Label-Free and Real-Time Detection of Protein Ubiquitination with a Biological Nanopore

Registration of activity of a single molecule of horseradish peroxidase using a detector based on a solid-state nanopore

This work demonstrates the use of a solid-state nanopore detector to monitor the activity of a single molecule of a model enzyme, horseradish peroxidase (HRP). This detector includes a measuring cell, which is divided into cis- and trans- chambers by a silicon nitride chip (SiN structure) with a nanopore of 5 nm in diameter. To entrap a single HRP molecule into the nanopore, an electrode had been placed into the cis-chamber; HRP solution was added into this chamber after application of a negative voltage. The reaction of the HRP substrate, 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS), oxidation by the enzyme molecule was performed in the presence of hydrogen peroxide. During this reaction, the functioning of a single HRP molecule, entrapped in the nanopore, was monitored by recording the time dependence of the ion current flowing through the nanopore. The approach proposed in our work is applicable for further studies of functioning of various enzymes at the level of single molecules, and this is an important step in the development of single-molecule enzymology.

A lumen-tunable triangular DNA nanopore for molecular sensing and cross-membrane transport

Synthetic membrane nanopores made of DNA are promising systems to sense and control molecular transport in biosensing, sequencing, and synthetic cells. Lumen-tunable nanopore like the natural ion channels and systematically increasing the lumen size have become long-standing desires in developing nanopores. Here, we design a triangular DNA nanopore with a large tunable lumen. It allows in-situ transition from expanded state to contracted state without changing its stable triangular shape, and vice versa, in which specific DNA bindings as stimuli mechanically pinch and release the three corners of the triangular frame. Transmission electron microscopy images and molecular dynamics simulations illustrate the stable architectures and the high shape retention. Single-channel current recordings and fluorescence influx studies demonstrate the low-noise repeatable readouts and the controllable cross-membrane macromolecular transport. We envision that the proposed DNA nanopores could offer powerful tools in molecular sensing, drug delivery, and the creation of synthetic cells.

Detection of phosphorylation post-translational modifications along single peptides with nanopores

Current methods to detect post-translational modifications of proteins, such as phosphate groups, cannot measure single molecules or differentiate between closely spaced phosphorylation sites. We detect post-translational modifications at the single-molecule level on immunopeptide sequences with cancer-associated phosphate variants by controllably drawing the peptide through the sensing region of a nanopore. We discriminate peptide sequences with one or two closely spaced phosphates with 95% accuracy for individual reads of single molecules.

Recent advances in nanopore-based analysis for carbohydrates and glycoconjugates

Saccharides are not only the basic constituents and nutrients of living organisms, but also participate in various life activities, and play important roles in cell recognition, immune regulation, development, cancer, etc. The analysis of carbohydrates and glycoconjugates is a necessary means to study their transformations and physiological roles in living organisms. Existing detection techniques can hardly meet the requirements for the analysis of carbohydrates and glycoconjugates in complex matrices as they are expensive, involve complex derivatization, and are time-consuming. Nanopore sensing technology, which is amplification-free and label-free, and is a high-throughput process, provides a new solution for the identification and sequencing of carbohydrates and glycoconjugates. This review highlights recent advances in novel nanopore-based single-molecule sensing technologies for the detection of carbohydrates and glycoconjugates and discusses the advantages and challenges of nanopore sensing technologies. Finally, current issues and future perspectives are discussed with the aim of improving the performance of nanopores in complex media diagnostic applications, as well as providing a new direction for the quantification of glycan chains and the study of glycan chain properties and functions.

Deep Learning-Assisted Single-Molecule Detection of Protein Post-translational Modifications with a Biological Nanopore

Protein post-translational modifications (PTMs) play a crucial role in countless biological processes, profoundly modulating protein properties on both spatial and temporal scales. Protein PTMs have also emerged as reliable biomarkers for several diseases. However, only a handful of techniques are available to accurately measure their levels, capture their complexity at a single molecule level, and characterize their multifaceted roles in health and disease. Nanopore sensing provides high sensitivity for the detection of low-abundance proteins, holding the potential to impact single-molecule proteomics and PTM detection, in particular. Here, we demonstrate the ability of a biological nanopore, the pore-forming toxin aerolysin, to detect and distinguish α-synuclein-derived peptides bearing single or multiple PTMs, namely, phosphorylation, nitration, and oxidation occurring at different positions and in various combinations. The characteristic current signatures of the α-synuclein peptide and its PTM variants could be confidently identified by using a deep learning model for signal processing. We further demonstrate that this framework can quantify α-synuclein peptides at picomolar concentrations and detect the C-terminal peptides generated by digestion of full-length α-synuclein. Collectively, our work highlights the advantage of using nanopores as a tool for simultaneous detection of multiple PTMs and facilitates their use in biomarker discovery and diagnostics.

