Talk:Hormone sensitive lipase

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Ideas for improvement

This was written as part of an assignment for a Biochemistry course at Westfield State University.

  1. My favorite figure: Figure "ligand pocket". The figure is based on the coordinates 3dnm and the script is http://proteopedia.org/wiki/scripts/58/580297/3dnm_cartoon_surface/4.spt. The primary citation [1] is from 2008, and available at https://onlinelibrary.wiley.com/doi/full/10.1002/prot.22313. Also available is a review paper[2] on the regulation of this and related enzymes through a lid at the opening of the substrate channel.
  2. This is my suggestion for a figure legend: Hormone-sensitive lipase (3dnm) has a deep ligand binding pocket. Surface representation of a monomer in lime green, with the ligand pocket facing the viewer in the initial orientation.
  3. What I like about the figure: It shows that there is a deep ligand pocket (different from other hydrolases with catalytic triads such as chymotrypsin).The surface representation gives a nice view of the ligand pocket.
  4. Corresponding figure in the primary citation: Figure 1d. In the figure, the protein is shown as a surface cut in half making it easy to see the extent of the pocket. Selected structural elements (active site serine, helices as the entrance of the ligand pocket) are shown. There is a scale bar showing a length of 16 Ångstrm, the approximate depth of the pocket.
  5. How I think the figure could be improved: It would be great to use color to show how hydrophobic or hydrophilic the pocket is. It would also be helpful to have a unique color for the active site serine at the bottom of the pocket. The primary citation has a figure showing the scale, making it easier to see that the pocket is about 16 Ångström deep. Showing a fatty acid at the same scale would be a nice illustration of the relevant dimensions. Once these elements are added, the figure legend would have to be updated to explain the color scheme.

References

  1. ↑ Nam KH, Kim MY, Kim SJ, Priyadarshi A, Kwon ST, Koo BS, Yoon SH, Hwang KY. Structural and functional analysis of a novel hormone-sensitive lipase from a metagenome library. Proteins. 2009 Mar;74(4):1036-40. PMID:19089974 doi:http://dx.doi.org/10.1002/prot.22313
  2. ↑ Khan FI, Lan D, Durrani R, Huan W, Zhao Z, Wang Y. The Lid Domain in Lipases: Structural and Functional Determinant of Enzymatic Properties. Front Bioeng Biotechnol. 2017 Mar 9;5:16. doi: 10.3389/fbioe.2017.00016., eCollection 2017. PMID:28337436 doi:http://dx.doi.org/10.3389/fbioe.2017.00016

Karsten Theis 14:22, 25 November 2018 (UTC)

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Karsten Theis

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