FoldIt!

So, FoldIt is a program that allows you to fold proteins. As you fold the protein, you get a score based on how well it is folded. Your goal is to reach a pre-determined score and then you get to move on to the next puzzle. So....

Puzzle 3-1 is called "Sheets Together"

Basically all I had to do with this was wiggle the protein by clicking the "Wiggle All" button. This created hydrogen bonds in the protein (the blue and white ones), which stabilized the protein. Doing this made the protein properly folded and allowed me to get the score I needed to move on.

Puzzle 3-2 is called "Lonely Sheets"

For this one, I had to match up the sheets and so I couldn't just use the "Wiggle All" button, but also had to drag the sheets to one another. I did this by hitting the shift key, clicking on the sheet, and dragging it. Then, I wiggled the protein because that allows the rubber bands to pull together. I put rubber bands across the areas of the puzzle where the protein sheets were too far apart. These were identified by red balls between the parts that were too far apart. I actually managed to finish this puzzle using only one rubber band. However, I had to reset the puzzle a couple of times before I was able to do this! At the end it looked like this:

The rubber band I used is shown in purple.

Puzzle 3-3 is called "Sheets and Ladders"

I managed to solve this puzzle using only one rubber band as well. I used the same method, making the rubber band and then hitting "wiggle". It immediately got me the points I needed, which was kind of surprising. I noticed that at the end there was still space between it, shown by the red ball, but I decided not to argue it. Hydrogen bonds were formed in the process. As usual, the rubber band is in purple and the hydrogen bonds are blue and white. Here is the completed puzzle:

I did puzzles 3-4 and 3-5 as well to get to puzzle 4-1. 3-4 or "Lock and Lower" introduced the concept of freezing a portion of the protein so that it doesn't move while the protein was wiggling. After freezing part of the protein, I was able to solve the puzzle using just one rubber band and then wiggling, which resulted in several hydrogen bonds that stabilized the protein.

I solved 3-4 or "Rebuild" by right clicking on a portion of the protein that seemed unstable and clicking rebuild. After I stopped the rebuilding, I clicked wiggle, which allowed some stabilizing hydrogen bonds to form.

Puzzle 4-1 was called "Hide the Hydrophobic"

Orange sidechains were hydrophobic and wanted to be buried inside the protein. If there was a yellow bubble around an orange sidechain, it signified that the sidecain was being exposed, and was not hidden in the middle of the protein. Blue sidechains needed space, and had to point outwards. Solving this puzzle was very simple. I just clicked and dragged the orange section to the middle (no pressing shift!) and then I clicked and dragged the blue sidechain so that it pointed outwards. I was able to finish this puzzle in two simple steps, with no wiggling, rebuilding, or rubber banding involved!

Basic Fold It Tips: If you are having trouble with the folding the first time you try, walk away from the computer. The first time I did this I wanted to chuck my computer against a wall. I suggest you don't do this unless it's your sibling's computer. Also, you can always undo a step or go back to the original settings. This helps a lot when you are first starting out. I found myself making a huge mess with the proteins, and undoing was the only way to get myself out of it. So, with that, have fun with your protein folding!