom, or go around the other way. Rosetta has to make a choice.

In some cases (like Phe & Tyr sidechains), that choice is arbitrary. It doesn't matter which one you choose because the geometry of the ring is more-or-less fixed in the representation Rosetta uses. Proline is different, in that there are flexible degrees of freedom both on the backbone side and the sidechain side of the ring. Because the two sides can move independently, you need some way of keeping the ring closed. That's what the pro_close term is for. It looks at the difference in position of where the nitrogen is according to the backbone, and where it should be according to the position of the sidechain, and applies a penalty if those two locations differ. It also has a component which accounts for the torsional energy around that N-Cdelta bond.

It really doesn't have a physical meaning, strictly speaking. It's a practically derived term which is there to keep the proline ring closed in the appropriate geometry. If it makes you feel better, you can think of it as analogous to the bonding energy of the N to Cdelta, but the functional form is not directly derived from the physical form of that bonding interaction, like it would be in a molecular mechanics force field.

Mon, 2013-11-18 08:15
rmoretti

Thanks a lot for answer. But ok then and what about cis and trans proline, is it posibble to differ them according to this energy term?

Tue, 2013-11-19 07:31
peony

They're treated separately, but not altogether differently. I misspoke a bit earlier. The torsional component of the pro_close term isn't centered around the N-Cdelta bond, it's actually centered around the peptide bond, so the torsional angle under scrutiny is that of Cdelta-N-C(n-1)-O(n-1). The angle is then classified as either cis or trans, and assigned a harmonic penalty based on how far away it is from the "ideal" cis/trans angle. (The spring constant varies slightly for cis versus trans, by not by much.) An ideal cis proline ( -2.9105 degree dihedral) has the same energy as an ideal trans proline (176.3 degrees). Both of them would get zero "bonus" to the pro_close term.

Tue, 2013-11-19 13:29
rmoretti

So can I say that the for high value of pro_close energy term the proline ring is build improper (not close)?

Sat, 2013-11-23 08:05
peony

Not closed properly, yes.

Sun, 2013-11-24 10:37
rmoretti