Nyeo2 Week 8

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Assignments

Individual Journals

Class Journals

Purpose

Since this assignment does not require the readings of any scientific articles, there is no scientific purpose. However, the overall purpose of this assignment is to navigate online scientific databases and evaluate the efficacy and background of each depending on the article at hand.

Questions

  1. In Google Scholar.
    1. Number of “hits”: 36,800
    2. Top 10 papers(APA format):
      • Wu, H., Myszka, D. G., Tendian, S. W., Brouillette, C. G., Sweet, R. W., Chaiken, I. M., & Hendrickson, W. A. (1996). Kinetic and structural analysis of mutant CD4 receptors that are defective in HIV gp120 binding. Proceedings of the National Academy of Sciences, 93(26), 15030-15035.
      • Pantophlet, R., Wilson, I. A., & Burton, D. R. (2003). Hyperglycosylated mutants of human immunodeficiency virus (HIV) type 1 monomeric gp120 as novel antigens for HIV vaccine design. Journal of virology, 77(10), 5889-5901.
      • Moebius, U., Clayton, L. K., Abraham, S., Harrison, S. C., & Reinherz, E. L. (1992). The human immunodeficiency virus gp120 binding site on CD4: delineation by quantitative equilibrium and kinetic binding studies of mutants in conjunction with a high-resolution CD4 atomic structure. The Journal of experimental medicine, 176(2), 507-517.
      • 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.
      • Ratcliff, A. N., Shi, W., & Arts, E. J. (2013). HIV-1 resistance to maraviroc conferred by a CD4 binding site mutation in the envelope glycoprotein gp120. Journal of virology, 87(2), 923-934.
      • Jacobs, A., Sen, J., Rong, L., & Caffrey, M. (2005). Alanine scanning mutants of the HIV gp41 loop. Journal of Biological Chemistry, 280(29), 27284-27288.
      • Roche, M., Salimi, H., Duncan, R., Wilkinson, B. L., Chikere, K., Moore, M. S., ... & Ellett, A. (2013). A common mechanism of clinical HIV-1 resistance to the CCR5 antagonist maraviroc despite divergent resistance levels and lack of common gp120 resistance mutations. Retrovirology, 10(1), 43.
      • Maeda, K., Das, D., Ogata-Aoki, H., Nakata, H., Miyakawa, T., Tojo, Y., ... & Arnold, E. (2006). Structural and molecular interactions of CCR5 inhibitors with CCR5. Journal of Biological Chemistry, 281(18), 12688-12698.
      • Ogert, R. A., Hou, Y., Ba, L., Wojcik, L., Qiu, P., Murgolo, N., ... & Howe, J. A. (2010). Clinical resistance to vicriviroc through adaptive V3 loop mutations in HIV-1 subtype D gp120 that alter interactions with the N-terminus and ECL2 of CCR5. Virology, 400(1), 145-155.
      • 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.
  2. Top 5 papers by date(APA format):
    • 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.
    • Lin, M., & Da, L. T. (2019). Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States During HIV-1 Entry. Journal of Chemical Information and Modeling.
    • Fischer, K., Nguyen, K., & LiWang, P. J. (2019). Griffithsin retains anti-HIV-1 potency with changes in gp120 glycosylation and complements broadly neutralizing antibodies PGT121 and PGT126. Antimicrobial agents and chemotherapy, 64(1).
    • Serra, P., Martins, A., Taveira, N., & Guedes, R. C. (2019). Structural elucidation and molecular dynamics study targeting the viral surface glycoproteins against HIV-2 infection. Annals of Medicine, 51(sup1), 151-151.
  3. Top 5 papers since 2019(APA format):
    • Zhuang, M., Vassell, R., Yuan, C., Keller, P. W., Ling, H., Wang, W., & Weiss, C. D. (2019). Mutations that increase the stability of the postfusion gp41 conformation of the HIV-1 envelope glycoprotein are selected by both an X4 and R5 HIV-1 virus to escape fusion inhibitors corresponding to heptad repeat 1 of gp41, but the gp120 adaptive mutations differ between the two viruses. Journal of virology, 93(11), e00142-19.
    • Serra, P., Martins, A., Taveira, N., & Guedes, R. C. (2019). Structural elucidation and molecular dynamics study targeting the viral surface glycoproteins against HIV-2 infection. Annals of Medicine, 51(sup1), 151-151.