Evidence of Cytolysin A nanopore incorporation in mammalian cells assessed by a graphical user interface

Technologies capable of assessing cellular metabolites with high precision and temporal resolution are currently limited. Recent developments in the field of nanopore sensors allow the non-stochastic quantification of metabolites, where a nanopore is acting as an electrical transducer for selective substrate binding proteins (SBPs). Here we show that incorporation of the pore-forming toxin Cytolysin A (ClyA) into the plasma membrane of Chinese hamster ovary cells (CHO-K1) results in the appearance of single-channel conductance amenable to multiplexed automated patch-clamp (APC) electrophysiology. In CHO-K1 cells, SBPs modify the ionic current flowing though ClyA nanopores, thus demonstrating its potential for metabolite sensing of living cells. Moreover, we developed a graphical user interface for the analysis of the complex signals resulting from multiplexed APC recordings. This system lays the foundation to bridge the gap between recent advances in the nanopore field (e.g., proteomic and transcriptomic) and potential cellular applications.

Registration of Functioning of a Single Horseradish Peroxidase Macromolecule with a Solid-State Nanopore

Currently, nanopore-based technology for the determination of the functional activity of single enzyme molecules continues its development. The use of natural nanopores for studying single enzyme molecules is known. At that, the approach utilizing artificial solid-state nanopores is also promising but still understudied. Herein, we demonstrate the use of a nanotechnology-based approach for the investigation of the enzymatic activity of a single molecule of horseradish peroxidase with a solid-state nanopore. The artificial 5 nm solid-state nanopore has been formed in a 40 nm thick silicon nitride structure. A single molecule of HRP has been entrapped into the nanopore. The activity of the horseradish peroxidase (HRP) enzyme molecule inserted in the nanopore has been monitored by recording the time dependence of the ion current through the nanopore in the course of the reaction of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) oxidation reaction. We have found that in the process of ABTS oxidation in the presence of 2.5 mM hydrogen peroxide, individual HRP enzyme molecules are able to retain activity for approximately 700 s before a decrease in the ion current through the nanopore, which can be explained by structural changes of the enzyme.

Detection of Unfolded Cellular Proteins Using Nanochannel Arrays with Probe-Functionalized Outer Surfaces

Nanochannel technology has emerged as a powerful tool for label-free and highly sensitive detection of protein folding/unfolding status. However, utilizing the inner walls of a nanochannel array may cause multiple events even for proteins with the same conformation, posing challenges for accurate identification. Herein, we present a platform to detect unfolded proteins through electrical and optical signals using nanochannel arrays with outer-surface probes. The detection principle relies on the specific binding between the maleimide groups in outer-surface probes and the protein cysteine thiols that induce changes in the ionic current and fluorescence intensity responses of the nanochannel array. By taking advantage of this mechanism, the platform has the ability to differentiate folded and unfolded state of proteins based on the exposure of a single cysteine thiol group. The integration of these two signals enhances the reliability and sensitivity of the identification of unfolded protein states and enables the distinction between normal cells and Huntington's disease mutant cells. This study provides an effective approach for the precise analysis of proteins with distinct conformations and holds promise for facilitating the diagnoses of protein conformation-related diseases.

Ubiquitination detection techniques

Ubiquitination is an intricately regulated post-translational modification that involves the covalent attachment of ubiquitin to a substrate protein. The complex dynamic nature of the ubiquitination process regulates diverse cellular functions including targeting proteins for degradation, cell cycle, deoxyribonucleic acid (DNA) damage repair, and numerous cell signaling pathways. Ubiquitination also serves as a crucial mechanism in protein quality control. Dysregulation in ubiquitination could result in lethal disease conditions such as cancers and neurodegenerative diseases. Therefore, the ubiquitination cascade has become an attractive target for therapeutic interventions. Enormous efforts have been made to detect ubiquitination involving different detection techniques to better grasp the underlying molecular mechanisms of ubiquitination. This review discusses a wide range of techniques stretching from the simplest assays to real-time assays. This includes western blotting/immunoblotting, fluorescence assays, chemiluminescence assays, spectrophotometric assays, and nanopore sensing assays. This review compares these applications, and the inherent advantages and limitations.

Protein Sizing with 15 nm Conical Biological Nanopore YaxAB

Nanopores are promising single-molecule tools for the electrical identification and sequencing of biomolecules. However, the characterization of proteins, especially in real-time and in complex biological samples, is complicated by the sheer variety of sizes and shapes in the proteome. Here, we introduce a large biological nanopore, YaxAB for folded protein analysis. The 15 nm cis-opening and a 3.5 nm trans-constriction describe a conical shape that allows the characterization of a wide range of proteins. Molecular dynamics showed proteins are captured by the electroosmotic flow, and the overall resistance is largely dominated by the narrow trans constriction region of the nanopore. Conveniently, proteins in the 35-125 kDa range remain trapped within the conical lumen of the nanopore for a time that can be tuned by the external bias. Contrary to cylindrical nanopores, in YaxAB, the current blockade decreases with the size of the trapped protein, as smaller proteins penetrate deeper into the constriction region than larger proteins do. These characteristics are especially useful for characterizing large proteins, as shown for pentameric C-reactive protein (125 kDa), a widely used health indicator, which showed a signal that could be identified in the background of other serum proteins.

