Valency-Limited Molecular Dynamics Simulations of Stickers-and-Spacers Polymers Reveal a Tradeoff Between Condensation and Organization

Abstract

Biomolecular condensates formed by intrinsically disordered proteins (IDPs) are often described using stickers-and-spacers models, in which specific sticker motifs form reversible crosslinks and spacer regions modulate phase behavior. Recent theory predicts that heterogeneous nonspecific spacer interactions can promote condensation but may also disrupt sticker-mediated organization. Here, we develop an off-lattice coarse-grained stickers-and-spacers polymer model for continuous molecular dynamics simulations and implement it in the GPU-accelerated OpenABC package. The model uses a directional sticker-sticker interaction to encode limited valency through interaction geometry, producing effectively one-to-one sticker binding without explicit bond assignment. Simulations of one-component systems show that sticker affinity and multivalency promote porous, network-like condensates, while nonspecific spacer interactions can also drive phase separation but produce more compact, spacer-dominated dense phases. When both interaction types are present, strong spacer heterogeneity reduces sticker conversion, suppresses sticker mobility, and disrupts the sticker-mediated network. In two-component systems, specific sticker interactions buffer client recruitment into host condensates, while nonspecific spacer interactions produce reservoir-dependent uptake. These results support a tradeoff in which spacer heterogeneity promotes condensation at the cost of condensate organization and compositional robustness, providing a physical rationale for the suppression of promiscuous spacer interactions in low-complexity IDP regions.