Hello,

 

I'm trying to do some biophysics - but I suck at it!

 

I have two beta-sheets and I'm trying to work out how they'll 'connect' together, i.e. which functional groups will associate. I know that hydrophobic ones (e.g. Ile) will cluster together. I also know that aromatic ones (i.e. Phe) might stack in pi-bonding.

 

But could anyone explain to me in simple terms which other amino acids would 'like' to be near each other? I'm not sure about the positive or negative charged ones, or the polar ones.

 

Thanks!!

Hydrogen bonding is a critical component to stable secondary protein structure, although this generally applies to the backbones interacting more so then the functional groups.

 

 

The above picture shows that pretty readily.

 

Polar, positive and negative residues will generally be interacting or not interacting with whatever the protein happens to be in (if in solution/water, they will interact with the water, if in a hydrophobic environment, they will interact with each other). Things like cysteine can often interact with other cysteine amino acids to form di-sulfide bonds.

 

Another factor is pH. This has a huge effect on the positive and negative residues, and controls what particular state they are in due to their weak acid/base nature. It can shift hydrogen bonding networks and how they interact with water and with each other.

 

I hope this helps.