Article
Biochemistry & Molecular Biology
Joseph W. F. Robertson, Madhav L. Ghimire, Joseph E. Reiner
Summary: Protein nanopores have evolved into an important class of sensors for studying biophysical processes and detecting biopolymers. This review focuses on the chemistry of biological pores and its impact on molecular detection at the single molecule scale.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2021)
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
Physics, Applied
Maurits R. R. de Planque
Summary: The ion flow through channel proteins embedded in a lipid bilayer membrane can be recorded as an electrical current, enabling biophysical characterization and pharmacological drug screening at a single-channel level. This concise review introduces the bilayer recording methodology, with an emphasis on the requirements for full electrophysiology assays. The self-assembled lipid bilayer, formed in a similar to 100 mu m diameter aperture in between two aqueous chambers, is critical. Various approaches to increase the measurement throughput by scaling to aperture arrays are discussed in terms of current-amplifier technology, bilayer stability, ion channel incorporation, system functionality and obtained single-channel data. The various bilayer recording platforms all have advantages and limitations. Combining the strengths of the different platform architectures, for example, the use of shaped apertures, will be essential to realize and also automate parallel ion channel recordings.
JAPANESE JOURNAL OF APPLIED PHYSICS
(2022)
Article
Engineering, Biomedical
Yasin Ozturk, Aliakbar Ebrahimi, Araz Norouz Dizaji, Ozge Kaygusuz, Jayesh Arun Bafna, Mathias Winterhalter, Guven Cankaya, Cihan Darcan, Fatma Dogan Guzel
Summary: The study investigates the reproducible generation of micropores in the range of 50-100 microns in diameter in a Teflon film. The multi-pulse method is more convenient for lipid bilayer formation and has a higher success rate. Experimental results show that the lipid bilayer on Teflon pores can last for more than 33 hours.
BIOMEDICAL MICRODEVICES
(2021)
Review
Chemistry, Analytical
Jiajun Wang, Yi-Lun Ying, Cheng-Bing Zhong, Li-Min Zhang, Feng Yan, Yi-Tao Long
Summary: Nanopore electrochemistry, a promising tool for single molecule sensing, requires appropriate nanopore sensing interface, advanced instrumentation, and multi-disciplinary collaboration for high resolution and throughput. Recent improvements in the nanopore sensing interface, nanopore arrays, and intelligent data analysis methods have enhanced the potential for widespread application in single-molecule research.
Article
Chemistry, Multidisciplinary
Rajan Shrivastava, Subhendu Ghosh
Summary: Ion channels self-organize into clusters on cellular and organelle membranes, mutually modulating their gating behavior. A statistical mechanical model has been proposed to study the collective dynamics in ion channel clusters, successfully describing the multichannel gating behavior and self-organization.
Article
Multidisciplinary Sciences
Lauren Ashley Mayse, Ali Imran, Motahareh Ghahari Larimi, Michael S. Cosgrove, Aaron James Wolfe, Liviu Movileanu
Summary: The authors convert a protein nanopore into a sensitive biosensor to detect and quantify the binding of WDR5 protein to a ligand, revealing a wide dynamic range and three modes of protein recognition.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Peter Kramar, Damijan Miklavcic
Summary: The study aimed to investigate the effects of different cholesterol concentrations on the behavior of planar lipid bilayers under an electric field. The results showed no statistical difference in capacitance but a significant impact on breakdown voltage with the addition of cholesterol.
BIOELECTROCHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Weichao Peng, Shuaihu Yan, Ke Zhou, Hai-Chen Wu, Lei Liu, Yuliang Zhao
Summary: By using a modified density gradient ultracentrifugation method, ultrashort single-walled carbon nanotubes (SWCNTs) with a narrow conductance range can be separated and inserted into lipid bilayers to construct high-resolution nanopore sensors. These SWCNT nanopores exhibit 3-5 times higher ion mobility compared to bulk mobility, and are capable of discriminating homologous and isomeric proteinogenic amino acids, which is challenging for other types of nanopore sensors. These findings hold great importance for the development of protein sequencing technologies.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Mitsuki Miyagi, Sotaro Takiguchi, Kazuaki Hakamada, Masafumi Yohda, Ryuji Kawano
Summary: The EXP2 nanopore has been shown to detect poly-L-lysine with single-molecule sensitivity and sufficient resolution to differentiate between two individual PLLs of different molecular weights. Exploring biological nanopores suitable for peptide sensing is key to achieving amino acid sequence determination.
Review
Chemistry, Physical
Ru-Jia Yu, Ke-Le Chen, Yi-Lun Ying, Yi-Tao Long
Summary: Nanopores offer high spatial and temporal resolutions for label-free measurement of single molecules, allowing for the study of molecular variations and dynamic behaviors. The design of sensing interface within the pore enables selectivity, making it possible for exciting applications in single-molecule biosensors.
