Cathryn Rapadas


 Journal/Papers  Review/Comments
Molecular Bio and Biochemistry Website

Jan 27, 2010

After the introduction to chemical bonds and interactions in biology, I decided it was best to brush up on biochemistry. I went to my old biochem class website and printed out hand-outs of the amino acids, which are classified according to acidic, basic, hydrophobic, polar, and the leftovers. I started to re-memorize the mnemonics for remembering the different ways to name  each amino acid. I brushed up on D and L amino acid configurations (CORN- I knew I learned it...) and I brushed up on how to tell the difference between a right-handed and left-handed helix.

 Biomedical Issues: AIDS

Jan 28, 2010

After reading through my Biomedical Issues in AIDS notes pamphlet, I've decided I want to study up on drugs, more specifically immunomodulators. I am interested in learning about new research that's going into using interleukin-2 and interferon to help aid the immune system. Also, I decided to research articles about CD4 proteins linked with Ig.


 Navigation Tutorial

Jan 31, 2010

I completed the RCSB PDB website navigation tutorial. In searching for calmodulin, at first I tried just using the search bar and input "calmodulin" for PDB ID or keyword. When I viewed the list and remembered that many of the structures are similiar, I decided to search in a different way. I clicked on "Advanced Search" on the left-hand sidebar and searched under "Macromolecule Name" and removed similar sequences at 90% identity. The rest of the navigation questions didn't seem too bad until I got to question 11. Is there a typo in this question? The sketch tool opened up and I drew the napthalene ring, but then what was I supposed to do? And when it said to search for instances of benzene, am I supposed to draw benzene and click search for exact molecule or was I supposed to keep the drawing of napthalene and search for similar substructures?

Leone, Amanda. "IL-2, IL-7 and IL-15 as Immuno-Modulators During SIV/HIV Vaccination and Treatment." Current HIV research7.1 (2009): 83 .

Feb 1, 2010

IL-2, IL-7 and IL-15 wee studied because of their role in immunotherapeutics, in increasing T cell levels and function and for enhancing vaccine-elicited viral-specific T-cell responses. When patients use the HAART therapy, CD4+ T cells remain lowand complete recovery does not always occur. Using immunomodulators may have the potential to enhance HIV-specific adaptive immune responses. IL-7 has been found to be well tolerated in both SIV+ macaque model and humans, but it needs to be administered in the context of HAART treated infection in order to be efficacious. IL-7 is the most promising candidate being developed for immune therapeutics.


Riva, D. A. "Two immunomodulators, curcumin and sulfasalazine, enhance IDV antiretroviral activity in HIV-1 persistently infected cells."

Archives of virology 153.3 (2008): 561.

Feb 3, 2010

If use curcumin and sulfasalazine together with a protease inhibitor, indinavir (IDV), HIV-1 production was found to be reduced in persistently infected cells. HIV targets the transcription factor NF-kappaB. Sulfasalazine inhibits this transcription factor with many immunomodulatory actions. This paper suggests that Sul and Cur both interfere with viral production. Since resistance to antiretroviral treatment is inevitable, the use of an immunomodulator with a different mechanism of action could help reduce HIV-replication in the presence of antiviral therapy.

Nikolaeva, Lyudmila G. "Effect of Immunomodulator Dzherelo on CD4 + T-Lymphocyte Counts and Viral
Load in HIV Infected Patients Receiving Anti-Retroviral Therapy."
Research Journal of Pharmacology 2.1 (2008): 8-12

Dzherelo, an oral immunomodulator, is used in Ukraine as a solution for effective and safe immunotherapy that could regulate immune ersponse and manage HIV infections. Studies show that Dzherelo increases CD4 T-lymphocytes significantly and has shown to achieve successful clinical response when taken with standard anti-retroviral therapy. Dzherelo also decreases incidence of opportunistic infections and the toxicity to the liver associated with ART. Patients have better prognosis because Dzherelo produces significant increase in total CD3+ lymphocytes, CD4 helper cells, better CD4/CD8 ratio.

Haim, Hillel. "Soluble CD4 and CD4-Mimetic Compounds Inhibit HIV-1 Infection by Induction of a Short-Lived Activated State."

