Protein Modeling C

Dhruvster
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Re: Protein Modeling C

Post by Dhruvster » March 17th, 2015, 2:22 pm

Yeah my idea was to just put it in some kind of crate to hold it all together and make sure nothing gets ruined. Lol I'm relieved to see others going crazy too with keeping the protein safe.

So I realize the DNA is an obvious addition which everyone is going to have. Its just that the proctors have always given me negative comments about how my pitch and amplitude is off, and how my placement could be better. Has anyone found a solid material that works well when building the DNA or knows how to calculate a pitch and amplitude in sync with the 2cm to 1 amino acids size?

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Re: Protein Modeling C

Post by annaphase » March 17th, 2015, 8:09 pm

Dhruvster wrote:Yeah my idea was to just put it in some kind of crate to hold it all together and make sure nothing gets ruined. Lol I'm relieved to see others going crazy too with keeping the protein safe.

So I realize the DNA is an obvious addition which everyone is going to have. Its just that the proctors have always given me negative comments about how my pitch and amplitude is off, and how my placement could be better. Has anyone found a solid material that works well when building the DNA or knows how to calculate a pitch and amplitude in sync with the 2cm to 1 amino acids size?
For your second question, a lot of jMol files include DNA in them, and you can adapt a scale from there, assuming the protein is being built at the same scale. I know there are acailable files of FokI bound to DNA so that souldn't be extremly difficult to locate.
As for the material, I posted earlier but what I finally settled on was actually leftover minitoobers from past competion years held together with jewlery wire bent in the general pentagoal/hexagonal shape of the bound DNA bases that represent FokI's binding sequence, and that stood up to trial and tribulation and I got a judge's complement on its accuracy (I just didn't know the tiebreaker quesiton pigeon I was so close :evil: :oops: :x :( but good luck to you!
"What are the squiggly things for?"~Protein Modeling
"150 degrees Celsius? Either this graph is wrong, or the only place this enzyme is active is in hell." ~Cell Bio

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Re: Protein Modeling C

Post by SAmoyo » March 20th, 2015, 4:58 am

Are questions about the zinc finger protein going to be asked at the state competition level, or is it going to be just on the TALE nuclease proteins?

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Re: Protein Modeling C

Post by Sushies » March 20th, 2015, 8:20 am

annaphase wrote:
Dhruvster wrote:Yeah my idea was to just put it in some kind of crate to hold it all together and make sure nothing gets ruined. Lol I'm relieved to see others going crazy too with keeping the protein safe.

So I realize the DNA is an obvious addition which everyone is going to have. Its just that the proctors have always given me negative comments about how my pitch and amplitude is off, and how my placement could be better. Has anyone found a solid material that works well when building the DNA or knows how to calculate a pitch and amplitude in sync with the 2cm to 1 amino acids size?
For your second question, a lot of jMol files include DNA in them, and you can adapt a scale from there, assuming the protein is being built at the same scale. I know there are acailable files of FokI bound to DNA so that souldn't be extremly difficult to locate.
As for the material, I posted earlier but what I finally settled on was actually leftover minitoobers from past competion years held together with jewlery wire bent in the general pentagoal/hexagonal shape of the bound DNA bases that represent FokI's binding sequence, and that stood up to trial and tribulation and I got a judge's complement on its accuracy (I just didn't know the tiebreaker quesiton butterfly I was so close :evil: :oops: :x :( but good luck to you!
Regarding your last sentence, you mention the specific sequence bound by FokI's binding domain. It was my understanding that we modeled the catalytic domain and the portion of DNA cleaved by our model is nonspecific. Did you additionally model the DNA-recognition domain?
2014: Circuit Lab, Designer Genes, MagLev. Trial: Environmental Chemistry
2015: Astronomy, Bridges, Protein Modeling, Chemistry Lab.

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Re: Protein Modeling C

Post by Giant Mole Squad » March 21st, 2015, 9:02 am

Does anyone know if the website provided on the event description for the visualization environment (MSOE CBM) is what will be used at the state competitions? Or is Jmol completely different? Our regionals used some downloaded software that I don't think was correct...

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Re: Protein Modeling C

Post by Dhruvster » March 23rd, 2015, 12:06 pm

SAmoyo wrote:Are questions about the zinc finger protein going to be asked at the state competition level, or is it going to be just on the TALE nuclease proteins?
I believe anything having to do with genome editing is fair game. What I'm worried about is a state proctor thinking the test is too short and decides to add their own supplemental questions.

