BIOL368/S20:Class Journal Week 13

Madeleine King

What new insights do you have into the article you read for journal club?

• New insights I have are how you can predict a lot about how a protein's structure and function will be like, just by looking at the amino acid sequence. I thought it was really cool how much PredictProtein's server predicted, from secondary structure, lethal mutations, and essential binding sites. I assumed that a lot of information about the protein was obtained by lots of laboratory work and experiments, but some can be predicted by using servers like PredictProtein, then testing your hypothesis by doing experiments.

Is FoldIt something that you would like to play and why?

• If I was more knowledgeable about structure/function relationships, I would play. I think it's a great way to use computer software to do research, especially during the quarantine. It's also cool that anyone can access it too, which allows way more people to participate in research rather than being in a lab with a small group of people.

Mking44 (talk) 13:03, 22 April 2020 (PDT)

Maya Paniagua

What new insights do you have into the article you read for journal club?

• I learned that a lot of the predictions can be made using a computer. So when they were making their predictions about 2019-nCoV they could use its sequence to discover a lot of information about it and that sometimes lab groups have their own way of labeling. I discovered this when I found positions numbered in iCn3D did not correspond to exactly what the paper did but was actually the inverse.

Is FoldIt something that you would like to play and why?

• I would play because I am very interested in structure-function relationships and especially now that research outside the home is limited it is a nice way to learn more and apply concepts learned in class to the research and how proteins fold.

Mpaniag1 (talk) 13:54, 22 April 2020 (PDT)

Christina Dominguez

After manipulating the protein structure yourself, what new insights to you have into the article you read for journal club? I have more confidence in the article that I read for journal club. It was a hypothesis paper that made predictions made on evidence and a predictive framework for SARS-CoV. However, by looking at the protein structure myself and comparing it to the paper, I was able to see the amino acids interactions that they mentioned. I have a new found appreciation and confidence in the paper and their hypothesis.

Please comment on whether this game is something that you would like to play and why (it might be a good "safer at home" distraction once the semester ends!). I think that this could be an interesting game that is played as a part of the class; however, I do not think that I would find myself playing the game on my own time. It was be a good activity in class to be able to use application skills from what is learned in class.

Cdominguez (talk) 17:49, 22 April 2020 (PDT)

Nicholas Yeo

1. After manipulating the protein structure yourself, what new insights to you have into the article you read for journal club?
   • I learned that the tools that we used are actually very accurate and useful in visualizing and predicting amino acid sequences and protein structures. The predictions must have a lot of scientific data to back up the site. It is cool to see the structures for the proteins that we read about in the paper last week. For example, I could clearly visualize the open and closed states of the S1 subunit on the spike glycoprotein.
2. Please comment on whether FoldIt game is something that you would like to play and why.
   • I would play the game if I had an idea of what questions I would want to answer with the game. I think that it could be something to do during the quarantine, since it is so accessible. Also, it would be cool to discover structure-function relationships because they ultimately determine how things work.

Nyeo2 (talk) 21:06, 22 April 2020 (PDT)

Annika Dinulos

After manipulating the protein structure yourself, what new insights to you have into the article you read for journal club?

• After manipulating the protein structure myself, I was able to get a better idea of the actual areas of the protein that were examined in the Wtapp et. al paper. Specific regions like the NTD and RBD were highlighted, and I was able to see those specific sequences better. I would like to develop more skill since I had a harder time finding the exact region they were located but I liked being able to specify those regions and make comparisons to the actual model of the protein.

Please comment on whether FoldIt game is something that you would like to play and why.

• I would play the game if I were especially interested in the structure/function of proteins, but if not, it wouldn't be something I would play on my own. I think it would be a good option for a class warm-up.

Adinulos (talk) 21:30, 22 April 2020 (PDT)

Jack Menzagopian

1. Because I was able to move the complex around, look at it from many different angles, and visualize or remove different parts of the protein, I was able to better understand the interaction between the RBD and ACE2, specifically with alpha1 in the PD described throughout Yan et al. (2020). Being able to label the termini, highlight the different secondary structures, and remove other parts of the protein helped put those interactions into perspective.
2. I think the game would be something cool to try out, it would definitely be a fun activity to do in class one time. I don't know if I know enough to do pretty well, but it would be interesting to be able to try to apply what I've learned in a non-academic or vocational way.

