GPCR structural components

Question 1

Common features in binding areas of a GPCR

Answer 1

Three extracellular loops with the N-terminal being of variable length and function

Seven (7) transmembrane α-helices embedded within the cell membrane

Three intracellular loops and a variable length C-terminus

Question 2

Variable functions of an N-terminus

Answer 2

1. Bind ligands
2. Mask binding pockets
3. introduce ligands to the binding pocket
4. act as a ligand

Question 3

Chemokine topographic receptor components

Answer 3

Sulphide bridge connects the N-terminus to ECL3 and and ECL1 to ECL2. These play an important in stabilizing the receptor inactive conformations

Question 4

Structure of chemokine classes

Answer 4

Defined by arrangrement of conserves cystine residues

Question 5

Chemokine receptor binding sequences

Answer 5

• Two step model whereby the ligand’s C-terminus anchors to the N-terminus of the receptor which is followed by the binding of the flexible N-terminus of the ligand to the ECL and TMD of the receptor.
• Aromatic residue on the GPCR N terminus allows binding, this motif also prevents the N-terminus from waving around
• Receptor dimerisation typically occurs prior to signalling , with numerous stoichometries
• N TERMINUS CONFERS THE ABILITY TO DISCRIMINATE AGAINST DIFFERENT LIGANDS

Question 6

Protease activated receptor activators

Answer 6

PAR1,3,4: thrombin

PAR2: trypsin

PAR1: MMPS

These enzymes are all zymogens, C termius lysine or arginine is cleaved resulting in increaed nucleophilicty.

Question 7

Activation of PAR

Answer 7

• Can be cleaved at different locations engerdering signal bias

Question 8

TM conformational changes

Answer 8

Confromation changes occur within TM 3, 5, 6, 7 and helix 8 which subsequently alter the conformation of i2 and i3 and the C terminal to enable G protein coupling

Question 9

Extracellular loops

Answer 9

Extremely variable and can sit over the ligand binding pocket or out of the way (can close when ligand is bound)

Question 10

Extracellular loop specific

Answer 10

Particularly important in regulating activity, mutations often confer constituitive activity.

In muscarinic receptors is a highly conserved cystine residue which confers a disulphide bond between ECL2 and TM 3

Question 11

Transmembrane helices general structural components

Answer 11

• each consists of 25-35 hydrophobic AA’s that confer stability in lipid environment
• Create orthosteric binding pocket
• Cytoplasmic surfaces are Important regulators of constraint

Question 12

Regulators of constraint

Answer 12

The NPXYY motif at the cytoplasmic curface of TM7 causes a distortion in the a-helical structure and the tyrosine faces into a pocket lined by TM2, TM3, TM6 and TM7. H2O solvate cage reinforces the helical deformation, stabilized the inactive state but also provides an entropic drive for activation

E/DRY motif on TM3 forms an ionic lock of H bond with glutamate residue on TM6, stabilizing the inactive conformer

If ionic lack is missing, DRY motif restrains the conformation of ICL2

Question 13

IC loops and tail + conformational change upon ligand binding

Answer 13

Directly bind to G-proteins and proviee sites for phosphorylation by intracellular kinases.

Outwarm movement of helix 5, thereby opening a crevice within the intracellular surface of the receptor (rhodspin)