BIOL368/F20:Class Journal Week 5

Aiden Burnett

1. After manipulating the protein structure yourself, what new insights to you have into the article we read for journal club?
   • I now have a better understanding of what the different structure visualizations are showing. I know what I am looking at in the figures, as well as what the writers may have intended to communicate (based on which visualization styles & colours are chosen).
2. 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 (scroll to the middle of the page where it says "Experiment results for coronavirus spike binders") 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 find foldit really interesting but don't really want to play it myself. I probably would if the "game" became available on the PS4 (where I play video games). I do think I'll talk to my younger brother (17) about the game though. He is waiting for a new gaming laptop to arrive in the mail and is very science minded.

Aiden Burnett (talk) 22:29, 7 October 2020 (PDT)

Yaniv Maddahi

1. After manipulating the protein structure yourself, what new insights do you have into the article we read for journal club?
   • After having used the software and manipulated the protein structure myself, I started being able to see the interactions between ACE2 and Spike protein at a much more nuanced level; I was able to manipulate the diagram to view it from different angles and further analyze it in different ways to understand the complexity of its interactions. From viewing it from a perspective of charge to perhaps simply the amount of space it occupies, I am able to learn about it in different ways. I was able to understand the location of interactions and what kind of amino acids were involved in them.
2. 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 (scroll to the middle of the page where it says "Experiment results for coronavirus spike binders") 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 an incredible software, linking the bridge between science and people. Aside from its ability to reach such a large audience and have so many people contribute to research to help progress scientific discovery at a fast rate, it also helps in that people are able to actually interact with science and learn from home. I would definitely like to play foldit because I think it is a fun way to contribute to science from one’s home and to learn.

Yaniv Maddahi (talk) 09:19, 7 October 2020 (PDT)

Nathan Beshai

1. After manipulating the protein structure yourself, what new insights do you have into the article we read for journal club?
   • After Manipulating the protein structure I believe that I have gained a lot of insight pertaining to the interactions of proteins. The 3-dimensional structure of the protein and interactions allowed me to understand a lot about receptor and protein binding. An example of this is that the article did not show the hydrogen bonding of the ACE-2 - Spike protein side chains. Another insight that I had after manipulating the protein is the difficulty of finding the specific 5 critical amino acids. While observing the ACE-2 and spike protein bonding, the proteins just looked like two peptides close together. I could not find the 5 amino acids by just eyeballing it. These insights are why viewing 3-dimensional proteins is a huge advancement for biologists and biochemists, as it helps view interactions of receptor and binding proteins better.
2. 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 (scroll to the middle of the page where it says "Experiment results for coronavirus spike binders") 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 I would play fold-it before an exam for protein folding or when I need refreshment on protein folding. I am a very visual learner so I believe that playing with a protein will help me better understand how it interacts with other proteins and how it folds. This can be useful for cell function and younger biologists who are first being introduced to protein folding and interactions.

Nathan R. Beshai (talk) 17:34, 7 October 2020 (PDT)

Owen Dailey

1. After manipulating the protein structure yourself, what new insights do you have into the article we read for journal club?
   • After Manipulating the protein structure I was able to see that a relatively small number of amino acids in the spike protein and ACE2 protein interact with one another. Being able to interact with the ACE2 and spike protein structures gave me a better understanding of the RBD of the spike protein, and just how small it is. Its interesting to me that such a small number of amino acids can control the binding/interaction of the virus with the receptor.
2. 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 (scroll to the middle of the page where it says "Experiment results for coronavirus spike binders") 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!).
   • It would definitely be hard to convince me to play Foldit rather than a more "mainstream" video game that I currently play; however, every time I play these "mainstream" videogames, I feel like I have wasted my time and not been productive. I would probably feel more accomplished by playing Foldit than with the videogames I play currently. Foldit does offer a good "safer at home" option, and I think it's cool that the data generated this game is actually being used to fuel scientific research.

Owen R. Dailey (talk) 19:49, 7 October 2020 (PDT)

Anna Horvath

1. After manipulating the protein structure yourself, what new insights do you have into the article we read for journal club?
   • After manipulating the protein structure, I was able to better understand just how small the interaction between the ACE2 protein and the RBD protein was. The protein, which had a quaternary structure, was very interesting to visualize. The protein structure was very large, and being able to change the components was very good for me to understand just how relatively small the critical amino acid residues were. The article, which outlines these residues, included very nice images of them, whereas I found it relatively difficult to locate and take an image of these residues.
2. 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 (scroll to the middle of the page where it says "Experiment results for coronavirus spike binders") 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 I would play Foldit as a way to look at protein folding in a different way. I think it is very useful and interactive, which can be helpful when trying to better visualize proteins. I feel that it can be a beneficial way for students to be introduced to the topic. However, I do not play any video games, so I am unsure whether I would take time to play Foldit, as I do not normally do things similar to it.

