Structural Features of Antibody-Peptide Recognition

Abstract

Antibody recognition of antigens is a critical element of adaptive immunity. One key class of antibody-antigen complexes is comprised of antibodies targeting linear epitopes of proteins, which in some cases are conserved elements of viruses and pathogens of relevance for vaccine design and immunotherapy. Here we report a detailed analysis of the structural and interface features of this class of complexes, based on a set of nearly 200 nonredundant high resolution antibody-peptide complex structures that were assembled from the Protein Data Bank. We found that antibody-bound peptides adopt a broad range of conformations, often displaying limited secondary structure, and that the same peptide sequence bound by different antibodies can in many cases exhibit varying conformations. Propensities of contacts with antibody loops and extent of antibody binding conformational changes were found to be broadly similar to those for antibodies in complex with larger protein antigens. However, antibody-peptide interfaces showed lower buried surface areas and fewer hydrogen bonds than antibody-protein antigen complexes, while calculated binding energy per buried interface area was found to be higher on average for antibody-peptide interfaces, likely due in part to a greater proportion of buried hydrophobic residues and higher shape complementarity. This dataset and these observations can be of use for future studies focused on this class of interactions, including predictive computational modeling efforts and the design of antibodies or epitope-based vaccine immunogens.

Keywords: antibody; immunology; linear epitope; peptide; structure.

Figure 1

Antibody-bound peptide lengths and secondary structures. (A) A histogram of the peptide residue lengths, (B) Peptide structural classes, and (C) Peptide residue DSSP structural classes are shown for the full set of antibody-peptide complexes (N = 188). The (D) Peptide lengths, (E) Peptide structural classes, and (F) Peptide residue structural classes are also shown for the “nr_epitope” complex set (N = 121), which corresponds to the full set of complexes filtered by grouping pairs or sets of complexes with matching peptide sequences and retaining one representative per pair/group. Peptide structural classes (B, E) were defined based on DSSP (33) residue-level secondary structure assignments, as noted in the Methods, and peptide residue secondary structure classes (C, F) correspond to DSSP-assigned classes. Classes are α-helix (“H”), β-bridge (“B”), extended strand (“E”), 3₁₀ helix (“G”), turn (“T”), bend (“S”), and no regular secondary structure (loop/irregular; “C”).

Figure 2

Examples of peptide-antibody complexes and structural classes. (A, D) SARS-CoV-2 spike stem in complex with antibody B6 (PDB code 7M53; Helix peptide), (B, E) HCV E2 peptide in complex with antibody HCV1 (PDB code 4DGY; Hairpin peptide), (C, F) P. falciparum circumsporozoite protein junctional epitope in complex with mAb668 (PDB code 6PBV; Coil peptide). Antibodies are shown in cyan (heavy chain) and tan (light chain), and peptides are magenta. (D–F) show selected interface side chains as sticks, with oxygen atoms red, nitrogen atoms red, and sulfur atoms yellow.

Figure 3

Buried solvent accessible surface area in antibody-peptide interfaces. (A) Change in accessible surface area (ΔSASA) for antibody-peptide interactions in comparison with length of the peptide (in residues) in the structure. (B) Change in accessible surface area for non-antibody-antigen (N = 190), antibody-protein (N = 54), and antibody-peptide (N = 188) interfaces. Non-antibody-antigen and antibody-protein complex structures are nonredundant sets previously reported in Protein Docking Benchmark 5.5 (7). Statistical significance tests between sets of values were calculated with Wilcoxon rank sum test (ns: p > 0.05; ****: p ≤ 0.0001). Two outlier points for the non-antibody-antigen set with very high ΔSASA values (6671 Ų, 6628 Ų) are not shown.

Figure 4

Contacts with antibody heavy chain and CDR loops for sets of antibody-protein (N = 54) and antibody-peptide (N = 188) interfaces. All atomic-level contacts between antigenic protein or peptide and the antibody (< 4.5 Å) were counted for each antibody-protein and antibody-peptide interface, and percentages of atomic contacts within each interface including the heavy chain (Heavy), light chain (Light), and the six heavy and light chain CDR loops were calculated. Statistically significant differences between sets of antibody-protein and antibody-peptide values (Wilcoxon rank sum test) are indicated (***: p ≤ 0.001).

Figure 5

Interface and energetic features of antibody-peptide complexes in comparison with antibody-antigen complexes. (A) Interface hydrogen bonds, (B) Calculated binding affinity (ΔG), and (C) Calculated affinity per unit interface surface area are represented for antibody-antigen (N = 54) and antibody-peptide (N = 188) complex structures. Statistical significance between sets of values are from Wilcoxon rank sum test (ns: p > 0.05; ****: p ≤ 0.0001).

Figure 6

Interface hydrophobicity and shape complementarity of antibody-peptide versus antibody-protein complexes. (A) Percent of hydrophobic buried interface surface area (ΔSASA), calculated by Rosetta and (B) Shape complementarity values (Sc (38), calculated by Rosetta) from antibody-protein (N = 54) and antibody-peptide (N = 188) interface structures are represented. Statistical significance between sets of values are from Wilcoxon rank sum test (****: p ≤ 0.0001).

Figure 7

Hydrophobic atom contacts in antibody-peptide and antibody-protein complexes. Percent of total atom contacts (< 4.5 Å distance to binding partner) for hydrophobic residue side chains were calculated separately for antibody and antigen in each antibody-protein (N=54) and antibody-peptide (N=188) interface. Statistical significance between sets of values were determined by Wilcoxon rank sum test (ns: p > 0.05; ****: p ≤ 0.0001).

Figure 8

Antibody binding conformational changes in antibody-antigen and antibody-peptide complexes. Comparison of unbound and bound antibody structures was performed for antibody-peptide (N = 32) and antibody-antigen (N = 54) structures. Calculated values are backbone atom root-mean-square distances, using interface residues proximal (< 10 Å) of the bound antigen (Interface), or individual CDR loops.

Figure 9

Peptide conformational variability in antibody-peptide complexes. Clusters of antibody-bound peptide structures (C1-C6), each with common epitope sequences, were used to calculate pairwise backbone root-mean-square distance between the observed peptide conformations within each set. Each point represents an RMSD value between two peptide conformations.

Figure 10

Structural variability of three peptide epitopes. Superposed structures of shared peptide residues from antibody-bound complexes for (A) Cluster 2, HIV fusion peptide (19 structures, 9 residues; AVGIGAVF), (B) Cluster 3, HCV E2 AS412 (7 structures, 9 residues; LINTNGSWH), and (C) Cluster 6, HIV Env MPER (5 structures, 6 residues; LELDKWA). For clarity, peptide structures are shown in semi-transparent cartoon representation, except for representative peptides from PDBs (A) 6PDU (blue) and 6NCP (magenta) (3.26 Å backbone RMSD), (B) 4DGY (green) and 4XVJ (salmon) (3.09 Å backbone RMSD), and (C) 1TJI (orange) and 5DD0 (cyan) (3.03 Å backbone RMSD).