    • Van Duyne, R., Kuo, L. S., Pham, P., Fujii, K., & Freed, E. O. (2019). Mutations in the HIV-1 envelope glycoprotein can broadly rescue blocks at multiple steps in the virus replication cycle. Proceedings of the National Academy of Sciences, 116(18), 9040-9049.
    • 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.
    • Yuan, C., Wang, J. Y., Zhao, H. J., Li, Y., Li, D., Ling, H., & Zhuang, M. (2019). Mutations of Glu560 within HIV-1 Envelope Glycoprotein N-terminal heptad repeat region contribute to resistance to peptide inhibitors of virus entry. Retrovirology, 16(1), 1-11.
  4. Top 5 papers since 2016(APA format):
    • Zhuang, M., Vassell, R., Yuan, C., Keller, P. W., Ling, H., Wang, W., & Weiss, C. D. (2019). Mutations that increase the stability of the postfusion gp41 conformation of the HIV-1 envelope glycoprotein are selected by both an X4 and R5 HIV-1 virus to escape fusion inhibitors corresponding to heptad repeat 1 of gp41, but the gp120 adaptive mutations differ between the two viruses. Journal of virology, 93(11), e00142-19.
    • Keller, P. W., Morrison, O., Vassell, R., & Weiss, C. D. (2018). HIV-1 gp41 residues modulate CD4-induced conformational changes in the envelope glycoprotein and evolution of a relaxed conformation of gp120. Journal of virology, 92(16), e00583-18.
    • Clark, A. J., Gindin, T., Zhang, B., Wang, L., Abel, R., Murret, C. S., ... & Kwong, P. D. (2017). Free energy perturbation calculation of relative binding free energy between broadly neutralizing antibodies and the gp120 glycoprotein of HIV-1. Journal of molecular biology, 429(7), 930-947.
    • Serra, P., Martins, A., Taveira, N., & Guedes, R. C. (2019). Structural elucidation and molecular dynamics study targeting the viral surface glycoproteins against HIV-2 infection. Annals of Medicine, 51(sup1), 151-151.
    • Powell, R. L., Totrov, M., Itri, V., Liu, X., Fox, A., & Zolla-Pazner, S. (2017). Plasticity and epitope exposure of the HIV-1 envelope trimer. Journal of virology, 91(17), e00410-17.
  5. List of the search terms used by each student in the class(on board):
    • Mutations in gp120
    • HIV gp120 mutation
    • HIV gp120 function
    • mutations gp120
    • HIV gp120
    • structure-fuction 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
    • My search terms:
      • HIV gp120 structure mutation
  6. Unrestricted search on assigned keywords on PubMed database by using the LMU-specific link
    • Number of hits: 258
    • Top 10 papers:
      1. Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5.
      2. Characterization of resistance to a potent D-peptide HIV entry inhibitor.
      3. Griffithsin Retains Anti-HIV-1 Potency with Changes in gp120 Glycosylation and Complements Broadly Neutralizing Antibodies PGT121 and PGT126.
      4. Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope.
      5. Concomitant Enhancement of HIV-1 Replication Potential and Neutralization-Resistance in Concert With Three Adaptive Mutations in Env V1/C2/C4 Domains.
      6. Systematic mutational analysis of human neutrophil α-defensin HNP4.
      7. Human Anti-HIV-1 gp120 Monoclonal Antibodies with Neutralizing Activity Cloned from Humanized Mice Infected with HIV-1.
      8. Structural Constraints at the Trimer Apex Stabilize the HIV-1 Envelope in a Closed, Antibody-Protected Conformation.
      9. Display of the HIV envelope protein at the yeast cell surface for immunogen development.
      10. CRISPR/Cas9 gene editing for the creation of an MGAT1-deficient CHO cell line to control HIV-1 vaccine glycosylation.
  7. Title/abstract search
    • Number of hits: 0
    • Top 10 papers
      1. No hits when "HIV gp 120 structure mutation" was searched under title/abstract in the advanced settings.
  8. Add the word “Review” to any articles that are review articles that you listed in question 8.
  9. Author search on Overbaugh JM
    • Do you find any new articles that you did not find before on PubMed? No.
    • List up to 5 new articles that were found on the author name search:
