User:Emily Jean Onufer

From OpenWetWare
Jump to navigationJump to search

I am a new member of OpenWetWare!

Contact Info

Emily Jean Onufer (an artistic interpretation)
  • Emily Jean Onufer
  • MIT 20.109
  • MIT Address: 479 Commonwealth Ave. Boston, MA 02115
  • Home Address: 2756 Ocean Shore Ave. VA Beach, VA 23451
  • Hometown: Virginia Beach, VA

Feel free to email me: ejonufer [at] is my resume on my Athena public which gives an overview of my accomplishments as a whole. Basically, I enjoy playing tennis for MIT and being involved in various leadership positions around campus. I love traveling, being outdoors, and learning anything new. I am also adore solving puzzles.


  • 2006, Princess Anne High School International Bacc. Graduate
  • Present, MIT student, Sophomore

Research interests

  1. Immunology
  2. Infectious Diseases
  3. Cardiovascular Research

Module 3 Research Project

Research Problem

  • Topic

Did you know that in 2007 alone, 33.2 million people lived with AIDS? Of this number, 2.1 million died, including 330,000 children.

AIDS is now a pandemic, ravaging sub-Saharan Africa and retarding economic growth. Research has been done in a multitude of labs across the country concerning HIV, its deadly retrovirus.

Recent researchers have identified antibodies in the first loop (ECL1) of CCR5 of HIV exposed but uninfected individuals. This means that these antibodies could resist the HIV infection. It would be interesting to analyze and target the specific amino acid residues in this loop to determine which amino acids are involved in antibody binding to CCR5. Studies have been done that showed that amino acid substitutions in positions Alanine-95 and Alanine-96 increased antibody-peptide binding compared to that of the wild-type peptide Aspartate-95 and Phenylalanine-96.

  • Idea

Because of this research and that of others, we would like analyze the binding antibodies for key characteristics that would contribute to their binding affinity. We would then like to target these same residues of Aspartate-95 and Phenylalanine-96 to determine if other types of amino acids would increase the binding affinity. We would use site-directed mutagenesis to test to see how mutating these residues would affect antibody binding to CCR5. If we can determine the residues that bind antibodies most effectively, then we can more easily prevent an HIV-positive patient from becoming infected with AIDS.

  • Current Research in the Field and Sources of Information

Source: Pastori, et al. “Two amino acid substitutions within the first external loop of CCR5 induce human immunodeficiency virus-blocking antibodies in mice and chickens.” J Virol. 2008 Apr;82(8):4125-34. Epub 2008 Feb 6.


The CCR5 coreceptor is a seven-transmembrane-spanning receptor involved in chemokine signaling. With regards to our research project, it also is used as a viral coreceptor by HIV, and it presumably mediates the first contacts between HIV and target host cells in mucosal sites, as CCR5-tropic HIV strains are generally the first in pioneering new hosts. Earlier studies have found that antibodies to the first loop (ECL1) of CCR5 have been identified in HIV-exposed uninfected individuals and in HIV-positive nonprogressing subjects. Thus, these antibodies may confer resistance against HIV infection.

To define which amino acids are involved in antibody binding to CCR5, the authors of the journal performed a peptide-scanning assay and studied the immunogenicity of peptides in animal models. A panel of synthetic peptides spanning the CCR5-ECL1 region and displaying glycine or alanine substitutions was assayed for antibody binding with a pool of natural anti-CCR5 antibodies. They used mice and chickens to study the immunogenicity of mutagenized peptide. Structural characterization by NMR spectroscopy and molecular dynamics simulations were performed to better understand the structural and conformational features of the mutagenized peptide. Amino acid substitutions in positions Ala95 and Ala96 increased antibody-peptide binding compared to that of the wild-type peptide (Asp(95)-Phe(96)).

Strikingly, chicken antibodies to the Ala95-96 peptide specifically recognize human CCR5 molecules, downregulate receptors from lymphocytes, inhibit CCR5-dependent chemotaxis, and prevent infection by several R5 viruses, displaying 50% inhibitory concentrations of less than 3 ng/ml. NMR spectroscopy and molecular dynamics simulations proved the high flexibility of isolated epitopes and suggested that A(95)-A(96) substitutions determine a slightly higher tendency to generate helical conformations combined with a lower steric hindrance of the side chains in the peptides. These findings may be relevant to the induction of strong and efficient HIV-blocking antibodies.

  • Earlier Study:

Source: Konigs, et al. “Peptide mimotopes selected with HIV-1-blocking monoclonal antibodies against CCR5 represent motifs specific for HIV-1 entry.” Immunology Cell Biology. October 2007.

Summary: CCR5 is a chemokine receptor that mediates entry of HIV-1. Two monoclonal antibodies that block HIV-1 entry, 3A9 and 5C7, were used to select peptide mimotopes of sequences on CCR5 from phage displayed peptide libraries. The selected mimotopes comprised motifs at the N-terminus and on the first and third extracellular loops (ECL1 and ECL3) of CCR5. Amino acids in these motifs were exchanged for alanines by site-directed mutagenesis in the cDNA for human CCR5. Ensuing effects on antibody binding to CCR5, cellular entry of HIV-1 and chemokine-induced signalling were analysed by transfection of mutant cDNAs into HEK293.CD4 cells. For both antibodies, fluorescence-activated cell sorting analysis was used to define overlapping conformational epitopes on CCR5 at the N-terminus, on ECL1 and ECL3. Mutation of the N-terminal motif 10YD11 prevented HIV-1 entry into transfected cells as judged by single round infection assays with R5 and R5X4 HIV-1 isolates, as did mutation of the motif 96FG97 in ECL1, whereas mutation of the motif 274RLD276 in ECL3 had only a minor effect. None of the motifs in CCR5 relevant to HIV-1 entry disrupted chemokine-induced signalling. Thus, peptide mimotopes of conformational contact sites of CCR5 with the paratope of monoclonal antibodies 3A9 and 5C7 represent sites on CCR5 that are essential for HIV-1 entry. Structural knowledge of these mimotopes could help elucidate the nature of the interaction between CCR5 and HIV-1, and thus the derivation of specific inhibitors of entry of HIV-1 into susceptible cells without interference with chemokine signalling. Note: We are particularly interested in the results of the study with regards to the ECL1 loop, as we intend to focus on it.

Useful links