Conformational changes in antibody Fab fragments upon binding and their consequences on the performance of docking algorithms

Background The existence of conformational changes in antibodies upon binding has been previously established. However, existing analyses focus on individual cases and no quantitative study provides a more global view of potential moves and repacking, especially on recent data. The present study focuses on analyzing the conformational changes in various antibodies upon binding, providing quantitative observations to be exploited for antibody-related modeling. Methods Cartesian and dihedral Root-Mean-Squared Deviations were calculated for different subparts of 27 different antibodies, for which X-ray structures in the bound and unbound states are available. Elbow angle variations were also calculated. Previously reported results of four docking algorithms were condensed into one score giving overall docking success for each of 16 antibody-antigen cases. Results Very diverse movements are observed upon binding. While many loops stay very rigid, several others display side-chain repacking or backbone rearrangements, or both, at many different levels. Large conformational changes restricted to one or more antibody hypervariable loops were found to be a better indicator of docking difficulty than overall conformational variation at the antibody-antigen interface. However, the failure of docking algorithms on some almost-rigid cases shows that scoring is still a major bottleneck in docking pose prediction. Conclusions This study is aimed to help scientists working on antibody analysis and design by giving insights into the nature and the extent of conformational changes at different levels upon antigen binding.