Improving Single-Molecule Antibody Detection Selectivity through Optimization of Peptide Epitope Presentation in OmpG Nanopore

Outer membrane protein G (OmpG) is a monomeric porin found in Escherichia coli, which possesses seven flexible loops. OmpG has been engineered as a nanopore sensor, where its loops can host affinity epitopes for selective detection of biological molecules. In this study, we investigated various loop positions to incorporate a FLAG peptide antigen epitope in the most flexible loop 6 and tested the efficacy and sensitivity of these nanopore constructs in antibody detection. We observed an OmpG construct containing inserted FLAG sequence, which exhibited strong interaction with anti-FLAG antibodies in flow cytometry; however, it could not translate molecule interactions into a readable signal in current recordings. Further optimization of the peptide presentation strategy by replacing specific sections of loop 6 sequences with the FLAG tag created a construct capable of generating unique and distinct signals when interacting with various monoclonal or polyclonal anti-FLAG clones IgG antibodies in the mixture. The peptide display scheme demonstrated in this study can be generalized for the engineering of OmpG sensors, which can be used for screening and validating positive clones during antibody development, as well as for real-time quality control of cell cultures in monoclonal antibody production.

Real-time label-free detection of dynamic aptamer-small molecule interactions using a nanopore nucleic acid conformational sensor

Nucleic acids can undergo conformational changes upon binding small molecules. These conformational changes can be exploited to develop new therapeutic strategies through control of gene expression or triggering of cellular responses and can also be used to develop sensors for small molecules such as neurotransmitters. Many analytical approaches can detect dynamic conformational change of nucleic acids, but they need labeling, are expensive, and have limited time resolution. The nanopore approach can provide a conformational snapshot for each nucleic acid molecule detected, but has not been reported to detect dynamic nucleic acid conformational change in response to small -molecule binding. Here we demonstrate a modular, label-free, nucleic acid-docked nanopore capable of revealing time-resolved, small molecule-induced, single nucleic acid molecule conformational transitions with millisecond resolution. By using the dopamine-, serotonin-, and theophylline-binding aptamers as testbeds, we found that these nucleic acids scaffolds can be noncovalently docked inside the MspA protein pore by a cluster of site-specific charged residues. This docking mechanism enables the ion current through the pore to characteristically vary as the aptamer undergoes conformational changes, resulting in a sequence of current fluctuations that report binding and release of single ligand molecules from the aptamer. This nanopore tool can quantify specific ligands such as neurotransmitters, elucidate nucleic acid-ligand interactions, and pinpoint the nucleic acid motifs for ligand binding, showing the potential for small molecule biosensing, drug discovery assayed via RNA and DNA conformational changes, and the design of artificial riboswitch effectors in synthetic biology.

Nanopore Single-molecule Analysis of Biomarkers: Providing Possible Clues to Disease Diagnosis

Biomarker detection has attracted increasing interest in recent years due to the minimally or non-invasive sampling process. Single entity analysis of biomarkers is expected to provide real-time and accurate biological information for early disease diagnosis and prognosis, which is critical to the effective disease treatment and is also important in personalized medicine. As an innovative single entity analysis method, nanopore sensing is a pioneering single-molecule detection technique that is widely used in analytical bioanalytical fields. In this review, we overview the recent progress of nanopore biomarker detection as new approaches to disease diagnosis. In highlighted studies, nanopore was focusing on detecting biomarkers of different categories of communicable and noncommunicable diseases, such as pandemic Covid-19, AIDS, cancers, neurologic diseases, etc. Various sensitive and selective nanopore detecting strategies for different types of biomarkers are summarized. In addition, the challenges, opportunities, and direction for future development of nanopore-based biomarker sensors are also discussed.

DNA nanostructure-assisted detection of carcinoembryonic antigen with a solid-state nanopore

In this paper, a novel detection technique for tumor marker carcinoembryonic antigen (CEA) has been developed by using a solid-state nanopore as a tool. The system utilizes the specific affinity between aptamer-modified magnetic Fe₃O₄ and CEA, rather than directly detecting the translocation of CEA through the nanopore. The aptamer-modified magnetic Fe₃O₄ was hybridized with tetrahedral DNA nanostructures (TDNs), and TDNs were released after CEA was added. We investigate the translocation behavior of individual TDNs through solid-state nanopores. The frequency of the blockage signals for TDNs is recorded for indirect detection of CEA. We realized the detection of CEA with a concentration as low as 0.1 nM and proved the specificity of the interaction between the aptamer. In addition, our designed nanopore sensing strategy can detect CEA in real samples.

The Mechanism of Overflow Amplitude in Nanopore Experiments and Its Application in Molecule Detection

The investigation of abnormal experimental phenomena observed in nanopore research improves our understanding of nanopores. In this article, we report and explore the unusual phenomenon that the amplitude of current blockage decreases beyond zero baseline (overflow amplitudes), which was observed in the translocation behavior of 100 bp double-stranded DNA molecules through SiN_x nanopores. In our experiments, the overflow amplitude decreases with the increase of salt concentration and also decreases when the dwell time is shortened as the normalized amplitude of the overflow current showed a reduction with the increase of voltage. Upon analyzing the electric double layer meanwhile, the overflow amplitudes were shown to be positively correlated with the depth of the electric double layer and the duration of interaction between biological molecules. The formation of overflow amplitude can be attributed to the double electric layer ionic perturbation and reconfiguration, which are the results of the interaction between the biomolecule and the electric bilayer. The validation of the assumption using biomolecules containing different charges demonstrated that the overflow amplitude increased with the increase of the charge. It was concluded that proteins that pass through the nanopore with different orientation were differentiated based on their different overflow amplitude patterns. The investigation of overflow amplitude helps to enhance the understanding and the performance of nanopores.

