BIOL368/F11:Class Journal Week 7

Robert W. Arnold

1. The easiest part of the article was that it continued on the topic of HIV. Now that we have some background and general information, it is easier to get more in depth on a molecular level. I tend to enjoy molecular and it was interesting to come from a project like Markham that dealt with things on a broad scale to something very specified like the V3 region of the gp120 protein.
2. I found the article extremely challenging to read. Hopefully, it is due to lack of sleep and general tiredness as it has been a stressful week so far. I could not get a good understanding of the paper due to the repetition of antibodies, loop regions, residues, conformations, etc. I will definitely need more time and some possible extracurricular research to fully grasp this article. I plan to reread the article and go back over my outline in the next few days.
3. My new question is about the gp160 protein, the one that codes for gp41 and gp 120. I wonder if there could an antibody that could suppress the gp160 from even encoding gp120. If there were, I would be curious to see what the effects would be, whether or not the virus would use other means to attach to receptors. If gp120 is responsible for binding and it is no longer made, I would assume the virus would not be able to infect healthy cells.

Robert W Arnold 19:37, 12 October 2011 (EDT)

Isaiah M. Castaneda

1. Perhaps the main factors in being able to navigate through the article were having already been introduced to the HIV-1 virus through previous assignments and Dr. Dahlquist’s pre-assignment explanations. Another helpful factor was that within the article, there were many vibrant animations with meaningful captions and labels. They really helped to visualize what was being discussed in the paper. The wording/grammar was easy to follow as well.
2. The frequent in-text citations were a bit of an annoyance. It felt similar to enjoying a smooth drive, until a barrage of discourteous drivers cut you off. Naturally, I understand the importance of citing sources throughout an article, but coming across so many of them was just the first thing I recall peeving me. I have always preferred an endnotes style of in-text citing. Similar to what is difficult in any situation, there were still plenty of things that I was unfamiliar with. There was a vast amount of programs, procedures, and jargon that I had not previously heard of. This is what contributed to the bulk of the difficulty in reading the article.
3. A question that the article inspired is, if a V3-based fusion inhibitor were to be created, what are the odds of the virus’ success? Do we know if such a specific inhibitor is enough to conquer HIV-1, or does the virus have other means of binding that it my utilize?

Isaiah M. Castaneda 22:34, 16 October 2011 (EDT)

Alex A. Cardenas

1. The easiest aspect of reading/understanding my journal club article was the step by step details that it provided in order to get to the conclusion. I took a step back and tried to look at the bigger picture of what was going on, and writing it down on a piece of paper also helped.
2. The most difficult aspect of reading/understanding my journal club article was that there was so much information. There are so many little details and didn't know if I should include them in my outline. Another hard part was trying to understand all the different numbers and abbreviations because once a protein or enzyme was named, they almost always had an abbreviation for the rest of the reading.
3. What biological functions does the flexibility of the V3 loop conformation possess?

Alex A. Cardenas Alex A. Cardenas 17:10, 17 October 2011 (EDT)

Nicolette S. Harmon

1. The easiest way for me to understand this article was to read the end of the introduction so that I knew what questions were going to investigated and hopefully answered. I also found it helpful to read the legends that go with each figure because they act as a narration for what's happening in the figure and what the results were.
2. It was difficult to follow along with this article because there was so much information. The way the article was organized also made it difficult to follow, the sections the article was broken up into felt random and I couldn't tell why they would suddenly switch topics.
3. My question is if it's possible to remove the water cavity from gp120, what would happen if an antibody could bind there?

Nicolette S. Harmon 21:36, 17 October 2011 (EDT)

Chris Rhodes

1. The easiest part of reading my article was actually the discussion section. It summed up very concisely and very clearly what the results and conclusions of the study were and helped me to better understand what all the other information in the paper was telling me.
2. This article was particularly difficult to follow when I read it through the first time. This is the first article I've ever read about protein structure so most of the data the article was presenting went right over my head. It took me a couple of reads to finally understand the significance of the article and what each figure, table, and section was telling me although I still don't fully understand the Materials and Methods section.
3. The main limitation of this paper is that it was only looking at truncated versions of the V3 peptide independent of the rest of gp120. I would like to see if the assertion that V3 loop conformation alters gp120 functionality is true by looking at various intact gp120-anitbody complexes.

Chris H. Rhodes 00:41, 18 October 2011 (EDT)

Zeb Russo

1. The easiest part of the article was probably the very beginning when they were discussing the general structure of HIV
2. The hardest section was probably everything else about this article. It immediately dived into technical discussion about the orientation and structure of gp120. Among all this the hardest was most likely the figures 2 and 3 which went into great detail about every facet of the interaction between CD4 and gp120
3. I would like to know more about how the chemokine receptor works and the obligate 2ndary receptor and its role. Also learning more about gp41 would be cool too.

Zeb Russo 22:59, 18 October 2011 (EDT)

Samantha Hurndon

1. The easiest part of understanding the article was when looking at the figures. The visual help to put everything together.
2. The most difficult part for me was when the article talked about antibody binding, also I was very confused with the carbon tracing figure.
3. I would like to know more about the V3 loop as well as the larger cavity that they did not go into great deal about as they did for the Phe cavity

Samantha Hurndon 22:59, 18 October 2011 (EDT)