These days I'm having fun with proteins on ChimeraX, mainly by creating videos and nice pictures. This is one of the first results that is worth publishing.

I'm following the tutorials available on the program site, and I found one focused on making movies. After some hours of playing with a couple of structures, I created this short movie animation, and I thought it would be a good idea to learn a little about the protein itself.

The animation show two different structures of a periplasmic glucose/galactose receptor isolated in Salmonella typhimurium. You can see the secondary structures of the protein, and how they "move" from the unbound conformation to the final ligand-bound structure.

The program took the two different structures and compute the animation by selecting the common residues and making them move around a central point. The surface as well is represented and helps us in seeing how the bound conformation creates an internal pocket that hosts the ligand.


This receptor is thought to be involved in the process of chemotaxis (movement of the organism in response to a chemical stimulus), and the active transport of sugars. In receptors, the presence of ligands often causes conformational changes in the proteins through allosteric interaction, similar to some enzyme mechanisms. After the conformational change, the "information" of the presence of ligand, is transferred across the cell by a series of cascade chemical reactions.

The structures come from different experiments:

  • free structure (PDB:2FW0): coming from E. coli, resolved by high-resolution X-ray diffraction 
  • bound structure (PDB: 3GBP): coming from S. typhimurium, resolved by X-ray diffraction at 2.4 Amstrong

Sequences alignment in protein BLAST, the query (reference sequence) is the unbound receptor, the subject is the sequence coming from S. typhimurium. We can see that both coverage and identity of the query sequence is higher than 94%.

The structures come from different organisms, but the level of similarities in the sequence and in the 3D structure makes them compatible for a cross-analysis like this one.

What researchers found is interesting: the observed change in conformation is due to the rotation of one domain of the protein in respect to the other one, in a hinge-fashion, causing a 31° rotation. Finally, it was found that the receptor is able to recognize only the Beta anomer of sugars, in contrast with other previous studies on similar receptors.