Chris Rhodes Week 7

From OpenWetWare
Jump to navigationJump to search

The paper we are preparing is "Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing Fabs" Stanfield et al. (1999) The full article can be found here Stanfield (1999)

10 Terms

  1. Chemokines: A class of molecules that can attract and activate white blood cells and other immune response cells. There are many different types of chemokines each of which serve different functions or interact with different immune cell types. They're most common purpose is inter-cellular communication. Chemokines 10/17/11
  2. Macrophage: A class of mammalian cells that are activated in response to foreign agents in the body. They function as immune cells attacking and killing certain bacteria, but also have a broader affect on immune system activation by stimulating other immune cells and exposing antigens. Macrophage 10/17/11
  3. Syncytia: Usually the result of cellular fusion, syncytia are giant cells containing multiple nuclei not separated by individual cellular membranes. As discussed by the paper, interactions between the cell membrane and viral gp120 and gp41 can cause accidental syncytia formation. Syncytia 10/17/11
  4. Lentivirus: The genus of retrovirus that contains HIV-1. This genus is characterized by viruses which show persistent infection of multiple organs and who require long incubation periods. Lentivirus 10/17/11
  5. CXCR4: Transmembrane cell receptors that react to alpha chemokines. They also serve as fusion cofactors during the fusion of the HIV-1 viral coat and the t-cell membrane. CXCR4 10/17/11
  6. CCR5: Transmembrane cell receptors that react to beta chemokines. They also serve as fusion cofactors during the fusion of the HIV-1 viral coat and the macrophage cell membrane. CCR5 10/17/11
  7. Epitope: An area of a large molecule which is sensitive to and will bind to an antibody specific to that large molecule. The binding of the antibody to this site will typically cause a conformational shift or other reaction that neutralizes the large molecule. Epitope 10/17/11
  8. Antihapten Antibody: Antibodies that target small molecule markers known as haptens. Haptens in conjunction with another protein will activate the immune responses of an organism. Anti-hapten antibodies will only be produced when the hapten complex activates the immune system and will target, bind, and neutralize specific haptens as a means of keeping the immune response regulated during and after infection. Antihapten Antibody 10/17/11
  9. Protease: An enzyme which facilitates the cleaving of peptides bonds within a protein in order to shorten the protein or create smaller protein segments. Proteases can by used to both active and neutralize proteins depending on the type of protease and the protein it acts on. Protease 10/17/11
  10. Tropism: The attractive or repulsive response to a given stimulus. In the case of the paper this was discussed as T-Tropic or M-Tropic viral strains meaning strains attracted to either T cells or Macrophages. Tropism 10/17/11



  • The V3 domain of gp120 of HIV-1 viruses represent essential sites of CD4-Virus interaction necessary to facilitate viral and CD4 membrane fusion allowing for the initiation of the viral infection of the CD4 cell.
  • The V3 peptide loop has multiple effects on viral interactions including tropism and antibody neutralization.
  • Previous research done by La Rosa has indicated that the amino acid sequences around the stems of the V3 loops of different viral variants were highly variable while the amino acid sequences comprising the tip of the loop (GPGR) were highly conserved among the variants suggesting that the amino acids that comprise the tip are essential for function.
  • Though the general functions of gp120 are fairly well understood, the in-depth mechanisms of reaction and the various structural conformations of the V3 amino acids and their effects on viral binding potential and viral progression are still unknown.
  • Previous studies have not been able to relate specific changes in the V3 sequence with a change in phenotype, however there could be a relationship between V3 amino acid conformations and gp120 functionality.
  • The lab has previously researched crystal structures of Fab 50.1-V3 and Fab 59.1-V3 complexes in an attempt to find the conformations adopted by the V3 peptide upon binding to various antibodies shown to have different styles of viral neutralization.
    • These two previous studies did not prioritize the study of the (GPGR) loop tip as the current study does.
  • Understanding how the structural conformation of the V3 peptide affects its function could provide invaluable insight into HIV-1 immunology and potential medical treatments for the disease.

