Depletion-Induced Interactions Modulate Nanoscale Protein Diffusion in Polymeric Crowder Solutions
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arXiv
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| Format: | Preprint |
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2025
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| author | Dargasz, Michelle Anthuparambil, Nimmi Das Retzbach, Sebastian Girelli, Anita Timmermann, Sonja Möller, Johannes Jo, Wonhyuk Lenonau, Aliaksandr Raza, Agha Mohammad Bin, Maddalena Savelkouls, Jaqueline Andronis, Iason Unger, Frederik Brausse, Felix Hallmann, Jörg Boesenberg, Ulrike Pudell, Jan-Etienne Rodriguez-Fernandez, Angel Wrigley, James Shayduk, Roman Youssef, Mohamed Zozulya, Alexey Madsen, Anders Lehmkühler, Felix Perakis, Fivos Zhang, Fajun Schreiber, Frank Paulus, Michael Gutt, Christian |
| author_facet | Dargasz, Michelle Anthuparambil, Nimmi Das Retzbach, Sebastian Girelli, Anita Timmermann, Sonja Möller, Johannes Jo, Wonhyuk Lenonau, Aliaksandr Raza, Agha Mohammad Bin, Maddalena Savelkouls, Jaqueline Andronis, Iason Unger, Frederik Brausse, Felix Hallmann, Jörg Boesenberg, Ulrike Pudell, Jan-Etienne Rodriguez-Fernandez, Angel Wrigley, James Shayduk, Roman Youssef, Mohamed Zozulya, Alexey Madsen, Anders Lehmkühler, Felix Perakis, Fivos Zhang, Fajun Schreiber, Frank Paulus, Michael Gutt, Christian |
| contents | Macromolecular crowding plays a crucial role in modulating protein dynamics in cellular and in vitro environments. Polymeric crowders such as dextran and Ficoll are known to induce entropic forces, including depletion interactions, that promote structural organization, but the nanoscale consequences for protein dynamics remain less well understood. Here, we employ megahertz X-ray photon correlation spectroscopy (MHz-XPCS) at the European XFEL to probe the dynamics of the protein ferritin in solutions containing sucrose, dextran, and Ficoll. We find that depletion-driven short-range attractions combined with long-range repulsions give rise to intermediate-range order (IRO) once the polysaccharide overlap concentration $c^*$ is exceeded. These IRO features fluctuate on microsecond to millisecond timescales, strongly modulating the collective dynamics of ferritin. The magnitude of these effects depends sensitively on crowder type, concentration, and molecular weight. Normalizing the crowder concentration by $c^*$ reveals scaling behavior in ferritin self-diffusion with a crossover near 2$c^*$, marking a transition from depletion-enhanced mobility to viscosity-dominated slowing. Our results demonstrate that bulk properties alone cannot account for protein dynamics in crowded solutions, underscoring the need to include polymer-specific interactions and depletion theory in models of crowded environments. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2509_04087 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Depletion-Induced Interactions Modulate Nanoscale Protein Diffusion in Polymeric Crowder Solutions Dargasz, Michelle Anthuparambil, Nimmi Das Retzbach, Sebastian Girelli, Anita Timmermann, Sonja Möller, Johannes Jo, Wonhyuk Lenonau, Aliaksandr Raza, Agha Mohammad Bin, Maddalena Savelkouls, Jaqueline Andronis, Iason Unger, Frederik Brausse, Felix Hallmann, Jörg Boesenberg, Ulrike Pudell, Jan-Etienne Rodriguez-Fernandez, Angel Wrigley, James Shayduk, Roman Youssef, Mohamed Zozulya, Alexey Madsen, Anders Lehmkühler, Felix Perakis, Fivos Zhang, Fajun Schreiber, Frank Paulus, Michael Gutt, Christian Soft Condensed Matter Macromolecular crowding plays a crucial role in modulating protein dynamics in cellular and in vitro environments. Polymeric crowders such as dextran and Ficoll are known to induce entropic forces, including depletion interactions, that promote structural organization, but the nanoscale consequences for protein dynamics remain less well understood. Here, we employ megahertz X-ray photon correlation spectroscopy (MHz-XPCS) at the European XFEL to probe the dynamics of the protein ferritin in solutions containing sucrose, dextran, and Ficoll. We find that depletion-driven short-range attractions combined with long-range repulsions give rise to intermediate-range order (IRO) once the polysaccharide overlap concentration $c^*$ is exceeded. These IRO features fluctuate on microsecond to millisecond timescales, strongly modulating the collective dynamics of ferritin. The magnitude of these effects depends sensitively on crowder type, concentration, and molecular weight. Normalizing the crowder concentration by $c^*$ reveals scaling behavior in ferritin self-diffusion with a crossover near 2$c^*$, marking a transition from depletion-enhanced mobility to viscosity-dominated slowing. Our results demonstrate that bulk properties alone cannot account for protein dynamics in crowded solutions, underscoring the need to include polymer-specific interactions and depletion theory in models of crowded environments. |
| title | Depletion-Induced Interactions Modulate Nanoscale Protein Diffusion in Polymeric Crowder Solutions |
| topic | Soft Condensed Matter |
| url | https://arxiv.org/abs/2509.04087 |