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Based on the project "Computational Exploration of Protein Function."
I have been doing this project on Peptidoglycan Recognition Protein 1 (PGLYRP1). The part i am currently stuck on is how to determine which part of the protein is important based on the multiple sequence alignment. I ran the alignment with 5 species.. Also from determining the important parts, how do i formulate and test a hypothesis about the protein's function(s) and the protein's 3D structure?
*Attached is the MSA results. (protein)
Analyzing a protein based on the multiple sequence alignment
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deleted-125401
- Posts: 3
- Joined: Mon Feb 25, 2013 7:51 am
- Occupation: Student 11th grade
- Project Question: Based on the project "Computational Exploration of Protein Function." I have been doing this project on Peptidoglycan Recognition Protein 1 (PGLYRP1). The part i am currently stuck on is how to determine which part of the protein is important based on the multiple sequence alignment. I ran the alignment with 5 species; human, gorilla, cat, water buffalo, and monkey. Also from determining the important parts, how do i formulate and test a hypothesis about the protein's function(s)?
- Project Due Date: March 5, 2013
- Project Status: I am conducting my experiment
Analyzing a protein based on the multiple sequence alignment
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deleted-71536
- Former Expert
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- Project Question: How do different animals adapt to their environment?
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Re: Analyzing a protein based on the multiple sequence align
Hi Kayla,
This is a really fun project! https://www.sciencebuddies.org/science- ... p002.shtml
To determine which part of your protein may be important, you want to look for areas where the protein sequence is conserved (exactly the same in all 5 species). Based on the data you posted, I see several areas for which you have 8-10 amino acids in a row that are conserved across all 5 species. These would be good areas to examine.
To understand how these domains may affect the proteins 3D structure, you'll want to use some of the online tools listed in the Background section of the project (https://www.sciencebuddies.org/science- ... background). The Basic Protein Analysis tools will help you look at the domains, whereas the Advanced Protein Analysis tools will help you examine the entire structure. I think those tools are your best bet for developing hypotheses regarding the importance of the conserved domains in your protein.
Why did you choose Peptidoglycan Recognition Protein 1? What is the normal function of that protein? Answering these questions may also help you as you try to understand your results.
I hope this helps. Please post again (in this same thread) if you have more questions.
Heather
This is a really fun project! https://www.sciencebuddies.org/science- ... p002.shtml
To determine which part of your protein may be important, you want to look for areas where the protein sequence is conserved (exactly the same in all 5 species). Based on the data you posted, I see several areas for which you have 8-10 amino acids in a row that are conserved across all 5 species. These would be good areas to examine.
To understand how these domains may affect the proteins 3D structure, you'll want to use some of the online tools listed in the Background section of the project (https://www.sciencebuddies.org/science- ... background). The Basic Protein Analysis tools will help you look at the domains, whereas the Advanced Protein Analysis tools will help you examine the entire structure. I think those tools are your best bet for developing hypotheses regarding the importance of the conserved domains in your protein.
Why did you choose Peptidoglycan Recognition Protein 1? What is the normal function of that protein? Answering these questions may also help you as you try to understand your results.
I hope this helps. Please post again (in this same thread) if you have more questions.
Heather
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deleted-125401
- Posts: 3
- Joined: Mon Feb 25, 2013 7:51 am
- Occupation: Student 11th grade
- Project Question: Based on the project "Computational Exploration of Protein Function." I have been doing this project on Peptidoglycan Recognition Protein 1 (PGLYRP1). The part i am currently stuck on is how to determine which part of the protein is important based on the multiple sequence alignment. I ran the alignment with 5 species; human, gorilla, cat, water buffalo, and monkey. Also from determining the important parts, how do i formulate and test a hypothesis about the protein's function(s)?
- Project Due Date: March 5, 2013
- Project Status: I am conducting my experiment
Re: Analyzing a protein based on the multiple sequence align
Heather,
Thank you for your input! i had been looking at the alignment results with my biology teacher and i think we were thinking the actual results would show us something. I had determined the larger parts but wasn't sure what i was suppose to take from them. Now i know i just needed to move forward a bit more.
If i have any more trouble or any other questions, i'll be sure to look here for help.
Thanks!
Kayla
Thank you for your input! i had been looking at the alignment results with my biology teacher and i think we were thinking the actual results would show us something. I had determined the larger parts but wasn't sure what i was suppose to take from them. Now i know i just needed to move forward a bit more.
If i have any more trouble or any other questions, i'll be sure to look here for help.
Thanks!
Kayla