Location of hydrophobic and hydrophilic AA side chains

[sanguinee]

I'm a little confused on the location of hydrophobic and hydrophilic amino acids in different protein structures and was hoping someone could clear this up for me:

In the secondary structure: hydrophilic AAs are pointing outside while hydrophobic are inside the chain, but does this change in tertiary/quaternary structures?

**question bank SPOILER ALERT **
A section from the question bank asks which AA are present at dimerization interface of proteins -- I assumed that hydrophilic AAs are still the ones that are outward and the outward hydrophilic AAs of the different proteins are engaged in protein-protein interaction, but apparently it is hydrophobic that are "free and most likely to participate in dimerization of" the protein. Could someone explain?

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[aldol16]

In the secondary structure: hydrophilic AAs are pointing outside while hydrophobic are inside the chain, but does this change in tertiary/quaternary structures?

I don't think you understand secondary structure. In secondary structure, the side chains are always on the outside. The inside of the chain cannot accommodate the relatively large side chains. So they all point outwards in an alpha helix. If you have hydrophobic residues, they're going to want to stick together with similar hydrophobic residues on other proteins or with lipid tails. So for instance, if you have a transmembrane helix that's part of a channel, the part of the helix facing the inside of the channel will be polar/hydrophilic while the part of the helix facing the membrane will be hydrophobic.

For beta sheet structures, the side chains alternate up and down on a strand. So every other protein will tend to have the same properties. And again, those properties will depend on what the beta structure is trying to interact with. If you have a beta barrel forming a transmembrane channel, the residues on the inside of that channel will be hydrophilic while the residues on the outside will be hydrophobic. So you would expect your beta sheet structures to alternate between hydrophilic and hydrophobic residues every other residue.

A section from the question bank asks which AA are present at dimerization interface of proteins -- I assumed that hydrophilic AAs are still the ones that are outward and the outward hydrophilic AAs of the different proteins are engaged in protein-protein interaction, but apparently it is hydrophobic that are "free and most likely to participate in dimerization of" the protein. Could someone explain?

At a dimerization interface, the residues must be buried. Otherwise, they'll want to interact with water and other polar solutes and so will break apart from one another easily - not something you want if you're trying to form a dimer. So in order to make a "sticky" contact region, the interface residues will be nonpolar, which will stick to each other and thus be buried in the tertiary structure.

 

[NextStepTutor_2]

I'm a little confused on the location of hydrophobic and hydrophilic amino acids in different protein structures and was hoping someone could clear this up for me:

In the secondary structure: hydrophilic AAs are pointing outside while hydrophobic are inside the chain, but does this change in tertiary/quaternary structures?

**question bank SPOILER ALERT **
A section from the question bank asks which AA are present at dimerization interface of proteins -- I assumed that hydrophilic AAs are still the ones that are outward and the outward hydrophilic AAs of the different proteins are engaged in protein-protein interaction, but apparently it is hydrophobic that are "free and most likely to participate in dimerization of" the protein. Could someone explain?

Hi @sanguine ! Protein dimers represent an aspect of the quaternary structure of a protein. They are found all over the body (antibodies, disulfide bridges, G-proteins, clotting factors....). Most of the time, we want these structures to interact with each other and form the dimer, not to be "distracted" by the aqueous environs of the cell. A hydrophobic set of residues would fit this bill quite nicely.

Hope this helps, good luck!