Alex J. George Week 7

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


  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


  • 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


  • 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


  • 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

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