PLoS pathogens 5.4 (2009): 100

Feb 4, 2010

HIV-1 envelope glycoproteins are induced to form a major structural rearrangement as a result of CD4 binding. The change exposes gp120 co-receptor binding site and the gp41 HR1 groove. (Where is the gp41 HR1 groove? N-terminal heptad repeat regions of the 3 gp41 subunits). This conformational stability of the sCD4-activated intermediate inhibit HIV-1 infection. However, the intermediate is only short-lived, even after continued sCD4 engagement and exposure of 48d epitope on gp120. The paper suggests perhaps sCD4 neutralization was due to competitive inhibition of envelope glycoprotein binding to the cell-surface CD4 receptor.


Meyuhas, Ronit. "Enhanced HIV-1 neutralization by a CD4-VH3-IgG1 fusion protein."

Biochemical and biophysical research communications 386.2 (2009): 402

I searched for the HIV-1 gp120 and viewed its structure. HIV-1 gp120 binds certain VH3+ human antibodies. I tried searching VH3 gene products (VH-23 and VH-30) in the PDB, but no results found. Also, I tried searching CD4-VH3-IgG1 fusion protein and none came up. This paper suggests that CD4 fusion proteins function better to inhibit HIV-1 than just human IgG1 immunoligands harboring VH3 human antibodies. The pairing of VH3 with CD4 causes a stabilization of an Ig Fv like structure, which contributes to the overall affinity.

I would like to continue researching on soluble CD4 proteins as potential entry inhibitors.




I was able to understand the material that was covered during today's meeting in regards to the PDB format file and the mmCIF format file. This is because I have previous knowledge of HTML and CSS, and this reminded me of it (even if it's not exactly the same, I was able to relate to it and it didn't completely go over my head.) 

Visualizing minute molecules may be very hard to an untrained eye. Even though I've learned about atoms, molecules, etc. for the past four years, visualizing can still be pretty tough. The computer models help me understand structures that are complicated, but the overall concept can still feel pretty abstract. Hopefully, in time, I will get used to viewing these molecules and be familiar with all its aspects.

In regards to what the big picture of my research project would be,  I want to focus on the mechanism of HIV-entry through binding of the gp120 and the CD4 receptor as the big picture. I want to focus on these structures and future structures that I may find that is relevant (perhaps the chemokine receptors?). But I also want to include drug interactions, like entry inhibitors or immunomodulators, that can interfere with this step.

Kwong, Peter. "Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody." Nature 393 (1998): 648-659

February 7, 2010

After viewing this article, I found other articles of interest through CrossRef. I spent about an hour reading through the journal article and spent another hour searching for and printing out articles of interest to read.

This article mentions that "the focus of CD4 positivity is displaced from the centre of greatest negativity on gp120." I don't really understsand what that means.

Two of the interfacial cavities are unusually large. The larger cavity, which is lined by hydrophilic residues derived from both gp120 and CD4, serves as a water buffer between gp120 and CD4. The article concludes that a "variational island" can be produced (because of the tolerance for variation in gp120 surface) which can help facilitate virus escape from antibodies directed against this CD4 binding site. I find this interesting and relevant to the big picture of my research project.

Residues that line the Phe43 cavity are hydrophobic, so they have little direct contact to CD4 but do affect the gp120-CD4 interaction.

  • Mutations at Thr 257 and Trp 427 can reduce binding.
  • Changes in cavity lining residues affect binding of antibodies directed against the CD4 bindin site
  • interaction between elements of the chemokine receptor binding region and the residues lining the Phe 43 cavity

Phe 43 cavity may have been formed as a consequence of CD4 induced conformational change.

Fab17b is a broadly neutralizing human monoclonal antibody isolated from blood of an HIV infected individual. Its contact surface is very acidic and it complenets with the basic surface of gp120. The 17b has hydrophobic contacts that predominate at the center. The gp120 surface that contacts 17b consists of a hydrophobic centre surrounded by basic periphery. However, there are no direct contacts between CD4 and 17b and none of the gp120 residues contacts both 17b and CD4. On gp120, the 17b epitope lies across the base of the 4 stranded bridging sheet- the integrity of the bridging sheet is necessary for 17b binding. CD4 binds on the opposite face of the bridging sheet, providing contacts that stabilize its conformation.

