Biomolecular condensates formed by intrinsically disordered proteins require molecular models that accurately describe proteins in both dilute solution and condensed phases. Explicit-solvent coarse-grained models offer an attractive balance between chemical resolution and computational efficiency. Yet, it remains unclear whether improving dilute-state properties is sufficient to obtain an accurate description of condensates. Here, we address this question by introducing minimal modifications to the Martini 3 force field that combine recent advances in bonded interactions with refined protein–water interactions and strengthened glycine self-interactions, while preserving the underlying chemical transferability of the model. The resulting model substantially improves the description of single-chain conformations across a diverse benchmark of disordered proteins. We then investigate phase separation of the well-characterized low-complexity domain of heterogeneous nuclear ribonucleoprotein A1 and its sequence variants. The model reproduces several key physicochemical properties of biomolecular condensates, including chain expansion in the dense phase, sequence-dependent intermolecular contacts, protein diffusion and its relation to single-chain dimensions, and hydration, while revealing quantitative limitations in condensate density, phase equilibria, and ion partitioning. Our results show that improving dilute-state behaviour translates into a better description of condensed-phase properties, including condensate density, but is not sufficient to quantitatively reproduce the equilibrium between the dilute and dense phases.
Fran Bačić Toplek, Luís Borges-Araújo, Kresten Lindorff-Larsen et al.· bioRxiv· 0 citations
Proteins destined for secretion typically contain N-terminal signal sequences that target nascent chains to the endoplasmic reticulum (ER). Following targeting, these sequences are cleaved by the heterotetrameric signal peptidase complex (SPC). Despite a conserved N-terminal (n), hydrophobic core (h) and C-terminal (c) tripartite organization, their sequences are highly variable. How SPC subunits contribute to recognition of these diverse sequences remains poorly understood. Sec11, the catalytic subunit of the SPC, contains an N-terminal transmembrane (TM) domain and a C-terminal hydrophobic region. The latter was unresolved in human SPC cryo-EM structures, likely due to intrinsic flexibility, yet AlphaFold predictions of the yeast SPC suggest that this region forms a C-terminal short helix (CTS) strategically positioned within the presumed signal sequence-binding site. This structural arrangement led us to hypothesize its possible role in substrate handling during signal peptide processing and we undertook to investigate its function using biochemical assays combined with molecular dynamics (MD) simulations. Topology mapping confirmed that the Sec11 CTS traverses the ER membrane and MD simulations showed that removal of the Sec11 CTS does not substantially alter overall SPC architecture or the proximal membrane environment. While N-terminal signal sequences of varying hydrophobicity were efficiently cleaved, internal signal sequences with extended n-region were selectively defective in cleavage in the absence of the Sec11 CTS. These data suggest that the Sec11 CTS specifically stabilizes internal signal sequences for productive engagement with SPC.
Yeonji Chung, Mariia Borbuliak, Sanghun Hwang et al.· Journal of Biological Chemis...· 0 citations
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