Hydrophobicity is the tendency of amino acids to avoid water. Hydrophobicity is thought to be important in how proteins fold up naturally. Amino acids can hide from water by moving into the core of a protein.
"Hide the hydrophobics" is a major goal in Foldit. Getting hydrophobic amino acids buried in the core of the protein is a key to good score. Foldit can highlight exposed hydrophobics, but it's not always possible to hide them all.
In Foldit, amino acids are considered either hydrophobic, wanting to hide from water, or hydrophilic, the opposite. Using default view options, the sidechains of hydrophobic amino acids are orange, and the sidechains of hydrophilic amino acids are blue.
Amino acids actually vary in hydrophobicity, and there's a hydropathy index, which gives each amino acid a number. The Amino Acids page has a table that gives the hydropathy index along with other information about each amino acid.
Foldit assumes that proteins are in a solvent which consists mainly of water. Proteins may start out in water, but they don't necessarily stay there.
Many proteins become part of the cell membrane. The cell membrane is made of lipids, which have the opposite effect of water:
- hydrophilic or "water loving" amino acids fear lipids
- hydrophobic or "water fearing" amino acids will love lipids
So, membrane proteins tend to have more exposed hydrophobics than others. In general, a membrane protein would have a worse score in Foldit than an intracellular protein of a similar size. Foldit puzzles sometimes include a special adjustment to scoring to compensate. For example, Puzzle 1347, "De-novo Freestyle 101", had modified scoring. The same protein had been featured in Puzzle 1344, which made it clear that it would be impossible to "hide the hydrophobics" in the usual sense.
There are also other exceptions. Some proteins are extracellular, especially the keratins found in skin, hair, fingernails, beaks, claws, and hooves. They tend to form polymers, long chains of the same protein (or closely related proteins).
Other proteins form oligomers, which is when a limited number of copies of the same protein bond to each other to form a stable unit. Foldit symmertry puzzles work with oligomers, which typically have two to six copies of a single protein.
Both protein polymers and oligomers may have slightly more exposed hydrophobics than other proteins, at least as a single protein "monomer". The exposed hydrophobics in the monomer may get buried when the monomer joins a polymer or an oligomer.
In general, there's a always a chance that a protein's function is to stick to another protein. An exposed hydrophobic may be part of the "interface" that lets two proteins stick together.
As usual, there's an easier way to say these things, but scientists like to use words based on ancient Greek. The word parts here are:
- hydro means "water"
- phobic means "fearing"
- philic means "loving"
So, hydrophobic fears water, while hydrophilic loves water.
The word "hydropathy" originally meant "water-cure", a kind of (pseudo-) medical treatment involving the external and internal application of water. It's not clear that the authors of the paper on the hydropathy index were aware of this 19th-century use of "hydropathy".
- hydrophobicity in Wikipedia