CURRENT OPINION IN ELECTROCHEMISTRY
(2022)
Article
Biochemical Research Methods
Xiaoyu Guan, Zhongnian Li, Yueying Zhou, Wei Shao, Daoqiang Zhang
Summary: Nanopore sequencing, as a high-throughput sequencing technology for DNA, RNA, and proteins, faces the challenge of high labeling costs for the enormous generated data. This study introduces active learning to select samples that need to be labeled, reducing the labeling costs significantly. Experimental results demonstrate that active learning can greatly reduce the labeling amount while achieving the best baseline performance for nanopore data analysis.
Article
Biochemistry & Molecular Biology
Sung-Tae Yang, Song-Yub Shin, Sung-Heui Shin
Summary: The PXXP motif in PMAP-23 plays a crucial role in its translocation across lipid bilayers by interacting with negatively charged bacterial membranes, and wild-type PMAP-23 has stronger antimicrobial activity compared to its Pro-substituted derivatives.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Xiaoyi Wang, Tina-Marie Thomas, Ren Ren, Yu Zhou, Peng Zhang, Jingjing Li, Shenglin Cai, Kai Liu, Aleksandar P. Ivanov, Andreas Herrmann, Joshua B. Edel
Summary: The analysis of proteins and their interactions at the single-molecule level has important implications for understanding biological processes and diseases, especially for proteins found in low copy numbers in biological samples. Nanopore sensing is a label-free detection technique that is well-suited for applications such as studying protein-protein interactions, biomarker screening, drug discovery, and protein sequencing. However, current limitations in protein nanopore sensing pose challenges in controlling protein translocation and relating protein structures and functions to nanopore readouts.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Analytical
Y. M. Nuwan D. Y. Bandara, Jugal Saharia, Buddini Karawdeniya, Patrick Kluth, Min Jun Kim
Summary: This study introduces an analysis platform with four baseline fitting methods adaptable to various nanopore traces for extracting events effectively. The performance was tested with stable and fluctuating current profiles, showing that event count increased significantly with increasing fitting robustness for fluctuating profiles. Event turning points were clustered using the dbscan method, with subsequent segmentation and iterative refinement to deduce final event levels.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Jiajun Wang, Jayesh Arun Bafna, Satya Prathyusha Bhamidimarri, Mathias Winterhalter
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2019)
Article
Chemistry, Multidisciplinary
Jiajun Wang, Remi Terrasse, Jayesh Arun Bafna, Lorraine Benier, Mathias Winterhalter
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
Article
Chemistry, Medicinal
Jigneshkumar Dahyabhai Prajapati, Crystal Mele, Mehmet Alphan Aksoyoglu, Mathias Winterhalter, Ulrich Kleinekathoefer
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2020)
Article
Biology
Julia Vergalli, Alessio Atzori, Jelena Pajovic, Estelle Dumont, Giuliano Malloci, Muriel Masi, Attilio Vittorio Vargiu, Mathias Winterhalter, Matthieu Refregiers, Paolo Ruggerone, Jean-Marie Pages
COMMUNICATIONS BIOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Sushil Pangeni, Jigneshkumar Dahyabhai Prajapati, Jayesh Bafna, Mohamed Nilam, Werner M. Nau, Ulrich Kleinekathoefer, Mathias Winterhalter
Summary: This study focused on quantifying the passage of the large peptide protamine (Ptm) across CymA, a passive channel for cyclodextrin uptake. Results showed that the kinetics of Ptm entry through CymA was independent of its concentration, with about 1-2 events per second and long dwell times observed per channel. Additionally, voltage-dependent entry of single Ptm peptide molecules into the channel was resolved, with extrapolation to zero voltage revealing a translocation rate of about one molecule per second per channel.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Chemistry, Multidisciplinary
Jigneshkumar Dahyabhai Prajapati, Ulrich Kleinekathoefer, Mathias Winterhalter
Summary: Traditional antibiotics are facing the challenge of Gram-negative bacteria developing resistance, prompting the urgent need for new antibacterial agents. Designing new antibiotic molecules that can rapidly penetrate Gram-negative bacteria and achieve lethal intracellular drug accumulation is a major challenge. The lack of simple experimental techniques to measure antibiotic uptake and local concentrations in subcellular compartments is a limiting factor.
