Non: Week 8

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Course Work
Assignments Journal Pages Shared Class Journal Pages
BIOL368/S20:Week 1 BIOL368/S20:Class Journal Week 1
BIOL368/S20:Week 2 Non: Week 2 BIOL368/S20:Class Journal Week 2
BIOL368/S20:Week 3 Non: Week 3 BIOL368/S20:Class Journal Week 3
BIOL368/S20:Week 4 Non: Week 4 BIOL368/S20:Class Journal Week 4
BIOL368/S20:Week 5 Non: Week 5 BIOL368/S20:Class Journal Week 5
BIOL368/S20:Week 6 Non: Week 6 BIOL368/S20:Class Journal Week 6
BIOL368/S20:Week 8 Non: Week 8 BIOL368/S20:Class Journal Week 8
BIOL368/S20:Week 10 Non: Week 10 BIOL368/S20:Class Journal Week 10
BIOL368/S20:Week 13 Non: Week 13 BIOL368/S20:Class Journal Week 13
BIOL368/S20:Week 14 Non: Week 14 BIOL368/S20:Class Journal Week 14

Purpose

The purpose of this lab to gain practice using a variety of scientific article/journal search engines to find optimal search results.

Assignment

Google Scholar

search term - "HIV-1 gp120 structure"

  • Number of hits = 53,100
  • Record the top 10 papers, this time using APA format:
    • 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.
    • 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.
    • Liu, J., Bartesaghi, A., Borgnia, M. J., Sapiro, G., & Subramaniam, S. (2008). Molecular architecture of native HIV-1 gp120 trimers. Nature, 455(7209), 109-113.
    • 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.
    • Huang, C. C., Lam, S. N., Acharya, P., Tang, M., Xiang, S. H., Hussan, S. S. U., ... & Wyatt, R. (2007). Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science, 317(5846), 1930-1934.
    • 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.
    • Pancera, M., Majeed, S., Ban, Y. E. A., Chen, L., Huang, C. C., Kong, L., ... & Schief, W. R. (2010). Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility. Proceedings of the National Academy of Sciences, 107(3), 1166-1171.
    • Koch, M., Pancera, M., Kwong, P. D., Kolchinsky, P., Grundner, C., Wang, L., ... & Wyatt, R. (2003). Structure-based, targeted deglycosylation of HIV-1 gp120 and effects on neutralization sensitivity and antibody recognition. Virology, 313(2), 387-400.
    • Do Kwon, Y., Finzi, A., Wu, X., Dogo-Isonagie, C., Lee, L. K., Moore, L. R., ... & Zhu, J. (2012). Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops. Proceedings of the National Academy of Sciences, 109(15), 5663-5668.
  • Sort your results by date (instead of relevance), and record the top 5 papers, using APA format:
    • Pandey, P. P. A. K., Mishra, A., Gupta, P., Tripathi, P. K., Menon, M. B., Gomes, J., & Vivekanandan, P. Coronavirus Wuhan outbreak 2020 withdrawn paper.
    • Intelligence, F., Cash, D. W. O., Matrix, G. T., & Bose, S. C. Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag. Methodology, 1, 2.
    • Andrianov, A. M., Nikolaev, G. I., Kornoushenko, Y. V., Karpenko, A. D., Huang, J., Jiang, S., & Tuzikov, A. V. (2019). Identification of functional mimetics of anti-hiv antibody n6 by methods of virtual screening and molecular modeling. Doklady of the National Academy of Sciences of Belarus, 63(5), 561-571.
    • Wenzel, E. (2019). Mechanisms of HIV-1 gp120 Neurotoxicity: The Role of Microtubules (Doctoral dissertation, Georgetown University).
    • Bello, M., Rodríguez-Fonseca, R. A., & Correa-Basurto, J. (2020). Complexation of peptide epitopes with G4-PAMAM dendrimer through ligand diffusion molecular dynamic simulations. Journal of Molecular Graphics and Modelling, 96, 107514.
  • Filter your results using “Since 2019”, and record the top 5 papers, using APA format:
    • 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.
    • Guan, Y. (2019). The first structure of HIV-1 gp120 with CD4 and CCR5 receptors. Cell & bioscience, 9(1), 2.
    • Galkin, A., Chen, Y., Guenaga, J., O’Dell, S., Acevedo, R., Steinhardt, J. J., ... & Grishaev, A. V. (2020). HIV-1 gp120–CD4-Induced Antibody Complex Elicits CD4 Binding Site–Specific Antibody Response in Mice. The Journal of Immunology.
    • Li, Y., Deng, L., Yang, L. Q., Sang, P., & Liu, S. Q. (2019). Effects of CD4 Binding on Conformational Dynamics, Molecular Motions, and Thermodynamics of HIV-1 gp120. International journal of molecular sciences, 20(2), 260.
    • Ding, S., Grenier, M. C., Tolbert, W. D., Vézina, D., Sherburn, R., Richard, J., ... & Abrams, C. (2019). A New Family of Small-Molecule CD4-Mimetic Compounds Contacts Highly Conserved Aspartic Acid 368 of HIV-1 gp120 and Mediates Antibody-Dependent Cellular Cytotoxicity. Journal of virology, 93(24).
  • Filter your results using “Since 2016”, and record the top 5 papers, using APA format:
    • 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).
    • Li, X., Grant, O. C., Ito, K., Wallace, A., Wang, S., Zhao, P., ... & Sharp, J. S. (2017). Structural analysis of the glycosylated intact HIV-1 gp120–b12 antibody complex using hydroxyl radical protein footprinting. Biochemistry, 56(7), 957-970.
    • Curreli, F., Belov, D. S., Do Kwon, Y., Ramesh, R., Furimsky, A. M., O'Loughlin, K., ... & Altieri, A. (2018). Structure-based lead optimization to improve antiviral potency and ADMET properties of phenyl-1H-pyrrole-carboxamide entry inhibitors targeted to HIV-1 gp120. European journal of medicinal chemistry, 154, 367-391.
    • Chan, K. W., Pan, R., Costa, M., Gorny, M. K., Wang, S., Lu, S., & Kong, X. P. (2018). Structural comparison of human anti-HIV-1 gp120 V3 monoclonal antibodies of the same gene usage induced by vaccination and chronic infection. Journal of virology, 92(18), e00641-18.
    • Pan, R., Qin, Y., Banasik, M., Lees, W., Shepherd, A. J., Cho, M. W., & Kong, X. P. (2018). Increased epitope complexity correlated with antibody affinity maturation and a novel binding mode revealed by structures of rabbit antibodies against the third variable loop (V3) of HIV-1 gp120. Journal of virology, 92(7), e01894-17.