Nanopore Detection Assisted DNA Information Processing

The deoxyribonucleotide (DNA) molecule is a stable carrier for large amounts of genetic information and provides an ideal storage medium for next-generation information processing technologies. Technologies that process DNA information, representing a cross-disciplinary integration of biology and computer techniques, have become attractive substitutes for technologies that process electronic information alone. The detailed applications of DNA technologies can be divided into three components: storage, computing, and self-assembly. The quality of DNA information processing relies on the accuracy of DNA reading. Nanopore detection allows researchers to accurately sequence nucleotides and is thus widely used to read DNA. In this paper, we introduce the principles and development history of nanopore detection and conduct a systematic review of recent developments and specific applications in DNA information processing involving nanopore detection and nanopore-based storage. We also discuss the potential of artificial intelligence in nanopore detection and DNA information processing. This work not only provides new avenues for future nanopore detection development, but also offers a foundation for the construction of more advanced DNA information processing technologies.

PlyAB Nanopores Detect Single Amino Acid Differences in Folded Haemoglobin from Blood

The real‐time identification of protein biomarkers is crucial for the development of point‐of‐care and portable devices. Here, we use a PlyAB biological nanopore to detect haemoglobin (Hb) variants. Adult haemoglobin (HbA) and sickle cell anaemia haemoglobin (HbS), which differ by just one amino acid, were distinguished in a mixture with more than 97 % accuracy based on individual blockades. Foetal Hb, which shows a larger sequence variation, was distinguished with near 100 % accuracy. Continuum and Brownian dynamics simulations revealed that Hb occupies two energy minima, one near the inner constriction and one at the trans entry of the nanopore. Thermal fluctuations, the charge of the protein, and the external bias influence the dynamics of Hb within the nanopore, which in turn generates the unique ionic current signal in the Hb variants. Finally, Hb was counted from blood samples, demonstrating that direct discrimination and quantification of Hb from blood using nanopores, is feasible.

Application of nanopore sensors for biomolecular interactions and drug discovery

Biomolecular interactions, including protein-protein, protein-nucleic acid, and protein/nucleic acid-ligand interactions, play crucial roles in various cellular signaling and biological processes, and offer attractive therapeutic targets in numerous human diseases. Currently, drug discovery is limited by the low efficiency and high cost of conventional ensemble-averaging-based techniques for biomolecular interaction analysis and high-throughput drug screening. Nanopores are an emerging technology for single-molecule sensing of biomolecules. Owing to the robust advantages of single-molecule sensing, nanopore sensors have contributed tremendously to nucleic acid sequencing and disease diagnostics. In this minireview, we summarize the recent developments and outlooks in single-molecule sensing of various biomolecular interactions for drug discovery applications using biological and solid-state nanopore sensors.

Quantification of Protein Glycosylation Using Nanopores

Although nanopores can be used for single-molecule sequencing of nucleic acids using low-cost portable devices, the characterization of proteins and their modifications has yet to be established. Here, we show that hydrophilic or glycosylated peptides translocate too quickly across FraC nanopores to be recognized. However, high ionic strengths (i.e., 3 M LiCl) and low pH (i.e., pH 3) together with using a nanopore with a phenylalanine at its constriction allows the recognition of hydrophilic peptides, and to distinguish between mono- and diglycosylated peptides. Using these conditions, we devise a nanopore method to detect, characterize, and quantify post-translational modifications in generic proteins, which is one of the pressing challenges in proteomic analysis.

Chemistry solutions to facilitate nanopore detection and analysis

Characteristic ionic current modulations will be produced in a single molecule manner during the communication of individual molecules with a nanopore. Hence, the information regarding the length, composition, and structure of a molecule can be extracted from deciphering the electrical message. However, until now, achieving a satisfactory resolution for observation and quantification of a target analyte in a complex system remains a nontrivial task. In this review, we summarize the progress and especially the recent advance in utilizing chemistry solutions to facilitate nanopore detection and analysis. The discussed chemistry solutions are classified into several major categories, including covalent/non-covalent chemistry, redox chemistry, displacement chemistry, back titration chemistry, chelation chemistry, hydrolysis-chemistry, and click chemistry. Considering the significant success of using chemical reaction-assisted nanopore sensing strategies to improve sensor sensitivity & selectivity and to study various topics, other non-chemistry based methodologies can undoubtedly be employed by nanopore sensors to explore new applications in the interdisciplinary area of chemistry, biology, materials, and nanotechnology.

