Assessing Domain Interactions in Fusion Proteins Through Structural Modeling

Chromosomal rearrangements can generate oncogenic gene fusions that alter protein structure and function. We investigated the FGFR3-KHSRP fusion, found to be present in pancreatic tumors, to understand the physical consequences of the fusion on domain interactions and antibody accessibility. Using AlphaFold, we predicted three-dimensional structures of FGFR3, KHSRP, and the fusion protein, validating their reliability through alignment with Protein Data Bank structures with the structures in good agreement. To understand the interactions between domains we used ZDock, a rigid-body docking algorithm that samples rotational and translational configurations in phase space and scores their binding likelihood using statistical potentials. Docking analysis suggested strong interactions between FGFR3 domain 4 and KHSRP domains 1 and 2, with higher scores than our control interactions. This analysis suggests the domain binding may introduce excluded-volume effects that reshape the free-energy landscape of protein–antibody interactions. These results provide an explanation for experiments that show KHSRP antibodies do not bind to the FGFR3-KHSRP fusion. This work emphasizes the value of physics-based modeling in uncovering how fusion proteins may bypass therapeutic recognition.