Quantum mechanics

Cytoplasm

Cell biology

Intracellular transport

Chemical physics

Biology

Materials science

Displacement (psychology)

Mean squared displacement

Nucleus

Biochemistry

Molecule

Thermal diffusivity

Computational biology

Mass diffusivity

Intracellular

Thermodynamics

Physics

Nanotechnology

Organic chemistry

Diffusion

Psychology

Molecular dynamics

Psychotherapist

Computational chemistry

Chemistry

Nanoscopic scale

Biophysics

Nature Methods

Intracellular diffusion underlies vital cellular processes. However, it remains difficult to elucidate how an unbound protein diffuses inside the cell with good spatial resolution and sensitivity. Here we introduce single-molecule displacement/diffusivity mapping (SMdM), a super-resolution strategy that enables the nanoscale mapping of intracellular diffusivity through local statistics of the instantaneous displacements of freely diffusing single molecules. We thus show that the diffusion of an average-sized protein in the mammalian cytoplasm and nucleus is spatially heterogeneous at the nanoscale, and that variations in local diffusivity correlate with the ultrastructure of the actin cytoskeleton and the organization of the genome, respectively. SMdM of differently charged proteins further unveils that the possession of positive, but not negative, net charges drastically impedes diffusion, and that the rate is determined by the specific subcellular environments. We thus unveil rich heterogeneities and charge effects in intracellular diffusion at the nanoscale.

Single-molecule displacement mapping unveils nanoscale heterogeneities in intracellular diffusivity