Label-Free Optical Analysis of Biomolecules in Solid-State Nanopores: Toward Single-Molecule Protein Sequencing

Sequence identification of peptides and proteins is central to proteomics. Protein sequencing is mainly conducted by insensitive mass spectroscopy because proteins cannot be amplified, which hampers applications such as single-cell proteomics and precision medicine. The commercial success of portable nanopore sequencers for single DNA molecules has inspired extensive research and development of single-molecule techniques for protein sequencing. Among them, three challenges remain: (1) discrimination of the 20 amino acids as building blocks of proteins; (2) unfolding proteins; and (3) controlling the motion of proteins with nonuniformly charged sequences. In this context, the emergence of label-free optical analysis techniques for single amino acids and peptides by solid-state nanopores shows promise for addressing the first challenge. In this Perspective, we first discuss the current challenges of single-molecule fluorescence detection and nanopore resistive pulse sensing in a protein sequencing. Then, label-free optical methods are described to show how they address the single-amino-acid identification within single peptides. They include localized surface plasmon resonance detection and surface-enhanced Raman spectroscopy on plasmonic nanopores. Notably, we report new data to show the ability of plasmon-enhanced Raman scattering to record and discriminate the 20 amino acids at a single-molecule level. In addition, we discuss briefly the manipulation of molecule translocation and liquid flow in plasmonic nanopores for controlling molecule movement to allow high-resolution reading of protein sequences. We envision that a combination of Raman spectroscopy with plasmonic nanopores can succeed in single-molecule protein sequencing in a label-free way.

Cataloguing the proteome: Current developments in single-molecule protein sequencing

The cellular proteome is complex and dynamic, with proteins playing a critical role in cell-level biological processes that contribute to homeostasis, stimuli response, and disease pathology, among others. As such, protein analysis and characterization are of extreme importance in both research and clinical settings. In the last few decades, most proteomics analysis has relied on mass spectrometry, affinity reagents, or some combination thereof. However, these techniques are limited by their requirements for large sample amounts, low resolution, and insufficient dynamic range, making them largely insufficient for the characterization of proteins in low-abundance or single-cell proteomic analysis. Despite unique technical challenges, several single-molecule protein sequencing (SMPS) technologies have been proposed in recent years to address these issues. In this review, we outline several approaches to SMPS technologies and discuss their advantages, limitations, and potential contributions toward an accurate, sensitive, and high-throughput platform.

Functionalised nanopores: chemical and biological modifications

Nanopore technology has established itself as a powerful tool for single-molecule studies. By analysing changes in the ion current flowing through a single transmembrane channel, a wealth of molecular information can be elucidated. Early studies utilised nanopore technology for sensing applications, and subsequent developments have diversified its remit. Nanopores can be synthetic, solid-state, or biological in origin, but recent work has seen these boundaries blurred as hybrid functionalised pores emerge. The modification of existing pores and the construction of novel synthetic pores has been an enticing goal for creating systems with tailored properties and functionality. Here, we explore chemically functionalised biological pores and the bio-inspired functionalisation of solid-state pores, highlighting how the convergence of these domains provides enhanced functionality.

The convergence of chemistry, biology, and solid-state approaches enables the construction hybrid nanopores with enhanced single-molecule applications.

Macromolecule sensing and tumor biomarker detection by harnessing terminal size and hydrophobicity of viral DNA packaging motor channels into membranes and flow cells

Biological nanopores for single-pore sensing have the advantage of size homogeneity, structural reproducibility, and channel amenability. In order to translate this to clinical applications, the functional biological nanopore must be inserted into a stable system for high-throughput analysis. Here we report factors that control the rate of pore insertion into polymer membrane and analyte translocation through the channel of viral DNA packaging motors of Phi29, T3 and T7. The hydrophobicity of aminol or carboxyl terminals and their relation to the analyte translocation were investigated. It was found that both the size and the hydrophobicity of the pore terminus are critical factors for direct membrane insertion. An N-terminus or C-terminus hydrophobic mutation is crucial for governing insertion orientation and subsequent macromolecule translocation due to the one-way traffic property. The N- or C-modification led to two different modes of application. The C-terminal insertion permits translocation of analytes such as peptides to enter the channel through the N terminus, while N-terminus insertion prevents translocation but offers the measurement of gating as a sensing parameter, thus generating a tool for detection of markers. A urokinase-type Plasminogen Activator Receptor (uPAR) binding peptide was fused into the C-terminal of Phi29 nanopore to serve as a probe for uPAR protein detection. The uPAR has proven to be a predictive biomarker in several types of cancer, including breast cancer. With an N-terminal insertion, the binding of the uPAR antigen to individual peptide probe induced discretive steps of current reduction due to the induction of channel gating. The distinctive current signatures enabled us to distinguish uPAR positive and negative tumor cell lines. This finding provides a theoretical basis for a robust biological nanopore sensing system for high-throughput macromolecular sensing and tumor biomarker detection.

