Jennymchua Week 8 Assignment

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Purpose

Google Scholar

  • Record the number of "hits" you found:
    • about 61,300 results
  • Record the top 10 papers, this time using APA format:
    • Rizzuto, C. D., Wyatt, R., Hernández-Ramos, N., Sun, Y., Kwong, P. D., Hendrickson, W. A., & Sodroski, J. (1998). A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding. Science, 280(5371), 1949-1953.
    • Wyatt, R., Kwong, P. D., Desjardins, E., Sweet, R. W., Robinson, J., Hendrickson, W. A., & Sodroski, J. G. (1998). The antigenic structure of the HIV gp120 envelope glycoprotein. Nature, 393(6686), 705-711.
    • Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J., & Hendrickson, W. A. (1998). Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature, 393(6686), 648-659.
    • Huang, C. C., Tang, M., Zhang, M. Y., Majeed, S., Montabana, E., Stanfield, R. L., ... & Wyatt, R. (2005). Structure of a V3-containing HIV-1 gp120 core. Science, 310(5750), 1025-1028.
    • Zhou, T., Xu, L., Dey, B., Hessell, A. J., Van Ryk, D., Xiang, S. H., ... & Burton, D. R. (2007). Structural definition of a conserved neutralization epitope on HIV-1 gp120. Nature, 445(7129), 732-737.
    • Kwong, P. D., Wyatt, R., Majeed, S., Robinson, J., Sweet, R. W., Sodroski, J., & Hendrickson, W. A. (2000). Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure, 8(12), 1329-1339.
    • McLellan, J. S., Pancera, M., Carrico, C., Gorman, J., Julien, J. P., Khayat, R., ... & O’Dell, S. (2011). Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9. Nature, 480(7377), 336-343.
    • Poignard, P., Saphire, E. O., Parren, P. W., & Burton, D. R. (2001). gp120: biologic aspects of structural features. Annual review of immunology, 19(1), 253-274.
    • Chen, L., Do Kwon, Y., Zhou, T., Wu, X., O’Dell, S., Cavacini, L., ... & Yang, Z. Y. (2009). Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120. Science, 326(5956), 1123-1127.
    • Myszka, D. G., Sweet, R. W., Hensley, P., Brigham-Burke, M., Kwong, P. D., Hendrickson, W. A., ... & Doyle, M. L. (2000). Energetics of the HIV gp120-CD4 binding reaction. Proceedings of the National Academy of Sciences, 97(16), 9026-9031.
  • Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    • Bontempo, A., Garcia, M. M., Rivera, N., & Cayabyab, M. J. (2020). A Systematic Approach to HIV-1 Vaccine Immunogen Selection. AIDS Research and Human Retroviruses, (ja).
    • Li, Y., Guo, Y. C., Zhang, X. L., Deng, L., Sang, P., Yang, L. Q., & Liu, S. Q. (2020). CD4-binding obstacles in conformational transitions and allosteric communications of HIV gp120. Biochimica et Biophysica Acta (BBA)-Biomembranes, 183217.
    • Silver, Z. A., Antonopoulos, A., Haslam, S. M., Dell, A., Dickinson, G. M., Seaman, M. S., & Desrosiers, R. C. (2020). Discovery of O-Linked Carbohydrate on HIV-1 Envelope and Its Role in Shielding against One Category of Broadly Neutralizing Antibodies. Cell Reports, 30(6), 1862-1869.
    • Kawashita, N. (2020). Interaction Analysis between HIV gp120 and the Antibodies by Fragment Molecular Orbital Method. Biophysical Journal, 118(3), 305a.
    • Le, C. B., LiWang, P., & Colvin, M. E. (2020). In-Silico Exploration of Antiviral Lectin Griffithsin. Biophysical Journal, 118(3), 505a.
  • Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • Shaik, M. M., Peng, H., Lu, J., Rits-Volloch, S., Xu, C., Liao, M., & Chen, B. (2019). Structural basis of coreceptor recognition by HIV-1 envelope spike. Nature, 565(7739), 318-323.
    • Li, Y., Guo, Y. C., Zhang, X. L., Deng, L., Sang, P., Yang, L. Q., & Liu, S. Q. (2020). CD4-binding obstacles in conformational transitions and allosteric communications of HIV gp120. Biochimica et Biophysica Acta (BBA)-Biomembranes, 183217.
    • Gorman, J., Mason, R. D., Nettey, L., Cavett, N., Chuang, G. Y., Peng, D., ... & Biris, K. (2019). Isolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan Shields. Immunity, 51(4), 724-734.
    • Morton, S. P., Phillips, J. B., & Phillips, J. L. (2019). The Molecular Basis of pH-Modulated HIV gp120 Binding Revealed. Evolutionary Bioinformatics, 15, 1176934319831308.
    • Gawron, M. A., Duval, M., Carbone, C., Jaiswal, S., Wallace, A., Martin, J. C., ... & Luban, J. (2019). Human Anti–HIV-1 gp120 Monoclonal Antibodies with Neutralizing Activity Cloned from Humanized Mice Infected with HIV-1. The Journal of Immunology, 202(3), 799-804.
  • Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    • Wang, H., Cohen, A. A., Galimidi, R. P., Gristick, H. B., Jensen, G. J., & Bjorkman, P. J. (2016). Cryo-EM structure of a CD4-bound open HIV-1 envelope trimer reveals structural rearrangements of the gp120 V1V2 loop. Proceedings of the National Academy of Sciences, 113(46), E7151-E7158.
    • Zheng, Y., Han, G. W., Abagyan, R., Wu, B., Stevens, R. C., Cherezov, V., ... & Handel, T. M. (2017). Structure of CC chemokine receptor 5 with a potent chemokine antagonist reveals mechanisms of chemokine recognition and molecular mimicry by HIV. Immunity, 46(6), 1005-1017.
    • Wibmer, C. K., Gorman, J., Ozorowski, G., Bhiman, J. N., Sheward, D. J., Elliott, D. H., ... & Druz, A. (2017). Structure and recognition of a novel HIV-1 gp120-gp41 interface antibody that caused MPER exposure through viral escape. PLoS pathogens, 13(1).
    • Shaik, M. M., Peng, H., Lu, J., Rits-Volloch, S., Xu, C., Liao, M., & Chen, B. (2019). Structural basis of coreceptor recognition by HIV-1 envelope spike. Nature, 565(7739), 318-323.
    • Gristick, H. B., von Boehmer, L., West Jr, A. P., Schamber, M., Gazumyan, A., Golijanin, J., ... & Bjorkman, P. J. (2016). Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site. Nature structural & molecular biology, 23(10), 906.
  • We will now make a list of the search terms that were used by each student in the class. Record the list written on the board here:
    • structure-function mutation gp120
    • structure and function of gp120
    • structure of gp120
    • gp120
    • gp120 structure and function
    • gp120 structure function
    • mutations in the gp120 protein
    • HIV-1 gp120 protein mutation
    • gp120 mutations structure function
    • mutations in gp120
    • HIV gp120 mutation
    • mutations gp120
    • HIV gp120
  • Record the search terms that have now been assigned specifically to you:
    • HIV
    • gp120
    • structure

