Depletion-induced interactions modulate nanoscale protein diffusion in polymeric crowder solutions
Abstract
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 2 c *, 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.
Article Details
Journal Info
Proceedings of the National Academy of Sciences
National Academy of Sciences
Authors (29)
Michelle Dargasz
Department Physik, Universität Siegen
Nimmi Das Anthuparambil
Department Physik, Universität Siegen
Sebastian Retzbach
Institut für Angewandte Physik, Universität Tübingen
Anita Girelli
Department of Physics, AlbaNova University Center, Stockholm University
Sonja Timmermann
Department Physik, Universität Siegen
Johannes Möller
European X-Ray Free-Electron Laser Facility
Wonhyuk Jo
European X-Ray Free-Electron Laser Facility
Aliaksandr Leonau
Department Physik, Universität Siegen
Mohammad Raza Agha
Department Physik, Universität Siegen
Maddalena Bin
Department of Physics, AlbaNova University Center, Stockholm University
Jaqueline Savelkouls
Fakultät Physik/DELTA
Iason Andronis
Department of Physics, AlbaNova University Center, Stockholm University
Frederik Unger
Department Physik, Universität Siegen
Felix Brausse
European X-Ray Free-Electron Laser Facility
Jörg Hallmann
European X-Ray Free-Electron Laser Facility
Ulrike Boesenberg
European X-Ray Free-Electron Laser Facility
Jan-Etienne Pudell
European X-Ray Free-Electron Laser Facility
Angel Rodriguez-Fernandez
European X-Ray Free-Electron Laser Facility
James Wrigley
European X-Ray Free-Electron Laser Facility
Roman Shayduk
European X-Ray Free-Electron Laser Facility
Mohamed Youssef
European X-Ray Free-Electron Laser Facility
Alexey Zozulya
European X-Ray Free-Electron Laser Facility
Anders Madsen
European X-Ray Free-Electron Laser Facility
Felix Lehmkühler
Deutsches Elektronen-Synchrotron
Fivos Perakis
Department of Physics, AlbaNova University Center, Stockholm University
Fajun Zhang
Institut für Angewandte Physik, Universität Tübingen
Frank Schreiber
Institut für Angewandte Physik, Universität Tübingen
Michael Paulus
Fakultät Physik/DELTA
Christian Gutt
Department Physik, Universität Siegen