Allosteric Switching of Calmodulin in a Mycobacterium smegmatis porin A (MspA) Nanopore-Trap

Recent developments concerning large protein nanopores suggest a new approach to structure profiling of native folded proteins. In this work, the large vestibule of Mycobacterium smegmatis porin A (MspA) and calmodulin (CaM), a Ca²⁺ -binding protein, were used in the direct observation of the protein structure. Three conformers, including the Ca²⁺ -free, Ca²⁺ -bound, and target peptide-bound states of CaM, were unambiguously distinguished. A disease related mutant, CaM D129G was also discriminated by MspA, revealing how a single amino acid replacement can interfere with the Ca²⁺ -binding capacity of the whole protein. The binding capacity and aggregation effect of CaM induced by different ions (Mg²⁺ /Sr²⁺ /Ba²⁺ /Ca²⁺ /Pb²⁺ /Tb³⁺ ) were also investigated and the stability of MspA in extreme conditions was evaluated. This work demonstrates the most systematic single-molecule investigation of different allosteric conformers of CaM, acknowledging the high sensing resolution offered by the MspA nanopore trap.

Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis

Proteins carry out life's essential functions. Comprehensive proteome analysis technologies are thus required for a full understanding of the operating principles of biological systems. While current proteomics techniques suffer from limitations in sensitivity and/or throughput, nanopore technology has the potential to enable de novo protein identification through single-molecule sequencing. However, a significant barrier to achieving this goal is controlling protein/peptide translocation through the nanopore sensor for processive strand analysis. Here, we review recent approaches that use a range of techniques, from oligonucleotide conjugation to molecular motors, aimed at driving protein strands and peptides through protein nanopores. We further discuss site-specific protein conjugation chemistry that could be combined with these translocation approaches as future directions to achieve single-molecule protein detection and sequencing of native proteins.

Enhanced identification of Tau acetylation and phosphorylation with an engineered aerolysin nanopore

Posttranslational modifications (PTMs) affect protein function/dysfunction, playing important roles in the occurrence and development of tauopathies including Alzheimer's disease. PTM detection is significant and still challenging due to the requirements of high sensitivity to identify the subtle structural differences between modifications. Herein, in terms of the unique geometry of the aerolysin (AeL) nanopore, we elaborately engineered a T232K AeL nanopore to detect the acetylation and phosphorylation of Tau segment (Pep). By replacing neutral threonine (T) with positively charged lysine (K) at the 232 sites, the T232K and K238 rings of this engineered T232K AeL nanopore corporately work together to enhance electrostatic trapping of the acetylated and phosphorylated Tau peptides. Translocation speed of the monophosphorylated Pep-P was decelerated by up to 46 folds compared to the wild-type (WT) AeL nanopore. The prolonged residences within the T232K AeL nanopore enabled to simultaneously identify the monoacetylated Pep-Ac, monophosphorylated Pep-P, di-modified Pep-P-Ac and non-modified Pep. The tremendous potential is demonstrated for PTM sensing by manipulating non-covalent interactions between nanopores and single analytes.

Real-Time and Label-Free Measurement of Deubiquitinase Activity with a MspA Nanopore

Covalently attaching ubiquitin (Ub) to cellular proteins as a post-translational modification can result in altered function of modified proteins. Enzymes regulating Ub as a post-translational modification, such as ligases and deubiquitinases, are challenging to characterize in part due to the low throughput of in-vitro assays. Single-molecule nanopore based assays have the advantage of detecting proteins with high specificity and resolution, and in a label-free, real-time fashion. Here we demonstrate the use of a MspA nanopore for discriminating and quantifying Ub proteins. We further applied the MspA pore to measure the Ub-chain disassembly activity of UCH37, a proteasome associated deubiquitinase. The implementation of this MspA system into nanopore arrays could enable high throughput characterizations of unknown deubiquitinases as well as drug screening against disease related enzymes.

Recent advances in biological nanopores for nanopore sequencing, sensing and comparison of functional variations in MspA mutants

Biological nanopores are revolutionizing human health by the great myriad of detection and diagnostic skills. Their nano-confined area and ingenious shape are suitable to investigate a diverse range of molecules that were difficult to identify with the previous techniques. Additionally, high throughput and label-free detection of target analytes instigated the exploration of new bacterial channel proteins such as Fragaceatoxin C (FraC), Cytolysin A (ClyA), Ferric hydroxamate uptake component A (FhuA) and Curli specific gene G (CsgG) along with the former ones, like α-hemolysin (αHL), Mycobacterium smegmatis porin A (MspA), aerolysin, bacteriophage phi 29 and Outer membrane porin G (OmpG). Herein, we discuss some well-known biological nanopores but emphasize on MspA and compare the effects of site-directed mutagenesis on the detection ability of its mutants in view of the surface charge distribution, voltage threshold and pore-analyte interaction. We also discuss illustrious and latest advances in biological nanopores for past 2-3 years due to limited space. Last but not the least, we elucidate our perspective for selecting a biological nanopore and propose some future directions to design a customized nanopore that would be suitable for DNA sequencing and sensing of other nontrivial molecules in question.

