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)
• Figure 5
  • A surface picture of Fab 58.2 indicating acidic regions (red), basic regions (blue) and neutral regions (white)
  • a) Shows the acidic binding pocket for Arg(P322) of Aib142
  • b) Shows the charge-charge interaction between Arg of peptide and Glu/Asp of Fab
• Table 2
  • Shows the number of Van der Waals contacts between Fab and the 3 peptides, Aib142, His loop and Ser loop
• Table 3
  • Shows the number of Hydrogen bonds between Fab and the 3 peptides, Aib142, His loop and Ser loop

• Various amino acids were substituted for other amino acids to determine their importance to the structure; Gly(P319) proved to be important, as did Arg (P322) and Pro(P320)
• The conformation of the V3 loop is different than others when it is bound to Fab 58.2
• Figure 6
  • The conformations of the V3 loop of 3 peptides bound to Fabs 50.1, 59.1 and 58.2
  • Fabs 50.1 and 59.1 overlap each other, but Fab 58.2 shows a different conformation (different turns)
  • Blue is the Aib142 peptide bound to V3, Green is the His loop
• Table 4
  • Indicates that the residue binding angles are similar despite the different turns

• NMR has supported the idea that glycosylation can affect V3 conformation

Discussion

• The high degree of conservation of GPGR region at the tip of the V3 loop suggests this is significant to biological function
• Altering the V3 loop changes tropism, but is it because the loop structure is different or just that the turn is different
• The results here help to understand the conformational flexibility of the V3 loop
• More knowledge of the V3 regions will always help to combating HIV-1

Group Journal Club

Protein Structure Presentation

Individual Journals

1. No Week 1 Journal
2. Alex J. George Week 2
3. Alex J. George Week 3
4. Alex J. George Week 4
5. Alex J. George Week 5
6. Alex J. George Week 6
7. Alex J. George Week 7
8. Alex J. George Week 8
9. Alex J. George Week 9
10. Alex J. George Week 10
11. Alex J. George Week 11
12. Alex J. George Week 12
13. Alex J. George Week 13

Shared Journals

1. Week 2
2. Week 3
3. Week 4
4. Week 5
5. Week 6
6. Week 7
7. Week 8
8. Week 9
9. Week 11
10. Week 12
11. Week 13
12. Week 14
13. Week 15

Links

Course Home Page

Alex George