Abstract
Molecular clustering at the plasma membrane has long been identified as a key process and is associated with regulating signalling pathways across cell types. Recent advances in microscopy, in particular the rise of super-resolution, have allowed the experimental observation of nanoscale molecular clusters in the plasma membrane. However, modelling approaches capable of recapitulating these observations are in their infancy, partly because of the extremely complex array of biophysical factors which influence molecular distributions and dynamics in the plasma membrane. We propose here a highly abstracted approach: an agent-based model dedicated to the study of molecular aggregation at the plasma membrane. We show that when molecules are modelled as though they can act (diffuse) in a manner which is influenced by their molecular neighbourhood, many of the distributions observed in cells can be recapitulated, even though such sensing and response is not possible for real membrane molecules. As such, agent-based offers a unique platform which may lead to a new understanding of how molecular clustering in extremely complex molecular environments can be abstracted, simulated and interpreted using simple rules.
Highlights
The plasma membrane (PM) has long been identified as a key component of cellular machinery
For our Standard Condition displacement profile (Fig 1b), we fix defined maximum (Dmax) at 3.5 nm. ms-1 which translates to a diffusion coefficient (DC) of ~0.1 μm2.s-1, i.e. within the range of expected values for transmembrane proteins[45,46,47] and Dmin = 0
The range of targeted L100 values recapitulates clustering observed at the cellular membrane using singlemolecule localisation, microscopy and quantitative cluster analysis techniques
Summary
The plasma membrane (PM) has long been identified as a key component of cellular machinery. An agent-based model of molecular aggregation at the cell membrane case of full convergence: < Lb 100 > has reached a horizontal asymptote within the 5 minutes timescale (Fig 2b(i)-(iii) and 2c(i)-(iii)).
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