PubMed

  • Record the total number of hits:
    • 1,763
  • Record the top 10 papers (you don't need to do APA format for this):
    • Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque Cd4 and CC45.
    • A Systematic Approach to HIV-1 Vaccine Immunogen Selection
    • Cryo-EM Structure of Full-length HIV-1 Env Bound With the Fab of Antibody PG16.
    • The Envelope-Based Fusion Antigen GP120C14K Forming Hexamer-Like Structures Triggers T Cell and Neutralizing Antibody Response Against HIV-1.
    • Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry.
    • Scaffold Simplification Strategy Leads to a Novel Generation of Dual Human Immunodeficiency Virus and Enterovirus-A71 Entry Inhibitors
    • Boosting with AIDSVAX B/E Enhances Env Constant Region 1 and 2 Antibody-Dependent Cellular Cytotoxicity Breadth and Potency.
    • Opening dynamics of HIV-1 gp120 upon receptor binding is dictated by a key hydrophobic core.
    • The lipid membrane of HIV-1 stabilizes the viral envelope glycoproteins and modulates their sensitivity to antibody neturalization.
    • Characterization of resistance to a potent D-peptide HIV entry inhibitor.
  • Perform a title/abstract search on your assigned keywords. Record the total number of hits:
    • 22
  • Record the top 10 papers (you don't need to do APA format for this):
    • Human Anti-HIV-1 gp120 Monoclonal Antibodies with Neutralizing Activity Cloned from Humanized Mice Infected with HIV-1.
    • In silico Analysis of HIV-1 Env-gp120 Reveals Structural Bases for Viral Adaptation in Growth-Restrictive Cells.
    • Range of CD4-Bound Conformations of HIV-1 gp120, as Defined Using Conditional CD4-Induced Antibodies.
    • REVIEW: HIV-1 gp120 as a therapeutic target: navigating a moving labyrinth.
    • The influence of N-linked glycans on the molecular dynamics of the HIV-1 gp120 V3 loop.
    • Highly conserved HIV-1 gp120 glycans proximal to CD4-binding region affect viral infectivity and neutralizing antibody induction.
    • Increasing the potency and breadth of an HIV antibody by using structure-based rational design.
    • Probing the HIV gp120 envelope glycoprotein conformation by NMR.
    • Correlated mutations at gp120 positions 322 and 440: implications for gp120 structure.
    • Effect of chloroquine on reducing HIV-1 replication in vitro and the DC-SIGN mediated transfer of virus to CD4+ T-lymphocytes.
  • Pick an author that shows up in multiple citations (if there isn’t one, just pick a last author from one of the papers) and perform an author search on the name.
      • Author name is Rizzuto CD.
    • Did you find any new articles that you did not find before on PubMed?
      • Yes, I found three new results.
    • List up to 5 new articles that were found on the author name search:
      • Mutagenic stabilization and/or disruption of a CD4-bound state reveals distinct conformations of the human immunodeficiency virus type 1 gp120 envelope glycoprotein.
      • A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding.
      • Contribution of virion ICAM-1 to human immunodeficiency virus infectivity and sensitivity to neutralization.

