Science Buddies: "Ask an Expert"

I was very interested in the Computational Exploration of Protein Function, and I have already chosen which protein I'm going to compare between different species. I have chosen an Ellis van Creveld protein, and will be comparing it with a Western lowland gorilla, killer whale, green monkey, and human. However, I haven't been able what problem I would be answering with that info and would really appreciate it if someone could give an idea of what I could use as my topic. Hopefully it'll help me in my science fair project.

Hi, Zero Infinity.

Going back to the project idea, it says: "...you will generate a hypothesis about which parts of the protein are likely to be most important to its function. This will be done by comparing the human version of the protein to other (non-human) versions of the protein. You will then use databases that identify signatures of common functional components of proteins and assess whether or not these analyses are consistent with your hypothesis."

What do you know, so far, about your protein and how it works? Once you understand it's structure and function, you should be able to come up with a hypothesis about which areas are more or least likely to be conserved between species.

Make sure you read all the tabs under https://www.sciencebuddies.org/science- ... p002.shtml. Especially the background and procedure as there is a lot of information there to guide you.

Once you've had a chance to review the info, let me know if you have a more specific question.

Good luck and have fun!

Thanks Lisa, but unfortunately I am having some trouble understanding the procedure. I have already compared the sequences, and used T-Coffee. Do you know what I would do after that?

Have you researched the different parts of the protein? You're looking to figure out where the differences occur. I'm more of a DNA person, but like DNA, proteins form secondary structures and have important sites for binding and other functions. You need to know where those sections are before you can go further. Then you would determine in which areas the changes occurring.

Does that make sense?

BLAST has some useful resources including nucleotide BLAST, protein BLAST, and primer BLAST. These search engines help you find matches for given DNA and protein sequences. You can also design primers. If you want to align multiple protein, DNA, or RNA sequences, you might want to visit this link at http://www.ebi.ac.uk/Tools/msa/clustalo/