Simulating structurally variable nuclear pore complexes for microscopy.

Area of Science:

• Cell Biology
• Biophysics
• Microscopy

Background:

• The nuclear pore complex (NPC) is crucial for nucleocytoplasmic transport and serves as a microscopy standard due to its large, ordered structure.
• While average NPC architecture is known, significant structural heterogeneity exists, posing challenges for image analysis.
• Distinguishing true NPC structural variability from single-molecule localization microscopy (SMLM) noise is difficult.

Purpose of the Study:

• To introduce CIR4MICS, a simulation pipeline for generating ground truth datasets of structurally variable NPCs.
• To enable users to simulate diverse geometric variations in NPCs based on architectural models.
• To provide annotated datasets for comparing simulated and real NPC data.

Main Methods:

• CIR4MICS synthesizes NPC datasets using configurable, irregular ring models.
• It allows simulation of N- or C-terminally tagged proteins and geometric variations.
• A spring-model simulates irregular shapes under user-defined forces.

Main Results:

• CIR4MICS generates ground truth data for structurally diverse NPCs.
• Simulated data successfully replicated analyses of real NPC radii, showing parameter-dependent results.
• The pipeline facilitates testing image analysis methods and informing experimental imaging strategies.

Conclusions:

• CIR4MICS provides a valuable tool for simulating NPC structural variability.
• It aids in validating image analysis software and optimizing experimental design for NPC studies.
• The simulator supports hypothesis-driven research by providing realistic, variable NPC models.