We have purchased the 3 D molecular design’s 2015-2016 Science Olympiad Protein Modeling Event Kit (pre- build Kit). The site says it is for 168 amino acids but this year’s protein needs 169 and we found the mini-toobers are short by 2 centimeters. Has anyone else ordered the kit and had the same problem? If so, how did you add the two centimeters?
A team from our state noticed the same issue. You can glue on your red and blue caps so they are only attached to 1 cm of the toober. Assuming that the caps are 2 cm each this will add 2 cm total to your protein.
There is no problem with the kit. The scale is 2 cm per amino acid, which really means that there are 2 cm between each amino acid. If you go on Jmol and color one amino acid you will see that the color covers one bend and halfway to the bend on either side. So each amino acid is represented by the turn - not the connection. The backbone structure connects amino acids linearly, rather than creating smooth turns like in the cartoon visualization. So, getting back to the kit, you need 2 cm between each amino acid. Say the protein was from amino acids 5 to 9 (hypothetically), that would mean your structure would be as follows with the dashes representing the 2 cm of tuber you need.
5 - 6 - 7 - 8 - 9
That's four dashes, 4 * 2 = 8 cm of tuber. More simply, (9-5) * 2 = 8. In the case of this years protein, we have to build amino acids 93 - 261. So, (261- 93) * 2 = (168) * 2 = 336 cm of tuber, which is what the kit provides.
I know it's confusing because there are 169 amino acids but you have to understand that the first and last amino acids are at the ends of the tuber. And when you restrict the amino acids visualized in Jmol, the program will eliminate one cm of backbone connecting to amino acid 92 and one cm of backbone connecting to amino acid 264, which is why the kit provides 2 cm less tuber than you might expect.