Materials and Methods

  • This experiment uses the neutralizing antibody Fab 58.2 crystallized in complex with three different truncated V3 peptides.
    • Histidine Loop: JHIGPGRAFGZG
    • Serine Loop: JSIGPGRAFGZG
  • Aib is used to replace the alanine in the V3 peptide in order to establish a stable and uniform structure for the peptide. If the alanine was not replaced, the structure of peptide would be too variable to perform accurate crystallization.
  • The Aib142 peptide was created using chemical synthesis while the Ser and His peptide loops were generated using solid phase synthesis.
  • The complexes were crystallized using the sitting drop, vapor diffusion method at 22.5 degrees Celsius
  • The structures determined through the use of the X-PLOR computer program, PC refinement, and an in-house Harada translation function. Various programs were used to generate the data and renderings given in the Tables and Figures.

Explanations of Figures and Tables

  • Figure 1: Figure 1 details the protein sequences of each of the peptides used to form complexes with the Fab 58.2 antibody as well as the complete sequence of the V3 peptide used to create the three experimental peptides. It also gives a pictorial representation of how the hydrazone linkage of the J and Z residues of the His and Ser-loop peptides forms the stabilized loop used in the formation of the final Fab 58.2-Peptide complexes.
  • Table 1: Table 1 describes the X-ray diffraction data and statistics for each of the three Fab 58.2-peptide complexes. Unfortunately, due to my limited knowledge of the in-depth details of X-ray crystallography, unfamiliarity with the conventions of data presentation in the field, and the lack of further explanation of this data in the paper I am unable to interpret most of the information given in this table.
  • Figure 2: Figure 2 shows computer generated representations of the crystalized structures of the entire Fab 58.2-Peptide complex for Fab 58.2 bound to (a) the linear Aib142 containing peptide, (b) the His-loop peptide, and (c) the Ser-loop peptide. The two loop peptide complexes show very similar Fab 58.2 structures while the linear Aib142 peptide complex shows a distinctly larger gap between the upper 2 domains containing the peptide and the lower 2 domains, which when compared to the loop peptide complexes seem much more compressed or tightly packed.
  • Figure 3: Figure 3 shows the structural conformation of the H1 loop of the Fab 58.2 antibody in comparison to the structure of the H1 loops of two other Fab antibodies, N10 (yellow) and AN02 (blue), with similar H1 loop length. The H1 loop structure of AN02 represents the expected canonical structure for the length of the loop. Fab 58.2 (red) shows a similar structure to the other two H1 loops from residues 20-29 and 35-37, but differs distinctly from the other two H1 loops between residues 31-34 forming pronounced inner(31-32) and outer(33-34) kinks.
  • Figure 4: Figure 4 shows the electron densities of some of the various structures examined in the experiment.(a) Displays the electron density of the GPGR residues in the Aib142 peptide complex and indicates a type 1 β turn. (b) Displays the electron density of the RAibFY residues in the Aib142 peptide complex. (c)and(d) Display the electron density of the entire peptide sequence of the His-loop and Ser-loop peptides excluding the J-Z hydrazone linkage due to insufficient density.
  • Figure 5: Figure 5 shows the Fab 58.2-Aib142 complex with the Fab 58.2 shown using the space-filling model with regions of polarity shown as red and blue, red representing negative charges and blue representing positive charges. The Aib142 is bound to a highly negative pocket of the Fab 58.2 structure. The stereoview of all the Fab 58.2 residues that interact with the peptide at the binding site is also shown.
  • Table 2: Table 2 gives a list of each of the Van der Waals interactions between the specific residues of Fab 58.2 and the specific residues of each of the three peptides in complex. The table shows the Fab 58.2 residues that interact with the common residues amongst all three of the peptides as well as the unique interactions between the Fab 58.2 residues and certain peptide specific residues. The common residue interactions are listed under the "In all complexes" column and the unique interactions are listed for each specific residue under each of the individual peptide columns. It is seen that there are 3 instances of interactions that are completely unique to a specific peptide and two instances in which there are no peptide specific interactions.
  • Table 3: Table 3 shows the various hydrogen bonds and salt bridges taking place between the Fab 58.2 residues and the various residues of the three peptides in complex. Again due to my lacking knowledge of crystallography data conventions and lack of explanation in the paper it is difficult to render further interpretation of the data.
  • Figure 6: Figure 6 shows the comparison of the structural data of the Fab 50.1-peptide and 59.1-peptide complexes obtained by the lab in previous experiments and the structural data of the Fab 58.2-Aib142 and Fab 58.2-His complexes studied in this experiment. The comparison shows that the main chain residues of all of the peptides share a similar structural configuration, but differ when examining the conformational structure developed by the GPGR loop residues. The peptides of Fab 50.1 and 59.1 show a type 2 β-turn at the GPGR residues while both of the Fab 58.2 peptide conformations show a type 1 β-turn at the GPGR residues.
  • Table 4: Table 4 lists the φ and ψ angle values for conserved residues among the peptides used to form the Fab 50.1-peptide and 59.1-peptide complexes from the previous experiments and the Fab 58.2-Aib142 complex. When examining the angles of the GPGR residues between the three peptides, the angles between the 50.1 and 59.1 residues are considerably similar, but are markedly different from the angles of the same residues in the Aib142 peptide. The difference in these angles represents the conformational differences between the GPGR residues of the previous experiment's peptides and the current experiment's peptides.


