Structural basis of condensate formation of VAPB protein

Abstract Vesicle-associated membrane protein-associated protein B (VAPB) is an endoplasmic reticulum protein implicated in amyotrophic lateral sclerosis (ALS) through its P56S mutation. Although pathological function loss and condensate formation of the VAPB P56S mutant are crucial for disease progression, the underlying molecular mechanism remains unclear. Here, we investigated the structural basis of VAPB condensate formation using nuclear magnetic resonance (NMR) spectroscopy, turbidity analysis, and microscopy. Our results show that the major sperm protein domain of VAPB undergoes temperature-dependent condensate formation, a process regulated by localized structural dynamics. We identified a pH-sensitive hydrogen bond that functions as a switch to autoinhibition of condensate formation, as well as a flexible loop whose slow dynamics facilitate the multivalent interactions essential for condensate formation. The ALS-linked P56S mutant exhibits markedly enhanced condensate formation, which is associated with increased conformational heterogeneity that may promote aberrant intermolecular contacts related to pathological function loss. These findings reveal how specific dynamic features within a folded protein can drive condensate formation, providing a molecular framework for understanding both VAPB function and its pathological condensate formation.