Talk:Fatty acid amide hydrolase

From Proteopedia

Ideas for improvement

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

1. My favorite figure: Figure “entry channel.” The figure is based on the coordinates 2vya and the script is /wiki/scripts/57/573125/2vya/16.spt. The primary citation [1] is from 2008, and available at https://www.rcsb.org/structure/2vya.
2. This is my suggestion for a figure legend: Fatty Acid Amide Hydrolase (2vya) has an amphipathic entry channel that allows lipid signaling molecules to move from the lipid bilayer to the enzymes active site. The amino acid residues in green are hydrophobic, which allow lipid signaling molecules with nonpolar tails to enter the channel. The amino acids on residues R486 and D403 are in black and allow polar head groups to enter the channel.
3. What I like about the figure: I like this figure because it displays the entry channel and clearly displays the differences between the residues that are hydrophobic versus those that are hydrophilic. I also like that the entry channel is amphipathic, due to it consisting of both hydrophobic and hydrophilic parts. I though that was interesting.
4. Corresponding figure in the primary citation: Figure 4b. In the figure, the opening of the MA channel in the structure is shown making it easy to see the channel. Although this channel is not the entry channel that is my favorite figure this figure is better at showing the channel itself as well as the depth in the channel. The figure on Proteopedia lacks diversity as it only display’s a basic scene of the channel.
5. How I think the figure could be improved: I believe that this is the best way to portray this entry channel. Instead of working on this figure itself I would maybe add in another figure, or maybe locate this channel on another figure. It was difficult for me to find this channel on any other figure that is presented. I was able to locate the amino acids R486 and D403 that I measured to be 0.77nm away from each other. So maybe including that on the structure itself so it is understood how far the residues are from one another.

References

Mileni M, Johnson DS, Wang Z, Everdeen DS, Liimatta M, Pabst B, Bhattacharya K, Nugent RA, Kamtekar S, Cravatt BF, Ahn K, Stevens RC. Structure-Guided Inhibitor Design for Human Faah by Interspecies Active Site Conversion. US National Library of Medicine National Institutes of Healthy 2008 Sep; 105(35): 12820-4. PMID:18753625 doi: http://dx.doi.org/10.1073/pnas.0806121105

--Karsten Theis 03:33, 17 December 2018 (UTC)