BIOL368/F16:Class Journal Week 9

Colin Wikholm

1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
   • Yes, I increased my understanding of protein structure. This is especially true in better grasping the affects of DNA mutation on amino acids. Specifically, certain differences in amino acids (ex size, charge, shape) can lead to greater or lesser affects due to mutations. I also learned about various tools on Biology Workbench that can determine degree of differences between amino acids. Finally, I now have a better grasp on how the gp120 gene is organized (including the location of the V3 coding region).
2. What is not (yet) clear?
   • I still do not yet understand how many of the tools on Biology Workbench determine greater or lesser differences in amino acids. Is this based on functional effects, shape effects, or evolutionary differences between amino acids? Also, I still wish to know why Markham et al. (1998) studied the parts of the gp120 gene that he did, and if studying other components of the gene would yield different results from what we plan to do in out protein structure analysis project.
3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV.
   • Explain whether you would be interested in playing this game and why or why not?
     • I would want to play this game. If it is really is a way to learn about protein structure that is more fun, I would love to take advantage of such an opportunity. What is more, I enjoyed playing the game EteRNA, which is a similar research-based game that uses human gamers to solve RNA folding.
   • Do you think that games like this could assist you in learning about protein structure? (I'm not asking you to play it, per se, although you can if you want; I just want you to comment based on reading the article.)
     • I think this game could definitely assist me in learning about protein structure. If the game really is a fun challenge, it would allow me to actively learn and problem solve in a way that requires considerably less effort. This is especially true because (as stated by the article), the game is puzzle-based. I love puzzles, so understanding the parts of the protein "puzzle" would make learning much more efficient for me.

Colin Wikholm 23:39, 31 October 2016 (EDT)

Isai Lopez

1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
   • Actually yes, the tools we used for the in-class activity made it easier to visualize how interactions like disulfide bridges and secondary structures correspond to a sequence of amino acids. Seeing it laid out for me in the UniProt website helped my understanding. In addition, much of the information in the UniProt database elucidated the functions of different protein structures and why structure and function are innately tied together.
2. What is not (yet) clear?
   • I'm still not exactly sure how these programs take the sequence and are able to decide exactly at what reside certain interactions, such as loops will begin, as well as defining where that loop ends.
3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV.
4. Explain whether you would be interested in playing this game and why or why not?
   • Certainly, because I think that tinkering without direction or a strict set of rules is often one of the best ways to explore the potential of a simulation. The joy of discovery can often be a strong driving factor.
5. Do you think that games like this could assist you in learning about protein structure?
   • Yes, because I think that what happens often when people play games is once they become adept at using the tools provided, they will seek new ways to explore their function, effectively tinkering with the "meta" of the game itself. In learning how to use the simulation and actively interacting with it I could answer for myself many of the questions I have that start with "what happens when..?"

• Isai Lopez 23:26, 31 October 2016 (EDT):

Will Fuchs

1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
   • The way that proteins can be analyzed in three dimensional space was very interesting and this is important because if you can anylze the structure of some proteins one may be able to infer on a possible function of that protein (complex).
2. What is not (yet) clear?
   • The multiple ways and facets of these programs and how they can be utilized to their full potential.
3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV.
4. Explain whether you would be interested in playing this game and why or why not?
   • This was an interesting approach to resource the public in solving complex scientific challenges. Personally, I'd like to at least try the game and see what I can do.
5. Do you think that games like this could assist you in learning about protein structure?
   • Absolutely because it is right up my alley. I love the idea of online competition and an interactive game such as this would fulfill that desire at an immersive level.

William P Fuchs 18:58, 31 October 2016 (EDT)

Anindita Varshneya

1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
2. What is not (yet) clear?
3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV.
   1. Explain whether you would be interested in playing this game and why or why not?
   2. Do you think that games like this could assist you in learning about protein structure? (I'm not asking you to play it, per se, although you can if you want; I just want you to comment based on reading the article.)

Avery Vernon-Moore

1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
   • No, I don't think I learned anything to deepen my understanding of protein structure. I didn't get through every aspect of this weeks assignment though. I think tomorrow will help me gain some better understanding.
2. What is not (yet) clear?
   • I still just know how the amino acid sequences relate to the function of the protein, or better yet how I am supposed to be able to distinguish that. I also am not sure how we are going to compare the sequences for our project.
3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV.
   • Explain whether you would be interested in playing this game and why or why not?
   • I think it is super cool that they are giving everyone an opportunity to help lead us towards a cure for HIV and AIDS. I would be interested in trying the game. It is cool that the general public can choose to get involved and help a good cause.
   • Do you think that games like this could assist you in learning about protein structure? (I'm not asking you to play it, per se, although you can if you want; I just want you to comment based on reading the article.)
   • Yes, I think something more engaging would make me more willing to learn about protein structure and some of the stuff we are learning at the moment.

