Carolyne week 8

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Purpose

The purpose of this activity is to determine optimal ways to search for journal articles related to the structure-function relationships in the gp120 region of the Env protein in HIV using Google Scholar, PubMed, and Web of Science. This way, a library of relevant articles can be made to use in developing a research project looking at structure-function related to HIV gp120.

Searching for Articles

HIV Structure Function

Class Search Term

  • Class generated search terms: mutations in gp120, HIV gp120 mutation, mutations gp120, HIV gp120, structure-function mutation gp120, structure and function of gp120, structure of gp120, gp120, gp120 structure and function, gp120 structure function, mutaions in the gp120 protein, HIV gp120 protein mutation, gp120 mutation structure
  • Assigned Search Term: HIV gp120 structure variation

Google Scholar

  • Hits with the assigned search term: 28,300
Top Ten Pages
    1. White, T. A., Bartesaghi, A., Borgnia, M. J., Meyerson, J. R., de la Cruz, M. J., Bess, J. W., Nandwani, R., Hoxie, J. A., Lifson, J. D., Milne, J. L., & Subramaniam, S. (2010). Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure. PLoS pathogens, 6(12), e1001249. https://doi.org/10.1371/journal.ppat.1001249
    2. 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.
    3. Siliciano, R. F., Lawton, T., Knall, C., Karr, R. W., Berman, P., Gregory, T., & Reinherz, E. L. (1988). Analysis of host-virus interactions in AIDS with anti-gp120 T cell clones: effect of HIV sequence variation and a mechanism for CD4+ cell depletion. Cell, 54(4), 561-575.
    4. Fouchier, R. A., Groenink, M., Kootstra, N. A., Tersmette, M., Huisman, H. G., Miedema, F., & Schuitemaker, H. (1992). Phenotype-associated sequence variation in the third variable domain of the human immunodeficiency virus type 1 gp120 molecule. Journal of virology, 66(5), 3183. Retrieved from http://jvi.asm.org/content/66/5/3183.abstract
    5. Huang, C.-c., Tang, M., Zhang, M.-Y., Majeed, S., Montabana, E., Stanfield, R. L., . . . Kwong, P. D. (2005). Structure of a V3-Containing HIV-1 gp120 Core. Science, 310(5750), 1025. doi:10.1126/science.1118398
    6. 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. doi:10.1038/31514
    7. 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. doi:https://doi.org/10.1016/S0969-2126(00)00547-5
    8. Merk, A., & Subramaniam, S. (2013). HIV-1 envelope glycoprotein structure. Current opinion in structural biology, 23(2), 268-276. https://doi.org/10.1016/j.sbi.2013.03.007
    9. 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. doi:10.1126/science.280.5371.1949
    10. Jiang, X., Burke, V., Totrov, M., Williams, C., Cardozo, T., Gorny, M. K., . . . Kong, X.-P. (2010). Conserved structural elements in the V3 crown of HIV-1 gp120. Nature Structural & Molecular Biology, 17(8), 955-961. doi:10.1038/nsmb.1861
Sort by Date
  • Salimi, H., Johnson, J., Flores, M. G., Zhang, M. S., O'Malley, Y., Houtman, J. C., ... & Haim, H. (2020). The lipid membrane of HIV-1 stabilizes the viral envelope glycoproteins and modulates their sensitivity to antibody neutralization. Journal of Biological Chemistry, 295(2), 348-362.
  • Vangala, R., Sivan, S. K., Peddi, S. R., & Manga, V. (2020). Computational design, synthesis and evaluation of new sulphonamide derivatives targeting HIV-1 gp120. Journal of Computer-Aided Molecular Design, 34(1), 39-54.
  • Wang, S., Voronin, Y., Zhao, P., Ishihara, M., Mehta, N., Porterfield, M., ... & Wells, L. (2020). Glycan profiles of gp120 protein vaccines from four major HIV-1 subtypes produced from different host cell lines under non-GMP or GMP conditions. Journal of Virology.
  • Schommers, P., Gruell, H., Abernathy, M. E., Tran, M. K., Dingens, A. S., Gristick, H. B., ... & Kreer, C. (2020). Restriction of HIV-1 escape by a highly broad and potent neutralizing antibody. Cell.
  • van Dorsten, R. T., Lambson, B. E., Wibmer, C. K., Weinberg, M. S., Moore, P. L., & Morris, L. (2020). Neutralization breadth and potency of single-chain variable fragments derived from broadly neutralizing antibodies targeting multiple epitopes on the HIV-1 envelope. Journal of Virology, 94(2).

