Talk:Glucagon receptor

From Proteopedia

Ideas for improvement

This "figure-review" was written by Jacqueline E. Amel as part of an assignment for a Biochemistry course at Westfield State University, and posted by the instructor with permission.

1. My favorite figure: My favorite figure is the one called “Binding Pocket.” The figure is based on the coordinates 4L6R and the script is available from www.proteopedia.org/wiki/scripts/72/721538/Binding_pocket/1.spt. The primary citation is from 2013 and available at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820480/. Another article (Wang & Xiao, 2014) is available that summarizes the pathophysiology roles of these receptors in metabolic diseases and energy homeostasis.
2. This is my suggestion for a figure legend: The class B Glucagon G protein-coupled receptor has the longest and widest binding pocket of all classes of Glucagon G protein-coupled receptors. The space between alpha helices 3 and 7 is 37.4 Å across and the space between alpha helices 2 and 6 is 32.63 Å across. The glucagon molecule binds deep inside the receptor and binds close to the cell membrane.
3. What I like about the figure: I like how the figure has labels corresponding to the alpha helices are a part of the binding pocket. I also like how the alpha helices 3 and 7 are colored the same color and alpha helices 2 and 6 are colored a different color than the other two helices but are both the same color. I like how the put the dimensions for the binding pocket on the figure. I like how you can move the figure around, so you can explore the protein and see the binding pocket from a different angle. I like how as you move the figure, you can still see the dimensions and the alpha helix labels. I also like how they show the shape of the binding pocket in a separate picture within the text (Figure 3), and the binding pocket itself can easily be seen in the side figure.
4. Corresponding figure in the primary citation: The corresponding figure in the primary citation is Figure 5, which is called “Model of GCGR bound to glucagon.” In the figure the protein is shown bound to the glucagon molecule, in which you can see the way it binds to the receptor protein. The protein’s extracellular domain is shown in magenta and the 7TM domain is shown in blue. Glucagon is shown in green. Shown in brown are residues 122-126 and 199-218, which are not defined in the extracellular domain and 7TM domain. Also highlighted in the figure is the GCGR-linker, which highlights where the glucagon binds to the receptor protein.
5. How I think the figure could be improved: I think it would be better if the other helices not involved in the binding pocket were a different color. I think it would be better if the helices 2 and 6 were a brighter color. I think it would be best to have the helices not involved in the binding pocket to be a much lighter color than the helices that are involved in the binding pocket. I would be interesting to see how the glucagon molecule binds in the binding pocket in 3D as shown in the primary article. I also think it would be beneficial to have similar but interactive figure as Figure 3 from the text. I think it would be interesting to see the binding pocket easier that way in 3D.

References

Siu, F.Y., He, M., de Graaf, C., Han, G.W., Yang, D., Zhang, Z., Zhou, C., Xu., Q., Wacker, D., Joseph, J.S., Liu, W., Lau, J., Cherezov, V., Katritch, V., Wang, M.W., and Stevens, R.C. 2013. Structure of the class B human glucagon G protein coupled receptor. Nature, 499(7459), 444-449.

Wang, J & Xiao, R. 2014. G protein receptors in energy homeostasis. Science China. Life Science, 57(7), 672-680.

--Karsten Theis 19:26, 16 December 2018 (UTC)