      1. Diversity and function of maternal HIV-1-specific antibodies at the time of vertical transmission.
      2. Dynamics of HIV DNA reservoir seeding in a cohort of superinfected Kenyan women.
      3. Schistosomiasis was not associated with higher HIV-1 plasma or genital set point viral loads among HIV seroconverters from four cohort studies.
      4. Virological failure in children living with HIV on antiretroviral therapy: correlates and predictive value of clinical measurements and CD4 cell count.
      5. Maternal Envelope gp41 Ectodomain-Specific Antibodies Are Associated With Increased Mother-to-Child Transmission of Human Immunodeficiency Virus-1.
  10. Unrestricted search onWeb of Science database
    • Total number of hits: 260
    • Top 10 papers:
      1. The Genetic Diversity of HIV-1 Quasispecies Within Primary Infected Individuals
      2. Refolding Dynamics of gp41 from Pre-fusion to Pre-hairpin States during HIV-1 Entry
      3. Griffithsin Retains Anti-HIV-1 Potency with Changes in gp120 Glycosylation and Complements Broadly Neutralizing Antibodies PGT121 and PGT126
      4. Topological analysis of the gp41 MPER on lipid bilayers relevant to the metastable HIV-1 envelope prefusion state
      5. Characterization of resistance to a potent d-peptide HIV entry inhibitor
      6. Conformational Engineering of HIV-1 Env Based on Mutational Tolerance in the CD4 and PG16 Bound States
      7. Systematic mutational analysis of human neutrophil alpha-defensin HNP4
      8. Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein-Protein Interfaces
      9. Identification of a Helical Segment within the Intrinsically Disordered Region of the PCSK9 Prodomain
      10. Human Anti-HIV-1 gp120 Monoclonal Antibodies with Neutralizing Activity Cloned from Humanized Mice Infected with HIV-1
  11. Now that we have our shared bibliography, each student will be assigned one article. Record the citation for your article in APA format: Wu, H., Myszka, D. G., Tendian, S. W., Brouillette, C. G., Sweet, R. W., Chaiken, I. M., & Hendrickson, W. A. (1996). Kinetic and structural analysis of mutant CD4 receptors that are defective in HIV gp120 binding. Proceedings of the National Academy of Sciences, 93(26), 15030-15035.
  12. 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: easy access to pre-made citations and the keywords are bolded in the title
    • Google Scholar disadvantages: search results can be too broad, not every single article is scholarly
    • PubMed advantages: helpful advanced search function and easy to navigate among review articles
    • Pubmed disadvantages: access to full-text journals is limited and the citations are not provided
    • Web of Science advantages: narrower search results and more organized
    • Web of Science disadvantages: not as specific search filters and keyword searches are not as accurate
  13. What impact does choice of keywords have on your results?
    • Keywords can make a search more or less specific, depending on how they are used. For example, the words "and" and "or" or the amount of keywords can drastically change the outcome of the search.
  14. Assigned article
    • Wu, H., Myszka, D. G., Tendian, S. W., Brouillette, C. G., Sweet, R. W., Chaiken, I. M., & Hendrickson, W. A. (1996). Kinetic and structural analysis of mutant CD4 receptors that are defective in HIV gp120 binding. Proceedings of the National Academy of Sciences, 93(26), 15030-15035. DOI: 10.1073/pnas.93.26.15030
    1. Link to the PubMed abstract
    2. Link to the full text on PubMed Central
      • N/A
    3. Link to the full text of the article (HTML format)
    4. Link to PDF version of the article
    5. Copyright: 1996 by the Proceedings of the National Academy of Sciences of the United States of America
    6. This article is from PNAS, which is not an open access database. According to the list on http://sq4ya5rf2q.search.serialssolutions.com/, LMU pays for access to this. PNAS is available by subscription, and all content is free after 6 months. Authors who choose the open access option can have their articles made available without cost to the reader immediately upon publication.
