Article
Chemistry, Multidisciplinary
Joshua C. Foster, Bach Pham, Ryan Pham, Minji Kim, Matthew D. Moore, Min Chen
Summary: Molecular detection via nanopore is a promising technology for multiplex sensing development. Two OmpG nanopores with unique peptide motifs displayed in specific loops were identified and utilized for single-molecule multiplex protein detection. A strategy to increase sensor sensitivity via avidity motif display was also reported. These sensing schemes can be further expanded to increase multiplicity and sensitivity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Analytical
Hye-Jin Hwang, Jin-Sik Kim, Jeonghyun Lee, Jun Sik Min, Ki-Baek Jeong, Eunha Kim, Mi-Kyung Lee, Seung-Wook Chi
Summary: Nanopore sensors are a promising platform for single-molecule sensing, such as sequencing, disease diagnostics, and drug screening. In this study, the interaction between Bcl-xL and Bak-BH3 was characterized using chemically modified OmpG nanopores, and specific inhibition of Bcl-xL was achieved using a small-molecule antagonist. The results demonstrate that chemically modified OmpG nanopores can serve as a valuable sensor platform for ultrasensitive, rapid, and single-molecule-based drug screening against protein-protein interactions.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Minji Kim, Joshua C. Foster, Matthew D. Moore, Min Chen
Summary: In this study, a nanopore construct capable of interacting with antibodies and generating readable signals was successfully engineered by inserting a FLAG sequence in the flexible loop of OmpG protein found in Escherichia coli. The peptide display scheme demonstrated in this study can be applied to the engineering of OmpG sensors for screening and validating positive clones during antibody development, as well as for real-time quality control of cell cultures in monoclonal antibody production.
Article
Biophysics
Monifa A. Fahie, Fanjun Li, Carolyn Palmer, Connie Yoon, Min Chen
Summary: This research identified critical residues that control the pH-dependent gating of the loop 6 in OmpG nanopore, and successfully created a mutant OmpG nanopore that can stay predominantly open at a broad range of pHs. The study demonstrates the utility of the OmpG nanopore for sensing complementary DNA and a DNA binding protein at an acidic pH.
BIOPHYSICAL JOURNAL
(2022)
Review
Chemistry, Multidisciplinary
Zheng-Li Hu, Ming-Zhu Huo, Yi-Lun Ying, Yi-Tao Long
Summary: Proteins play a crucial role in disease occurrence and treatment, making protein sequencing a game changer for proteomics and clinical diagnostics. While the biological nanopore approach has shown success in single-molecule DNA sequencing, challenges remain in sequentially identifying each amino acid of single proteins.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Analytical
Ting Li, Xinying Li, Xiaoxue Li, Li Yang, Hailong Wang
Summary: Developing a new method for bleomycin detection using dumbbell DNA as probe on the nanopore sensor platform is described in this study, which shows a quantitative relationship between event intervals (tau(on)) and the concentration of bleomycin with high selectivity and ultra-low detection limit.
MICROCHEMICAL JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Juan Zhou, Qing Lan, Wang Li, Li-Na Ji, Kang Wang, Xing-Hua Xia
Summary: Obtaining sequential and conformational information on proteins is important for understanding their functions. This study combines surface enhanced Raman scattering (SERS) with a nanopore to observe the unfolding and multistep sequential translocation of single molecule (SM) cytochrome c (cyt c). The high bias voltage unfolds the SM protein, slowing down the translocation and allowing specific SERS traces of different SM cyt c segments to be recorded. This research provides insight into protein segments and accelerates the development of nanopore-based SM protein sequencing.
Article
Nanoscience & Nanotechnology
Pablo Martin-Baniandres, Wei-Hsuan Lan, Stephanie Board, Mercedes Romero-Ruiz, Sergi Garcia-Manyes, Yujia Qing, Hagan Bayley
Summary: Electro-osmosis in an anion-selective alpha-hemolysin nanopore is utilized for capturing, unfolding, and transporting polypeptides with more than 1,200 residues. By monitoring the ionic current at a single-molecule resolution, this method enables the mapping of post-translational modifications in polypeptide chains. The application of nanopore technology holds potential for identifying full-length proteoforms.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Analytical
Hong Sun, Chuan Yao, Kaibo You, Can Chen, Shuoshuo Liu, Zhihong Xu
Summary: In this study, a dynamic monitoring approach based on nanopore single-molecule biosensor was developed to detect the folding and unfolding transitions of proteins. By gradually increasing the concentration of denaturant guanidine hydrochloride (GdmCl), sensitive responses were observed with lysozyme unfolding. The existence of a stable intermediate was experimentally confirmed, providing insights into the conformation of the intermediate and the manner of denaturant towards lysozyme.
ANALYTICA CHIMICA ACTA
(2023)
Review
Chemistry, Multidisciplinary
Xiaoqing Zeng, Yang Xiang, Qianshan Liu, Liang Wang, Qianyun Ma, Wenhao Ma, Delin Zeng, Yajie Yin, Deqiang Wang
Summary: Protein is the material basis of life and plays a crucial role in proteomics and human biology. Current protein analysis techniques face limitations, but nanopore single-molecule detection technology offers a solution with its wide applications and potential for development.
Article
Biophysics
David Rodriguez-Larrea
Summary: The study demonstrates the use of simple neural networks to identify protein mutants, with poor generalization ability. By utilizing a thermal annealing protocol and examining multiple mutants in repeated experiments, the generalizability of the neural network can be improved.
