Talk:Hox protein

From Proteopedia

Ideas for improvement

This "figure-review" was written by Courtney Capitan 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 3: 3D-Representation of Exd-Scr-DNA ternary complex with Scr specific site”. This figure is based on the coordinates 2R5Z, and script: http://proteopedia.org/wiki/index.php/Hox_protein/wiki/scripts/Sandbox_Reserved_169/Scr_mg/8.spt . The page is featured in a publication from 2012, appearing in the Journal of Biochemistry and Molecular Biology Education, available at https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20650.
2. This is my suggestion for a figure legend: Hox Protein SCR forms a heterodimer with it’s cofactor EXT around DNA. SCR is shown in yellow, and it’s cofactor EXT shown in blue, both surrounding the orange DNA molecule.
3. What I like about the figure: This is the best representation of this figure because it shows the HOX protein of interest SCR, it’s cofactor EXT, and the DNA all together. This is the best representation because it gives context to the spatial and structural relationships which give rise to the function of the HOX protein complex.
4. Corresponding figure in the primary citation: In the BAMBED paper, Figure 1 shows the 3D crystalline structure of SCR and EXT surrounding and binding to DNA. This figure shows a clear overall picture representation of the biological view of the complex. There are no scale bars, but the inclusion of DNA in the representation provides ample context.
5. How I think the figure could be improved: One small change that would be helpful is the ability to exclude any of the molecules shown. It may be of benefit to explore the HOX Protein complex without the DNA in the viewers way at some angles. It would also be helpful for further understanding of the molecular relationships if there was an option to show the hydrophobic bonds with a transparent glow in one color and the hydrogen bonds in a glow of another color. This feature may help distinguish the specificity that is at work within the HOX complex and DNA binding, while simultaneously differentiating further between SCR, EXT, and the major and minor grooves overall. These added details would allow the figure to fully demonstrate the capabilities of the HOX protein. Otherwise, there is little improvement that could be done to this figure, it is very well done overall.

--Karsten Theis 20:19, 20 December 2018 (UTC)