  • The GPGR region of the V3 peptide is highly conserved throughout different viral variants and can be considered biologically relevant to the binding of antibodies to gp120.
  • The GPGR region of the V3 peptide has been seen to adopt multiple different structural conformations based on it's environment and binding partner. These variations may relate to variations in biological function or binding potential of the V3 loop.
  • This lab's findings disagree with some of its own previous studies of V3 peptide structure in the different conformational structures taken by the GPGR β-turn, however this disagreement actually furthers their theory that different types of antibodies will cause different conformational shifts in the V3 structure.
    • These results also show the conformational flexibility of the V3 loop
  • In agreement with the epitope mapping of the Jellis study, this paper concludes that the residues GlyP319, ProP320 and ArgP322 are especially important for anti-body binding to gp120 and thus the functionality of gp120.
  • Although not conclusively shown by their results, this paper asserts that the effects of different V3 loop conformations could lead to changes in biological functions and interactions of gp120 and should be considered as a potential area for further study.
  • To date (1999), there haven't been any studies crystallizing the total gp120 structure. The paper suggests that future experiments should include the crystallization of a complete V3 peptide sequence rather than truncated versions of the peptide which have been used so far. The study of intact gp120 complexes would provide for more definite conclusions to be made.

Journal Club Presentation

Chris Rhodes, Alex Cardenas Week 7 Journal Club


  1. Chris Rhodes User Page
  2. Week 2 Journal
  3. Week 3 Journal
  4. Week 4 Journal
  5. Week 5 Journal
  6. Week 6 Journal
  7. Week 7 Journal
  8. Week 8 Journal
  9. Week 9 Journal
  10. Week 10 Journal
  11. Week 11 Journal
  12. Week 12 Journal
  13. Week 13 Journal
  14. Week 14 Journal
  15. Home Page
  16. Week 5 Assignment Page
  17. Week 6 Assignment Page
  18. Week 7 Assignment Page
  19. Week 8 Assignment Page
  20. Week 9 Assignment Page
  21. Week 10 Assignment Page
  22. Week 11 Assignment Page
  23. Week 12 Assignment Page
  24. Week 13 Assignment Page
  25. Week 14 Assignment Page