From Heteropolymer Stiffness Distributions to Effective Homopolymers: A Conformational Analysis of Intrinsically Disordered Proteins
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arXiv
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| Format: | Preprint |
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2025
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| _version_ | 1866915590611927040 |
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| author | Witzky, Yannick Schmid, Friederike Nikoubashman, Arash |
| author_facet | Witzky, Yannick Schmid, Friederike Nikoubashman, Arash |
| contents | Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To investigate these effects, we employ a discretized heterogeneous worm-like chain model, where the local persistence lengths are drawn from a Gaussian distribution. In the first part, we develop a theoretical model that maps such heterogeneous chains to homogeneous chains with a single effective persistence length. For uncorrelated disorder, our model predicts that this effective stiffness is systematically smaller than the arithmetic mean of the local persistence lengths, indicating that flexible segments have a bigger influence on the overall chain stiffness than rigid segments. We validate our model predictions using off-lattice Monte Carlo simulations, considering both ideal and self-avoiding chains in good solvent, and find excellent agreement in the regime, where the persistence lengths are on the order of a few bond lengths, consistent with typical values observed in polypeptides. In the second part, we performed simulations using various coarse-grained models of intrinsically disordered proteins (IDPs), finding that the simulated IDPs have similar shapes like the corresponding homogeneous and heterogeneous worm-like chains. However, the IDPs are systematically larger than ideal worm-like chains, yet slightly more compact when excluded volume interactions are considered. We attribute these differences to intramolecular interactions between non-bonded monomers, which our theoretical models do not account for. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2504_11027 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | From Heteropolymer Stiffness Distributions to Effective Homopolymers: A Conformational Analysis of Intrinsically Disordered Proteins Witzky, Yannick Schmid, Friederike Nikoubashman, Arash Soft Condensed Matter Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To investigate these effects, we employ a discretized heterogeneous worm-like chain model, where the local persistence lengths are drawn from a Gaussian distribution. In the first part, we develop a theoretical model that maps such heterogeneous chains to homogeneous chains with a single effective persistence length. For uncorrelated disorder, our model predicts that this effective stiffness is systematically smaller than the arithmetic mean of the local persistence lengths, indicating that flexible segments have a bigger influence on the overall chain stiffness than rigid segments. We validate our model predictions using off-lattice Monte Carlo simulations, considering both ideal and self-avoiding chains in good solvent, and find excellent agreement in the regime, where the persistence lengths are on the order of a few bond lengths, consistent with typical values observed in polypeptides. In the second part, we performed simulations using various coarse-grained models of intrinsically disordered proteins (IDPs), finding that the simulated IDPs have similar shapes like the corresponding homogeneous and heterogeneous worm-like chains. However, the IDPs are systematically larger than ideal worm-like chains, yet slightly more compact when excluded volume interactions are considered. We attribute these differences to intramolecular interactions between non-bonded monomers, which our theoretical models do not account for. |
| title | From Heteropolymer Stiffness Distributions to Effective Homopolymers: A Conformational Analysis of Intrinsically Disordered Proteins |
| topic | Soft Condensed Matter |
| url | https://arxiv.org/abs/2504.11027 |