Distinguishing between Similar Miniproteins with Single-Molecule Nanopore Sensing: A Computational Study

Area of Science:

• Biotechnology
• Nanotechnology
• Computational Biology

Background:

• Nanopore technology offers label-free, high-throughput single-molecule sensing.
• Protein analysis using nanopores is challenging due to protein size, charge, and structural variability.
• Miniproteins present a simplified system for studying protein sensing due to their defined structures.

Purpose of the Study:

• To computationally evaluate the sensing of two similar human miniproteins using a silicon nitride nanopore.
• To develop a method for distinguishing between miniproteins with comparable structural features.
• To explore an alternative to computationally intensive molecular dynamics simulations for translocation events.

Main Methods:

• Utilized molecular dynamics to calculate ionic current magnitudes within the nanopore.
• Employed electronic structure calculations to determine interaction strengths between the nanopore and miniproteins.
• Derived miniprotein dwell times using combinatorics and numerical solutions based on interaction strengths.

Main Results:

• Occupied-pore ionic current magnitudes showed minimal variation between the two miniproteins.
• Dwell times for the two miniproteins differed by one order of magnitude.
• The computational approach successfully differentiated between structurally similar miniproteins.

Conclusions:

• The developed method, focusing on dwell time differences, offers a viable strategy for identifying similar miniproteins.
• This approach circumvents the extensive computational resources typically required for simulating protein translocation events.
• The findings suggest a promising label-free identification protocol for challenging protein samples using nanopore technology.