Avery Vernon-Moore 23:30, 31 October 2016 (EDT)

User: Zachary T. Goldstein

1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
   • I don't feel like I have learned anything new about understanding protein structure from this assignment, but I believe that is largely due to the fact that the assignment covered surface level information (or at least the parts that I was able to complete). I learned that there exists a database which holds a ton of information about specific proteins such as gp160, but have learned nothing new about protein structure.
2. What is not (yet) clear?
   • What is not yet clear is how protein structure and amino acid composition relates to function of proteins. I'm curious to see how nonsynonymous mutations can effect how proteins function within a cell through our HIV-1 structural project. I hope to learn how to use software that can project how these physical changes effect protein function.
3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV. Explain whether you would be interested in playing this game and why or why not? Do you think that games like this could assist you in learning about protein structure? (I'm not asking you to play it, per se, although you can if you want; I just want you to comment based on reading the article.)
   • I would probably be interested in playing the game, although I think only in a classroom setting; I can't really see myself playing a "game" like this outside of a direct school-related setting. I think the concept of combining human and computer power is a really strong and powerful tool as we look into the future of scientific discovery, but it just doesn't seem like something I would do in my free time. On the other hand, I do think a lot could be learned from a program like this and it would be a very interesting assignment if students had to join the game and demonstrate progress. This game provides a necessary framework for bringing the power of humans and computer together which results in discoveries such as the molecular structure of a retroviral protease which plays a critical role in AIDS progression. Additionally I like the idea of public people working on a project and then submitting it to researchers who specialize in the field, as long as due credit is given to the gamers who make the discovery.

Zachary T. Goldstein 18:20, 27 October 2016 (EDT)Zachary T. Goldstein

Jordan T. Detamore

1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
   • I learned more details about silent deviations in proteins and also proteins that are different but function very similarly. This could explain how some changes in base pairs don't necessarily change the function of the protein
2. What is not (yet) clear?
   • It is not clear what new programs we are going to need to work with for our new project.
3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV.
   1. Explain whether you would be interested in playing this game and why or why not?
      • I would be interested in this game if it could help me with a project or gain a better understanding of a certain protein structure. I would use it for educational purposes, not necessarily for personal enjoyment.
   2. Do you think that games like this could assist you in learning about protein structure? (I'm not asking you to play it, per se, although you can if you want; I just want you to comment based on reading the article.)
      • I absolutely do think that this game could help me learn about protein structure. Seeing a 3D model of proteins and being able to work with them could absolutely allow for a better understanding of the structure of proteins. The fact that it is also both interactive and a "game" would make it a more approachable way to learn about proteins.

• Jordan T. Detamore 23:11, 31 October 2016 (EDT):

Matthew K. Oki

1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
   • Reading frames were a very new concept for me, and it was interesting to see which reading frame was actually the one used. However, other than the reading frames, there was not anything new learned from this assignment. There were more convenient methods learned. I think all of the programs greatly increased the efficiency at which we can complete our project. I didn't realize that there was such a large amount of protein sequence information in one place. We will definitely use these programs to aid our project.
2. What is not (yet) clear?
   • I wasn't able to reach the last "in-class" bullet point, which was to compare the sequences from Markham et al. (1998) to Kwong et al. (1998). We need to find an efficient way to compare the protein sequences of multiple visits/clones in order to complete our study. Furthermore, it will be interesting to see if any of these specific changes from the sequences will show any functionality difference.
3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV.
   • Explain whether you would be interested in playing this game and why or why not?
     • I think I would be interested in playing the game. It interests me for two reasons. First, it's just intriguing that a group of scientists made a "game" all about science that gamers would want to play at all. So, it would just be fun to see exactly how the game works in that aspect. Secondly, I like pattern folding types of problems. It makes me think outside of the 2-D dimensions of a piece of paper. It is also very challenging. Overall, it sounds like an interesting game.
   • Do you think that games like this could assist you in learning about protein structure? (I'm not asking you to play it, per se, although you can if you want; I just want you to comment based on reading the article.)
     • I believe I could contribute at some level. Maybe not the extent of finding the confirmation of an entire enzyme of a retrovirus, but something smaller scale. I'm not sure exactly what that would be, maybe a portion of the virus, but I think it's very possible for many people to make a difference.

