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(Exceptions)
(Add new image, rework content a bit. Learned there's a such a thing as a wikipedia link.)
 
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Hydrophobicity is one of the component considerations that goes into making up your score on a fold.
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[[File:Hydrophobicity.png|thumb|400px|Using default view options, <span style="color:blue;">hydrophilic</span> sidechains are blue, <span style="color:orange;">hydrophobic</span> sidechains are orange.]]
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[[Hydrophobicity]] is the tendency of [[Amino Acids|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|core]] of a protein.
   
== Intro ==
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"Hide the hydrophobics" is a major goal in Foldit. Getting hydrophobic amino acids [[Buried|buried]] in the core of the protein is a key to good score. Foldit can highlight [[Exposed|exposed]] hydrophobics, but it's not always possible to hide them all.
[[Image:Sidechains.jpg|left|thumb|230px|A protein fold showing hydrophobic and hydrophilic sidechains. The two hydrophobics appear near the top center of the picture; the others are hydrophilic.]][[Amino Acids|Amino acids]] are either <span style="color:orange;">hydrophobic</span>, or <span style="color:blue;">hydrophilic</span>. The [[Sidechain|sidechains]] of an amino acid will be orange or blue depending on whether they are hydrophobic or hydrophilic.
 
   
; Hydrowhat?
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In Foldit, amino acids are considered either [[Hydrophobic|hydrophobic]], wanting to hide from water, or [[Hydrophilic|hydrophilic]], the opposite. Using default [[View Options|view options]], the [[Sidechain|sidechains]] of hydrophobic amino acids are orange, and the sidechains of hydrophilic amino acids are blue.
* ''hydro'' means "water"
 
* ''phobic'' means "that fears"
 
* ''philic'' means "that loves"
 
   
So, ''hydrophobic'' fears water, while ''hydrophilic'' loves water.
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Amino acids actually vary in hydrophobicity, and there's a [[Hydropathy index|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.
   
; Ok that's great for them, but how can that help me?
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== Exceptions ==
The proteins in all cells are immersed in water. So:
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Foldit assumes that proteins are in a [[Solvent|solvent]] which consists mainly of water. Proteins may start out in water, but they don't necessarily stay there.
* all the "water fearing" amino-acids will tend to be inside the protein (where they can't touch the surrounding water)
 
* all the "water loving" amino acids will tend to be outside the protein (where they can be in contact with the water)
 
   
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Many proteins become part of the cell membrane. The cell membrane is made of lipids, which have the opposite effect of water:
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* hydrophilic or "water loving" amino acids fear lipids
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* hydrophobic or "water fearing" amino acids will love lipids
   
When folding, you should then try to get as much <span style="color:orange;">hydrophobic</span> inside, and as much <span style="color:blue;">hydrophilic</span> outside. Exceptions, however, will almost always exist. While hydrophobic hiding is a good [[strategy]] to follow, it is almost never possible to put every single hydrophobic amino acid on the inside of a fold. Often, in fact, the biological function of the protein requires some hydrophobic amino acids on the outside.
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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, [http://fold.it/portal/node/2003490 Puzzle 1347], "De-novo Freestyle 101", had modified scoring. The same protein had been featured in [http://fold.it/portal/node/2003465 Puzzle 1344], which made it clear that it would be impossible to "hide the hydrophobics" in the usual sense.
   
== Exceptions ==
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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).
Proteins are not all in water. A lot of them are actually implanted in the cell membrane. The cell membrane is made of lipids, that has the opposite effect of water:
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* the "water loving" amino acids will fear lipids
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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 [[Symmetry puzzle|symmertry puzzles]] work with oligomers, which typically have two to six copies of a single protein.
* the "water fearing" amino acids will love lipids
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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.
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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.
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==Greek roots==
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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:
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* ''hydro'' means "water"
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* ''phobic'' means "fearing"
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* ''philic'' means "loving"
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So, ''hydrophobic'' fears water, while ''hydrophilic'' loves water.
   
Some parts of the proteins can actually be inside the membrane, and some other parts outside, for real.
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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".
   
 
== See also ==
 
== See also ==
 
* [[wikipedia:hydrophobicity|hydrophobicity]] in Wikipedia
 
* [[wikipedia:hydrophobicity|hydrophobicity]] in Wikipedia
 
[[Category:Protein Structure]]
 
[[Category:Protein Structure]]
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[[Category:Glossary]]
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[[Category:Biochemistry]]

Latest revision as of 03:23, April 4, 2017

Hydrophobicity

Using default view options, hydrophilic sidechains are blue, hydrophobic sidechains are orange.

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.

Exceptions Edit

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.

Greek rootsEdit

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".

See also Edit

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