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Comparative Study
. 2005 Oct;79(20):13060-9.
doi: 10.1128/JVI.79.20.13060-13069.2005.

Structure of the Fab fragment of F105, a broadly reactive anti-human immunodeficiency virus (HIV) antibody that recognizes the CD4 binding site of HIV type 1 gp120

Royce A Wilkinson  1 , Chayne Piscitelli, Martin Teintze, Lisa A Cavacini, Marshall R Posner, C Martin Lawrence
Affiliations
Comparative Study

Structure of the Fab fragment of F105, a broadly reactive anti-human immunodeficiency virus (HIV) antibody that recognizes the CD4 binding site of HIV type 1 gp120

Royce A Wilkinson et al. J Virol. 2005 Oct.

Abstract

We have determined the crystal structure of the Fab fragment from F105, a broadly reactive human antibody with limited potency that recognizes the CD4 binding site of gp120. The structure reveals an extended CDR H3 loop with a phenylalanine residue at the apex and shows a striking pattern of serine and tyrosine residues. Modeling the interaction between gp120 and F105 suggests that the phenylalanine may recognize the binding pocket of gp120 used by Phe(43) of CD4 and that numerous tyrosine and serine residues form hydrogen bonds with the main chain atoms of gp120. A comparison of the F105 structure to that of immunoglobulin G1 b12, a much more potent and broadly neutralizing antibody with an overlapping epitope, suggests similarities that contribute to the broad recognition of human immunodeficiency virus by both antibodies. While the putative epitope for F105 shows significant overlap with that predicted for b12, it appears to differ from the b12 epitope in extending across the interface between the inner and outer domains of gp120. In contrast, the CDR loops of b12 appear to interact predominantly with the outer domain of gp120. The difference between the predicted epitopes for b12 and F105 suggests that the unique potency of b12 may arise from its ability to avoid the interface between the inner and outer domains of gp120.

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Figures

FIG. 1.
FIG. 1.
(A) Amino acid sequences of F105 CDRs (Kabat definition). Color coding of the CDR name corresponds to the coloring of the respective CDR in Fig. 1B, while color coding of the amino acid sequence corresponds to the coloring of the residue type in Fig. 1C. For example, “CDR L1” is shown in orange, as is the CDR L1 loop in Fig. 1B, all serine residues in the sequence of Fig. 1A are in pink, and all serine side chains are depicted in pink in Fig. 1C. (B) Tyrosine residues across the top of the F105 antigen recognition site. The nine tyrosine residues found in the F105 CDRs are shown. The color coding is indicative of the CDR loop, with CDR L1 in orange, CDR L2 in red, etc. (C) Serine and tyrosine residues in the CDRs of F105. The orientation is related to the structure in Fig. 1B by a 90o rotation such that one is looking down upon the antigen combining site, rather than looking from the side. The side chains of all serine (pink) and tyrosine (blue) residues within the CDRs are shown. In addition, PheH100A is shown in yellow and ArgL31A is shown in orange. Tyrosine residues are concentrated in the center of the antigen recognition site, at positions that commonly interact with the antigen (the “contact CDR”) (8, 34), whereas the serine residues are found in higher concentration along the periphery of the antigen recognition site, within the Kabat definition of the CDR but outside the contact CDR. (D) Superposition of F105 and antibody b12. The variable domains of F105 (green) and b12 (blue) have been superimposed, demonstrating the similarities between the extended CDR H3 loops of these two antibodies. The side chains for PheH100A (yellow) and TyrH100B (cyan) of F105 are shown, as is the tryptophan at the apex of the H3 loop of antibody b12 (red). (E) The superimposed F105 (green) and b12 (blue) structures shown in Fig. 1D were rotated 90o to highlight the differences between the two CDR H3 loops.
FIG. 2.
FIG. 2.
(A) Ribbon structure of CD4-bound monomeric HIV gp120. Mutational analysis of the antigen binding site of F105 suggests a critical role for gp120 residues 255 to 257, 368, 370, 375, 384, 421, 470, and 473 through 477 (45, 59, 61, 69) (magenta and red). The crystal structure of the gp120/CD4 complex shows that 26 residues from gp120 are involved in direct interactions with CD4 (yellow and red) (27). These include residues 368, 370, 473, and 474, which are also critical for binding of F105 (red). Residues 276, 279, and 282 within the D loop of gp120 that affect the binding of b12 are shown in orange (45). (B) Ribbon structure of unliganded SIV monomeric gp120. The outer domain of unliganded SIV gp120 (6) has been superimposed upon the outer domain structure of CD4-bound HIV gp120. The orientations of the outer domain structures in Fig. 2A and B are thus identical and serve as a common reference point. The sequence alignment of Chen et al. (6) was used to color the corresponding residues as described for Fig. 2A. Conformational differences with respect to the inner domains are easily seen. These include a very significant reorganization of the inner domain elements, including helix α1, and elements of the bridging sheet. (C) Residues critical to binding of F105 and those known to contact CD4 are mapped on the surface of CD4-bound HIV gp120. The orientation and color coding of the surface of HIV gp120 are identical to those in Fig. 2A, with the additional tan color showing the residual carbohydrate present in the deglycosylated structure. The mutational evidence clearly shows an overlap of the CD4 (yellow and red) and F105 (red and magenta) binding sites, including the use of residues involved in formation of the Phe43 binding pocket. The heavy chain of b12 is thought to interact with the Phe43 pocket of gp120 and the ridge formed by β-strand 15, residues also recognized by CD4 and F105 (yellow and red). The light chain of b12 is believed to interact with residues within the D loop of gp120, including residues 276, 279, and 282, which are shown in orange (45, 53, 75). (D) Surface of unliganded monomeric SIV gp120. The orientation and color coding of the surface of SIV gp120 are identical to those in Fig. 2B, with the additional tan color showing the carbohydrate residues. The masking of the F105 binding site (red and magenta) by residues at the N terminus of helix α1 suggests that F105 does not bind to this conformation of gp120. (E) Proposed interactions of b12 with gp120. The b12 Fab fragment is colored as in Fig. 1A and B, whereas schematic symbols corresponding to regions of gp120 are colored as in Fig. 2A to D. Mutagenesis experiments and modeling exercises (45, 53, 75) suggest key interactions between b12 and gp120, specifically that TrpH100 inserts into the Phe43 binding pocket (red crescent), a ridge formed by β15 (CD4 binding loop, red/yellow triangle) is straddled by a cleft between CDR H3 and CDR H1&2, and the light chain interacts with gp120 D-loop residues (orange oval, behind the plane of the page). b12 does not appear to interact with residues in helix α5 (magenta oval). (F) F105 is unable to bind in a fashion similar to that proposed for b12. F105 lacks the deeper cleft between CDR H3 and CDR H1&2 (coloring as in Fig. 2E). The reduced cleft would prohibit F105 from extending across the ridge formed by β15 (CD4 binding loop) in the manner proposed for b12. If F105 does indeed bind to a conformation of gp120 similar to that bound by b12, it is likely to tilt away from β15, shifting the light chain down and away from the D loop and onto the N terminus of helix α5. Note that the D loop is behind and above helix α5 in these orientations (2E and F), such that the orientation for b12 is slightly rotated with respect to F105. The lateral extension of the H3 loop in b12 may allow this rotation while preserving the interaction with the Phe43 pocket.
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