Web of Science

  • Record the total number of hits:
    • 1,294
  • Record the top 10 papers (you don't need to use APA format for this):
    • Discoveries and developments of CXCR4-targeted HIV-1 entry inhibitors.
    • Boosting with AIDSVAX B/E Enhances Env Constant Region 1 and 2 Antibody-Dependent Cellular Cytotoxicity Breadth and Potency.
    • The lipid membrane of HIV-1 stabilizes the viral envelope glycoproteins and modulates their sensitivity to antibody neutralization.
    • Scaffold Simplification Strategy Leads to a Novel Generation of Dual Human Immunodeficiency Virus and Enterovirus-A71 Entry Inhibitors.
    • The Genetic Diversity of HIV-1 Quasispecies Within Primary Infected Individuals.
    • Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry.
    • Catalytic antibody (catabody) platform for age-associated amyloid disease: From Heisenberg's uncertainty principle to the verge of medical interventions.
    • HIV-1 Coreceptor Usage and Variable Loop Contact Impact V3 Loop Broadly Neutralizing Antibody Susceptibility
    • Griffithsin Retains Anti-HIV-1 Potency with Changes in gp120 Glycosylation and Complements Broadly Neutralizing Antibodies PGT121 and PGT126.
    • SOS and IP Modifications Predominantly Affect the Yield but Not Other Properties of SOSIP.664 HIV-1 Env Glycoprotein Trimers.

Questions

What are the relative merits of searching with Google Scholar, PubMed, and Web of Science? Name two advantages and disadvantages for each.

    • Google Scholar
      • advantages: gives pre-made citations, bolds keywords in titles
      • disadvantages: can be too broad, "search by relevance" is arbitrary (what is considered relevant?)
    • PubMed
      • advantages: monitored and funded by the U.S. National Library of Medicine, can search by specific filters (i.e., species of subjects)
      • disadvantages: not as many broad articles as Google Scholar, does not give pre-made citation
    • Web of Science
      • advantages: has information needed for a citation on search page, easy to read interface
      • disadvantages: comes out of LMU tuition dollars (not free), redirects to Kopernio to read PDF (Google Chrome extension)

What impact does choice of keywords have on your results?

Using the example we did in class, "structure-function," "structure and function," and "structure function" can produce different results and journal articles, even though there are subtle differences between all three. Thus, it is important to know the intent behind what one is trying to achieve before searching so as to get the best and most narrowed-down results.

Now we will begin to evaluate your assigned article in three areas availability, the journal, and the article metadata. Again, provide a citation for the article in APA format, this time including the DOI. For the following questions, for information that is not available, answer n/a).

Bontempo, A., Garcia, M. M., Rivera, N., & Cayabyab, M. J. (2020). A Systematic Approach to HIV-1 Vaccine Immunogen Selection. AIDS Research and Human Retroviruses, (ja). doi:10.1089/AID.2019.0239.

Provide a link to the abstract of the article on PubMed.

https://www.ncbi.nlm.nih.gov/pubmed/32056466

Provide a link to the full text of the article in PubMed Central.

n/a

Provide a link to the full text of the article (HTML format) from the publisher website.

n/a

Provide a link to the full PDF version of the article from the publisher website.

https://www.liebertpub.com/doi/abs/10.1089/AID.2019.0239

Who owns the rights to the article? Look at the first page of the PDF version of the article for the © symbol. Generally, either the journal/publisher or the authors will hold the copyright.

