Quantification of Biomolecular Dynamics Inside Real and Synthetic Nuclear Pore Complexes Using Time-Resolved Atomic...

Area of Science:

• Biophysics
• Nanotechnology
• Molecular Biology

Background:

• Atomic force microscopy (AFM) is crucial for studying biomolecular dynamics at the nanoscale.
• Distinguishing stochastic biomolecular dynamics from AFM noise is challenging, especially for intrinsically disordered proteins.

Purpose of the Study:

• To observe and quantify the dynamics of intrinsically disordered proteins in native and mimetic nuclear pore complexes (NPCs) using AFM.
• To develop and apply an autocorrelation analysis for quantifying stochastic fluctuations in biomolecular systems.

Main Methods:

• Utilized AFM with 50-200 ms temporal resolution to study protein dynamics.
• Employed drift correction and baseline measurements for accurate data analysis.
• Developed an autocorrelation analysis to quantify dynamics and assess their veracity.

Main Results:

• Observed dynamics of intrinsically disordered proteins in both native NPCs and DNA origami-based mimetic NPCs.
• Highlighted the importance of data processing techniques like drift correction.
• Revealed surprisingly slow collective transition rates within mimetic NPCs.

Conclusions:

• The autocorrelation analysis protocol is effective for quantifying stochastic fluctuations in biomolecular systems.
• FG-nucleoporin (FG-nup) cohesive interactions play a significant role in the dynamics of the NPC transport barrier.
• AFM is a powerful tool for investigating complex biomolecular dynamics, even with inherent stochasticity.