Alex J. George Week 7

Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing Fabs

Vocabulary

1. X-Ray crystallography- a method of determining the arrangement of atoms within a molecule by looking at diffraction patterns of X-rays
2. syncytium- a cell-like structure filled with cytoplasm containing many nuclei
3. Fab fragment- "fragment antigen binding" region on antibody that binds to the antigen
4. paucity- smallness or insufficient number; scarcity
5. GPGR tip- a relatively conserved region within the V3 Loop
6. Ramachandran space- way to visualize dihedral angles ψ against φ of amino acid residues in protein structure
7. isomorphously- similarity in form
8. hydrazone bond- a double bond between a Carbon atom and Nitrogen atom
9. Aib142- α- aminoisobutyric acid [NHC(CH3)2C(O)]
10. His loop and Ser loop- Histidine and Serine loops
11. residue- amino acid

Paper Outline

Introduction

• The third hypervariable (V3) loop of gp120 is required for viral entry into the cell membrane
• Sequence changes in V3 can affect receptor usage- controlling which types of cells are infected
• CXCR4 is the coreceptor for T-Cell tropic and CCR5 is the coreceptor for macrophage tropic
• V3 loop is about 40 amino acids
• Exposure of V3 loop depends on viral type which affects tropism-- CD4 increases exposure
• T-Tropic sequences around V3 loop are basic
• Highly conserved sequences have key structural role to protein
• Knowing conformations of loop could help explain progression of disease
• Fab 50.1 and 59.1 have turns similar to Aib amino acid
• Replacing Alanine with Aib residue didn't change rigidity of Fab 59.1

Results/Discussion

• Figure 1
  • Indicates Amino acid sequences of RP70, Histidine loop, Serine loop and Aib142
  • RP70 loop has disulfide bond, the two loops have hydrazone bonds between J and Z (this is shown in detail)
  • J is called Arn(P1); Z is called Gly(P11)
• Table 1
  • Data collection and refinement statistics
  • Rmsd- Deviation from ideal bond length/ angle
• Figure 2
  • Views of Fab 58.2- A) with Aib142, B) with His loop C) with Ser loop
  • Cyan is the light chain, Blue is heavy chain, Red is highly conserved sequence
• Figure 3
  • Comparing the H1 loop of different Fabs (58.2, AN02 and N10)
  • The structures are very similar until regions 32-37
• Figure 4
  • Electron density for the Aib142 peptide loop (a,b), His loop peptide (c) and Ser loop peptide (d)