Simulating structurally variable Nuclear Pore Complexes for Microscopy

The Nuclear Pore Complex (NPC) is a massive, 8-fold symmetrical protein assembly that enables macromolecular exchange between the cytoplasm and nucleus. The average architecture of proteins within the NPC has been resolved with pseudo-atomic precision, however observed NPC heterogeneities such as varying diameters, elongated shapes, 9-fold symmetry, and irregular shapes evidence a high degree of divergence from this average. Single Molecule Localization Microscopy (SMLM) images NPCs at protein-level resolution, whereupon image analysis software studies their heterogeneity. Antithetically, NPCs have been used as a reference standard for SMLM due to their abundance, size, and symmetry. Ground truth annotations would ultimately aid both lines of research, however SMLM noise impedes such annotations and complicates image analysis. Here, we introduce a pipeline that simulates structurally variable NPCs based on architectural models of the NPC. Users can specify one of several N- or C-terminally tagged NPC proteins, as well as geometric variability in radius, height, internal twist, and elongation. We represent the NPC as a spring-model such that arbitrary deforming forces, of user-defined magnitudes, simulate irregularly shaped variations. We provide an open-source simulation pipeline, as well as a reference dataset of simulated human NPCs, with multiple types of geometric variability and increasing magnitudes of deforming forces. ### Competing Interest Statement The authors have declared no competing interest.