Jmenzago (talk) 21:58, 22 April 2020 (PDT)

Sahil Patel

• After manipulating the protein structure yourself, what new insights to you have into the article you read for journal club?
  • Because I was able to actually manipulate the protein structure myself, I was able to understand more clearly how different proteins/enzymes bind to receptor binding domains. By examining this relationship, we can compare the affinity by which these bond and thus make assumptions about the function of the protein.
• I think this would be a fun activity, and could be a group warmup exercise for many different classes as well. I tried some of the beginner puzzles and it did not take too long to navigate my way around the program.

Sahil Patel (talk) 22:27, 22 April 2020 (PDT)

Jenny Chua

After manipulating the protein structure yourself, what new insights to you have into the article you read for journal club? I was able to more fully understand the proteins that bound to the receptor binding domain. As I mentiioned previously, the article was hard to read, since there was no separation between parts of the paper, so the various names such as SD1 and RBD were a bit confusing. Now, though, having a 3D image where I can turn and see the different structures that make up SARS-CoV-2 and how those parts in turn bind to ACE2.

Please comment on whether FoldIt game is something that you would like to play and why. This game would work really well as a class warm-up, and if a particular protein that we learned about intrigued me enough to pursue out of class research, then I think it would be a good way to take that learning and apply it elsewhere in a fun setting.

Jennymchua (talk) 23:12, 22 April 2020 (PDT)

Drew Cartmel

1. After manipulating the protein structure myself, I was able to gain a better understanding of just how the viral spike protein attaches to the host ACE2 protein by seeing the actual 3-D structures interacting with each other.
2. I think that this would be a fun activity to do in class because of how relevant it is to our topic of the structure of particular proteins. I would most likely not try this game on my own but it would be interesting to see how much of the game I could understand and follow based on the concepts that I have learned in class.

Dcartmel (talk) 12:05, 23 April 2020 (PDT)

Nathan On

• After manipulating the protein structure yourself, what new insights to you have into the article you read for journal club?
  • I have better insights into the various secondary structural elements that make up the spike glycoprotein.
• The "protein folding problem", i.e., the difficulty of predicting protein structure from sequence information alone, has prompted a group to create Foldit, a protein-folding game that anyone can play on the web. Scientific papers have been published based on the crowd-sourced work of gamers playing Foldit, with the gamers as co-authors. Read the blog post about how Foldit is contributing to coronavirus research. I'm not asking you to play Foldit, but please comment on whether this game is something that you would like to play and why (it might be a good "safer at home" distraction once the semester ends!).
  • I think Foldit is a good tool to utilize the massive number of minds and computers out there to help gain better understandings of a complex problem like protein folding. The gamification aspect will also allow for a different group of individuals to get involved in science.

Non (talk) 23:19, 22 April 2020 (PDT)

Carolyn Egekeze

• After manipulating the protein structure yourself, what new insights to you have into the article you read for journal club?
  • After spending time looking at and manipulating the protein structures, I understand how the location of particular amino acids are important for determining if the SARS-CoV-2 can bind to ACE2 with strong affinity. It is surprising to me how involved these interactions are.
• Please comment on whether this game is something that you would like to play and why.
  • I think Foldit would be an interesting game to try in class, especially in classes like this class, biochemistry, or molecular biology. In each class, I've spent a lot of time thinking protein structure and how amino acids are important for determining the final structure of the protein. Having a game that illustrates how difficult that problem is could be a new way to think about the protein-folding problem.

Carolyne (talk) 23:46, 22 April 2020 (PDT)

Karina Vescio

• After manipulating the protein structure yourself, what new insights do you have into the article you read for journal club?
  • After manipulating the structure myself, I understand the tables/charts in Yan et al. better. I also understand the interaction between the ACE2 receptor and the SARS-CoV-02 protein. I was able to select which parts of the structure to look closer at, in addition to being able to rotate image to my liking.

• The "protein folding problem", i.e., the difficulty of predicting protein structure from sequence information alone, has prompted a group to create Foldit, a protein-folding game that anyone can play on the web. Scientific papers have been published based on the crowd-sourced work of gamers playing Foldit, with the gamers as co-authors. Read the blog post about how Foldit is contributing to coronavirus research. I'm not asking you to play Foldit, but please comment on whether this game is something that you would like to play and why (it might be a good "safer at home" distraction once the semester ends!).
  • I believe that the game would be beneficial in a class similar to bioinformatics. It is an interactive way to gain an understanding on protein sequences. I would play it myself if I had more time on my hands.

(Kvescio (talk) 22:53, 27 April 2020 (PDT))