Talk:Hormone sensitive lipase
From Proteopedia
(Difference between revisions)
(→Ideas for improvement) |
|||
| Line 1: | Line 1: | ||
== 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". | + | # '''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 is from 2008, and available at https://onlinelibrary.wiley.com/doi/full/10.1002/prot.22313. |
| - | # ''' | + | # '''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. | # '''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. | ||
| - | As an aside, here is a paper discussing the lid | + | '''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. |
| + | |||
| + | As an aside, here is a paper discussing the lid regulating enzyme activity in this protein and in many related lipases: PMID:28337436 | ||
Revision as of 13:49, 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 is from 2008, and available at https://onlinelibrary.wiley.com/doi/full/10.1002/prot.22313.
- 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.
As an aside, here is a paper discussing the lid regulating enzyme activity in this protein and in many related lipases: PMID:28337436
