Dramatic influence of patchy attractions on short-time protein diffusion under crowded conditions
Saskia Bucciarelli 1, Jin Suk Myung 1,2, Bela Farago 3, Shibananda Das 2, Gerard A. Vliegenthart 2, Olaf Holderer 4, Roland G. Winkler 2, Peter Schurtenberger 1, Gerhard Gompper 2 and Anna Stradner 1,5,*
- Author Affiliations
1Division of Physical Chemistry, Department of Chemistry, Lund University, Naturvetarvägen 16, SE-221 00 Lund, Sweden.
2Theoretical Soft Matter and Biophysics, Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany.
3Institut Laue-Langevin (ILL), F-38042 Grenoble Cedex 9, France.
4Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstr. 1, D-85748 Garching, Germany.
5Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland.
↵*Corresponding author. Email: anna.stradner@fkem1.lu.se
Science Advances 07 Dec 2016:
Vol. 2, no. 12, e1601432
Abstract
In the dense and crowded environment of the cell cytoplasm, an individual protein feels the presence of and interacts with all surrounding proteins. While we expect this to strongly influence the short-time diffusion coefficient Ds of proteins on length scales comparable to the nearest-neighbor distance, this quantity is difficult to assess experimentally. We demonstrate that quantitative information about Ds can be obtained from quasi-elastic neutron scattering experiments using the neutron spin echo technique. We choose two well-characterized and highly stable eye lens proteins, bovine α-crystallin and γB-crystallin, and measure their diffusion at concentrations comparable to those present in the eye lens. While diffusion slows down with increasing concentration for both proteins, we find marked variations that are directly linked to subtle differences in their interaction potentials. A comparison with computer simulations shows that anisotropic and patchy interactions play an essential role in determining the local short-time dynamics. Hence, our study clearly demonstrates the enormous effect that weak attractions can have on the short-time diffusion of proteins at concentrations comparable to those in the cellular cytosol.
Keywords Protein crowding short-time dynamics protein-protein interactions anisotropic interactions protein diffusion neutron spin echo technique hydrodynamic interactions computer simulations multiparticle collision dynamics
Copyright © 2016, The Authors
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