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

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Abstract

Non-membrane-bound biomolecular condensates have been proposed to represent an important mode of subcellular organization in diverse biological settings. However, the fundamental principles governing the spatial organization and dynamics of condensates at the atomistic level remain unclear. The S. cerevisiae Lge1 protein is required for histone H2B ubiquitination and its N-terminal intrinsically disordered fragment (Lge1_1-80) undergoes robust phase separation. This study connects single- and multi-chain all-atom molecular dynamics simulations of Lge1_1-80 with the in vitro behavior of Lge1_1-80 condensates. Analysis of modelled protein-protein interactions elucidates the key determinants of Lge1_1-80 condensate formation and links configurational entropy, valency and compactness of proteins inside the condensates. A newly derived analytical formalism, related to colloid fractal cluster formation, describes condensate architecture across length scales as a function of protein valency and compactness. In particular, the formalism provides an atomistically resolved model of Lge1_1-80 condensates on the scale of hundreds of nanometers starting from individual protein conformers captured in simulations. The simulation-derived fractal dimensions of condensates of Lge1_1-80 and its mutants agree with their in vitro morphologies. The presented framework enables a multiscale description of biomolecular condensates and embeds their study in a wider context of colloid self-organization.

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All data generated or analysed during this study are included in the manuscript and supporting files (Supplementary Files 1 and 2); source data files have been provided for Figure 2 (Figure 2 -source data 1), Figure 1-figure supplement 1 (Figure 1-figure supplement 1-source data 2), Figure 1-figure supplement 2 (Figure 1-figure supplement 2-source data 1), Figure 5-figure supplement 2 (Figure 5-figure supplement 2-source data 1); compressed folders containing source data files have been provided for Figure 1 (Figure 1 -source data 1), Figure 2 (Figure 2 -source data 2), Figure 3 (Figure 3 -source data 1), Figure 4 (Figure 4 -source data 1), Figure 5 (Figure 5 -source data 1), Figure 6 (Figure 6 -source data 1), Figure 1-figure supplement 1 (Figure 1-figure supplement 1-source data 1), Figure 2-figure supplement 1 (Figure 2-figure supplement 1-source data 1), Figure 3-figure supplement 1 (Figure 3-figure supplement 1-source data 1), Figure 4-figure supplement 1 (Figure 4-figure supplement 1-source data 1), Figure 6-figure supplement 1 (Figure 6-figure supplement 1-source data 1). These source files contain the numerical data used to generate the figures.

Article and author information

Author details

Anton A Polyansky

Department of Structural and Computational Biology, University of Vienna, Vienna, Austria

For correspondence
anton.polyansky@univie.ac.at

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1011-2706
Laura D Gallego

Max F Perutz Laboratories, Medical University of Vienna, Vienna, Austria

Competing interests
The authors declare that no competing interests exist.
Roman G Efremov

Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation

Competing interests
The authors declare that no competing interests exist.
Alwin Köhler

Max F Perutz Laboratories, Medical University of Vienna, Vienna, Austria

Competing interests
The authors declare that no competing interests exist.
Bojan Zagrovic

Department of Structural and Computational Biology, University of Vienna, Vienna, Austria

For correspondence
bojan.zagrovic@univie.ac.at

Competing interests
The authors declare that no competing interests exist.

Funding

Austrian Science Fund (P 30550)

Bojan Zagrovic

Austrian Science Fund (P 30680-B21)

Bojan Zagrovic

NOMIS Stiftung (Pioneering Research Grant)

Alwin Köhler

Austrian Science Fund (F79)

Alwin Köhler

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.