Prerequisites

UCSF Chimera https://www.cgl.ucsf.edu/chimera/download.html or ChimeraX https://www.cgl.ucsf.edu/chimerax/download.html.

Paper

Elucidating the active δ-opioid receptor crystal structure with peptide and small-molecule agonists

Task

Delta-opioid recepor is a GPCR protein, the signalling cascade is triggered by ligand binding, followed by conformational changes in the receptor, it's activation and biological response.

The authors studied the conformational changes in the binding site (BS) upon activation and revealed which of them play the essential role.

What we want to visualize:

1. Superposition of active and inactive states of receptor, showing the location of the BS and membrane borders.
2. Close view of the BS, displaying the residues that undergo the most drastic conformational changes upon activation and ligands superposition (agonist and antagonist).
3. Difference in ligand binding - change in the electrostatic environment and distance from specific ligand atom and key residue.

What you learn

1. Selection, editing
2. Representations, styling
3. Structural alignment
4. Surfaces
5. Binding site

Tutorial

ChimeraX (video)