Google Scholar Results Since 2019

  1. Morton, S. P., Phillips, J. B., & Phillips, J. L. (2019). The Molecular Basis of pH-Modulated HIV gp120 Binding Revealed. Evolutionary Bioinformatics. https://doi.org/10.1177/1176934319831308
  2. Palmer, J., & Poon, A. F. (2019). Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes. Virus evolution, 5(2), https://doi.org/10.1093/ve/vez022.
  3. Lamers, S. L., Fogel, G. B., Nolan, D. J., Barbier, A. E., Rose, R., Singer, E. J., ... & McGrath, M. S. (2019). Emerging patterns in HIV-1 gp120 variable domains in anatomical tissues in the absence of a plasma viral load. AIDS research and human retroviruses, 35(6), 588-596. https://doi.org/10.1089/aid.2018.0267
  4. 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. https://doi.org/10.1016/j.immuni.2019.09.007
  5. Kumar, S., Sarkar, A., Pugach, P., Sanders, R. W., Moore, J. P., Ward, A. B., & Wilson, I. A. (2019). Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide. Nature communications, 10(1), 1-10. https://doi.org/10.1038/s41467-019-08738-5

Google Scholar Results Since 2016

  1. Yolitz, J., Schwing, C., Chang, J., Van Ryk, D., Nawaz, F., Wei, D., ... & Fauci, A. S. (2018). Signal peptide of HIV envelope protein impacts glycosylation and antigenicity of gp120. Proceedings of the National Academy of Sciences, 115(10), 2443-2448.
  2. Morton, S. P., Phillips, J. B., & Phillips, J. L. (2019). The Molecular Basis of pH-Modulated HIV gp120 Binding Revealed. Evolutionary Bioinformatics. https://doi.org/10.1177/1176934319831308
  3. Munro, J. B., & Lee, K. K. (2018). Probing structural variation and dynamics in the HIV-1 Env fusion glycoprotein. Current HIV research, 16(1), 5-12.
  4. Palmer, J., & Poon, A. F. (2019). Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes. Virus evolution, 5(2), https://doi.org/10.1093/ve/vez022.
  5. Lamers, S. L., Fogel, G. B., Nolan, D. J., Barbier, A. E., Rose, R., Singer, E. J., ... & McGrath, M. S. (2019). Emerging patterns in HIV-1 gp120 variable domains in anatomical tissues in the absence of a plasma viral load. AIDS research and human retroviruses, 35(6), 588-596. https://doi.org/10.1089/aid.2018.0267

Pubmed Search Results

  • Hits: 188
Top 10 Papers
  1. The HIV-1 gp120 V1V2 loop: structure, function and importance for vaccine development (Review)
  2. Structure and immune recognition of trimeric pre-fusion HIV-1 Env.
  3. Range of CD4-Bound Conformations of HIV-1 gp120, as Defined Using Conditional CD4-Induced Antibodies.
  4. Signal peptide of HIV envelope protein impacts glycosylation and antigenicity of gp120.
  5. The V1V2 Region of HIV-1 gp120 Forms a Five-Stranded Beta Barrel.
  6. HIV Subtypes B and C gp120 and Methamphetamine Interaction: Dopaminergic System Implicates Differential Neuronal Toxicity.
  7. HIV/SIV glycoproteins: structure-function relationships.
  8. The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins.
  9. Prediction of the secondary structure of HIV-1 gp120.
  10. Antigenic variation in gp120s from molecular clones of HIV-1 LAI.
Author Search
  • I was able to find a couple of articles that I did not find on Pubmed before, which are shown in the list below.
  • New articles
    1. Crystal structure of an HIV-binding recombinant fragment of human CD4
    2. A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding
    3. Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody
    4. Probability analysis of variational crystallization and its application to gp120, the exterior envelope glycoprotein of type 1 human immunodeficiency virus (HIV-1)
    5. Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates

