Talk:Hormone sensitive lipase

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Revision as of 14:23, 25 November 2018 by Karsten Theis (Talk | contribs)
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Ideas for improvement

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

  1. Which figure did I like the best? 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 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 about the figure do you like? 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. Is there a corresponding figure in the primary citation? Yes, 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). There is a scale bar showing a length of 16 Angstroem, the approximate depth of the pocket.
  5. What I think could be improved? It would be great to use color to show how hydrophobic or hydrophylic 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 Angstroem 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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