Macromolecular Crowding: How Shape and Interactions Affect Diffusion

The Journal of Physical Chemistry B, vol. 124, pp. 7537–7543

Abstract

A significant fraction of the cell volume is occupied by various proteins, polysaccharides, nucleic acids, etc., which considerably reduces the mobility of macromolecules. Theoretical and experimental work so far have mainly focused on the dependence of the mobility on the occupied volume, while the effect of a macromolecular shape received less attention. Herein, using fluorescence correlation spectroscopy (FCS) and Brownian dynamics (BD) simulations, we report on a dramatic slowdown of tracer diffusion by cylindrically shaped double-stranded (ds) DNAs (16 nm in length). We find, for instance, that the translational diffusion coefficient of a streptavidin tracer is reduced by about 60% for a volume fraction of dsDNA as low as just 5%. For comparison, for a spherical crowder (Ficoll70) the slowdown is only 10% at the same volume fraction and 60% reduction occurs at a volume fraction as high as 35%. BD simulations reveal that this reduction can be attributed to a larger volume excluded to a tracer by dsDNA particles, as compared with spherical Ficoll70 at the same volume fraction, and to the differences in the tracer-crowder attractive interactions. In addition, we find using BD simulations that rotational diffusion of dsDNA is less affected by the crowder shape than its translational motion. Our results show that diffusion in crowded systems is determined not merely by the occupied volume fraction, but that the shape and interactions can determine diffusion, which is relevant to the diverse intracellular environments inside living cells.

Authors 4

1. Tomasz Skóra

   Polish Academy of Sciences · Institute of Physical Chemistry

   Affiliation as printed

   Polish Academy of Sciences , , Kasprzaka 44/52 , ,

   Department of Complex Systems, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland

2. Farzaneh Vaghefikia Aachen I. Physikalisches Institut

   RWTH Aachen University

   Affiliation as printed

   RWTH Aachen University , , ,

   I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen University, 52074 Aachen, Germany

3. Jörg Fitter corresponding Aachen I. Physikalisches Institut

   RWTH Aachen University · Forschungszentrum Jülich

   Affiliation as printed

   Forschungszentrum Jülich , , ,

   RWTH Aachen University , , ,

   I. Physikalisches Institut (IA), AG Biophysik, RWTH Aachen University, 52074 Aachen, Germany

   Institut für Biologische Informationsprozesse (IBI-6), Forschungszentrum Jülich, 52425 Jülich, Germany

4. Svyatoslav Kondrat corresponding

   Polish Academy of Sciences · Max Planck Institute for Intelligent Systems · Max Planck Society · University of Stuttgart · Institute of Physical Chemistry

   Affiliation as printed

   Max-Planck-Institut für Intelligente Systeme , Heisenbergstraße 3 , ,

   Polish Academy of Sciences , , Kasprzaka 44/52 , ,

   Universität Stuttgart , , Pfaffenwaldring 57 , ,

   Department of Complex Systems, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland

   Institut für Theoretische Physik IV, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany

   Max-Planck-Institut für Intelligente Systeme, Heisenbergstraße 3, 70569 Stuttgart, Germany