• Matthew K. Oki 21:34, 27 October 2016 (EDT):

Courtney L. Merriam

1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
   • Yes I did. Working with specific amino acid sequences so closely helped me begin to understand them as actual physical structures, instead of abstract concepts that only interact in the setting of academia. I think the ability to consider them more properly as real, physical structures helps make the entire discipline of genetic interaction more easy to grasp and understand.
2. What is not (yet) clear?
   • I want to know if the frequency an amino acid mutates or changes had as effect on the number of present CD4 cells.
3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV.
4. Explain whether you would be interested in playing this game and why or why not?
   • I would very much be interested in playing this game. This is exactly what I was talking about in the first question. Being able to consider these seemingly impossibly small and abstract structures as real physical things helps reduce their confusing nature. Especially working with them as if it were a game would further increase comfort of interacting with them and make them seem more simple and easy to understand.
5. Do you think that games like this could assist you in learning about protein structure? (I'm not asking you to play it, per se, although you can if you want; I just want you to comment based on reading the article.)
   • I think games like this would absolutely assist in learning about protein structure. Repetition aids in understanding, and the visually manipulability of the rendering of the protein structures would allow for a more dynamic perspective for a student to examine.

• Courtney L. Merriam 15:48, 1 November 2016 (EDT):

Mia Huddleston

1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
   • I learned that it is not always clear what is the correct reading frame is of a sequence, I guess I never really thought about how we have to choose which one we are going to look at.
2. What is not (yet) clear?
   • I am still not sure what the best way to compare sequences is and say "how different" they are from each other.

• Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV.

1. Explain whether you would be interested in playing this game and why or why not?
   • I think this game would be really interesting to play especially because you can both be potentially helping science and find an anti-AIDS drug and having fun at the same time. I think it is a great way to get a large amount of people to help in this very important research (especially without paying them).
2. Do you think that games like this could assist you in learning about protein structure? (I'm not asking you to play it, per se, although you can if you want; I just want you to comment based on reading the article.)
   • Yes, I think this game would definitely help to understand more about protein structure much better than most other ways. Because it is both interactive and fun, it would encourage people to learn about protein structure.

Mia Huddleston 13:45, 31 October 2016 (EDT)

Shivum Desai

1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
   • I am not sure if i learned something particular about protein structure that deepended my understanding. But I did learn about reading frames in nucleic acid sequences. I learned that the only valid reading sequence is the one that does not have a stop or stop codon, because those are not full sequences.
2. What is not (yet) clear?
   • What is not yet clear for me is the purpose behind this experiment. Im just not sure how being able to come up with a new research idea, analyzing amino acids and their starker, has to do with the bioinformatics portion of the class. From my view, we are doing the same thing we have been doing for weeks, simply looking at it a little differently, but the methods are the same.
3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV. Explain whether you would be interested in playing this game and why or why not?
   • I think that putting this matter into a game form is a really good idea. This will help bring awareness to the issue because it is not in a 'work' form. Its a game, therefore people can fun playing it while learning about the antiviral drug at the same time.
4. Do you think that games like this could assist you in learning about protein structure? (I'm not asking you to play it, per se, although you can if you want; I just want you to comment based on reading the article.
   • I think creating a game out of almost any subject is a more efficient form of learning a subject. I think this because while someone is playing a game they are enjoy themselves and still processing information. Sometimes even memorizing information so they can beat the game. Plus, the different structures of protein structure could add levels and diverse aspects to the game, helping add to the learning experience.

Shivum A Desai 18:43, 31 October 2016 (EDT):

Matthew Allegretti

1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
   • I learned some surface level information that I would still need to revisit in order to understand protein structures more fully. Exploring and manipulating the structure of actual proteins was very helpful as it showed me how little I knew. I realized how difficult it was for me to identify various structures on the proteins.
2. What is not (yet) clear?
   • How the sequence of amino acids affects the overall function and structure. Is it possible to get two proteins with identical function that have completely different amino acid sequences with completely different conformations? How much of a role does conformation play in protein function in relation to amino acid sequence?
3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV.
   • Explain whether you would be interested in playing this game and why or why not?
     • I would be interested in playing this game to some degree. The fact that an entertaining pastime could potentially contribute to understanding of many proteins and diseases is definitely enticing.
   • Do you think that games like this could assist you in learning about protein structure? (I'm not asking you to play it, per se, although you can if you want; I just want you to comment based on reading the article.)
     • Yes. My knowledge of protein structure is definitely limited and could benefit from this. It would also provide a more interactive and less conventional way of learning it that I might actually find to be enjoyable to do in my free time.

Matthew R Allegretti 02:10, 1 November 2016 (EDT)