Mary Ann Liebert, Inc. Publishers

How is the article available to you:

    • Is the article available “open access” (look for the words “open access” or the “unlocked” icon on the article website or the first page of the PDF) If YES, stop here.
      • No.
    • If the article is not “open access” is it available for free after a certain period of time has elapsed? You would not find the words “open access” or the “unlocked” icon, but you would still be able to access the article. If YES, stop here.
      • No.
    • Did LMU buy a subscription or pay a fee for your access to this article? You might see “Loyola Marymount University” or “LMU” on the article website. Alternately, a list of the journals that LMU pays for can be found at: http://sq4ya5rf2q.search.serialssolutions.com/ If YES, stop here.
      • No.
    • Is the article behind a paywall or “subscription-only”? Your attempts to access it when on the LMU network have failed. In this case, if you needed the article, you would use the ILLIAD system to request it by logging in here: https://lmu.illiad.oclc.org/illiad/illiad.dll?Action=99. Note that you don’t need to actually request it for this assignment.
      • Yes.
    • Is the article available online-only or both in print and online? Look on the journal website for a “subscription” link. If that page talks about subscribing to the print edition, then it is available in print. If not, it is available online-only.
      • The article is available online and in print, though they are both behind a "pay wall" in which one has to pay to access the full text.

Evaluating the source: the journal.

Who is the publisher of the journal?

Mary Ann Liebert, Inc. Publishers.

Is the publisher for-profit or non-profit?

It is unclear whether or not Mary Ann Liebert, Inc. Publishers is for-profit or non-profit, as some of the journals it publishes are for-profit and some are non-profit.

Is the publisher a scientific society? (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)

The publisher is a scientific society.

Does the publisher belong to the Open Access Publishers Association?

No.

What country is the journal published in?

The United States.

How long has the journal been in operation? (e.g., browse the archive for the earliest article published)

Since 1983 (37 years).

Are articles in this journal peer-reviewed?

Yes.

Provide a link to the scientific advisory board/editorial board of the journal.

https://home.liebertpub.com/publications/aids-research-and-human-retroviruses/2/editorial-board

What is the journal impact factor? (look to see if it is provided on the journal home page; often you can also find it through a Google search)

1.805.

Evaluating the source: the article.

Is the article a review or primary research article?

The article is a primary research article.

On what date was the article submitted?

It is unclear as to when the article was submitted.

On what date was the article accepted?

It is unclear as to when the article was accepted.

Did the article undergo any revisions before acceptance?

It is unclear as to whether or not the article underwent revisions before acceptance.

When was the article published?

The article was published on February 14, 2020.

What is the approximate elapsed time between submission and publication?

The approximate elapsed time between submission and publication is unclear.

What are the institutions with which the authors are affiliated?

All four authors are associated with the Forsyth Institute in Cambridge, Massachusetts.

Have the authors published other articles on this subject?

Yes. Bontempo has published an article called, "Molecular iodine impairs chemoresistance mechanisms, enhances doxorubicin retention and induces downregulation of the CD44+/CD24+ and E-cadherin+/vimentin+ subpopulations in MCF-7 cells resistant to low doses of doxorubicin."

Is there a conflict of interest for any other authors?

All of the authors have associations and background information with oncology, which is not related to HIV-1.

Read the abstract. Write 1-2 sentences about the relevance of this article to understanding the structure-function relationship of mutations in the HIV-1 gp120 protein.

The purpose of this paper is to find a vaccine that best targets certain proteins, including gp120, in order to produce antibodies to the HIV-1 virus. With regards to the structure-function relationship of mutations in the HIV-1 gp120 protein, the paper does not directly address the mechanism of the relationship.

Make a recommendation--based on the information you have gathered, should we do a journal club on this article? Why or why not?

We should probably not do a journal club on this article, mainly because it does not focus on the structure-function relationship of mutations in the HIV-1 gp120 protein nor is the paper available in an accessible format.

Conclusion

This exercise helped me to learn how important searching literature databases are, mostly in terms of keywords and how they align with one's purpose. I was taught before that words like "and" and "in" were not important, but after searching "structure function" and "structure and function," we are presented with two totally different search results. Thus, I think it is crucial to go into a database search with a goal of what one is looking for, so as to narrow down the results as efficiently and appropriately as possible.

Acknowledgments

  • I worked with my homework partner Nick Yeo in class.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Jennymchua (talk) 19:54, 25 March 2020 (PDT)

References

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