Due to conformational changes in core gp120, most of the envelope protein surface can hide from immune response by glycolsylation and oligomeric occlusion. Antibodies access two surfaes of the virus: one that overlaps the CD4 binding site, shielded by the V1/V2 loop and the other that overlaps the chemokine-receptor-binding site, shielded by the V2/V3 loops. CD4i epitopes tend to be masked from immune surveillance by the adjacent V2 and V3 loops. How are the viruses evading the immune responses? What are the underlying specific mechanisms of this immune evasion?



February 8, 2010

Chimera exercise - I spent about 2 hours on this exercise. (I had to do it a second time because I forgot I had to save the images, and I played around with the other functions.)

The question asks: How many different chains are there in this structure? Are all these chains identical? If not, which ones are different?

I know that hemoglobin is a tetramer = 4 chains (2 alpha, 2 beta) but Chimera shows hemoglobin's subunits in 4 different colors. Does that mean that they're all different and neither are identical to each other?

Also, after I click on Matchmaker, a new window doesn't pop up. Where is the MultiAlignViewer window??

The exercise was a little frustrating, and also I think the exercise should explain all of the functions a little bit more.. like a tutorial. There are still a bunch of functions that I don't know how to use..

I finished the exercise and saved the images, but I will try to tackle the next two questions another time.



February 10, 2010

I spent about 45 minutes and answered the last two questions of the Chimera exercise. I wasn't exactly sure what question 2 was asking for...

 "Mechanisms for HIV-1 Entry: Current Strategies to Interfere with This Step." Current Infectious Disease Reports 3 (2001): 93-99

I spent about an hour reading and understanding this journal article.

HIV Entry

Step 1: Attachment step- requires high affinity recognition of the cell surface CD4 receptor for virus binding to occur.

Inhibition: PRO 542, a tetravalent form of soluble CD4 based proteins, through covalent attachment to the Fc portion of IgG may or may not prove to be efficacious in blocking the initial step of HIV entry. HIV+ individuals produce significant quantities of antibodies that target the viral envelope which neutralizes therapy with soluble CD4.

Step 2: Interaction of the gp120 viral envelope- CD4 complex with a chemokine co-receptor.

Inhibition: The natural ligands for the chemokine receptors (RANTES, MIP1-alpha and beta (CCR5) and SDF-1 (CXCR4) do inhibit HIV infection. Problem- infection can occur if just use a single chemokine co receptor inhibitor. Must use in combination with RT and protease inhibitors to be effective.

Step 3: Fusion - close alignment of the viral and cell membranes and their subsequent fusion

Inhibition: Structural studies of the gp41 trimeric core have led to the suggestion that a cavity within the coiled coil interface may be a desirable drug target. HR2-derived peptide (T649) that covers this region of gp41 exhibits increased in virtro anti retroviral potency and appears to be less susceptible to the evolution of resistant viruses than T-20 (DP178, a gp41 peptide mimetic that inhibits fusion step), which lacks this region.

Gp120 surface holds onto the virus through noncovalent associations with the gp41 transmembrane glycoprotein. CD4 molecule on the target cell can interact with gp120 through its most amino-terminal of the four immunoglobulin-like domains. Once CD4 binds with gp120, a conformational change occurs in gp120 which exposes a high affinity binding site for the chemokine coreceptor (CCR5 or CXCR4) found within the third variable loop (V3). Further interaction with the CCR5/CXCR4 also lead to exposure of the fusion-peptide domain of gp41 and insertion of this hydrophobic region into the target cell membrane, results in fusion of the viral and cell membranes.

Consequently, the RNA genome can access the host's cellular machinery and undergo viral replication.

This article is easily readable and understandable than the rest of the journal articles I've read. It summarizes the history of HIV therapeutic agents and HIV entry and inhibition of the steps described above. It helps formulate the big picture I have in mind, but I think I should focus on the conformational changes that occur in the viral envelopes and interactions with CD4 in regards to HIV-1 entry inhibitors.


 February 11, 2010

Today, we learned more of  the functions of Chimera in depth, which will now allow us to use the Chimera more efficiently in order to highlight and focus on specific parts of the structures we want to show for our research.

