The tubes represent "electron density", the area where the electrons holding the atoms together are most likely to be. Only the "heavy" non-hydrogen atoms are shown by default. In the standard "cartoon" view, sidechains appear to be made of thin tubes. You should hide sidechains using "Don't Show (Fast)" to speed up tools like shake and wiggle, or when running a recipe. For looking at sidechains, the "View Sidechains" option "Show All (Slow)" is best. The Foldit view options control when sidechains appear and what they look like. Tryptophan, the amino acid with the largest sidechain, shown in EnzDes coloring Many Foldit tools work on bases in the same way they do on sidechains. The base portion of a DNA or RNA nucleotide is similar to the sidechain of an amino acid. The Foldit Lua function rotamer.SetRotamer can be used in a recipe to set a specific rotamer position.įoldit puzzles may also contain DNA and RNA, which are chains of nucleotides usually referred to as bases. The "wiggle sidechains" option of the wiggle tool can make further small adjustments to sidechain position.
The shake moves one or more sidechains to what seems to be a better rotamer position. Sidechains have different positions called rotamers. Sidechains help determine what other chemicals a protein interacts with (including other proteins), which is key to the function of the protein. The sidechains in a protein can bond with each other, helping to stabilize the protein. The sidechain is what makes each amino acid different.
The Amino Acid Gallery shows all the different sidechains seen in Foldit. It's important for hydrophobic sidechains to be buried in the core of the protein. Using its default color options, Foldit shows hydrophobic sidechains in orange and hydrophilic sidechains in blue. Sidechains can be either hydrophobic or hydrophilic.
Other tools can also cause sidechains to move to different positions. Shake and wiggle can also help move sidechains to their best position. In Foldit, you can click and drag on a sidechain to move it to another position. Some sidechains have only one position, but others can be "flipped" to multiple positions. Sidechains are the shapes that stick out from the backbone of a protein.
0 kommentar(er)
