BCMB20002 question - hydrogen bonding!!

[ChickenCh0wM1en]

Hey all you smarties out there!

I had a few questions regarding hydrogen bonds, VDW and hydrophobic effect in proteins. If anyone could help I would greatly appreciate it!

1) With regards to hydrogen bonding in the proteins lets say...in both alpha helices and b-sheets, I understand that hydrogen bonds occur within the mainchain between the C=O and NH group but 4 residues down, but do hydrogen bonds occur between the side chains of the amino acids? Do these contribute to the a-helical structure/b-structure?

2) With the VDW radii, these interactions mostly occur between hydrophobic residues which are buried deep in the folded protein right? --> tightly packed/no space in the protein

3) Are most hydrophobic residues orientated inwards from the watery environment AKA buried in the protein while the hydrophilic residues are generally orientated outwards? obviously there are exceptions right?

Sorry for so many silly questions!

Thanks!!!

[scribble]

1.side chains can be involved in hydrogen bonding (given theyre the right side chains), however they do not contribute to the secondary structure. their interactions can influence the tertiary/quaternary structure, as well as be involved in protein ligand binding.

2. i havent watched todays lecture yet, so parhaps im missing something, but im pretty sure everything has a van der walls radius. its just to describe the "size" of an atom.

3. yes. and yes. usually they will be packed away inside of proteins, where they dont interact with the solvent and hydrophilic residues are orientated outwards because that is energetically favourable. however exceptions do exist; oftentimes due to functional purposes.

[rery]

Hey all you smarties out there!
2) With the VDW radii, these interactions mostly occur between hydrophobic residues which are buried deep in the folded protein right? --> tightly packed/no space in the protein

Yes, residues within the core of the protein will usual have proximities nearer to their VDW radii than those on the outside, with some structures that feature strong hydrogen bonds being even closer. I think this is all just an illustration of the relative compactness of a typical protein.