    7. The article is available online-only.
  15. Evaluating the source--the journal
    1. Publisher: PNAS
    2. It was difficult to find out if the publisher was non-profit or for-profit, but judging from how they have payment rates for subscription, they most likely are a for-profit organization.
    3. The publisher is not a part of any scientific society; however, it is considered highly credible and prestigious.
    4. The publisher does not belong to the Open Access Publishers Association.
    5. The journal is published in the United States.
    6. The journal has been in operation since 1914.
    7. The articles in this journal are peer-reviewed.
    8. Link to the scientific advisory board/editorial board of the journal: https://www.pnas.org/page/about/editorial-board
    9. Journal impact factor: according to Journal Citation Reports, the journal has a 2018 impact factor of 9.58.
  16. Evaluating the source--the article
    1. The article is a primary research article
    2. Could not find date that the article was submitted.
    3. The article was accepted on October 18, 1996
    4. Not sure whether or not the article underwent any revisions before acceptance, but I am assuming it did.
    5. The article was published in December 1996.
    6. Approximate elapsed time between submission and publication: N/A
    7. What are the institutions with which the authors are affiliated? The authors are affiliated with the Department of Biochemistry and Molecular Biophysics at Howard Hughes Medical Institute at Columbia University in New York, SmithKline Beecham Pharmaceuticals, and Southern Research Institute in Birmingham, AL.
    8. Have the authors published other articles on this subject? Yes, most of the authors on this paper published articles on this subject. For example, David G. Myszka was published on a paper titled "Energetics of the HIV gp120-CD4 binding reaction". These were found by searching each of the authors' names on PNAS to see what other articles they published.
    9. Is there a conflict of interest for any of the authors? All the authors are involved in papers that research some element of biological binding.
    10. 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.
      • This article tries to find the characteristics of mutant CD4 receptors, which bind to the gp120 glycoprotein of HIV-1. It was found that while mutations on the receptor proteins can alter the binding affinity at this site, there is some element of conformational adaptation that still allows for this binding and therefore allows the function to maintain.
    11. Make a recommendation--based on the information you have gathered, should we do a journal club on this article? Why or why not?
      • I think that it would be worth a shot to do a journal club on this article because although there is no substantial conclusive evidence, the entire paper is centered around the structure of the CD4 receptor proteins for gp120. It also provides a view on the ability of HIV to mutate, which has been a large topic of discussion in this class.

Scientific Conclusion

This assignment made me realize how powerful of a tool online scientific databases are. More specifically, the importance of keywords and noting where the information is coming from. Small changes in search terms, such as the addition of another keyword or omission of an "and" or an "or" can make drastic changes in the results that appear after the search. It is crucial to pay attention to these and try to be as precise as possible in the language that we use, because in the end it could be the difference between finding good sources or not. One should go into the search with a goal of what he or she wants to find first. I learned that even the database one chooses can make a difference in this as well.

Acknowledgements

  • I worked with my homework partner Jenny Chua during the class period.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Nyeo2 (talk) 23:35, 25 March 2020 (PDT)

References

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