BIOSENSORS & BIOELECTRONICS
(2021)
Review
Chemistry, Multidisciplinary
Yanfang Wu, J. Justin Gooding
Summary: This review provides an overview of the concepts, fabrication, and applications of nanopore sensors, with a focus on their potential and recent developments in quantitative analysis.
CHEMICAL SOCIETY REVIEWS
(2022)
Review
Chemistry, Multidisciplinary
Xin Guan, Haijuan Li, Limei Chen, Guohua Qi, Yongdong Jin
Summary: A glass capillary-based nanopore (G-nanopore) with tapered tip and flexible surface modifications provides a powerful sensing platform for diverse biological measurements. It enables noninvasive single molecule and subcellular single cell detections and shows potential for cancer diagnosis and treatment applications. However, current bottlenecks limit its widespread use in clinical applications.
Article
Multidisciplinary Sciences
Mohammad Ahmad, Jeung-Hoi Ha, Lauren A. Mayse, Maria F. Presti, Aaron J. Wolfe, Kelsey J. Moody, Stewart N. Loh, Liviu Movileanu
Summary: Protein detection is important in molecular diagnostics. Nanopores and the resistive-pulse technique have been used to analyze proteins. However, there is still a challenge in implementing specific interfaces for detecting proteins without the restrictions of the nanopore interior.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Shuanghong Yan, Jinyue Zhang, Yu Wang, Weiming Guo, Shanyu Zhang, Yao Liu, Jiao Cao, Yuqin Wang, Liying Wang, Fubo Ma, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: Proteins exhibit diverse functions due to their variable amino acid sequences, but current technology for direct protein sequence analysis remains inadequate. The development of nanopore sequencing has sparked efforts to sequence peptides in a similar manner, successfully achieving direct observation of peptide's ratcheting motion and showing potential for peptide fingerprinting.
Article
Chemistry, Analytical
Monifa A. Fahie, Bib Yang, Martin Mullis, Matthew A. Holden, Min Chen
ANALYTICAL CHEMISTRY
(2015)
Article
Chemistry, Physical
Monifa A. Fahie, Min Chen
JOURNAL OF PHYSICAL CHEMISTRY B
(2015)
Article
Chemistry, Multidisciplinary
Monifa A. Fahie, Bib Yang, Bach Pham, Min Chen
Article
Chemistry, Multidisciplinary
Alan Perez-Rathke, Monifa A. Fahie, Christina Chisholm, Jie Liang, Min Chen
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2018)
Article
Multidisciplinary Sciences
Monifa A. Fahie, Lucas Liang, Alzira R. Avelino, Bach Pham, Patanachai Limpikirati, Richard W. Vachet, Min Chen
SCIENTIFIC REPORTS
(2018)
Article
Biophysics
Bo Lu, Chris Stokes, Monifa Fahie, Min Chen, Jene A. Golovchenko, Lene Vestergaard Hau
BIOPHYSICAL JOURNAL
(2018)
Article
Biochemistry & Molecular Biology
Monifa Fahie, Fabian B. Romano, Christina Chisholm, Alejandro P. Heuck, Mark Zbinden, Min Chen
JOURNAL OF BIOLOGICAL CHEMISTRY
(2013)
Article
Biophysics
Bach Pham, Scott J. Eron, Maureen E. Hill, Xin Li, Monifa A. Fahie, Jeanne A. Hardy, Min Chen
BIOPHYSICAL JOURNAL
(2019)
Article
Biochemistry & Molecular Biology
Bach Pham, Christina M. Chisholm, Joshua Foster, Emily Friis, Monifa A. Fahie, Min Chen
Summary: Enhancing electrostatic repulsion forces between extracellular loops can suppress the pH-dependent gating of OmpG nanopores, while mutant containing additional negative charges in loops 6 and 1 show reduced sensitivity to pH changes, providing new evidence for the mechanism of OmpG gating. The pH-independent OmpG pores could potentially serve as a sensing platform operating at a broad range of pH conditions.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2021)
Article
Chemistry, Multidisciplinary
Monifa A. Fahie, Jonathan Candido, Gisele Andree, Min Chen
Summary: Nanopore sensors with different loops of OmpG as anchoring points for affinity ligands were developed for protein sensing. Analytes weakly attracted to the surface are only detectable when the ligand is tethered to loop 6, while those forming a strong interaction with the surface are distinguishable by all seven OmpG nanopore constructs.
Article
Biophysics
Monifa A. Fahie, Fanjun Li, Carolyn Palmer, Connie Yoon, Min Chen
Summary: This research identified critical residues that control the pH-dependent gating of the loop 6 in OmpG nanopore, and successfully created a mutant OmpG nanopore that can stay predominantly open at a broad range of pHs. The study demonstrates the utility of the OmpG nanopore for sensing complementary DNA and a DNA binding protein at an acidic pH.
BIOPHYSICAL JOURNAL
(2022)
Article
Multidisciplinary Sciences
Eve E. Weatherill, Monifa A. Fahie, David P. Marshall, Rachel A. Andvig, Matthew R. Cheetham, Min Chen, Mark Wallace
Summary: Compared to globular proteins, the folding and insertion of beta-barrel membrane proteins are slow but rapid, occurring within seconds upon arrival at the membrane interface. This combination of infrequent yet fast folding events resolves the apparent contradiction between slow ensemble kinetics and typical biomolecular folding timescales.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Meishan Lin, Ge Zhang, Monifa Fahie, Leslie K. Morgan, Min Chen, Timothy A. Keiderling, Linda J. Kenney, Jie Liang
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2017)