1. Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing Fabs RL Stanfield, E Cabezas, AC Satterthwait, EA Stura, AT Profy, IA Wilson, Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing Fabs, Structure, Volume 7, Issue 2, 15 February 1999, Pages 131-142 Chris Rhodes and Alex Cardenas Loyola Marymount University Department of Biology BIOL 398 10/19/11

2. Outline The V3 peptide loop of gp120 of HIV-1 viruses has many effects on viral interactions and may affect antibody binding ability. Previous studies show conserved GPGR residues in V3 sequence variants indicating functional significance. The crystal structure of Fab 58.2-Peptide complex are found to show differences in GPGR β-turn conformation when compared to previous studies. The effects of different V3 loop conformations could lead to changes in biological functions and interactions of gp120. Future experiments should focus on determining the structure of intact gp120 in order to provide more definite conclusions.

3. Gp120 plays an essential role in HIV-1 viral infection gp120 is a protein complex found on the exterior of HIV-1 viral coats gp120 facilitates viral-CD4 receptor binding essential for infection The V3 peptide domain is located within gp120 – ~40 amino acid sequence –High sequence diversity among viral variants.

4. The V3 peptide loop of gp120 of HIV-1 viruses may affect antibody binding and gp120 functionality In previous experiments changes in the sequence of the V3 domain have shown multiple effects on: –Viral Tropism –Antibody binding ability –Syncytium-Formation –Chemokine Receptor usage

5. Previous studies show conserved GPGR residues indicating functional significance Studies by La Rosa et al. (1990) show conserved region among V3 amino acid sequence variations. GPGR residues near tip of loop are highly conserved “Stem” amino acids are highly variable Results agree with previous Stanfield studies of crystal structures. –Fab 50.1-V3 and 59.1-V3 complexes show conserved GPGR type II β-turn conformation High conservation of GPGR indicates GPGR is required for functionality

6. Experiment analyzes Aib 142,His-Loop, and Ser-Loop crystallized in complex with the Fab 58.2 Peptide Synthesis: –Aib 142 : Chemical Synthesis –His and Ser loops: Solid phase synthesis Crystallization: –Sitting drop, vapor diffusion method at 22.5 degrees Celsius Determination of Structure: –X-PLOR computer program – PC refinement –Modified Harada translation function

7. Outline The V3 peptide loop of gp120 of HIV-1 viruses has many effects on viral interactions and may affect antibody binding ability. Previous studies show conserved GPGR residues in V3 sequence variants indicating functional significance. The crystal structure of Fab 58.2-Peptide complexes are found to show differences in GPGR β-turn conformation when compared to previous studies. The effects of different V3 loop conformations could lead to changes in biological functions and interactions of gp120. Future experiments should focus on determining the structure of intact gp120 in order to provide more definite conclusions.

8. Residues and 2-D Structure of Experimental Peptide Sequences Amino Acid Sequences of 3 Experimental peptides J-Z Hydrazone linkage shown Aib142 replaces Ala142 to stabilize peptide structure

9. Data and Statistics gathered from X-ray Diffraction of Fab 58.2-Peptide Complexes

10. Crystallized structure of Fab 58.2- Peptide complexes A)Fab 58.2-Aib 142 Complex B)Fab 58.2-His Loop Complex C)Fab 58.2-Ser Loop Complex * Fab 58.2 shown as blue and cyan * Binding peptides shown in red

11. H1 Loop structure of Fab 58.2 and two other H1 loops of similar length Red: Fab 58.2 H1 loop Blue: AN02 H1 loop Yellow: N10 H1 loop Fab 58.2 H1 loop differs from expected structure shown by AN02 H1 loop is used when binding peptide but makes only minor contacts

12. Electron Density Maps of Peptides bound to Fab 58.2 A)GPGR β-Turn of Aib 142 peptide B)RAibFY residues of Aib 142 peptide C)Complete His-Loop peptide D)Complete Ser-Loop peptide J-Z Hydrazone linkage of His and Ser loops not shown

13. Experimental Peptides Bind to Fab 58.2 in Essentially Identical Manners A)Fab 58.2-Aib 142 Complex Red Regions: (-) Charge Blue Regions: (+) Charge Aib 142 binds to dense negatively charged pocket B) Fab 58.2 contacts to Aib 142 Yellow Structure: Aib 142 Blue and Cyan: Fab 58.2 Experimental peptides all bind in the same pocket Each peptide has specific and distinct contacts with 58.2

14. Residue Contacts Between Fab 58.2 and Bound Peptides Common Contacts Among all Peptides Contacts Specific to Aib 142 Contacts Specific to His-Loop Contacts Specific to Ser-Loop

15. Hydrogen Bonds and Salt Bridge Interactions in Fab 58.2-Peptide Complexes Bond Lengths (Å)Interacting Peptide ResidueInteracting Fab 58.2 Residue

16. Fab 58.2 Peptides are found to show differences in GPGR β-turn conformation when compared to previous studies Purple: Fab 59.1-Peptide Yellow: Fab 50.1-Peptide Blue: Fab 58.2-Aib 142 Peptide Green: Fab 58.2-His Loop Peptide Fab 59.1 and 50.1 Peptides show type II β-turn GPGR conformation Fab 58.2 Peptides show type I β-turn GPGR conformation

17. Differences in GPGR conformations are seen through bond angles. Fab 50.1 and 59.1 peptides share fairly similar bond angles for GPGR residues Fab 58.2-Aib 142 peptide GPGR residue angles differ distinctly from 50.1 and 59.1 peptide angles. Differences in bond angles corresponds to differences seen in peptide conformation.

18. Outline The V3 peptide loop of gp120 of HIV-1 viruses has many effects on viral interactions and may affect antibody binding ability. Previous studies show conserved GPGR residues in V3 sequence variants indicating functional significance. The crystal structure of Fab 58.2-Peptide complex are found to show differences in GPGR β-turn conformation when compared to previous studies. The effects of different V3 loop conformations could lead to changes in biological functions and interactions of gp120. Future experiments should focus on determining the structure of intact gp120 in order to provide more definite conclusions.

19. The effects of different V3 loop conformations could lead to changes in biological functions of gp120. The GPGR region of the V3 loop can be considered biologically relevant to gp120 functionality. Based on epitope mapping Gly P319, Pro P320 and Arg P322 have been found to affect antibody binding affinity to gp120. GPGR has been shown to adopt different conformations based on environment and binding partner. These variations may relate to the binding potential of the V3 peptide in the gp120 complex and thus gp120 functionality.

20. Future Experiments Should Focus on Crystallization of Intact gp120 Complex To date (1999) the intact structure of the gp120 complex has not been studied. Can’t show conclusive findings about V3-gp120 functionality without studying the two in complex Future experiments: –Structure of intact gp120 complex –Structural studies of complete V3 peptides –Determining effects of antibodies on V3 conformation in gp120 complex

21. Summary The V3 domain of gp120 of HIV-1 viruses has multiple effects on viral-CD4 receptor interactions Specifically the GPGR tip region of the V3 loop has been suspected for functional significance The β-turn conformations adopted by the GPGR residues are shown to change with binding partner and environment The various conformations of the GPGR residues of the V3 loop could affect gp120 functionality In order to properly study V3-gp120 functionality, future studies should research the two in complex

22. Acknowledgements Kam D. Dahlquist, Ph.D Stanfield et al. (1999)