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bioRxiv · 10.1101/2024.07.08.602299

Backbone-mediated weakening of pairwise interactions enables percolation in mimics of protein condensates

Zeng, X.·Pappu, R. V.
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Abstract

Biomolecular condensates formed by intrinsically disordered proteins (IDPs) condensates are semidilute solutions. These can be approximated as solutions of blob-sized segments, which can be as small as peptide-sized motifs. We leveraged the blob picture to quantify differences between inter-residue interactions in model compound and peptide-based mimics of dense versus dilute phases. The all-atom molecular dynamics simulations use the polarizable AMOEBA forcefield. In model compound solutions, the interactions between aromatic residues are stronger than interactions between cationic and aromatic residues. This holds in dilute and dense phases. Cooperativity within dense phases enhances pairwise interactions leading to finite-sized nanoscale clusters. The results for peptide-based condensates paint a different picture. Backbone amides add valence to the associating molecules. While this maintains or enhances pairwise inter-residue interactions in dilute phases, it weakens pair interactions in dense phases. Weakening of pair interactions enables fluidization characterized by short-range order and long-range disorder. The higher valence afforded by the peptide backbone becomes a generator of system-spanning networks. As a result, dense phases of peptides are best described as percolated network fluids. Overall, our results show how peptide backbones enhance pairwise interactions in dilute phases whole weakening these interactions in dense phases to enable percolation within dense phases.

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Zeng, X., Pappu, R. V.. 2024-07-08. Backbone-mediated weakening of pairwise interactions enables percolation in mimics of protein condensates. https://doi.org/10.1101/2024.07.08.602299

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