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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

Spring 2020

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Primary Research Articles

  • Altman, J. B., Liu, X., Itri, V., Zolla‐Pazner, S., & Powell, R. L. R. (2018). Optimized protocol for detection of native, full‐length HIV‐1 envelope on the surface of transfected cells. Health science reports, 1(9), e74. Adinulos (talk) 16:14, 5 March 2020 (PST)
    • In relation to structure-function, the article aims to detect surface expression of wild type env to help identify native env structures using cytometry. I don't think we should use a journal club on this article, it was hard for me to determine how much it related to the other information that we've been learning in class, especially in relation to cytometry. I don't know how much information can be gained from the article that we actually will use.
  • Shen, R., Raska, M., Bimczok, D., Novak, J., & Smith, P. D. (2014). HIV-1 envelope glycan moieties modulate HIV-1 transmission. Journal of virology, 88(24), 14258-14267. Adinulos (talk) 15:22, 5 March 2020 (PST)
  • Da, L. T., & Lin, M. (2019). Opening dynamics of HIV-1 gp120 upon receptor binding is dictated by a key hydrophobic core. Physical Chemistry Chemical Physics, 21(47), 26003-26016. Adinulos (talk) 15:18, 5 March 2020 (PST)
  • 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. Non (talk) 15:02, 5 March 2020 (PST)
    • 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." 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.

