Exploring Competitive Protein–Protein Interaction Mechanisms through Dynamic Residue Energy Landscapes for Antizyme Design and Validation

Abstract

Whether binding specificity and partner selection in protein–protein interactions (PPIs) can be reliably inferred from static structures or require more dynamic, pathway-resolved energetic analyses remains an open question. To explore this, we focus on the ornithine decarboxylase (ODC)-antizyme isoform 1 (Az1)-antizyme inhibitor (AzIN) system, a well-characterized competitive PPI network that plays a critical role in regulating polyamine homeostasis. By combining extensive all-atom molecular dynamics simulations with biochemical experiments and the development of a new tool, we uncover key dynamic features of the static and recognition pathway interaction. Based on these, we designed novel antizyme isoforms (NAZs). Our analysis, using residue-resolved energetic landscapes, reveals critical determinants of binding specificity and partner selection that static structures alone cannot capture. These insights guide the engineering of NAZs that either directly engage ODC or modulate Az1 availability. This work provides a new perspective, demonstrating that dynamic energetic landscapes, rather than static structures, are key to understanding and modulating competitive protein recognition. Additionally, our DyResEL tool enables broader, more detailed analyses of energetic contributions, offering a versatile approach for exploring PPIs in various biological contexts.