Article
Multidisciplinary Sciences
Samira Sadeghi, Siddharth Deshpande, Girish Vallerinteavide Mavelli, Alphan Aksoyoglu, Jayesh Bafna, Mathias Winterhalter, R. Manjunatha Kini, David P. Lane, Chester L. Drum
Summary: In vitro protein folding often leads to aggregation and low yields. Researchers have used nanoscale exoshells to enhance soluble yield, functional yield, and specific activity of folded proteins.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Tanzir Ahmed, Jayesh Arun Bafna, Roland Hemmler, Karsten Gall, Richard Wagner, Mathias Winterhalter, Michael J. Vellekoop, Sander van den Driesche
Summary: This work presents a microsystem setup for sensitive biological membrane translocation measurements. Thin free-standing synthetic bilayer lipid membranes (BLM) are constructed in microfabricated silicon nitride apertures and used for electrophysiological measurements of pore proteins. The integration of pore-forming proteins is achieved through direct reconstitution or reconstitution via outer membrane vesicles (OMVs) released from Gram-negative bacteria. This microsystem allows for investigation of fast gating events, pore blocking, and gating events of small pores.
Article
Chemistry, Multidisciplinary
Jiajun Wang, Jigneshkumar Dahyabhai Prajapati, Fan Gao, Yi-Lun Ying, Ulrich Kleinekathoefer, Mathias Winterhalter, Yi-Tao Long
Summary: Chirality is important but often overlooked in biological and chemical processes due to technical limitations. Researchers have used an electrostatically asymmetric membrane channel to successfully identify chiral amino acids in single peptides. This study provides a new approach for developing chiral recognition and protein sequencing methods.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biology
Muriel Masi, Julia Vergalli, Ishan Ghai, Andrea Barba-Bon, Therese Schembri, Werner M. Nau, Daniel Lafitte, Mathias Winterhalter, Jean-Marie Pages
Summary: This study investigated the translocation and killing effects of different cephalosporins on Gram-negative bacteria. The results revealed that the activity and efficiency of the drugs were influenced by the expression of specific porins. Through experimentation and analysis, it was found that the net negative charge of one of the cephalosporins contributed to its higher permeation through less cation-selective porins. These findings provide insights into the susceptibility of specific bacteria strains to cephalosporins.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Igor V. Bodrenko, Tsedenia Alemu Zewdie, Jiajun Wang, Eshita Paul, Susanne Witt, Mathias Winterhalter
Summary: This study investigates protein-protein interaction using electrophysiology, focusing on the structure of the TolC-AcrA-AcrB complex and the inhibitory effect of potential efflux pump inhibitors. The findings suggest that the fluctuation of ion current and the average current through the TolC channel can be used as complementary measures to assess the interaction of the complex.
Article
Chemistry, Medicinal
Abhishek Acharya, Ishan Ghai, Claudio Piselli, Jigneshkumar Dahyabhai Prajapati, Roland Benz, Mathias Winterhalter, Ulrich Kleinekathoefer
Summary: In this study, the molecular mechanism of an antibiotic permeating through a bacterial channel is revealed, with a focus on the role of conformational dynamics of the constriction loop. The dynamics of the L3 loop, specifically the F118 to S125 segment, at the constriction regions of the OmpF porin is investigated using temperature accelerated sliced sampling approach. The importance of hydrogen-bond stabilization in the conformational dynamics of the L3 loop is demonstrated through single channel electrophysiology experiments and applied-field simulations. The findings suggest that conformational dynamics of the constriction loop may play a general role in antibiotic permeation through porins.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Multidisciplinary
Yao Chen, Andrea Barba-Bon, Bohumir Gruner, Mathias Winterhalter, M. Alphan Aksoyoglu, Sushil Pangeni, Maryam Ashjari, Klaudia Brix, Giulia Salluce, Yeray Folgar-Camean, Javier Montenegro, Werner M. Nau
Summary: Cobalt bisdicarbollides (COSANs) are used as selective and efficient molecular carriers to transport hydrophilic oligopeptides through membranes. They can permeate lipid bilayer membranes without causing membrane damage. COSANs transport arginine-rich and lysine-rich peptides effectively, but cannot transport small molecules or anionic cargos. The transportation mechanism is a molecular carrier mechanism, and living cell experiments show that a fluorescent peptide cargo can be delivered into the cytosol.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Physical
Stefan Milenkovic, Jiajun Wang, Silvia Acosta-Gutierrez, Mathias Winterhalter, Matteo Ceccarelli, Igor V. Bodrenko
Summary: Transmembrane beta-barrel proteins are versatile candidates for various technological applications and their behavior is influenced by environmental conditions. Comparing two highly homologous porins, OmpF and OmpC, we observed subtle amino acid substitutions that can modulate mass transport properties. These differences can be attributed to the disparities in the environmental conditions under which the porins are expressed. Our analysis not only highlights the advantages of enhanced sampling methods, but also provides valuable insights into the biological function and technical applications of these proteins.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Jiajun Wang, Jigneshkumar Dahyabhai Prajapati, Ulrich Kleinekathoefer, Mathias Winterhalter
