Protein compactness and interaction valency define the architecture of a biomolecular condensate across scales

Abstract

Formation of biomolecular condensates via liquid-liquid phase separation (LLPS) contributes to the organization and function of living cells, but the general physicochemical principles involved are not fully understood. The present study provides a quantitative, multiscale framework that connects single- and multi-copy, microsecond molecular dynamics simulations with the experimentally observed, micrometer-scale LLPS behavior of an 80-aa N-terminal fragment of yeast Lge1 (Lge1 1-80), a regulator of histone H2B ubiquitination. Analysis of protein self-interactions modeled at all-atom resolution elucidates the impact of key residues on interaction valency and establishes a link between configurational entropy, valency and compactness of proteins inside a model condensate. An analytical formalism derived from first principles describes condensate structure across different length scales as a function of the interaction valency and compactness of its molecular components. In analogy to fractal cluster formation seen in biological and non-biological colloids, the formalism provides an atomistically resolved model of a micrometer-size condensate starting from the simulated ensemble of individual protein conformers. Finally, the simulation-derived fractal dimensions of the condensates of Lge1 1-80 and its mutants are shown to be consistent with their in vitro LLPS behavior. The presented framework provides a general, experimentally testable description of the multiscale features of biomolecular condensates and embeds their study in a wider context of self-organization in colloidal systems.

Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range

“…As additional test systems, we considered constructs of the 1–80 N-terminal fragment of yeast Lge1, which have been recently investigated using turbidity measurements 71 . CALVADOS 2 correctly predicts that the WT Lge1 1–80 construct undergoes PS at the experimental conditions, albeit with a hundred times larger c sat (50 ± 6 µM at c s = 100mM) compared to experiments ( < 1 µM).…”

Improved Predictions of Phase Behaviour of Intrinsically Disordered Proteins by Tuning the Interaction Range

“…As additional test systems, we considered constructs of the 1–80 N-terminal fragment of yeast Lge1, which have been recently investigated using turbidity measurements [43]. CALVADOS 2 correctly predicts that the WT Lge1 1−80 construct undergoes PS at the experimental conditions, albeit with a hundred times larger c sat (50 ± 6 µM at c s = 100 mM) compared to experiments ( < 1 µM).…”

RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding

“…Such profound insights suggest that the composition of highly multicomponent condensates can be anticipated based on the critical parameters (like temperature, pH, and salt concentration) of their constituent biomolecules. Further atomistic exploration 408 emphasizes the importance of configurational entropy, valency, and protein compactness in condensate formation. Such comprehensive knowledge could remarkably widen our lens to perceive the intricate mechanisms governing cellular behavior (see section RNA-Driven Physiological Crowding).…”