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Re: Protein Modeling C

Post by Dhruvster » March 23rd, 2015, 12:19 pm

Sushies wrote:
annaphase wrote:
Dhruvster wrote:Yeah my idea was to just put it in some kind of crate to hold it all together and make sure nothing gets ruined. Lol I'm relieved to see others going crazy too with keeping the protein safe.

So I realize the DNA is an obvious addition which everyone is going to have. Its just that the proctors have always given me negative comments about how my pitch and amplitude is off, and how my placement could be better. Has anyone found a solid material that works well when building the DNA or knows how to calculate a pitch and amplitude in sync with the 2cm to 1 amino acids size?
For your second question, a lot of jMol files include DNA in them, and you can adapt a scale from there, assuming the protein is being built at the same scale. I know there are acailable files of FokI bound to DNA so that souldn't be extremly difficult to locate.
As for the material, I posted earlier but what I finally settled on was actually leftover minitoobers from past competion years held together with jewlery wire bent in the general pentagoal/hexagonal shape of the bound DNA bases that represent FokI's binding sequence, and that stood up to trial and tribulation and I got a judge's complement on its accuracy (I just didn't know the tiebreaker quesiton butterfly I was so close :evil: :oops: :x :( but good luck to you!
Regarding your last sentence, you mention the specific sequence bound by FokI's binding domain. It was my understanding that we modeled the catalytic domain and the portion of DNA cleaved by our model is nonspecific. Did you additionally model the DNA-recognition domain?
According to the MSOE website the DNA recognition domain is fair game as a creative addition. It requires a lot of effort and skillful bending. But what we were referring to here is placing DNA in an appropriate position and conformation accordance to the Dimer. More of the shape of the DNA rather than the actual sequence. But what I do is just put the specific DNA recognition sequence on there anyway and just show the actual cut being staggered.

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Re: Protein Modeling C

Post by Dhruvster » March 23rd, 2015, 12:23 pm

Giant Mole Squad wrote:Does anyone know if the website provided on the event description for the visualization environment (MSOE CBM) is what will be used at the state competitions? Or is Jmol completely different? Our regionals used some downloaded software that I don't think was correct...
According to the letter sent to the state directors, there is a package sent to the state proctor with materials and there should be an visualization environment included in that package. This should be the case for all competitions. I do know some proctors like to download jmol and just upload the file on the environment and keep it locally as it doesn't require an internet connection. I've encountered both, but I imagine state and nats uses the MSOE environment.

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Re: Protein Modeling C

Post by annaphase » March 23rd, 2015, 4:44 pm

Dhruvster wrote:
Sushies wrote:
Regarding your last sentence, you mention the specific sequence bound by FokI's binding domain. It was my understanding that we modeled the catalytic domain and the portion of DNA cleaved by our model is nonspecific. Did you additionally model the DNA-recognition domain?
According to the MSOE website the DNA recognition domain is fair game as a creative addition. It requires a lot of effort and skillful bending. But what we were referring to here is placing DNA in an appropriate position and conformation accordance to the Dimer. More of the shape of the DNA rather than the actual sequence. But what I do is just put the specific DNA recognition sequence on there anyway and just show the actual cut being staggered.
Oh yeah, I went all out and I had the entire protein, too, which also helps with DNA positioning because it really does suddenly make conformational sense when you put all the pieces together. Also, I love proteins with all my little nerdy heart <3
"What are the squiggly things for?"~Protein Modeling
"150 degrees Celsius? Either this graph is wrong, or the only place this enzyme is active is in hell." ~Cell Bio

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Re: Protein Modeling C

Post by Dhruvster » April 4th, 2015, 10:57 am

annaphase wrote:
Dhruvster wrote:
Sushies wrote:
Regarding your last sentence, you mention the specific sequence bound by FokI's binding domain. It was my understanding that we modeled the catalytic domain and the portion of DNA cleaved by our model is nonspecific. Did you additionally model the DNA-recognition domain?
According to the MSOE website the DNA recognition domain is fair game as a creative addition. It requires a lot of effort and skillful bending. But what we were referring to here is placing DNA in an appropriate position and conformation accordance to the Dimer. More of the shape of the DNA rather than the actual sequence. But what I do is just put the specific DNA recognition sequence on there anyway and just show the actual cut being staggered.
Oh yeah, I went all out and I had the entire protein, too, which also helps with DNA positioning because it really does suddenly make conformational sense when you put all the pieces together. Also, I love proteins with all my little nerdy heart <3
Jesus that's like 10 meters of toober total. So much monies lol

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