This
Tuesday (February 5th), I went to RPI to continue my project from last week.
Last week, I identified possible α helix binding sites on the
protein. SInce last week, JP has worked on using the color coded model to come
up with amino acid sequences that would form an α helix structure and bind to one of the sites. My job
was to test the possible structure of the amino acid sequences by entering them
into a program called PEP-FOLD. This program uses the amino acid sequence to
identify possible reactions between the amino acids that would make the
protein's secondary structure. Ideally, the amino acid sequence we are looking
for should have an almost perfect α helix secondary structure in order to bind well with
the binding site on the protein. The figure below was the most successful α helix model we made.
We also
built the amino acid sequence using the MOE software. We set the program to
make the sequence into the ideal α helix
shape to determine where the bases would be located on the α helix. This allowed us to align our α helix sequence with its binding site on the protein
model to identify the possible reaction sites and see how we could change the
amino acid sequence to improve the binding.
Overall,
my work today really increased my knowledge about amino acid sequences and
protein structure. I look forward to continuing to work on this project!
Wow, that model is so cool! I am quite impressed with what you are coming up with in your internship.
ReplyDeleteRelated to a recent comment of mine, include some general information about your work to put your blog post in context. While this all makes sense to you, your readers (like me) cannot easily follow your technical steps. A few sentences for the lay person would make for wonderful additions to your work.
Otherwise, well done!!
Kailin, it was good to have conversation with you during the meeting on last Thursday. It seems like you are really enjoying making proteins. I asked you about what is the goal of assembling proteins. The purpose was to open the gap of the cell so that medicine can go into the cell. As I said during the meeting, I have done an experiment on opening the bacteria cell's plasma membrane and transform the bacteria in AP biology class. For my experiment, I used calcium and heat to open the plasma membrane. It was good to know that different methods can be used to make a entrance for other chemicals to enter the cell.
ReplyDeleteThanks, Lauren - very thorough!
DeleteHi Kailin,
ReplyDeleteYour blog is really interesting! How long is your amino acid sequence? How do you manipulate your protein? Are you changing amino acids and seeing what happens? Tell me a little bit more about that.
Is there any particular reason why different colors were used in the model?
I look forward to your next entry!
Ms. Maier
Hi Kailin:
ReplyDeleteDuring our past conversations, you have described more of the details about the goal of these experiments. For example, you explained that one of the goals is to have the protein bond to the endothelial cells to open the tight junctions, which would allow larger molecules to pass into the cells. It was very interesting to see that these techniques could be used so that medicines that contain larger and more complex molecules would be able to get through to the cell and then be able to be able to perform there designed functions.
At the AAAS Conference, it was very nice to have someone who was familiar with the programs used to model proteins when we attended the lecture on ancestral proteins. With your help I could better understand their diagrams and therefore was able to gain a better understanding of the process being used to formulate the amino acid sequences of ancient proteins.
Hope to hear more about your work and your real excitement for what you are accomplishing!
Moriah
Very thoughtful comment, Moriah!
Delete