G-protein coupled receptors (GPCRs) are the target of 50-60% of drugs, including many of those involved in the treatment of cancer and cardiovascular disease. Over 100 GPCR crystal structures are now available, but these are for only around 30 different receptors, and there are still hundreds more receptors for which no structure exists. There is huge diversity in the ligands which bind to GPCRs, so it may often be difficult to predict the shape of a binding pocket for a specific receptor of interest, especially if no close relatives have a structure solved.
Helix kinks (see previous blog posts) are a structural feature of GPCRs which are thought to be important for function. An ability to predict their presence and the magnitude of helix direction change is important for obtaining an accurate structure. A kink prediction method has already been used in the context of GPCR structure prediction, which scored the overall structures after replacing kink segments with others from a database. This made it possible to predict the change in a kink angle based on the stability of the whole GPCR structure.
To better inform this kind of modelling, we wanted to investigate specifically how much variation there is in kink angles between GPCRs. To do this we used the tool Kink Finder to measure angles in all of the transmembrane helices of the GPCRs in the GPCRDB, and estimate a confidence interval on those angles. Then we could state whether the variation that we see in GPCR kink angles is greater than what we would expect from measurement error alone.
Each helix appears to show different behaviour. Some helices were very well conserved, but others showed a huge amount of variation. For these helices with very variable angles, it would be interesting to know if this is a change related to sequence differences, or conformational flexibility between more than one preferred conformation. We found an example where significantly different angles were found even in the same receptor. In this case, the kink angle size is related to whether the structure has an agonist or an antagonist bound, so we propose that this is a functionally relevant and flexible kink.
We also carried out the same analysis on helices from other families of membrane and soluble proteins, and found many more highly variable kinks (one example shown below). This shows that they should be a very important consideration when carrying out homology modelling, and that their conformational flexibility could also be important for function in many other contexts.