Nanopore systems for protein characterization and biomimicry

Nanopore technology stands at the forefront of molecular analysis, offering unparalleled capabilities in single-molecule detection and sequencing. Its applications encompass genomics, proteomics, and biosensing, providing profound insights into biomolecular structures and functions. This technology enables real-time, label-free analysis of nucleic acids and proteins, promising transformative impacts in diagnostics, personalized medicine, and basic biological research. This thesis focuses on three primary applications of nanopore technology: sequencing, sensing, and biomimicry. The initial chapter introduces a method to transform nanoscale pores into highly selective, anion-conducting channels, leveraging a significant electro-osmotic effect. This approach facilitates the unidirectional movement of proteins through nanopores, accompanied by an analysis of the forces impacting peptides during electro-osmotic flow. The subsequent chapter shifts focus to the biosensing capabilities of nanopore technology. Rather than achieving single-amino acid resolution, this segment explores the translocation of entire proteins through nanopores. Specifically, we investigated the translocation mechanisms by applying external electric fields to push small proteins, such as cytochrome c₂, through ultrathin silicon nitride membranes. Additionally, this section explores the impact of protein knots on translocation dynamics. Finally, we developed a proof-of-concept proteome characterization system that identifies proteins based on their ionic current signatures as they traverse a series of nanopores. The third chapter discusses biomimicry, where nanopore technology is employed to mimic human skin structure, leading to the development of vapor-permeable, dehydrated nanoporous biomimetic membranes utilizing nanopore proteins. The final chapter investigates the engineering of a switchable artificial metalloprotein aimed at enhancing hydrogen bonding, presenting a Gln-responsive biological probe for future biosensing applications.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biophysics & Quant Biology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2024

Author dc:creator

• Mehrafrooz, Behzad

Contributors dc:contributor

• Aksimentiev, Aleksei
• Wanunu, Meni
• Sing, Charles E.
• Pogorelov, Taras

• Nanopore
• Molecular Dynamics Simulations
• Sequencing
• Protein Engineering

Statement dc:rights

• Copyright 2024 Behzad Mehrafrooz

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/127427

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F127427