The loop is one of three basic structures in FoldIt. It appears as a narrow cylindrical cord of arbitrary length, with kinks and sidedchains corresponding to the constituent amino acids. From a Foldit perspective, it is the most basic structure, representing any kind of structure that does not conform well enough to the helix or sheet forms. It is highly flexible, being easily reshaped by use of the various tools in Pull Mode. It is possible for loops to hydrogen bond with adjacent amino acids, but this will not be visible unless the area of interest is turned into sheets using Structure Mode.
Helices and sheets serve to stabilize the core of the protein. Loops are found on the outside of the protein and, not surprisingly, are rich in hydrophilic sidechains. Loops make hydrogen bonds with the surrounding water more than with adjacent amino acids, and thus are more flexible than helices and sheets.
The Purpose of Loops
Far from just being “connectors,” loops are often involved in the function of the protein, such as being part of the active site of an enzyme, or the binding site of a ligand or receptor. Their flexibility sometimes allows them to assume more than one local conformation, such as an “open” and “closed” position that either allows or blocks the protein’s function.
Since loops are found on the outside of proteins, their frequent role in protein function isn’t surprising, but it’s easy to ignore them and focus on helices and sheets as the star players. Loops are already water-facing and very flexible, so there are fewer points to be gained from manipulating them than there are for resolving sidechain clashes or getting hydrophobic regions hidden from water. Nevertheless, the conformation of the loops must be correct as well for maximum points. It’s doubtful that Foldit gives extra points for getting good loop conformations in spite of their often key roles. Still, we’re trying to advance science by predicting the most accurate structures possible, so do your loops.
Loop Classes
Loops can be loosely classified according to their shapes. For example, loop regions connecting two adjacent sheets (anti-parallel ones) are called Hairpin Loops. The shortest Hairpin Loops, just 2-5 amino acids long, are called reverse turns, or U-turns. Another common shape is the Omega loop. The beginning and end of the loop sequence will be close together, with middle part open; this is similar to the shape of the Greek letter omega.