Order–disorder interfaces in viral pRb inactivation: molecular dynamics insights into SLiM-mediated recognition and implications for interaction databases

Abstract

Intrinsically disordered regions (IDRs) mediate protein interactions through poorly understood mechanisms. We studied the retinoblastoma protein (pRb) and its interaction with the SV40 Large T antigen (LTSV40), a viral oncoprotein that displaces E2F factors. Using molecular dynamics and umbrella sampling, we show the LTSV40 LXCXE motif is part of a conserved Order–Motif–IDR architecture. The ordered N-terminal region drives initial pRb recognition via induced folding, adding over 6 kcal/mol to affinity. Simultaneously, the C-terminal IDR undergoes a bent-to-extended transition, sterically occluding the pRb AB cleft to prevent E2F binding. These coupled phenomena are evolutionarily conserved across 14 polyomaviruses, as confirmed by AlphaFold and MobiDB, suggesting a common pRb inactivation strategy. These results highlight a broader challenge for the field: functionally decisive IDR behaviors such as binding-induced folding and steric occlusion are not yet representable within current interaction data models, even when complementary evidence exists in resources such as DisProt or MobiDB. Bridging this gap through systematic integration of IDR annotations into databases such as IntAct and Complex Portal, supported by projection onto AlphaFold3-predicted complex structures, would enable community-scale identification of complexes where disorder is mechanistically decisive. ECCB 2026 online poster platform