An inter-residue network model to identify mutational-constrained regions on the Ebola coat glycoprotein

Abstract

Recently, progress has been made in the development of vaccines and monoclonal antibody cocktails that target the Ebola coat glycoprotein (GP). Based on the mutation rates for Ebola virus given its natural sequence evolution, these treatment strategies are likely to impose additional selection pressure to drive acquisition of mutations in GP that escape neutralization. Given the high degree of sequence conservation among GP of Ebola viruses, it would be challenging to determine the propensity of acquiring mutations in response to vaccine or treatment with one or a cocktail of monoclonal antibodies. In this study, we analyzed the mutability of each residue using an approach that captures the structural constraints on mutability based on the extent of its inter-residue interaction network within the three-dimensional structure of the trimeric GP. This analysis showed two distinct clusters of highly networked residues along the GP1-GP2 interface, part of which overlapped with epitope surfaces of known neutralizing antibodies. This network approach also permitted us to identify additional residues in the network of the known hotspot residues of different anti-Ebola antibodies that would impact antibody-epitope interactions.

Prediction of the binding interface between monoclonal antibody m102.4 and Nipah attachment glycoprotein using structure-guided alanine scanning and computational docking

“…Similar to the method for expressing GPs 52 , pcDNA 3.1(−) expression vectors containing encoding gene for different anti-Nipah mAbs was transiently transfected into HEK 293-F FreeStyle cells. After seven days, supernatant was harvested, filtered, and purified using Pierce ProteinA Agarose (Thermo Fisher Scientific).…”

“…ELISA protocol was adapted from Quinlan et al 52 . Briefly, 100 μL of the wild-type GP in PBS was adsorbed to clear 96-well Maxisorp plates (Nunc) at a concentration of 1 μg/mL and left at 4 °C overnight.…”

Tracking ebolavirus genomic drift with a resequencing microarray

“…The positions where substitutions were detected illustrate several different patterns of genomic drift. At position N(506) the Ebolavirus-RMA results, confirmed by NGS, identified an amino acid substitution known to block binding of the KZ52 antibody [ 48 , 49 ] that only appears in the 3rd round of passage under pressure from the KZ52 antibody. This is a tangible example of the genomic drift that the Ebolavirus-RMA is designed to detect.…”

Molecular basis for dengue virus broad cross-neutralization by humanized monoclonal antibody 513

“…Aside from binding energetics and SASA calculations, we employed an orthogonal inter-residue interactions approach 30 , 31 to investigate the contributions of ScFv513 residues on DIII binding. This approach enables a quantitative analysis of interactions by computing a numerical network score for each residue based on its interatomic interactions with other residues in its neighborhood 30 , 31 . The numerical network score for a residue can be correlated to its mutability; the higher the network score, the lower the mutability.…”