Gpcr Computational Chemistry Prac

EXPERIMENT 2. Analysis of a 7-transmembrane G-protein coupled receptor protein structure

Aim: To gain an understanding of GPCR protein structure and the amino acids involved in binding (ant)agonists using the β2-adrenergic receptor as an example.

Pre-lab question: An inverse agonist is an agent that occupies to the same receptor-site as an agonist for that receptor however; the resulting pharmacological outcome is the opposite of what it would be if the agonist was bound. So for an inverse agonist this would mean a decreasing the activity of the receptor.

The structure of carazolol is shown below:

Questions:

• Diagram of GPCR from the view of looking across the membrane with helix 1 on your right:

• Diagram of GPCR from the view of looking down on top (from outside the cell uppermost):

• Q. What interactions (i.e. within 5Е) does this cholesterol molecule make with the protein and adjacent substructures?

The cholesterol molecule makes significant interactions with the following residues; cholesterol (CLR412), ALA59, ILE55, THR73, CYS77, LEU80, VAL81, LEU84, ALA85, ILE112.

• Q. What (primarily) is the nature of these interactions?

All of the above listed residues are hydrophobic molecules with aliphatic side-chains (except THR and CYS which both make H-bonds with the cholesterol molecule).

• Q. How does this observation relate to the position of the cell membrane relative to this section of the protein?

The lipophilic side chains illustrate that they are like-like interactions present, between the lipophilic residues and the lipophilic cell membrane.

• Q. Which helix does this aspartate belong to?

The ASP113 residue belongs to helix number 3 (residue 32).

• Q. What is the role of these serine residues with regard to binding of the natural neurotransmitter for this receptor?

The serine residues (especially 203), naturally form H-bonds between their oxygen’s and the hydrogen’s from the catechol group of noradrenaline (as shown below).

The serine residues

interact with this catechol

group.

• Q. What other interactions does carazolol make with the receptor? For this question merely list the amino acid residues involved.

Tyrosine 119, Serine 203, Serine 207, Valine 114, Valine 117, Tryptophan 286, Aspartate 113, Tyrosine 316, Asparagine 312, Tryptophan 109, Phenylalanine 289, Phenylalanine 193.

Here (left) we can see carazolol and it’s interactions with the neighbouring residues.

• Diagram(s) illustrating some of the key interactions between carazolol and the protein binding site:

This image represents carazolol sitting in the receptor site, as the receptor site (and the molecule) is obviously 3D this image only represents one side view, the image below this one shows the other side view.