Chih-chin Huang, et al. "Structure of a V3-Containing HIV-1 gp120 Core" Science 310 (2005): 1025

 February 12, 2010

This is actually the second time I'm redoing the summary for this article. The first time I didn't notice that my laptop was running out of battery so then it suddenly died and shut off my computer without being able to restore everything I've written and the second time Mozilla crashed before I had the chance to save. There should be some sort of automatic saving that occurs so that we won't lose any data that we've put in... like Gmail. Now I'm going to save before I start!

This article presents the structure of V3 of the HIV-1 gp120 core in a complex with CD4 receptor and X5 antibody at 3.5 angstrom resolution. It was determined by using variational crystallization to obtain crystals suitable for x-ray structural analysis. The HIV envelope spike is trimeric and mediates binding to the receptors and virus entry. The binding of CD4 to gp120 in the spike causes conformational changes that allow binding to a coreceptor, either CCR5 or CXCR4. V3, which consists of 35 amino acids, is critical for determining which  coreceptor will be used for entry. If the 11th or 25th positions of V3 are positively charged, CXCR4 will be used; all other times, CCR5 is used. Gp120 is composed of inner and outer domains due to difference in orientation in the oligomeric viral spike. V3 arises from the outer domain and is subdivided into three structural regions: a conserved base, a flexible stem, and beta-hairpin tip (Pro-Gly). Gp120 has two important regions for coreceptor binding: the V3 tip and the gp120 core around the bridging sheet, the V3 base and neighboring residues.

They hypothesize that V3 acts as molecular hook due to its many features (ie high relative surface area, chemically reactive backbone,conformational flexibility, and overall extended nature) to catch the co-receptor and to modulate subunit interactins within the viral spike. These features allow V3 to grasp the neighboring protomers on the viral spike. The N terminus  of the coreceptor reaches  up and binds to the core and V3 base while the V3 tip of the  gp120 reaches down to interact with the second extracellular loop of the coreceptor.This is supported by biochemical studies that show that the binding of CCR5 N-terminus to gp120 is affected by gp120 alterations only  on the core and around the V3 base and that the small-molecule inhibitors of HIV entry that bind to the second extracellular loop of the coreceptor  no longer affect mutant viruses with V3 truncations. These attributes further allow V3 to influence HIV evasion of the immune system and trigger HIV entry into the cells.

V3 is an important structure of gp120 that I would like to include in my research topic.


 February 14, 2010

Today,I found 4 articles that I think will be relevant to my research. The first article is about the conformational changes when CD4 is bound to gp120 inner domain. The second article is about the ENV protein which mediates viral binding and entry. The third article is about the structural basis of HIV evasion (talked about in the article above on V3 loop). The fourth article is about the antbibody b13, which is a broadly neutralizing antibody that exploits the vulernable, functionally conserved and structurally invariant CD4-binding site (CD4BS) on HIV-1 gp120 to achieve neutralization.

PDB structures: 1GC1, 3DNN, 3IDX

 Kassa, A. "Transitions to and from the CD4-Bound Conformation Are Modulated by a Single-Residue Change in the Human Immunodeficiency Virus Type 1 gp120 Inner Domain" Journal of virology 83.17 (2009):8364


 Liu, Jun.

"Molecular architecture of native HIV-1 gp120 trimers" Nature (London) 455.7209 (2008): 109
 Chen, L. "Structural Basis of Immune Evasion at the Site of CD4 Attachment on HIV-1 gp120" Science 326.5956 (2009): 1123  
Zhou, T.

"P04-38. Crystal structure of gp120 in complex with the CD4-binding-site antibody b13 suggests precise targeting is needed for neutralization" Retrovirology 6(2009):P66

 Chimera  I updated the two images of chain D of hemoglobin and myoglobin. I highlighted the H bonds and the histidine structures on both hemoglobin and myoglobin. Notice that myoglobin has more H bonds with the atoms in the cavity than hemoglobin. Also, hemoglobin has only 2 histidine structures, whereas myoglobin has 4 histidine structures. Myoglobin also contains a sulfate ion H bonded to the heme structure and many water molecules.