  • Reitz Jr, M. S., Wilson, C., Naugle, C., Gallo, R. C., & Robert-Guroff, M. (1988). Generation of a neutralization-resistant variant of HIV-1 is due to selection for a point mutation in the envelope gene. Cell, 54(1), 57-63. Sahil Patel (talk) 15:20, 5 March 2020 (PST)
  • Davis, M. R., Jiang, J., Zhou, J., Freed, E. O., & Aiken, C. (2006). A mutation in the human immunodeficiency virus type 1 Gag protein destabilizes the interaction of the envelope protein subunits gp120 and gp41. Journal of virology, 80(5), 2405-2417. Sahil Patel (talk) 15:20, 5 March 2020 (PST)
    • Initial interactions between HIV-1 particles and target cells occur between gp120 and CD4. CD4 binding elicits a conformational change within gp120 that reveals a binding site for the viral coreceptor. Subsequent engagement of coreceptor initiates further conformational changes in gp41 that lead to membrane fusion.
    • I believe that this article would be good for a journal club because it pertains to prior topics discussed, but it may be a bit too long since this journal does not have a limit on the page count.
  • 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. Cdominguez (talk) 15:03, 5 March 2020 (PST)
  • Haim, H., Strack, B., Kassa, A., Madani, N., Wang, L., Courter, J. R., ... & Smith III, A. B. (2011). Contribution of intrinsic reactivity of the HIV-1 envelope glycoproteins to CD4-independent infection and global inhibitor sensitivity. PLoS pathogens, 7(6). Cdominguez (talk) 15:03, 5 March 2020 (PST)
    • This paper discusses specific HIV variants and how their requirement for CD4 binding changes glycoproteins. It speaks on how CD4 requirements changes reactivity of glycoproteins and causes sesitivity to neutralization by antibodies. I do not think that it would be a good journal club article. It is fairly complicated and the language in which it is written seems to be on a professional level where a lot of knowledge on background information and specific dynamics of HIV mechanisms would be needed to get the full benefits and information from the article.
  • Yolitz, J. (2019). Variations in protein processing lead to variations in structure and function of the HIV-1 envelope protein (Doctoral dissertation, Johns Hopkins University). Cdominguez (talk) 15:03, 5 March 2020 (PST)
  • Roop, J. I., Cassidy, N. A., Dingens, A. S., Bloom, J. D., & Overbaugh, J. (2020). Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5. Viruses, 12(2), 241. Jmenzago (talk) 15:03, 5 March 2020 (PST)
    • HIV-1 strains do not replicate well in Rhesus macaque cells due to a non-synonymous mutation in macaque CD4 that restricts HIV-1 env-mediated entry. Several induced mutations from this study have been found in gp120 that enhance binding of HIV-1 to macaque CD4. I think that it would be interesting to do a journal club on this article. Based on the abstract, it could provide useful information about the structure-function relationship of the mutations in the gp120 sequence of HIV-1. The journal is open access since the publisher has been committed to that movement in the research community, so the class will be able to easily read the article. There were no conflicts of interest, and the chief overseeing researcher (Julie Overbaugh) has published other articles on the subject. However, the article is new so there is no information about its relevance to HIV research. The journal and publisher are also relatively new, the former being created just over 10 years ago and the latter being established in 1996. The impact factor of the journal (3.811) is decent, but nothing notable. Because everything from the publisher to the article is fairly new, it is difficult to really get an idea of the quality of the article, but I think it would be interesting to give it a shot.
  • Ogert, R. A., Ba, L., Hou, Y., Buontempo, C., Qiu, P., Duca, J., ... & Howe, J. A. (2009). Structure-function analysis of human immunodeficiency virus type 1 gp120 amino acid mutations associated with resistance to the CCR5 coreceptor antagonist vicriviroc. 'Journal of virology, 83(23), 12151-12163.Mpaniag1 (talk) 15:04, 5 March 2020 (PST)
    • In this study, the authors looked at vicriviroc, a coreceptor antagonist of CCR5 that is used in treatment for HIV-1. The results of the study should that the VCV-resistant virus modified itself to use the drug-bound receptor, increasing the reliance on the N-terminus of CCR5.No, we should not use this article for journal club because the article was not organized in a manner that was easy to follow along with.
  • Ahmed, F. K., Clark, B. E., Burton, D. R., & Pantophlet, R. (2012). An engineered mutant of HIV-1 gp120 formulated with adjuvant Quil A promotes elicitation of antibody responses overlapping the CD4-binding site. Vaccine, 30(5), 922-930.Mpaniag1 (talk) 15:04, 5 March 2020 (PST)
  • Yuan, Y., Maeda, Y., Terasawa, H., Monde, K., Harada, S., & Yusa, K. (2011). A combination of polymorphic mutations in V3 loop of HIV-1 gp120 can confer noncompetitive resistance to maraviroc. Virology, 413(2), 293-299.Mpaniag1 (talk) 15:04, 5 March 2020 (PST)
  • 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 (New York, N.Y.), 280(5371), 1949–1953. Mking44 (talk) 15:05, 5 March 2020 (PST)
    • By using different mutants of the gp120 protein, the authors of this paper discovered a highly conserved gp120 structure that is adjacent to the V3 loop as well as contains neutralization antibodies. Therefore, this conserved structure can be used as a potential drug target or a starting point for preventing HIV diseases. I think the article has a potential spot for being used as a journal club article; it seems very interesting, it's not too complex as a paper, and it is cited by many people. However, I also think it is too old to use (1998), since Markham et. al was written in 1998 as well. I think it would be more interesting to hear from a more recent paper about HIV-1.
  • 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), 3183–3187. Mking44 (talk) 15:07, 5 March 2020 (PST)
  • Nguyen, D. N., Redman, R. L., Horiya, S., Bailey, J. K., Xu, B., Stanfield, R. L., ... & Montefiori, D. C. (2020). The impact of sustained immunization regimens on the antibody response to oligomannose glycans. ACS Chemical Biology. Jmenzago (talk) 15:08, 5 March 2020 (PST)
  • 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.Nyeo2 (talk) 15:15, 5 March 2020 (PST)
  • 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.Nyeo2 (talk) 15:15, 5 March 2020 (PST)
  • 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.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.
  • 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). Jennymchua (talk) 15:21, 5 March 2020 (PST)
  • Kawashita, N. (2020). Interaction Analysis between HIV gp120 and the Antibodies by Fragment Molecular Orbital Method. Biophysical Journal, 118(3), 305a. Jennymchua (talk) 15:21, 5 March 2020 (PST)
  • 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. Proc Natl Acad Sci U S A, 115(10), 2443–2448. Carolyne (talk) 15:25, 5 March 2020 (PST)
    • 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.
  • 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. Carolyne (talk) 15:25, 5 March 2020 (PST)
  • Pancera, M., Zhou, T., Druz, A. et al. Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature 514, 455–461 (2014). Lurbinah (talk) 15:28, 5 March 2020 (PST)
    • The structure at 3.5-Å resolution for an HIV-1-Env trimer shows the prefusion conformation of gp41, useful for immune evasion and immune recognition
  • 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. Lurbinah (talk) 15:28, 5 March 2020 (PST)
  • Blish, C. A., Nguyen, M. A., & Overbaugh, J. (2008). Enhancing exposure of HIV-1 neutralization epitopes through mutations in gp41. PLoS medicine, 5(1).Dcartmel (talk) 15:40, 5 March 2020 (PST)
  • Zanini, F., & Neher, R. A. (2013). Quantifying selection against synonymous mutations in HIV-1 env evolution. Journal of virology, 87(21), 11843-11850.Dcartmel (talk) 15:50, 5 March 2020 (PST)
    • In terms of the structure-function relationship of mutations in the HIV-1 gp120 protein, this article found that synonymous mutations that were located around gp120 loops in RNA were more likely to be lost than synchronous mutations that were located elsewhere on RNA strands.This observation of selection against synonymous mutations showed that this process slowed down the rate of evolution of the HIV-1 protein. Based on the information I have gathered about this article, I think that it would be worthwhile to do a journal club on this article because it investigated how synonymous mutations on the HIV-1 protein relate to the rate of evolution of the protein as a whole and I think that this is very relevant to the topic of the original paper by Markham et al.
  • Delwart, E. L., Shpaer, E. G., Louwagie, J., McCutchan, F. E., Grez, M., Rubsamen-Waigmann, H., & Mullins, J. I. (1993). Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes. Science, 262(5137), 1257-1261. (Kvescio (talk) 21:56, 1 April 2020 (PDT))
  • Do Kwon, Y., Pancera, M., Acharya, P., Georgiev, I. S., Crooks, E. T., Gorman, J., ... & Soto, C. (2015). Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env. Nature structural & molecular biology, 22(7), 522. (Kvescio (talk) 21:58, 1 April 2020 (PDT))