Detection of single peptide with only one amino acid modification via electronic fingerprinting using reengineered durable channel of Phi29 DNA packaging motor

Protein post-translational modification (PTM) is crucial to modulate protein interactions and activity in various biological processes. Emerging evidence has revealed PTM patterns participate in the pathology onset and progression of various diseases. Current PTM identification relies mainly on mass spectrometry-based approaches that limit the assessment to the entire protein population in question. Here we report a label-free method for the detection of the single peptide with only one amino acid modification via electronic fingerprinting using reengineered durable channel of phi29 DNA packaging motor, which bears the deletion of 25-amino acids (AA) at the C-terminus or 17-AA at the internal loop of the channel. The mutant channels were used to detect propionylation modification via single-molecule fingerprinting in either the traditional patch-clamp or the portable MinION™ platform of Oxford Nanopore Technologies. Up to 2000 channels are available in the MinION™ Flow Cells. The current signatures and dwell time of individual channels were identified. Peptides with only one propionylation were differentiated. Excitingly, identification of single or multiple modifications on the MinION™ system was achieved. The successful application of PTM differentiation on the MinION™ system represents a significant advance towards developing a label-free and high-throughput detection platform utilizing nanopores for clinical diagnosis based on PTM.

Instrumentational implementation for parallelized nanopore electrochemical measurements

Nanopore electrochemistry, as one of the promising tools for single molecule sensing, has proved its capability in DNA sequencing and protein analysis. To achieve a high resolution for obtaining molecular information, the nanopore electrochemical technique not only urgently requires an appropriate nanopore sensing interface with atomic resolution but also requires advanced instrumentation and its related data processing methods. In order to reveal the fundamental biological process and process the point-of-care diagnosis, it is necessary to use a nanopore sensing instrument with a high amperometric and temporal resolution as well as high throughput. The development of the instrumentation requires multi-disciplinary collaboration involving preparing a sensitive nanopore interface, low-noise circuit design, and intelligent data analysis. In this review, we have summarized the recent improvements in the nanopore sensing interface as well as discussed the higher throughput achieved by nanopore arrays and intelligent nanopore data analysis methods. The parallelized nanopore instrumentation could be popularized to all ranges of single-molecule applications.

The emerging landscape of single-molecule protein sequencing technologies

Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.

DNA barcodes using a double nanopore system

The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbone, we demonstrate that due to large variation of velocities of the chain segments between the tags, it is inevitable to under/overestimate the genetic lengths from the experimental current blockade and time of flight data. We demonstrate that it is the tension propagation along the chain's backbone that governs the motion of the entire chain and is the key element to explain the non uniformity and disparate velocities of the tags and DNA monomers under translocation that introduce errors in measurement of the length segments between protein tags. Using simulation data we further demonstrate that it is important to consider the dynamics of the entire chain and suggest methods to accurately decipher barcodes. We introduce and validate an interpolation scheme using simulation data for a broad distribution of tag separations and suggest how to implement the scheme experimentally.

Nanopores: a versatile tool to study protein dynamics

Proteins are the active workhorses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now readily available, observing the functional cycle of proteins - involving conformational changes and interactions - remains very challenging, e.g., due to ensemble averaging. However, time-resolved information is crucial to gain a mechanistic understanding of protein function. Single-molecule techniques such as FRET and force spectroscopies provide answers but can be limited by the required labelling, a narrow time bandwidth, and more. Here, we describe electrical nanopore detection as a tool for probing protein dynamics. With a time bandwidth ranging from microseconds to hours, nanopore experiments cover an exceptionally wide range of timescales that is very relevant for protein function. First, we discuss the working principle of label-free nanopore experiments, various pore designs, instrumentation, and the characteristics of nanopore signals. In the second part, we review a few nanopore experiments that solved research questions in protein science, and we compare nanopores to other single-molecule techniques. We hope to make electrical nanopore sensing more accessible to the biochemical community, and to inspire new creative solutions to resolve a variety of protein dynamics - one molecule at a time.

PROTACs, molecular glues and bifunctionals from bench to bedside: Unlocking the clinical potential of catalytic drugs

The vast majority of currently marketed drugs rely on small molecules with an 'occupancy-driven' mechanism of action (MOA). Therefore, the efficacy of these therapeutics depends on a high degree of target engagement, which often requires high dosages and enhanced drug exposure at the target site, thus increasing the risk of off-target toxicities (Churcher, 2018 [1]). Although small molecule drugs have been successfully used as treatments for decades, tackling a variety of disease-relevant targets with a defined binding site, many relevant therapeutic targets remain challenging to drug due, for example, to lack of well-defined binding pockets or large protein-protein interaction (PPI) interfaces which resist interference (Dang et al., 2017 [2]). In the quest for alternative therapeutic approaches to address different pathologies and achieve enhanced efficacy with reduced side effects, ligand-induced targeted protein degradation (TPD) has gained the attention of many research groups both in academia and in industry in the last two decades. This therapeutic modality represents a novel paradigm compared to conventional small-molecule inhibitors. To pursue this strategy, heterobifunctional small molecule degraders, termed PROteolysis TArgeting Chimeras (PROTACs) have been devised to artificially redirect a protein of interest (POI) to the cellular protein homeostasis machinery for proteasomal degradation (Chamberlain et al., 2019 [3]). In this chapter, the development of PROTACs will first be discussed providing a historical perspective in parallel to the experimental progress made to understand this novel therapeutic modality. Furthermore, common strategies for PROTAC design, including assays and troubleshooting tips will be provided for the reader, before presenting a compendium of all PROTAC targets reported in the literature to date. Due to the recent advancement of these molecules into clinical trials, consideration of pharmacokinetics and pharmacodynamic properties will be introduced, together with the biotech landscape that has developed from the success of PROTACs. Finally, an overview of subsequent strategies for targeted protein degradation will be presented, concluding with further scientific quests triggered by the invention of PROTACs.

