Protein ModelingitsDerk wrote: ↑Tue Jan 21, 2020 6:34 pmThis is what I've seen thru the available literature as well. It's just interesting that even the original 5td5 pdb file didn't match up with BE4 in the first version of the rules. Thanks for the feedback everyone. Hopefully there will be some rule clarification or response soon, but for MIT I guess we're just gonna have to run with it.svph300 wrote: ↑Tue Jan 21, 2020 11:47 amFrom my interpretation, the competitors are expected to create a theoretical model of APOBEC3A (which is the prebuild for this year and also different from APOBEC-1) within the larger fusion protein of the BE4 expression plasmid. I think that competitors need to build a schematic representation of APOBEC3A and how it could theoretically fit within the BE4 expression plasmid, since it's actually APOBEC-1 that interacts with the BE4 expression plasmid. Also, I've read research articles to make sure that there's no known relationship between APOBEC3A and BE4 expression plasmid and I haven't seen any relationships whatsoever between these two. In other words, you would have two models: a model of APOBEC3A (prebuild) and a theoretical model of BE4 expression plasmid (add-on; what competitors need to create). Also, don't forget to consider other regions of the fusion protein and their connections to each other as well (this is explicitly stated in the rules). I hope this interpretation made sense.huppada wrote: ↑Tue Jan 21, 2020 4:02 am
In that case, (for those who are going) is everyone sticking to the BE4 plasmid for the MIT Invitational this weekend?
Also, I’ve submitted requests for rules clarifications, asking whether BE4 is the correct plasmid we’re supposed to model and if we’re supposed to model the expression plasmid separately to the cytidine deaminase protein.
I agree that there seems to be a disconnect between MSOE and SOINC. As I mentioned, I haven't read any research papers discussing the relationship of APOBEC3A with the BE4 expression plasmid. From the addgene website and the papers I've read, it's APOBEC-1 that has a direct relationship with the BE4 expression plasmid. However, I have read papers about APOBEC3A and the BE3 plasmid, and I think it would make more sense for competitors to make a model of the BE3 instead of the BE4 expression plasmid.
TL;DR: Make a schematic representation of the relationship between APOBEC3A, BE4 expression plasmid, and other regions of the fusion protein in the correct linear order. Possible disconnect between MSOE and SOINC regarding the rules.
Good luck to all those going to MIT! It'll be a good one.
Rules Clarification (4.b.iii.3): The National level of competition requires that teams include "schematic representations of the other regions of the fusion protein and their connections to each other." We will score the event by awarding the same credit for all models, regardless of completeness, that have at least some representation of the other regions of the fusion protein. Models should provide enough evidence to substantiate that competitors know of and have depicted the other regions of the fusion protein, their connections to each other, and that these regions are depicted in the correct linear order.
^^^I found this on MIT's SciOly website. It seems like they will give credit as long as we make an attempt. Hope to see everyone at MIT this Saturday!