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:

  • mutations gp120
  • HIV gp120
  • 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 mutation structure function
  • mutations in gp120
  • HIV gp120 mutation


  • Record the search terms that have now been assigned specifically to you:
    • "HIV-1 gp120 structure"

PubMed

Now access the PubMed database by using the LMU-specific link. Perform an unrestricted search on your assigned keywords.

  • search term - HIV-1 gp120 structure
  • total number of hits: 1490
  • Record the top 10 papers (you don't need to do APA format for this): best match
    • "Hidden" dUTPase sequence in human immunodeficiency virus type 1 gp120.
    • Gp120 on HIV-1 Virions Lacks O-Linked Carbohydrate.
    • The HIV-1 gp120 V1V2 loop: structure, function and importance for vaccine development.
    • A non-canonical binding interface in the crystal structure of HIV-1 gp120 core in complex with CD4.
    • Structure and Dynamics of the Native HIV-1 Env Trimer.
    • The SPL7013 dendrimer destabilizes the HIV-1 gp120-CD4 complex.
    • Partially Open HIV-1 Envelope Structures Exhibit Conformational Changes Relevant for Coreceptor Binding and Fusion.
    • Metabolic labeling of HIV-1 envelope glycoprotein gp120 to elucidate the effect of gp120 glycosylation on antigen uptake.
    • Structural Constraints at the Trimer Apex Stabilize the HIV-1 Envelope in a Closed, Antibody-Protected Conformation.
    • The V1V2 Region of HIV-1 gp120 Forms a Five-Stranded Beta Barrel.

Perform a title/abstract search on your assigned keywords.


  • Record the total number of hits: 21
  • Record the top 10 papers (you don't need to do APA format for this):
    • HIV-1 gp120 as a therapeutic target: navigating a moving labyrinth.
    • Human Anti-HIV-1 gp120 Monoclonal Antibodies with Neutralizing Activity Cloned from Humanized Mice Infected with HIV-1.
    • Range of CD4-Bound Conformations of HIV-1 gp120, as Defined Using Conditional CD4-Induced Antibodies.
    • In silico Analysis of HIV-1 Env-gp120 Reveals Structural Bases for Viral Adaptation in Growth-Restrictive Cells.
    • The influence of N-linked glycans on the molecular dynamics of the HIV-1 gp120 V3 loop.
    • A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding.
    • Highly conserved beta16/beta17 beta-hairpin structure in human immunodeficiency virus type 1 YU2 gp120 is critical for CCR5 binding.
    • Highly conserved HIV-1 gp120 glycans proximal to CD4-binding region affect viral infectivity and neutralizing antibody induction.
    • gp120: Biologic aspects of structural features.
    • Towards a structure of the HIV-1 envelope glycoprotein gp120: an immunochemical approach.

Add the word “Review” to any articles that are review articles that you listed in question 8.

  • Total number of hits: 1
    • HIV-1 gp120 as a therapeutic target: navigating a moving labyrinth.

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: Kwong PD
  • Do you find any new articles that you did not find before on PubMed? yes
  • List up to 5 new articles that were found on the author name search:
    • Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1.
    • A human monoclonal antibody prevents malaria infection by targeting a new site of vulnerability on the parasite.
    • Hemagglutinin-stem nanoparticles generate heterosubtypic influenza protection.
    • HIV-1 Vaccines Based on Antibody Identification, B Cell Ontogeny, and Epitope Structure.
    • Trispecific broadly neutralizing HIV antibodies mediate potent SHIV protection in macaques.

