Depletion-induced interactions modulate nanoscale protein diffusion in polymeric crowder solutions

• 成果类型: Article
• 署名作者: Dargasz, Michelle; Das Anthuparambil, Nimmi; Retzbach, Sebastian; Girelli, Anita; Timmermann, Sonja; Moller, Johannes; Jo, Wonhyuk; Leonau, Aliaksandr; Raza Agha, Mohammad; Bin, Maddalena; Savelkouls, Jaqueline; Andronis, Iason; Unger, Frederik; Brausse, Felix; Hallmann, Jorg; Boesenberg, Ulrike; Pudell, Jan-Etienne; Rodriguez-Fernandez, Angel; Wrigley, James; Shayduk, Roman; Youssef, Mohamed; Zozulya, Alexey; Madsen, Anders; Lehmkuhler, Felix; Perakis, Fivos; Zhang, Fajun; Schreiber, Frank; Paulus, Michael; Gutt, Christian
• 署名单位: Universitat Siegen; Helmholtz Association; Deutsches Elektronen-Synchrotron (DESY); Eberhard Karls University of Tubingen; Stockholm University; European XFEL; Dortmund University of Technology
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2524733123
• 发表日期: 2026-08-04
• 页码: e2524733123
• 关键词: macromolecular crowding; diffusion; depletion interaction; X-ray photon correlation spectroscopy; free electron laser; CLUSTER FORMATION; MACROMOLECULAR STRUCTURE; phase-separation; EXCLUDED-VOLUME; self-diffusion; SERUM-ALBUMIN; DYNAMICS; SEMIDILUTE; nanoparticles; SCATTERING

摘要

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, yet their nanoscale consequences for protein dynamics remain poorly understood. Here, we employ megahertz X-ray photon correlation spectroscopy (MHz-XPCS) at the European X-ray Free Electron Laser (XFEL) to probe the dynamics of the protein ferritin in solutions containing sucrose, dextran, and Ficoll. We find pronounced changes in collective protein dynamics in polymeric crowders, revealing depletion-driven short-range attractions that, combined with long-range repulsions, give rise to intermediate-range organization. These mesoscale correlations undergo collective relaxation on microsecond to millisecond timescales, as directly resolved by XPCS through the decay of ferritin density fluctuations. The magnitude of this depends sensitively on crowder molecular weight and type. Normalizing the crowder concentration by c* reveals scaling behavior of ferritin self-diffusion with a crossover near 2c*, marking a transition from depletion-enhanced mobility to viscosity-dominated slowing. Our results demonstrate that bulk properties alone are insufficient to describe protein dynamics in crowded solutions, highlighting the need to include polymer-specific interactions and depletion theory in models of crowded environments.