Web of Science Search Results

  • Hits: 88
Top 10 Hits
  1. The lipid membrane of HIV-1 stabilizes the viral envelope glycoproteins and modulates their sensitivity to antibody neutralization
  2. Strain-Dependent Activation and Inhibition of Human Immunodeficiency Virus Entry by a Specific PF-68742 Stereoisomer
  3. Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies
  4. Signal peptide of HIV envelope protein impacts glycosylation and antigenicity of gp120
  5. Insights into the molecular mechanism underlying CD4-dependency and neutralization sensitivity of HIV-1: a comparative molecular dynamics study on gp120s from isolates with different phenotypes
  6. Protein structural disorder of the envelope V3 loop contributes to the switch in human immunodeficiency virus type 1 cell tropism
  7. Chemical optimization of macrocyclic HIV-1 inactivators for improving potency and increasing the structural diversity at the triazole ring
  8. Determinants of HIV-1 CD4-Independent Brain Adaptation
  9. Antigenicity-defined conformations of an extremely neutralization-resistant HIV-1 envelope spike
  10. Evidence of Divergent Amino Acid Usage in Comparative Analyses of R5-and X4-Associated HIV-1 Vpr Sequences

Advantages vs. Disadvantages of Each Search Engine

  • Advantages of Google Scholar: Google scholar returns a wide number of results. In addition, it bolds the keywords in the results and gives easy access to the citations for the articles.
  • Disadvantages of Google Scholar: Because google scholar gives so many results, it's hard to tell which ones are useful to a research project. In addition, some of these results are not scientific papers, but citations, doctoral theses, or patents.
  • Advantages of PubMed: PubMed is more specialized, so it returns fewer search results but they are more closely related to the search topic. In addition, I can be specific in my search for an article (ex. only looking for review articles, only looking for primary journal articles, etc.).
  • Disadvantages of Pubmed: PubMed is limited to biomedical research primarily. In addition, it does not tell you which papers you have access to as a student at LMU.
  • Advantages of Web of Science: Web of Science is the easiest to use if I am looking for articles that newer articles that cited a specific paper, or to determine the articles a published paper cited. Web of Science is also useful because it has a wider range of focus beyond biomedical research.
  • Disadvantages of Web of Science: Searching with Web of Science gave a really small number of search results. In addition, the search function is not as specific is the one in PubMed.

Impact of Key Words

In doing the searches on each search engine, I found that the keywords I used could impact the articles that I received. For example, when I searched with my assigned term (HIV gp120 structure variation) in Google Scholar, I primarily received articles that focused solely on the structure of HIV gp120. But when I use the term "HIV gp120 structure-function," I get papers that specifically look at how the structure impacts HIV function that did not appear in my other search. Thus choosing the right keywords is important to find journal articles that are relevant to what I want to research and study.

Analyzing an Article

  • Assigned article: Yolitz, J., Schwing, C., Chang, J., Van Ryk, D., Nawaz, F., Wei, D., Cicala, C., Arthos, J., & Fauci, A. S. (2018). Signal peptide of HIV envelope protein impacts glycosylation and antigenicity of gp120. Proceedings of the National Academy of Sciences of the United States of America, 115(10), 2443–2448. https://doi.org/10.1073/pnas.1722627115
  • My article has 56 cited references.
  • My article has been cited 7 times by other articles.

Article Availability

Article Availability

Evaluating the Source: The Journal

  • The article was published in the Proceedings of the National Academy of Sciences of the United States of America (PNAS)
    • Journal Publisher: The National Academy of Sciences (NAS)
      • NAS is a non-profit organization
      • NAS is a very prestigious honors society for distinguished scientists ("Mission").
      • The publisher does not belong to the Open Access Publishers Association.
      • The journal is published in the United States of America.
      • The journal has been in operation since 1915.
      • The articles in the journal are peer-reviewed.
      • PNAS Editorial Board: https://www.pnas.org/page/about/editorial-board
      • Journal Impact Factor: 9.5804 ("PNAS Article and Journal Metrics")