 February 16, 2010

I spent 2 hours reading the journal articles above and highlighting certain parts of the articles that were important to my research.

Later today, I reread and reviewed the research articles and thought a lot about the big picture of the project and what I wanted to focus on. I worked on a draft for about an hour and sent a copy to Dr. Shuchi for feedback.


 February 18, 2010

Today, I found two review articles on HIV interactions with CD4.

 Eiden, Lee. "HIV Interactions with CD4: A continuum of conformations and consequences" Immunology Today 13.6 (1992): 201-206

CD4 as the principal receptor for HIV

CD4   has 4 immunoglobulin-like domains V1-V4 (three with intra-loop disulfide  bonds), the transmembrane segment, and intracytoplasmic tail (CYT).

CD4-gp120-gp41 complex  progresses through a series of conformational rearrangement required to:

  1. facilitate the dissociation of gp120 from the gp120-gp41 complex
  2. correctly position gp41 relative to the surface membrane of the target cells
  3. allow fusion of the virion envelope with the cell membrane
 Moore, John. "The HIV gp120-CD4 interaction: A target for pharmacological or immunological intervention?" Perspectives in Drug Discovery and Design 1.1 (1993): 235-250  Too old of an article- must find newer version.
 PDB at CABM  Today, we went over my abstract. The first draft of my abstract was too specific for the general audience. Therefore, I needed to make it general so that I do not confine myself to a specific topic. I went to the PDB site and searched for HIV gp120 to find any structures and associated papers. In this time, I also revised my abstract.
   I took a look at my abstract and decided to add more information to it. I finished, sent it to Dr.  Dutta, and submitted the abstract application to the Aresty Research Symposium.

 February 19, 2010

Today I started viewing articles related to the PDB structures that I have found.


Crystal structure of a 3B3 variant—A
broadly neutralizing HIV-1 scFv antibody

3B3 variant, derived from b12 antibody, possess enhanced binding affinity and neutralization activity against several forms of HIV-1. The antibody b12, targets the recessed CD4-binding site on gp120. The binding epitope of b12 partially overlaps with the CD4-binding site thus blocking the initial viral gp120-host CD4 interaction and inhibiting viral fusion with the host cell membrane and infection.

The structures of bound and unbound forms of b12 were compared and results indicate close resemblance with 2 exceptions.

I tried finding where they found the structure, but everything is getting confusing. I'll try to find a review article that gives an overview on what this article is talking about.

WILLEY, S. "Humoral immunity to HIV-1:
neutralisation and antibody effector functions." Trends in microbiology 16.12 (2008): 596

 February 24, 2010

It's important to understand that since HIV continually evolves, antibodies weakly neutralize the majority of the virus in an infected person.

HIV entry

  1.  GP120 binds to CD4, triggering conformational changes that expose the co-receptor binding site.
  2. GP120 binds to the co-receptor (CCR5 or CXCR4)
  3. The N-terminus of the co-receptor interacts with the bridging sheet and surrounding residues of gp120, and the second extracellular loop contacts the tip of the gp120 V3 loop.
  4. Co-receptor binding triggers further conformational changes in the envelope spike that lead to the insertion of the gp41 fusion peptide into the target cell membrane.
  5. Complementary regions of the 3 gp41 subunits fold back on themselves to form a 6-helix bundle, which brings the viral and cellular membranes into close proximity and precipitates membrane mixing and fusion.
  6. A membrane pore is subsequently created, allowing delivery of the viral core into the cytoplasm of the cell.

Sattentau, Q. "The role of CD4 in HIV binding and entry. " Philos Trans R Soc Lond B Biol Sci. 342.1299 (1993):59-66.

CD4's role in HIV binding and entry

CD4 antigen is the common primary cellular receptor for HIV-1, HIV-2, and SIV. There is a high-affinity interaction between the first domain of CD4 and outer glycoprotein of HIV, gp120. To see its role, they used a soluble recombinant form of CD4 as a "receptor mimic" to bind with gp120, which induces conformational changes in gp120. Gp120 completely disscoates from the transmembrane glycoprotein, gp41, and exposes the epitopes of gp41. They also observed this same interaction with cell-anchored CD4, in which gp41 epitopes were also exposed at the fusion interfase between clusters of CD4 expressing and HIV-infected cells. CD4 binding induces receptor-mediated activation of fusion of gp41.