Anna Horvath (talk) 21:07, 7 October 2020 (PDT)

JT Correy

1. I think that the model was very helpful in understanding physically how the proteins interact. Through my many chemistry and biology classes at LMU I think I have a decent understanding of the forces and such that cause the interaction. It was the model that really helped me visualize and understand not the forces, but the shape and proteins as a whole.
2. I think the Foldit game is super interesting. There were definitely some parts of the description that I did not quite understand, but I think that I got the gist of it. I think once the stress of the semester is over and I could see myself playing a little bit. I also sent it to my younger brother. He is big into computer science and coding so I think he will enjoy it!

Jcorrey (talk) 21:24, 7 October 2020 (PDT)

Macie Duran

1. After manipulating the protein structure yourself, what new insights do you have into the article we read for journal club?
   • Being able to manipulate the protein structure myself gave me a much better understanding of the interactions between ACE2 receptors and spike proteins. It’s nice to have a visual representation of what is actually occurring when a viral spike protein binds to a host cell receptor.
2. 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 (scroll to the middle of the page where it says “Experiment results for coronavirus spike binders”) 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!).
   • The Foldit game is really interesting, and I think it would be a fun activity to learn how to do once I have more free time. Being able to manipulate and visualize the structures would be helpful in learning, and it’s also contributing to useful research. I also think it’s pretty cool that the people playing the game are included as co-authors in the published scientific papers.

(Macie Duran (talk) 21:43, 7 October 2020 (PDT))

Fatimah Alghanem

1. After manipulating the protein structure yourself, what new insights do you have into the article we read for journal club?
   • by manipulating the protein structure myself I had a better understanding of the bond between spike proteins and ACE2.
2. 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 (scroll to the middle of the page where it says “Experiment results for coronavirus spike binders”) 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!).
   • Although the game is interesting, I don't think I would want to play it because simply I am not into games.

Falghane (talk) 23:16, 7 October 2020 (PDT)

Kam Taghizadeh

1. After manipulating the protein structure yourself, what new insights do you have into the article we read for journal club?
   • After modifying the protein structure, I have a new insight into how residues react with one another inside of proteins, and can evaluate why binding affinity could increase or decrease between two proteins, depending on their charge, hydrophobic regions, or hydrophilic regions.
2. 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 (scroll to the middle of the page where it says “Experiment results for coronavirus spike binders”) 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!).
   • This game is something I would like to play during my free time as it shows a different, fun perspective on the way proteins fold.

Kam Taghizadeh (talk) 23:41, 7 October 2020 (PDT)

Ian Wright

1. After manipulating the protein structure yourself, what new insights to you have into the article we read for journal club?
   • I now understand how Wan et al was able to analyse the interactions between the critical residues. How they identified that this was the region of interaction, I still do not know. However, if I was told that the main interactions between two proteins were within a specific region of residues, I would now be able to map the interactions between the proteins.
2. 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 (scroll to the middle of the page where it says “Experiment results for coronavirus spike binders”) 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 would totally play this game! It seems like a very powerful engine for both education and citizen science. I think a game like this would really open up the opportunities for the everyday scientist. One of the largest stigmas on molecular biology is that it’s just so complicated that you can only participate in the community if you’ve had rigorous training. I would love to participate in something so forward thinking, technologically involved. This would probably teach me so much about the intricacies of protein structure.

Ian R. Wright (talk) 23:55, 7 October 2020 (PDT)

Taylor Makela

1. After manipulating the protein structure yourself, what new insights do you have into the article we read for journal club?
   • After manipulating the protein structures myself, I have a much greater understanding of both the Figure 1C SARS-CoV RBD (optimized for human ACE2 recognition) and human ACE2: 3SCI, and the civet ACE2-spike protein structure shown in Figure 4B. I feel like I not only better understand the overall structure, but I also better understand the bonding, atoms, and structures involved within the proteins.
2. Comment on whether the Foldit 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 the Foldit game is something that I would play! As someone who is interested in science, I think it would be fun to play this game and I appreciate that it encourages everyone to be creative and try to get involved in science!

Taylor Makela (talk) 01:23, 15 October 2020 (PDT)