Role of Non-local Interactions between CDR Loops in Binding Affinity of MR78 Antibody to Marburg Virus Glycoprotein

Abstract

SUMMARY An atomic-detail model of the Marburg virus glycoprotein in complex with a neutralizing human monoclonal antibody designated MR78 was constructed using Phenix.Rosetta starting from a 3.6Å crystallographic density map. The Asp at T6 in the HCDR3’s bulged torso cannot form the canonical salt bridge as position T2 lacks an Arg or Lys residue. It instead engages in a hydrogen bond interaction with a Tyr contributed by the HCDR1 loop. This inter-CDR loop interaction stabilizes the bulged conformation needed for binding to the viral glycoprotein: a Tyr to Phe mutant displays a binding affinity reduced by a factor of at least 10. We found that 5% of a database of 465 million human antibody sequences has the same residues at T2 and T6 positions in HCDR3 and Tyr in HCDR1 that could potentially form this Asp-Tyr interaction and that this interaction might contribute to a non-canonical bulged torso conformation.

A Comprehensive Analysis of Anion–Quadrupole Interactions in Protein Structures

“…As regular anion–quadrupole interactions are weak, there can be a significant difference in stability between the wild type and the mutant in this example. As another example, an aspartate-tyrosine-mediated HB-anion–quadrupole interaction between the CDR loops of the monoclonal antibody MR78 contributes significantly to the binding affinity for its antigen 53 (i.e., the Marburg virus glycoprotein), and substitution of this tyrosine residue with phenylalanine significantly compromises the binding affinity 53 , justifying the perception of the weak nature of anion–quadrupole interactions. Even though the energy of the anion–quadrupole component of the HB-anion–quadrupole interaction is low, an anion–quadrupole interaction can still make a significant contribution to the behavior of an HB-anion–quadrupole interaction.…”

Discovery of Marburg virus neutralizing antibodies from virus-naïve human antibody repertoires using large-scale structural predictions

“…Only the tip of the HCDR3 loop differed from that of MR78 Ab. Interestingly, while the torso conformation in the naïve-1 Ab is very close to the one in the MR78 Ab, it is not stabilized by the same amino acid pair (Asp101-Tyr32) interaction that was suggested to be important for the MR78 Ab structure (20). That observation again emphasizes the lack of the full understanding of principles of the long loops' structure formation.…”

“…4C). This finding suggests that, despite the presence of both Tyr32 and Asp101 that form a hydrogen bond in MR78 and stabilize its kinked torso conformation (20), the naïve-1 Ab establishes an alternate paradigm.…”

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

“…(B) Schematic of the AbPredict protocol, which assembles an antibody from templates in four fragment databases, containing VL, LCDR3, VH, and HCDR3 templates. Antibody fragments displayed in panels A and B were taken from PDB entries 5ITB, 65 5JRP, 66 5CGY, 67 5CHN, 67 3QHZ, 68 4GXV, 69 6MEE, 70 and 5XRQ. 71 (C) Schematic overview of RosettaCM, which creates models by threading and hybridization of template structures based on user-provided sequence alignments (used PDB entries 4HT1, 72 5UKP, 73 5JRP, 66 2EKS, 74 4JPW, 75 5TF1, 76 5T4Z, 77 6B0H, 78 2R0K, 79 4KMT, 80 1WT5, 81 5UMN, 82 and 4HS6( 83 )).…”