Advances in rational membrane protein design, molecular recognition, and single-molecule technology will be employed to enable biochemical sampling at high temporal and spatial resolution, as well as the detection, exploration, and characterization of individual biomolecules. We will use Ferric hydroxamate uptake component A (FhuA), one of the members of the superfamily of bacterial outer membrane proteins. Molecular engineering of the FhuA protein will be used in single-molecule stochastic sensing, because this system exhibits a remarkable array of advantageous characteristics, including its monomeric structure, robustness, versatility, tractability, and the availability of its high-resolution crystal structure. Our studies will be aimed at developing engineered nanopore-based biosensors that feature a wider pore diameter to accommodate bulky biopolymers, including proteins, double-stranded DNA, and their complexes with the interacting ligands. The partitioning of a single analyte into an engineered FhuA-based nanopore will be detected by a transient single- channel current blockade, the nature of which dependents on several factors that will be well-controlled by protein engineering and single-molecule design. The obtained data will be further processed through established protocols of single-molecule electric detection, macroscopic currents, and the analysis of current noise fluctuations produced by the analyte. The expected immediate outcomes will be the following: (1) the unusual stabilization of engineered FhuA-based nanopores by placing critical covalent and noncovalent intra- molecular contacts at strategic positions within the pore lumen;(2) the single-molecule stochastic sensing of highly specific HIV-1 aptamers;(3) the determination of the precise nature of the DNA aptamer-HIV-1 nucleocapsid protein interactions by obtaining the entropic and enthalpic contributions to the kinetic and thermodynamic constants, providing key information about which process in the DNA-protein interaction is dominant;(4) the single-molecule stochastic sensing of folded proteins and their complexes with the interacting ligands;(5) the improvement of the detection capabilities of the nanopore-based devices for proteins by engineering internal electrostatic traps;(6) the development of label-free diagnostic assays for drug-DNA complexes. The adaptation of these approaches to a microfabricated chip platform not only will provide a new generation of research tools in nanomedicine for examining the details of complex recognition events in a quantitative manner, but also will represent a crucial step in designing nanopore-based biosensors and high- throughput devices for biomedical molecular diagnosis, environmental monitoring, and homeland security.

Public Health Relevance

Engineered nanopores will represent a crucial step in the design of high-throughput devices for biomedical molecular diagnosis, biotherapeutics, and biosensing technology. They will also provide a new generation of research tools in nanomedicine for examining the details of complex recognition events in a quantitative manner.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Nanotechnology Study Section (NANO)
Program Officer
Lewis, Catherine D
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Syracuse University
Schools of Arts and Sciences
United States
Zip Code
Thakur, Avinash Kumar; Movileanu, Liviu (2018) Real-time measurement of protein-protein interactions at single-molecule resolution using a biological nanopore. Nat Biotechnol :
Wolfe, Aaron J; Gugel, Jack F; Chen, Min et al. (2018) Kinetics of Membrane Protein-Detergent Interactions Depend on Protein Electrostatics. J Phys Chem B 122:9471-9481
Wolfe, Aaron J; Gugel, Jack F; Chen, Min et al. (2018) Detergent Desorption of Membrane Proteins Exhibits Two Kinetic Phases. J Phys Chem Lett 9:1913-1919
Thakur, Avinash Kumar; Larimi, Motahareh Ghahari; Gooden, Kristin et al. (2017) Aberrantly Large Single-Channel Conductance of Polyhistidine Arm-Containing Protein Nanopores. Biochemistry 56:4895-4905
Wolfe, Aaron J; Si, Wei; Zhang, Zhengqi et al. (2017) Quantification of Membrane Protein-Detergent Complex Interactions. J Phys Chem B 121:10228-10241
Wolfe, Aaron J; Hsueh, Yi-Ching; Blanden, Adam R et al. (2017) Interrogating Detergent Desolvation of Nanopore-Forming Proteins by Fluorescence Polarization Spectroscopy. Anal Chem 89:8013-8020
Mohammad, Mohammad M; Tomita, Noriko; Ohta, Makoto et al. (2016) The Transmembrane Domain of a Bicomponent ABC Transporter Exhibits Channel-Forming Activity. ACS Chem Biol 11:2506-18
Couoh-Cardel, Sergio; Hsueh, Yi-Ching; Wilkens, Stephan et al. (2016) Yeast V-ATPase Proteolipid Ring Acts as a Large-conductance Transmembrane Protein Pore. Sci Rep 6:24774
Wolfe, Aaron J; Mohammad, Mohammad M; Thakur, Avinash K et al. (2016) Global redesign of a native ?-barrel scaffold. Biochim Biophys Acta 1858:19-29
Cheneke, Belete R; van den Berg, Bert; Movileanu, Liviu (2015) Quasithermodynamic contributions to the fluctuations of a protein nanopore. ACS Chem Biol 10:784-94

Showing the most recent 10 out of 31 publications