Talk:Hormone sensitive lipase
From Proteopedia
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== Ideas for improvement == | == Ideas for improvement == | ||
This was written as part of an assignment for a Biochemistry course at Westifeld State University. | This was written as part of an assignment for a Biochemistry course at Westifeld State University. | ||
| - | # '''From which figure did you learn the most?''' 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 <ref>PMID:19089974</ref> is from 2008, and available at https://onlinelibrary.wiley.com/doi/full/10.1002/prot.22313. | + | # '''From which figure did you learn the most?''' 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 <ref>PMID:19089974</ref> is from 2008, and available at https://onlinelibrary.wiley.com/doi/full/10.1002/prot.22313. Also available is a review paper<ref>PMID:28337436</ref> on the regulation of this and related enzymes through a lid at the opening of the substrate channel. |
# '''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. | # '''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. | ||
# '''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. | # '''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. | ||
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'''Figure legend for the current figure:''' Hormone-sensitive lipase (3dnm) has a deep ligand pocket. Surface representation of a monomer in lime green, with the ligand pocket facing the viewer in the initial orientation. | '''Figure legend for the current figure:''' Hormone-sensitive lipase (3dnm) has a deep ligand pocket. Surface representation of a monomer in lime green, with the ligand pocket facing the viewer in the initial orientation. | ||
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| - | As an aside, here is a paper discussing the lid regulating enzyme activity in this protein and in many related lipases: PMID:28337436 | ||
<references /> | <references /> | ||
Revision as of 14:18, 25 November 2018
Ideas for improvement
This was written as part of an assignment for a Biochemistry course at Westifeld State University.
- From which figure did you learn the most? 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.
- 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.
- 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.
- What 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, it would be a good idea to have a figure legend explaining the color scheme.
Figure legend for the current figure: Hormone-sensitive lipase (3dnm) has a deep ligand pocket. Surface representation of a monomer in lime green, with the ligand pocket facing the viewer in the initial orientation.
- ↑ 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
- ↑ 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