Review Articles

  • Stefic, K., Bouvin-Pley, M., Braibant, M., & Barin, F. (2019). Impact of HIV-1 Diversity on Its Sensitivity to Neutralization. Vaccines, 7(3), 74. Jmenzago (talk) 14:59, 5 March 2020 (PST)
  • 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. Non (talk) 15:04, 5 March 2020 (PST)
  • O'Connell, R. J., Kim, J. H., & Excler, J. L. (2014). The HIV-1 gp120 V1V2 loop: structure, function and importance for vaccine development. Expert review of vaccines, 13(12), 1489–1500. Mking44 (talk) 15:11, 5 March 2020 (PST)
  • O'Connell, R. J., Kim, J. H., & Excler, J. L. (2014). The HIV-1 gp120 V1V2 loop: structure, function and importance for vaccine development. Expert review of vaccines, 13(12), 1489–1500. Carolyne (talk) 15:21, 5 March 2020 (PST)
  • Shah VK, Firmal P, Alam A, Ganguly D, Chattopadhyay S. Overview of Immune Response During SARS-CoV-2 Infection: Lessons From the Past. Front Immunol. 2020 Aug 7;11:1949. doi: 10.3389/fimmu.2020.01949. PMID: 32849654; PMCID: PMC7426442. [1] Taylor Makela (talk) 16:12, 5 November 2020 (PST)

Other Articles

  • Nakra NA, Blumberg DA, Herrera-Guerra A, Lakshminrusimha S. Multi-System Inflammatory Syndrome in Children (MIS-C) Following SARS-CoV-2 Infection: Review of Clinical Presentation, Hypothetical Pathogenesis, and Proposed Management. Children (Basel). 2020 Jul 1;7(7):69. doi: 10.3390/children7070069. PMID: 32630212; PMCID: PMC7401880. [2] Taylor Makela (talk) 16:09, 5 November 2020 (PST)