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Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10.

Rujas E, Gulzar N, Morante K, Tsumoto K, Scott JK, Nieva JL, Caaveiro JM - J. Virol. (2015)

Bottom Line: The conclusions of our structure-function analysis strengthen the idea that to exert effective neutralization, the hydrophobic apex of the solvent-exposed CDR-H3 loop must recognize an antigenic structure more complex than just the linear α-helical epitope and likely constrained by the viral membrane lipids.However, 4E10 (or 4E10-like) antibodies are rarely found in HIV-1-infected individuals or elicited through vaccination.We conclude that the difference between neutralizing and nonneutralizing antibodies of 4E10 is neither structural nor energetic but is related to the capacity to recognize the HIV-1 gp41 epitope inserted in biological membranes.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain.

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Crystal structures of neutralizing and nonneutralizing 4E10 Fabs. (A) Superposition of the backbone atoms of WT (gray), WDWD (white), and ΔLoop (black). The RMSD of the backbone coordinates of the heavy chain of WT with those of WDWD was 0.20 Å, and that determined with those of ΔLoop was 0.29 Å. The arrows indicate differences in the conformation of the apex region of the CDR-H3 loop. The 4E10ep bound to WT, WDWD, and ΔLoop Fab is shown in orange, magenta, and blue, respectively. (B to D) Close-up view of the conformation of the CDR-H3 loop (residues 95-100J) of WT (B), WDWD (C), and ΔLoop (D) with respect to the peptide. Residues with side chains within the region 100-100D are depicted.
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Figure 1: Crystal structures of neutralizing and nonneutralizing 4E10 Fabs. (A) Superposition of the backbone atoms of WT (gray), WDWD (white), and ΔLoop (black). The RMSD of the backbone coordinates of the heavy chain of WT with those of WDWD was 0.20 Å, and that determined with those of ΔLoop was 0.29 Å. The arrows indicate differences in the conformation of the apex region of the CDR-H3 loop. The 4E10ep bound to WT, WDWD, and ΔLoop Fab is shown in orange, magenta, and blue, respectively. (B to D) Close-up view of the conformation of the CDR-H3 loop (residues 95-100J) of WT (B), WDWD (C), and ΔLoop (D) with respect to the peptide. Residues with side chains within the region 100-100D are depicted.

Mentions: High-resolution crystal structures of WDWD or ΔLoop in complex with 4E10ep were determined at 1.81 and 1.70 Å, respectively (Table 2). The two complexes crystallized in the same space group as that reported for the WT Fab obtained either from papain-treated IgG or by heterologous expression in E. coli (11, 19). The superposition of the three crystal structures showed that they are nearly indistinguishable from each other (Fig. 1). The root mean square deviation (RMSD) values between the coordinates of WT and WDWD and between WT and ΔLoop were 0.20 and 0.29 Å, respectively. A significant difference was found in the conformation of the CDR-H3 apex of WT compared to that of ΔLoop, possibly because the latter construct is two residues shorter in this region. This conformational change brings the apex of the CDR-H3 of ΔLoop Fab closer to the peptide, generating an H-bond between residue Trp680 of the peptide and the backbone oxygen of the residue GlyH100A of ΔLoop (distance = 2.7 Å) (Fig. 2; see also Table S1 in the supplemental material). A similar H-bond was observed in one copy of the crystal structure of WT Fab in complex with a peptide containing α-aminoisobutyric acid at position Trp678 (11).


Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10.

Rujas E, Gulzar N, Morante K, Tsumoto K, Scott JK, Nieva JL, Caaveiro JM - J. Virol. (2015)

Crystal structures of neutralizing and nonneutralizing 4E10 Fabs. (A) Superposition of the backbone atoms of WT (gray), WDWD (white), and ΔLoop (black). The RMSD of the backbone coordinates of the heavy chain of WT with those of WDWD was 0.20 Å, and that determined with those of ΔLoop was 0.29 Å. The arrows indicate differences in the conformation of the apex region of the CDR-H3 loop. The 4E10ep bound to WT, WDWD, and ΔLoop Fab is shown in orange, magenta, and blue, respectively. (B to D) Close-up view of the conformation of the CDR-H3 loop (residues 95-100J) of WT (B), WDWD (C), and ΔLoop (D) with respect to the peptide. Residues with side chains within the region 100-100D are depicted.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4645341&req=5

Figure 1: Crystal structures of neutralizing and nonneutralizing 4E10 Fabs. (A) Superposition of the backbone atoms of WT (gray), WDWD (white), and ΔLoop (black). The RMSD of the backbone coordinates of the heavy chain of WT with those of WDWD was 0.20 Å, and that determined with those of ΔLoop was 0.29 Å. The arrows indicate differences in the conformation of the apex region of the CDR-H3 loop. The 4E10ep bound to WT, WDWD, and ΔLoop Fab is shown in orange, magenta, and blue, respectively. (B to D) Close-up view of the conformation of the CDR-H3 loop (residues 95-100J) of WT (B), WDWD (C), and ΔLoop (D) with respect to the peptide. Residues with side chains within the region 100-100D are depicted.
Mentions: High-resolution crystal structures of WDWD or ΔLoop in complex with 4E10ep were determined at 1.81 and 1.70 Å, respectively (Table 2). The two complexes crystallized in the same space group as that reported for the WT Fab obtained either from papain-treated IgG or by heterologous expression in E. coli (11, 19). The superposition of the three crystal structures showed that they are nearly indistinguishable from each other (Fig. 1). The root mean square deviation (RMSD) values between the coordinates of WT and WDWD and between WT and ΔLoop were 0.20 and 0.29 Å, respectively. A significant difference was found in the conformation of the CDR-H3 apex of WT compared to that of ΔLoop, possibly because the latter construct is two residues shorter in this region. This conformational change brings the apex of the CDR-H3 of ΔLoop Fab closer to the peptide, generating an H-bond between residue Trp680 of the peptide and the backbone oxygen of the residue GlyH100A of ΔLoop (distance = 2.7 Å) (Fig. 2; see also Table S1 in the supplemental material). A similar H-bond was observed in one copy of the crystal structure of WT Fab in complex with a peptide containing α-aminoisobutyric acid at position Trp678 (11).

Bottom Line: The conclusions of our structure-function analysis strengthen the idea that to exert effective neutralization, the hydrophobic apex of the solvent-exposed CDR-H3 loop must recognize an antigenic structure more complex than just the linear α-helical epitope and likely constrained by the viral membrane lipids.However, 4E10 (or 4E10-like) antibodies are rarely found in HIV-1-infected individuals or elicited through vaccination.We conclude that the difference between neutralizing and nonneutralizing antibodies of 4E10 is neither structural nor energetic but is related to the capacity to recognize the HIV-1 gp41 epitope inserted in biological membranes.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain.

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Related in: MedlinePlus