Web of Science

  • Record the total number of hits: 1592
  • 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

Journal Search Engine Evaluations

  • Google Scholar
    • Pros: very easy to use, lenient with search terms, easy citations
    • Cons: often very broad results, not too specific to topic at hand
  • PubMed
    • Pros: huge amount of supplemental information, easy to search for specific authors
    • Cons: ugly interface, search results can be finicky
  • Web of Science
    • Pros: allows easy access to articles that have referenced article at hand, clear interface
    • Cons: smaller database of journals, requires more specific terms
  • What impact does choice of keywords have on your results?
    • Keywords are very important in limiting or expanding results. Some search engines are more lenient on the search terms you use but usually, words must be chose very carefully. A too broad word will lead to a large amount of results that may not be very specific to your topic. On the other hand, a very specific or technical word might limit your results too much.

Assigned Article

Now that we have our shared bibliography, each student will be assigned one article. Record the citation for your article in APA format:

  • In Web of Science, search for the specific article that you have been assigned.
    • How many cited references does that article have? 35
    • How many articles have cited the article you have been assigned? 580

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).

Huang, C. C., Tang, M., Zhang, M. Y., Majeed, S., Montabana, E., Stanfield, R. L., Dimitrov, D. S., Korber, B., Sodroski, J., Wilson, I. A., Wyatt, R., & Kwong, P. D. (2005). Structure of a V3-containing HIV-1 gp120 core. Science (New York, N.Y.), 310(5750), 1025–1028. https://doi.org/10.1126/science.1118398

       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. 
       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. Yes, free on PubMed.
       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.
       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.
   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.

Evaluating the source--the journal

  • Who is the publisher of the journal? Science
  • Is the publisher for-profit or non-profit? 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)? American Association for the Advancement of Science
  • Does the publisher belong to the Open Access Publishers Association? no
  • What country is the journal published in? United States
  • How long has the journal been in operation? (e.g., browse the archive for the earliest article published) since 1880
  • Are articles in this journal peer-reviewed? yes
  • Provide a link to the scientific advisory board/editorial board of the journal: https://www.sciencemag.org/advisory-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)? 2014 impact factor of 33.61

Evaluating the source--the article

  • Is the article a review or primary research article? Primary research article
  • On what date was the article submitted? Received for publication August 4, 2005
  • On what date was the article accepted? Accepted for publication October 17, 2005
  • Did the article undergo any revisions before acceptance? no mention of revisions
  • When was the article published? 11 Nov 2005
  • What is the approximate elapsed time between submission and publication? 3 months
  • What are the institutions with which the authors are affiliated?
    • Chih-chin Huang1, Min Tang1, Mei-Yun Zhang2, Shahzad Majeed1, Elizabeth Montabana1, Robyn L. Stanfield4, Dimiter S. Dimitrov3, Bette Korber5, Joseph Sodroski6, Ian A. Wilson4, Richard Wyatt1,*, Peter D. Kwong1,
   1 Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA.
   2 Basic Research Program, SAIC-Frederick, Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA.
   3 Protein Interaction Group, Center for Cancer Research Nanobiology Program, National Cancer Institute, Frederick, MD 21702, USA.
   4 Department of Molecular Biology and Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
   5 Theoretical Biology (T10), Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
   6 Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
  • Have the authors published other articles on this subject? (How will you find this out?)
    • Clicking on the author's name yields an automatically generated author record.
      • Huang, Chih-chin has published 26 articles, many mentioning HIV-1 gp120 and CD4
      • Kwong, Peter D. has published 468 articles with dozens mentioning HIV and other viruses
  • Is there a conflict of interest for any of the authors? There are no conflicts of interest mentioned in the article

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 V3 region of the HIV-1 gp120 protein has a coreceptor-binding tip that likely plays an important role in HIV entry and neutralization. "The extended nature and antibody accessibility of V3 explain its immunodominance."

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

I do not think it is a journal club worthy article, mainly because the article contains a lot of specific and technical information that may not be easily understandable. The article also contains figures and structures that are hard to interpret based on only the pictures.

Copy your 1-2 sentence statement about the relevance and the recommendation (plus justification) and paste into the class shared bibliography as a bullet point underneath your assigned paper.

Scientific Conclusion

Depending on the search engine, the search terms and punctuation you use can have a great effect on the results that the engine returns. It is important to you choose words that will either greatly restrict or expand the possible results by using either very specific words or very broad words.

Acknowledgements

  • I worked with Carolyn as my partner to find articles and answer questions.
  • I worked with Maya and Madeleine in class going through the questions, asking for help on finding information on sources, and going through the protocol.
  • I copied and used the Week 8 Protocol to answer questions.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Non (talk) 23:31, 25 March 2020 (PDT)

References