 February 25, 2010

Today, I found



February 26, 2010

Image- Shows different residues of CD4 (in blue), but highlighting Phe 43, which makes a significant contribution to the high  affinity interaction between CD4 and gp120.


 March 2, 2010



 March 3, 2010

Conformational Model for the V3 Loop of Gp120

V3 loop of gp120 has an essential role in infection process. It is composed of 35 amino acids and is closed by a disulfide bond between two invariant cysteines at positions 303 and 338 of gp120. It is the principal domain of HIV-1 targeted by the immune system. Variable V3 loop is predicted to be close to a conserved area of gp120 that is thought to interact with the coreceptors.

The residue Glu25 (highlighted in gray) is part of the first turn of the helix and studies show that acidic residues are highly favored in the first helical turn , making this residue important for the stability of the observed helix.


9108481 View PubMed Abstract at NCBI

Core structure of gp41 from the envelope glycoprotein

Gp41 mediates fusion between viral and cellular membranes. There is an alpha helical domain within gp41, composed of a trimer of 2 interacting peptides (N36 and C34) into a 6-helical bundle. 3 N36 helices form an interior, parallel coiled-coil trimer, while 3 C34 helices pack in an oblique, antiparallel manner into highly conserved, hydrophobic grooves on the surface of this trimer.

CD4 induces conformational changes in membrane fusion, which are thought to expose the hydrophobic, glycine rich fusion peptide r egion of gp41 that is essential for that membrane-fusion activity.


17901336 View PubMed Abstract at NCBI 

CCR5 Co-receptor

CCR5 and CXCR4 are members of a family of chemokine receptors that are G protein-coupled receptors characterized by seven transmembrane helices, an extracellular N terminus, which is variable in length, and three extracellular loops. The N terminus and around its second extracellular loop are elements of critical importance in interactions with HIV-1. N-terminus interacts with 4-stranded bridging sheet in gp120, which assembles upon CD4 binding. The ECL2 region interacts with the tip of the V3 loop in gp120. These two interactive regions are independent because considerable distance separates them.

The N terminus of  CCR5 approaches from the same face of gp120 as CD4 but binds to an orthogonal surface at the intersection of the bridging sheet and the V3 loop. Ser 7 and Pro 8 interact with the V3 stem. Tyrosine 14 binding pocket- completely sequestered in the crevice between V3 and the bridging sheet so to form this pocket, structural rearrangements would be expected to rigidify the V3 stem.


11258890 View PubMed Abstract at NCBI 


HIV gp41 core containing an Ile573 to Thr substitution

Gp41 undergoes conformational changes when Gp120 binds to CD4. A buried isoleucine (Ile573) in a central trimeric coild coil within the gp41 ectodomain core is thought to favor conformational activation. Its role was determined by mutating Ile573 to Thr 573. The introduction of Thr stabilized the gp41 core and the structure was very similar to the original. Between the burried Thr 573 and Thr 569 residues, a new hydrogen-bonding interaction appears to allow formation of trimer-of-hairpins structure at physiological temperature. The hydrophobicity of the side chain at 573 affects the proper folding of the gp41 core as well as the in vivo phenotypes of the gp120-gp41 complex. The mutation exhibits only a moderate reduction in fusion activity and virion infectivity. Conserved coiled-coil interactions within the N-terminal heptad repeat are important determinents of gp41 conformational change required for HIV-1 membrane fusion.


---having a hard time finding the residues and the hydrogen bonding interaction




10520998 View PubMed Abstract at NCBI 


10520998 View PubMed Abstract at NCBI 

Inhibitor of HIV entry

GP41 mediates fusion of the viral and cellular membranes. IQN17 was designed to target the prominent pocket on the surface of a central trimeric coild coil within gp41.



17125793 View PubMed Abstract at NCBI

4E10 - epitope: target for vaccine design

4E10 is the broadest HIV-1 neutralizing antibody known to date and recognizes a
contiguous and highly conserved helical epitope in the
membrane-proximal region of gp41.


