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688b: H-Bonding the Hydrogen-producing Catalyst Dimer
Status: Closed

Summary

Name: 688b: H-Bonding the Hydrogen-producing Catalyst Dimer
Status: Closed
Created: 03/19/2013
Points: 100
Expired: 03/26/2013 - 23:00
Difficulty: Intermediate
Description: This is the sequel to puzzle 675, where you folded two symmetric chains attached to a central catalyst molecule. We've kept the catalyst and the chains identical, but we're moving beyond just folding: it's time to make this catalyst go turbo. It needs protons fed to its inner nitrogen (an H-bond acceptor) to go faster, so we're giving you a large bonus for making an H-bond to this atom. Fair warning: it's a bit crowded in there, so the angle has to be just-right to avoid a clash. This is the atom in the central, bent ring that attaches to the flat outer ring. It looks blue in CPK mode and glows red when "show bondable atoms" and "show bonds (non-protein)" are turned on, under "View". Try to come up with stable folds that reach this atom!
Categories: Design, Overall, Symmetry

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Comments

Joined: 06/04/2012
H-Bond

Please explain again what an H-Bond exactly is. I believe i have made some but they don't score so i assume there are more kind of bonds possible between the catalyst and the protein

thanks in advance.

Joined: 08/10/2010
Groups: None
An H-bond is a bond between a

An H-bond is a bond between a polar hydrogen atom and an oxygen or nitrogen atom with a "free spot". (Or sometimes chlorine, fluorine, and a few other atom types that don't show up in Foldit.) These H-bonds aren't nearly as strong or as permanent as covalent chemical bonds (The solid lines, or sticks, in Foldit) but they still matter, and they help keep a protein in a specific shape.

In game terms, H-bonds show up as the bright lines that link parts of the protein; they look like shiny barber-poles or psychedelic candy canes. How these appear, where they appear, and whether all atoms involved appear, all depends on the "View" options you have selected. Though H-bonds technically involve a polar hydrogen and a free-spot on an oxygen or nitrogen atom, we simplify it a bit for display. If you turn on "show bondable atoms" under "View", the oxygen or nitrogen that wants to accept an H-bond appears as red, and an oxygen or nitrogen that wants to DONATE an H-bond appears as blue. (Nitrogens and oxygens covalently attached to hydrogens are said to "donate" these hydrogens to other oxygen or nitrogen "acceptor" atoms - atoms with a free spot - when they form H-bonds.)

Hydrogens are the atoms that are being donated or accepted, but these don't normally show up in Foldit; normally people just use the color codes: pulsing blue means that atom (nitrogen or oxygen) will donate a hydrogen and pulsing red means that atom (nitrogen or oxygen) will accept a hydrogen. But if you want to see the details - actually look at what is being donated or accepted, and how it's oriented - then turn on "Stick+PolarH" under the "View Protein" submenu of "View". (You might need to check "show advanced GUI" under "General Options", the screwdriver/wrench icon, for these View options to appear.)

When you can actually see the hydrogens that the nitrogen and oxygen atoms are sharing around, it becomes a lot easier to see what's going on. When you move polar hydrogens (hydrogens attached to nitrogen or oxygen) close enough to "open spaces" on different nitrogen or oxygen atoms, and viola, the shining dotted line will appear, and you have an H-bond! (Assuming you're showing all the H-bonds that you form. Check your view settings, and make sure all of the "Show Bonds" options are checked.) Since Foldit's proteins are a lot more busy looking (and possibly slower) this way, most players stick with the red and blue pulsing balls. Oh, or purple; atoms that can both donate and accept a hydrogen pulse purple. (These are serine, threonine, and tyrosine oxygen atoms, and the polar atoms of some ligands like sugars. They have a hydrogen pointing out one way, but free space to accept a different hydrogen on the opposite side. To see which side is which, turn on "Stick+PolarH" - but generally if you shake or wiggle a sidechain with a purple ball, it will rotate its hydrogen around and form the best H-bond available to it, so this is rarely necessary.)

Since H-bonds are drawn between the oxygen and nitrogen atoms (not they hydrogens), they can occasionally look a little weird. For example, glutamine, asparagine, lysine and arginine sidechains have donor atoms (pulsing blue) that have multiple polar hydrogens on them. They can form multiple H-bonds. This in and of itself is not weird, but confusion can arise when they form multiple H-bonds to the same acceptor atom. In this case, there's just one candy-cane H-bond line drawn between the donor and acceptor atoms, but technically it counts as 2 H-bonds because two hydrogens are involved. Luckily, I can't think of any cases where this is a big deal - even this puzzle, which gives a huge bonus for a specific H-bond, only gives a bonus for 1 or more; 2 H-bonds aren't any better than 1 here, so don't worry about super-fine-tuned analysis of the exact orientation of a hydrogen-bond-donating atom.

To complicate visualization a bit, oxygen and nitrogen atoms can be distinguished by color if you turn on "Score/Hydro+CPK" in the "Color" submenu of "View". This turns atoms different colors depending on what element they are; this is different from whether they're a donor or acceptor. Though it's true that acceptors are usually oxygen and donors are usually nitrogen, this is not always the case, and in this particular puzzle it is a nitrogen atom that needs to accept a hydrogen to form an H-bond. (So the atom can show up as a red pulsing ball overtop of its blue atom color.)

Hope that helps! Happy H-bonding! :)

Susume's picture
User offline. Last seen 1 day 2 hours ago. Offline
Joined: 10/02/2011
If you are not getting a

If you are not getting a bonus for your bonds to the catalyst, you may be bonding to the wrong red atom. Make sure show bonds non-protein is on, as well as show bondable atoms, and if you check H-bond in the bonus/penalty window it will put an extra glow on the target atom.

Joined: 05/19/2009
Groups: Contenders
Why are we not able to load

Why are we not able to load the old designs ?
This is an incredible waste of time recreating the previous design by hand.

Joined: 05/28/2012
can the hydrogen bond only

can the hydrogen bond only form on the side of the dimer where the atom protrudes a little bit or can it be formed on both sides?

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