Protein Modeling C

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Re: Protein Modeling C

Post by ericlepanda » January 19th, 2020, 9:09 am

itsDerk wrote:
January 18th, 2020, 8:25 pm
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.
is there a difference? structure might be the same/similar enough
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Re: Protein Modeling C

Post by exla23 » January 19th, 2020, 12:09 pm

ericlepanda wrote:
January 19th, 2020, 9:09 am
itsDerk wrote:
January 18th, 2020, 8:25 pm
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.
is there a difference? structure might be the same/similar enough
They’re very similar proteins but not quite the same, but it is confusing that they reference how the A3A model should “fit within” BE4. My team interpreted the rules as possibly meaning a separate model should be made for the BE4 plasmid.
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Re: Protein Modeling C

Post by eagerlearner102 » January 20th, 2020, 1:38 pm

How are you guys studying for the JMOL Exploration test? I couldn't find any paper tests online from invitationals or regionals for this portion of the exam.
Would I just practice typing in JMOL commands on proteins?
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Re: Protein Modeling C

Post by AlfWeg » January 20th, 2020, 4:44 pm

exla23 wrote:
January 19th, 2020, 12:09 pm
ericlepanda wrote:
January 19th, 2020, 9:09 am
itsDerk wrote:
January 18th, 2020, 8:25 pm
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.
is there a difference? structure might be the same/similar enough
They’re very similar proteins but not quite the same, but it is confusing that they reference how the A3A model should “fit within” BE4. My team interpreted the rules as possibly meaning a separate model should be made for the BE4 plasmid.
I'll throw in my two cence.....APOBEC1 and APOBEC3A have very different amino acid sequences. But 1r5t A(idk if that's the best representation of APOBEC1) and 5keg structure are.....somewhat close. imo, I dont think they want us to build a whole new model. I really hope this turns out to be another rule clarification, however irritating that is.
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Re: Protein Modeling C

Post by huppada » January 20th, 2020, 7:03 pm

AlfWeg wrote:
January 20th, 2020, 4:44 pm
exla23 wrote:
January 19th, 2020, 12:09 pm
ericlepanda wrote:
January 19th, 2020, 9:09 am


is there a difference? structure might be the same/similar enough
They’re very similar proteins but not quite the same, but it is confusing that they reference how the A3A model should “fit within” BE4. My team interpreted the rules as possibly meaning a separate model should be made for the BE4 plasmid.
I'll throw in my two cence.....APOBEC1 and APOBEC3A have very different amino acid sequences. But 1r5t A(idk if that's the best representation of APOBEC1) and 5keg structure are.....somewhat close. imo, I dont think they want us to build a whole new model. I really hope this turns out to be another rule clarification, however irritating that is.
I just thought of something:
The official SciOly rules are incorrect, right? They told us to model the cytidine deaminase protein from the 5td5 PDB file, while we are supposed to build the protein from the 5keg PDB file. Do you think they are also wrong in telling us to model the BE4 expression plasmid? Like, are they asking us to model the expression plasmid that correlates with the 5td5 PDB file instead of the 5keg PDB file?
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Re: Protein Modeling C

Post by ericlepanda » January 20th, 2020, 7:15 pm

huppada wrote:
January 20th, 2020, 7:03 pm
AlfWeg wrote:
January 20th, 2020, 4:44 pm
exla23 wrote:
January 19th, 2020, 12:09 pm


They’re very similar proteins but not quite the same, but it is confusing that they reference how the A3A model should “fit within” BE4. My team interpreted the rules as possibly meaning a separate model should be made for the BE4 plasmid.
I'll throw in my two cence.....APOBEC1 and APOBEC3A have very different amino acid sequences. But 1r5t A(idk if that's the best representation of APOBEC1) and 5keg structure are.....somewhat close. imo, I dont think they want us to build a whole new model. I really hope this turns out to be another rule clarification, however irritating that is.
I just thought of something:
The official SciOly rules are incorrect, right? They told us to model the cytidine deaminase protein from the 5td5 PDB file, while we are supposed to build the protein from the 5keg PDB file. Do you think they are also wrong in telling us to model the BE4 expression plasmid? Like, are they asking us to model the expression plasmid that correlates with the 5td5 PDB file instead of the 5keg PDB file?
very possible -- there seems to be a huge disconnect between MSOE and soinc. We should probably request rule clarifications
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Re: Protein Modeling C

Post by huppada » January 21st, 2020, 4:02 am

ericlepanda wrote:
January 20th, 2020, 7:15 pm
huppada wrote:
January 20th, 2020, 7:03 pm
AlfWeg wrote:
January 20th, 2020, 4:44 pm

I'll throw in my two cence.....APOBEC1 and APOBEC3A have very different amino acid sequences. But 1r5t A(idk if that's the best representation of APOBEC1) and 5keg structure are.....somewhat close. imo, I dont think they want us to build a whole new model. I really hope this turns out to be another rule clarification, however irritating that is.
I just thought of something:
The official SciOly rules are incorrect, right? They told us to model the cytidine deaminase protein from the 5td5 PDB file, while we are supposed to build the protein from the 5keg PDB file. Do you think they are also wrong in telling us to model the BE4 expression plasmid? Like, are they asking us to model the expression plasmid that correlates with the 5td5 PDB file instead of the 5keg PDB file?
very possible -- there seems to be a huge disconnect between MSOE and soinc. We should probably request rule clarifications
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.
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Re: Protein Modeling C

Post by svph300 » January 21st, 2020, 11:47 am

huppada wrote:
January 21st, 2020, 4:02 am
ericlepanda wrote:
January 20th, 2020, 7:15 pm
huppada wrote:
January 20th, 2020, 7:03 pm

I just thought of something:
The official SciOly rules are incorrect, right? They told us to model the cytidine deaminase protein from the 5td5 PDB file, while we are supposed to build the protein from the 5keg PDB file. Do you think they are also wrong in telling us to model the BE4 expression plasmid? Like, are they asking us to model the expression plasmid that correlates with the 5td5 PDB file instead of the 5keg PDB file?
very possible -- there seems to be a huge disconnect between MSOE and soinc. We should probably request rule clarifications
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.
From 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.

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.
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Re: Protein Modeling C

Post by voisinet22 » January 21st, 2020, 1:24 pm

On the pdb site, on the structural tab, does anyone have ideas for what the two random red colored "A"s represent?

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Re: Protein Modeling C

Post by itsDerk » January 21st, 2020, 6:34 pm

svph300 wrote:
January 21st, 2020, 11:47 am
huppada wrote:
January 21st, 2020, 4:02 am
ericlepanda wrote:
January 20th, 2020, 7:15 pm


very possible -- there seems to be a huge disconnect between MSOE and soinc. We should probably request rule clarifications
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.
From 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.

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.
This 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.

Good luck to all those going to MIT! It'll be a good one.
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