**Currently visualizing.



 March 4, 2010

Today, I showed and explained what I wanted to highlight in the PDB structures in relation to the big picture to Dr. Dutta. I have to alter some of the images to make it clearer for the general audience to see it and know what's going on. 

I also started the powerpoint presentation for tomorrow. It's not yet complete, and will continue to work on it tomorrow and the weekend.


 March 8, 2010

Today, I am reading articles to better understand the structures that I am making in Chimera. Sometimes it can be difficult to fully understand the articles and then try to make the structure based on it... 


 March 9, 2010

I was unable to change the structure of 3JWD into surface from ribbons. I wanted to show the binding site of CD4 and gp120. Instead I used 1GC1 to obtain the GP120 structure and then used 1CDI to obtain the CD4 structure and was able to pinpoint the Phe43 cavity within the GP120 structure. See below.



 March 10, 2010

I am continuing my power point presentation to incorporate the ideas and improvements suggested to me by Dr. Dutta. 



 March 11, 2010

Still in the process of doing the powerpoint presentation. I have yet to include the gp41 structure and the development of new therapy. 


 March 22, 2010

I viewed this website ( and found an animation pertaining to HIV binding/fusion and cell entry as well as inhibition of attachment, co-receptor, and fusion.


 March 23, 2010

I am re-reading this paper ( and ( to review and get back the overall sense in my presentation.

 March 25, 2010

Gp120 is noncovalently associated with gp41. Gp120 is located on the exterior and gp41 is a transmembrane envelope glycoprotein. Binding of gp120 to its receptors on target cell changes the gp120-gp41 interaction and activates gp41 to fuse with membrane. When gp120 interacts with CD4, V3 loop is exposed, which contributes to the binding of the chemokine receptors (CCR5 or CXCR4). CD4 dismantles the gp120 element (V3 loop + adjacent beta strands) and alters gp120-gp41 link, allowing the hydrophobic patch in the V3 tip to b available for chemokien receptor binding.


Viral evasion

Glycosylation and oligomeric occlusion protect HIV from the immune response.

Antibodies access only two surfaces:

  1. one that overlaps the CD4 binding site
    •  which is shielded by the V1/V2 loop
  2. another that overlaps the chemokine-receptor binding site
    •  which is shielded by the V2/V3 loops

Conformational change in chemo-receptor region may hide the conserved epitope (unformed before CD4 binding)

Steric occlusion may take place between the CD4 anchored viral spike and the proximal target membrane.

  • Steric occlusion: recessed nature of the binding pocket.

: encloses a variational island or a "hot spot".

An ‘anti-hotspot’ equivalent may camouflage chemokine-receptor-binding residues on the V3 loop in surrounding variability.



Chan, D. C., Fass, D., Berger, J. M. & Kim, P. S. Core structure of gp41 from the HIV envelope
glycoprotein. Cell 89, 263–273 (1997).

Weissenhorn, W., Dessen, A., Harrison, S. C., Skehel, J. J. & Wiley, D. C. Atomic structure of the
ectodomain from HIV-1 gp41. Nature 387, 426–430 (1997)


Must find articles on:

  • the conformational changes that trigger reorganization of the gp41 ectodomain
  • structural basis for insertion of the fusion peptide of gp41 into the target membrane
 Zwick, Michael. "gp41: HIV's shy protein" Nature Medicine 10 (2004)

 March 30, 2010

I am continuing my research on the gp41 molecule. I spent 2 hours looking for relevant articles and found an article that talks about the structure of gp41 and fusion inhibitors that were developed. I spent an hour reading. 

gp 41

  • transmembrane glycoprotein
  • strong tendency to aggregate
  • apparatus of viral fusion
  • activated when gp120 undergoes conformational changes after bound to CD4
  • uses conserved structural elements to mediate fusion of host and viral membranes
  • these vulnerable conserved regions on gp41 remain hidden as much as possible



March 31, 2010

I attended the Workshop: Effective Posters and Presentations provided by the Aresty Research Program (1 hour).  The speaker presented to us the different modes of presenting (oral speaking, power point presentation, poster presentation) and advised us what not to do and what we can do to enhance our presentation.



 April 1, 2010

I spent 3 hours creating the MAP depositions.