Structural insights into a high affinity nanobody:antigen complex by homology modelling

• Published in: Journal of molecular graphics & modelling 2017-09, Vol.76, p.305-312
• Main Author: Skottrup, Peter Durand
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Antibody Affinity - immunology; Antigen; Antigens - chemistry; Antigens - immunology; Catalytic Domain; Models, Molecular; Molecular Conformation; Molecular docking; Molecular Docking Simulation; Molecular Dynamics Simulation; Molecular modelling; Nanobody; Protein Binding; Protein Interaction Domains and Motifs; Single domain antibody; Single-Domain Antibodies - chemistry; Single-Domain Antibodies - immunology; Structure-Activity Relationship
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2017.07.008

[Display omitted] •In this study a homology model of a high affinity RgpB-nanobody (VHH7) was build.•Epitope residues and paratope residues were identified and used as input to an information-driven flexible docking approach.•The VHH7 binding epitope was found in the immunoglobulin-like domain.•Computational alanine scanning identified residue pairs at the molecular interface that was important for complex stability.•The molecular interaction data can be used in the design of an antibody-drug conjugate for specific RgpB targeting. Porphyromonas gingivalis is a major periodontitis-causing pathogens. P. gingivalis secrete a cysteine protease termed RgpB, which is specific for Arg-Xaa bonds in substrates. Recently, a nanobody-based assay was used to demonstrate that RgpB could represent a novel diagnostic target, thereby simplifying. P. gingivalis detection. The nanobody, VHH7, had a high binding affinity and was specific for RgpB, when tested towards the highly identical RgpA. In this study a homology model of VHH7 was build. The complementarity determining regions (CDR) comprising the paratope residues responsible for RgpB binding were identified and used as input to the docking. Furthermore, residues likely involved in the RgpB epitope was identified based upon RgpB:RgpA alignment and analysis of residue surface accessibility. CDR residues and putitative RgpB epitope residues were used as input to an information-driven flexible docking approach using the HADDOCK server. Analysis of the VHH7:RgpB model demonstrated that the epitope was found in the immunoglobulin-like domain and residue pairs located at the molecular paratope:epitope interface important for complex stability was identified. Collectively, the VHH7 homology model and VHH7:RgpB docking supplies knowledge of the residues involved in the high affinity interaction. This information could prove valuable in the design of an antibody-drug conjugate for specific RgpB targeting.