Journal Article

FZJ-2020-02881

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Macromolecular Crowding: How Shape and Interactions Affect Diffusion

Skóra, T. ; Vaghefikia, F. ; Fitter, J. (Corresponding author)FZJ* ; Kondrat, S. (Corresponding author)

2020
Soc. Washington, DC

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Please use a persistent id in citations: http://hdl.handle.net/2128/25622  doi:10.1021/acs.jpcb.0c04846

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.

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Contributing Institute(s):

1. Zelluläre Strukturbiologie (IBI-6)

Research Program(s):

1. 551 - Functional Macromolecules and Complexes (POF3-551) (POF3-551)

Appears in the scientific report 2020

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Database coverage:
; ; ; Clarivate Analytics Master Journal List ; Current Contents - Physical, Chemical and Earth Sciences ; Ebsco Academic Search ; Essential Science Indicators ; IF < 5 ; JCR ; NCBI Molecular Biology Database ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Web of Science Core Collection

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