Evaluating the Source: The Article

  • The article is a primary research article.
  • The article was submitted on January 2, 2018. It was accepted on January 29, 2018.
  • They do not state if the article underwent any revisions before being accepted.
  • The article was published online on published February 20, 2018. It was also included in the issue of PNAS released on March 6, 2018.
  • The elapsed time between submission and publication was about four weeks.
  • The authors are affiliated with the National Institute of Allergy and Infectious Diseases and National Institutes of Health–Johns Hopkins University Graduate Partnership Program. Both of these are ultimately affiliated with the National Institutes of Health.
  • The authors have published other articles on this subject. By looking at the publications in PubMed for author J. Yolitz, it appears that this author has published several papers studying gp120 in HIV. The corresponding author, Dr. Anthony S. Fauci, has published many studies related to HIV, but not all of them are specifically related to gp120.
  • The authors declared they had no conflicts of interest.
  • Relevance: So far, we have looked at sequences of the V3 region in gp120 to study HIV evolution. This paper is relevant because it talks about the structure of the HIV gp120 region in the ENV protein. Specifically, the found that the amino acid residues at the Env signal peptide gange the glycosylation sites in the protein, which affects the antigenicity of HIV gp120.
  • Recommendation: Since gp120 is important for the HIV virus to enter the cell and the next project is focused on HIV structure, I think this paper would be an ok paper to read. While it isn't focused on the V3 region specifically, the fact that they analyzed the amino acids and determined how that could impact the HIV virus might help to provide ideas about the structure project. The only downside is that just based on the abstract alone, it seems like it would be a jargon-heavy and challenging paper to understand in detail.

Conclusion

The purpose of this activity was to find the best methods for finding relevant scientific articles on HIV's gp120 region and to create a list of resources that can be used to develop a project studying HIV's gp120 region. Based on this activity, I believe I have found a good amount of articles that are informative about HIV gp120's structure-function relationships.

Going into this assignment, I was already quite comfortable with using Google Scholar and PubMed because I have had to use these resources in the past to find journal articles for literature reviews and research papers I've written in my classes. I knew that picking the right keywords was important and that having the wrong keywords could prevent me from finding articles relevant to me. After this assignment, I learned about how using the same keywords in different search engines/databases can lead to different results. I also learned about Web of Science, which I think will be useful in my HIV project. Finally, I learned about the importance of examining a journal article to see who wrote and published it, since that could affect how I read and understand the paper.

Acknowledgements

I copied and modified the assignment from the Week 8 assignment page to complete the sections about the search engines and the journal article. I used the PNAS site and NAS site to find more information about the PNAS journal. My homework partner Nathan helped me find the publishing and copyright information for my article. Except for what is noted above, this individual journal entry was completed by me and not copied from another source Carolyne (talk) 22:29, 25 March 2020 (PDT)

Refrences

User Page and Template Links

Individual Journal Pages

  1. Carolyne week 2
  2. Carolyne week 3
  3. Carolyne week 4
  4. Carolyne week 5
  5. Carolyne week 6
  6. Carolyne week 8
  7. Carolyne week 9
  8. Carolyne week 10
  9. Carolyne week 13
  10. Carolyne week 14

Weekly Assignments

  1. BIOL368/S20:Week 1
  2. BIOL368/S20:Week 2
  3. BIOL368/S20:Week 3
  4. BIOL368/S20:Week 4
  5. BIOL368/S20:Week 5
  6. BIOL368/S20:Week 6
  7. BIOL368/S20:Week 8
  8. BIOL368/S20:Week 9
  9. BIOL368/S20:Week 10
  10. BIOL368/S20:Week 13
  11. BIOL368/S20:Week 14

Class Journal Pages

  1. BIOL368/S20:Class Journal Week 1
  2. BIOL368/S20:Class Journal Week 2
  3. BIOL368/S20:Class Journal Week 3
  4. BIOL368/S20:Class Journal Week 4
  5. BIOL368/S20:Class Journal Week 5
  6. BIOL368/S20:Class Journal Week 6
  7. BIOL368/S20:Class Journal Week 8
  8. BIOL368/S20:Class Journal Week 9
  9. BIOL368/S20:Class Journal Week 10
  10. BIOL368/S20:Class Journal Week 13
  11. BIOL368/S20:Class Journal Week 14