Quantitative Measurements of Protein Volume and Concentration using Hydrogel-Backed Nanopores

Accurate identification and quantification of proteins in solution using nanopores is technically challenging in part because of the large fraction of missed translocation events due to short event times and limitations of conventional current amplifiers. Previously, we have shown that a nanopore interfaced with a poly(ethylene glycol)-dimethacrylate hydrogel with an average mesh size of 3.1 nm significantly enhances the protein residence time within the pore, reducing the number of missed events. We used hydrogel-backed nanopores to sense unlabeled proteins as small as 5.5 kDa in size and 10 fM in concentration. We show that the frequency of protein translocation events linearly scales with bulk concentration over a wide range of concentrations and that unknown protein concentrations can be determined from an interpolation of the frequency-concentration curve with less than 10% error. Further, we show an iterative method to determine a protein volume accurately from measurement data for proteins with a diameter comparable to a nanopore diameter. Our measurements and analysis also suggest several competing mechanisms for the detection enhancement enabled by the presence of the hydrogel.

Single-molecule analysis of interaction between p53TAD and MDM2 using aerolysin nanopores

Protein-protein interactions (PPIs) are regarded as important, but undruggable targets. Intrinsically disordered p53 transactivation domain (p53TAD) mediates PPI with mouse double minute 2 (MDM2), which is an attractive anticancer target for therapeutic intervention. Here, using aerolysin nanopores, we probed the p53TAD peptide/MDM2 interaction and its modulation by small-molecule PPI inhibitors or p53TAD phosphorylation. Although the p53TAD peptide showed short-lived (<100 ms) translocation, the protein complex induced the characteristic extraordinarily long-lived (0.1 s ∼ tens of min) current blockage, indicating that the MDM2 recruitment by p53TAD peptide almost fully occludes the pore. Simultaneously, the protein complex formation substantially reduced the event frequency of short-lived peptide translocation. Notably, the addition of small-molecule PPI inhibitors, Nutlin-3 and AMG232, or Thr18 phosphorylation of p53TAD peptide, were able to diminish the extraordinarily long-lived events and restore the short-lived translocation of the peptide rescued from the complex. Taken together, our results elucidate a novel mechanism of single-molecule sensing for analyzing PPIs and their inhibitors using aerolysin nanopores. This novel methodology may contribute to remarkable improvements in drug discovery targeted against undruggable PPIs.

Strategies for enzymological studies and measurements of biological molecules with the cytolysin A nanopore

Pore-forming toxins are used in a variety of biotechnological applications. Typically, individual membrane proteins are reconstituted in artificial lipid bilayers where they form water-filled nanoscale apertures (nanopores). When a voltage is applied, the ionic current passing through a nanopore can be used for example to sequence biopolymers, identify molecules, or to study chemical or enzymatic reactions at the single-molecule level. Here we present strategies for studying individual enzymes and measuring molecules, also in highly complex biological samples such as blood.

X-ray crystallography shines a light on pore-forming toxins

A common form of cellular attack by pathogenic bacteria is to secrete pore-forming toxins (PFTs). Capable of forming transmembrane pores in various biological membranes, PFTs have also been identified in a diverse range of other organisms such as sea anemones, earthworms and even mushrooms and trees. The mechanism of pore formation by PFTs is associated with substantial conformational changes in going from the water-soluble to transmembrane states of the protein. The determination of the crystal structures for numerous PFTs has shed much light on our understanding of these proteins. Other than elucidating the atomic structural details of PFTs and the conformational changes that must occur for pore formation, crystal structures have revealed structural homology that has led to the discovery of new PFTs and new PFT families. Here we review some key crystallographic results together with complimentary approaches for studying PFTs. We discuss how these studies have impacted our understanding of PFT function and guided research into biotechnical applications.

Autonomous and Active Transport Operated by an Entropic DNA Piston

We present a synthetic nanoscale piston that uses chemical energy to perform molecular transport against an applied bias. Such a device comprises a 13 by 5 nm protein cylinder, embedded in a biological membrane enclosing a single-stranded DNA (ssDNA) rod. Hybridization with DNA cargo rigidifies the rod, allowing for transport of a selected DNA molecule across the nanopore. A strand displacement reaction from ssDNA fuel on the other side of the membrane then liberates the DNA cargo back into solution and regenerates the initial configuration. The entropic penalty of ssDNA confinement inside the nanopore drives DNA transport regardless of the applied bias. Multiple automated and reciprocating cycles are observed, in which the DNA piston moves through the 10 nm length of the nanopore. In every cycle, a single DNA molecule is transported across the nanopore against an external bias force, which is the hallmark of biological transporters.