Protein Modeling C

[svph300]

Since we don't have to put functionally relevant features for regionals, what should we put on the notecard?

On the rules, it specifically says that the functionally relevant features will be explained in the notecard. Therefore, I believe the notecard will not be required in the regional level, and you do not have to put anything on it.

However, I still encourage having the notecard and functionally relevant features to be prepared for invitationals and the state competition. You may also put a quick blurb about the secondary structures on the notecard, if you really wish. For instance, you can state that the purple region are "alpha helices." Hope I helped!

[svph300]

Could anyone explain what is expected for the nationals specific addition to the prebuild? My partners and I were confused as to what is actually meant by a "schematic representation" as it says in the rules for the fusion protein model.

The rules state that the scoring will focus on "how the structure modeled fits within the larger fusion of the BE4 expression plasmid" and that "teams are expected to include schematic representations of the other regions of the protein and their connections to each other."

From my interpretation, you and your teammates need to decide the regions on the fusion protein of the BE4 expression plasmid that are relevant. After making that decision, you would then create a model of that region of the fusion protein only, which is the "schematic representation". Take note that your additions "must be arranged in the correct linear order." The grading and scoring would then focus on how your pre-build model (cytidine deaminase; 85% of the pre-built model score) fits within the larger fusion protein (schematic representation; 15% of the pre-built model score).

Feel free to correct me or offer more advice on this topic for anyone on this forum!

[eagerlearner102]

How do you guys study for CRISPR aside from the cbm msoe website and the research papers? I tried one of the invitational tests at home but I had no idea what was going on. CRISPR is a pretty new topic so i wouldn't find it in the textbook.

[AlfWeg]

How do you guys study for CRISPR aside from the cbm msoe website and the research papers? I tried one of the invitational tests at home but I had no idea what was going on. CRISPR is a pretty new topic so i wouldn't find it in the textbook.

I would read last year's papers, and do last year's tests. Try the Molecule of the Month article as well.

From my interpretation, you and your teammates need to decide the regions on the fusion protein of the BE4 expression plasmid that are relevant. After making that decision, you would then create a model of that region of the fusion protein only, which is the "schematic representation".

Yikes, this sounds really hard. Not complaining, but looks like a lot of time reading the papers over and over again.

[yummymangosdigested]

I have a question concerning the discrepancy in the protein prebuild model. Is it supposed to be one centimeter for the amino acid at the beginning of the model and one centimeter for amino acid at the end of the mode and two centimeters per amino acid for the rest of the model?

[Tailsfan101]

I have a question concerning the discrepancy in the protein prebuild model. Is it supposed to be one centimeter for the amino acid at the beginning of the model and one centimeter for amino acid at the end of the mode and two centimeters per amino acid for the rest of the model?

You are interpreting it right; that is correct.

[voisinet22]

Dose anyone know why the MSOE site prebuild visualzation dosen't show the beta bridges and do we have to show them on our models since theyre not shown?

[svph300]

Dose anyone know why the MSOE site prebuild visualzation dosen't show the beta bridges and do we have to show them on our models since theyre not shown?

Not sure why the MSOE site does not show the beta bridges because I'm only familiar with Jmol for modeling the protein. I believe you only need to show the protein backbone (alpha helices and beta sheets, possibly 310 helix) for the regional level, creative additions for the state level, and the BE4 expression plasmid model for the national level. Like I mentioned earlier, I used Jmol to build the protein backbone when I competed last year. The secondary structures (e.g. alpha helices, beta sheets, beta bridges) should be apparent if the protein backbone is bent correctly (considering angle, distances between residues, etc.) I recommend checking your model with the Jmol representation since it's accurate.

[voisinet22]

Since we don't have to put functionally relevant features for regionals, what should we put on the notecard?

On the rules, it specifically says that the functionally relevant features will be explained in the notecard. Therefore, I believe the notecard will not be required in the regional level, and you do not have to put anything on it.

However, I still encourage having the notecard and functionally relevant features to be prepared for invitationals and the state competition. You may also put a quick blurb about the secondary structures on the notecard, if you really wish. For instance, you can state that the purple region are "alpha helices." Hope I helped!

The rules say "For Regional competitions, scoring will be based primarily on the accuracy of the 3D folded structure of the alpha-carbon backbone of the protein"
I think we still need to include the functionally relevant features, but they aren't as large for points during scoring on the regional level.

[itsDerk]

Hey so for people prepping the Nats build for invitationals like MIT, was wondering what you guys were thinking/doing about BE4 seeing as it seems to include APOBEC1 rather than APOBEC3A (5keg) in it's sequence.