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Updated: Jun 23, 2026
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Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution
Published on: August 16, 2016
Engineering a Biological Nanopore for Monitoring Protein Dynamics and Conformational Changes at the Single-Molecule
Kumar Sarthak1,2, Veerle Van Meervelt3, Misha Soskine3
1Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.
ACS Nano
|June 22, 2026
Summary
Researchers engineered biological nanopores to observe protein conformational changes in real-time. Mutagenesis and simulations improved signal resolution for detecting glutamine binding by a substrate-binding domain protein.
Area of Science:
- Biophysics
- Nanotechnology
- Biochemistry
Background:
- Biological nanopores offer real-time, single-molecule monitoring of enzymatic reactions.
- Understanding the molecular basis for nanopore-based conformational dynamics measurement is crucial for engineering.
- Current methods lack sufficient resolution for precise protein transition monitoring.
Purpose of the Study:
- To elucidate the molecular mechanism of substrate-binding domain (SBD) protein recognition within ClyA nanopores.
- To enhance the resolution of single-molecule measurements for protein conformational transitions.
- To rationally engineer nanopore systems for improved biochemical reaction monitoring.
Main Methods:
- Combined all-atom molecular dynamics (MD) simulations with electrophysiology experiments.
- Utilized mutagenesis to engineer ClyA nanopores for SBD protein recognition.
- Analyzed simulated and experimental current data to determine protein location and conformational states.
Main Results:
- Identified the SBD protein's location near the ClyA nanopore constriction, where conformational changes cause significant current differences.
- Achieved a 3-fold signal amplification by introducing tryptophan residues to narrow the nanopore.
- MD simulations indicated electro-osmotic flow contributes to prolonged SBD protein residence time.
Conclusions:
- Nanopore systems can be rationally engineered for precise, single-molecule monitoring of biochemical reactions.
- Mutagenesis strategies can significantly enhance signal resolution in nanopore sensing.
- Understanding protein-nanopore interactions is key to optimizing nanopore-based biosensing applications.
