Homology modeling of a Camelid antibody fragment against a conserved region of Acinetobacter baumannii biofilm associated protein (Bap)

VHH or the single-domain antibodies (sdAb), are studied for therapeutic applications in cancers, infections and other diseases. In our previous study, we expressed and produced a soluble VHH against a conserved region of Acinetobacter baumannii biofilm associated protein (Bap). The present study was undertaken to predict the 2D and 3D structure of the receptor and ligand as well as residues involved in their interactions. Apart from ab initio, other rational methods such as homology modeling and threading were invoked to achieve the 3D structures. For homology modeling, BLAST was run on the sequences in order to find the best templates. Pocket detection and identification of functionally and structurally important residues of VHH 3D structure as well as determination of its clefts and ligand binding site were carried out on the structure. ZDOCK docking server predicted all possible binding modes in the translational and rotational space between the selected region of Bap as an antigen and the VHH structure as an antibody. We identified the amino acids involved in antigen-VHH interactions. Some functional conserved residues located in the largest cleft that participate in ligand binding site are identified. It seems that these amino acids are involved in antigen-VHH interactions. •Homology modeling of a VHH against conserved region of A. baumannii Bap was studied.•Important VHH 3D structure residues and its clefts, ligand binding site were studied.•Binding modes between Bap as an antigen and the VHH as an antibody were predicted.•Amino acids involved in antigen-VHH interactions were identified.•Functional residues in the largest cleft acting in ligand binding were identified.