Which atoms does Wiggle Backbone move?
| Case number: | 845813-2008625 |
| Topic: | Game: Tools |
| Opened by: | jeff101 |
| Status: | Open |
| Type: | Question |
| Opened on: | Sunday, January 19, 2020 - 15:59 |
| Last modified: | Sunday, February 9, 2020 - 19:44 |
For all amino acids in Foldit, atoms 1-4 are backbone atoms.
Are the H's hanging off the alpha-carbon and backbone nitrogen
also considered backbone atoms? Are the extra H's and O's on the
N- and C- terminal amino acids also considered backbone atoms?
These H's and the extra O's won't have atom #'s from 1-4.
Does Wiggle Backbone in Foldit only wiggle atoms 1-4 on each
segment, or does it also wiggle the backbone and terminal
H's and O's? Do the non-backbone (sidechain) atoms on each
segment move together like a rigid body, rotating and translating
as a unit, with the amount of rotation and translation set by the
motions of the segment's backbone atoms? I ask because
different amino acids will have different atom #'s for the
backbone H's; for example, I think usually the H attached to
cysteine's backbone N is atom 7 while the H attached to
histidine's backbone N is atom 11. Does Wiggle Backbone keep all
covalent bond lengths fixed? Does Wiggle Backbone just vary the
phi,psi dihedral angles, since these angles (with fixed covalent
bond lengths) are enough to determine the positions of all
backbone atoms?
Thanks!
Wed, 02/05/2020 - 14:44
#2
Great question and interesting answer ! Thanks jeff !
It's the first time I understand what wiggle power actually does !
Sat, 02/08/2020 - 07:13
#3
What happens if one uses Low Power after using Medium or High Power?
Will the bond lengths now stay fixed at the values obtained at Medium
or High Power, or will they revert to the original bond lengths used
at Low Power?
As an example, say one starts at Low Power with the C-N bond length
fixed at 1.32 Angstroms. Then one uses Med Power, and a certain C-N
bond length becomes 1.39 Angstroms. When one switches back to Low
Power, will this C-N bond length stay fixed at 1.39 Angstroms, or
will it get changed back to 1.32 Angstroms? Will wiggles, shakes,
rebuilds, remixes, and mutations done at Low Power keep the new C-N
bond length fixed at 1.39 Angstroms, or will none/some/all of them
switch this length back to 1.32 Angstroms?
Perhaps your answers will help me understand better why things seem
to get stuck or lose flexibility at Low Power if one has already
folded them some at Medium or High Power.
Good question! The answer depends on your Wiggle Power settings:
Low Power: All bond lengths and angles are fixed. Only torsion dihedrals (e.g. phi, psi) are allowed to rotate. When you Wiggle Backbone, the sidechain atoms and backbone hydrogens will follow the rotation of the backbone torsions as rigid bodies, with fixed bond lengths and angles (I think of them as "passengers" of the backbone torsions).
Medium Power: Same as Low Power, but now we can also vary the length of the bond between two segments (and the related bond angles on either side of this bond). This is really useful for closing cut-points, which is the most common way to disrupt the length/angles of this bond. Still, when you Wiggle Backbone, the sidechain and atoms and backbone hydrogens will follow as rigid bodies.
High Power: Now we can vary the lengths and angles of all bonds. Normally, bond angles and lengths are unlikely to deviate from their ideal values, so high-power wiggle rarely improves the scientific accuracy of a solution (this is why it is disabled in most puzzles). Now, when you Wiggle Backbone, the backbone hydrogens can wiggle a little bit on their own; the sidechain atoms will still follow as rigid bodies.