Insights into protein sequencing with an α-Hemolysin nanopore by atomistic simulations

Molecular Determinants of Current Blockade Produced by Peptide Transport Through a Nanopore

The nanopore sensing method holds the promise of delivering a single molecule technology for identification of biological proteins, direct detection of post-translational modifications, and perhaps de novo determination of a protein's amino acid sequence. The key quantity measured in such nanopore sensing experiments is the magnitude of the ionic current passing through a nanopore blocked by a polypeptide chain. Establishing a relationship between the amino acid sequence of a peptide fragment confined within a nanopore and the blockade current flowing through the nanopore remains a major challenge for realizing the nanopore protein sequencing. Using the results of all-atom molecular dynamics simulations, here we compare nanopore sequencing of DNA with nanopore sequencing of proteins. We then delineate the factors affecting the blockade current modulation by the peptide sequence, showing that the current can be determined by (i) the steric footprint of an amino acid, (ii) its interactions with the pore wall, (iii) the local stretching of a polypeptide chain, and (iv) the local enhancement of the ion concentration at the nanopore constriction. We conclude with a brief discussion of the prospects for purely computational prediction of the blockade currents.

Hydrophobically gated memristive nanopores for neuromorphic applications

Signal transmission in the brain relies on voltage-gated ion channels, which exhibit the electrical behaviour of memristors, resistors with memory. State-of-the-art technologies currently employ semiconductor-based neuromorphic approaches, which have already demonstrated their efficacy in machine learning systems. However, these approaches still cannot match performance achieved by biological neurons in terms of energy efficiency and size. In this study, we utilise molecular dynamics simulations, continuum models, and electrophysiological experiments to propose and realise a bioinspired hydrophobically gated memristive nanopore. Our findings indicate that hydrophobic gating enables memory through an electrowetting mechanism, and we establish simple design rules accordingly. Through the engineering of a biological nanopore, we successfully replicate the characteristic hysteresis cycles of a memristor and construct a synaptic device capable of learning and forgetting. This advancement offers a promising pathway for the realization of nanoscale, cost- and energy-effective, and adaptable bioinspired memristors.

Engineering Biological Nanopore Approaches toward Protein Sequencing

Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.

Oligomer Dynamics of LL-37 Truncated Fragments Probed by α-Hemolysin Pore and Molecular Simulations

Oligomerization of antimicrobial peptides (AMPs) is critical in their effects on pathogens. LL-37 and its truncated fragments are widely investigated regarding their structures, antimicrobial activities, and application, such as developing new antibiotics. Due to the small size and weak intermolecular interactions of LL-37 fragments, it is still elusive to establish the relationship between oligomeric states and antimicrobial activities. Here, an α-hemolysin nanopore, mass spectrometry (MS), and molecular dynamic (MD) simulations are used to characterize the oligomeric states of two LL-37 fragments. Nanopore studies provide evidence of trapping events related to the oligomer formation and provide further details on their stabilities, which are confirmed by MS and MD simulations. Furthermore, simulation results reveal the molecular basis of oligomer dynamics and states of LL-37 fragments. This work provides unique insights into the relationship between the oligomer dynamics of AMPs and their antimicrobial activities at the single-molecule level. The study demonstrates how integrating methods allows deciphering single molecule level understanding from nanopore sensing approaches.

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.

Detection of Biological Molecules Using Nanopore Sensing Techniques

Modern biomedical sensing techniques have significantly increased in precision and accuracy due to new technologies that enable speed and that can be tailored to be highly specific for markers of a particular disease. Diagnosing early-stage conditions is paramount to treating serious diseases. Usually, in the early stages of the disease, the number of specific biomarkers is very low and sometimes difficult to detect using classical diagnostic methods. Among detection methods, biosensors are currently attracting significant interest in medicine, for advantages such as easy operation, speed, and portability, with additional benefits of low costs and repeated reliable results. Single-molecule sensors such as nanopores that can detect biomolecules at low concentrations have the potential to become clinically relevant. As such, several applications have been introduced in this field for the detection of blood markers, nucleic acids, or proteins. The use of nanopores has yet to reach maturity for standardization as diagnostic techniques, however, they promise enormous potential, as progress is made into stabilizing nanopore structures, enhancing chemistries, and improving data collection and bioinformatic analysis. This review offers a new perspective on current biomolecule sensing techniques, based on various types of nanopores, challenges, and approaches toward implementation in clinical settings.

Portable nanopore-sequencing technology: Trends in development and applications

Sequencing technology is the most commonly used technology in molecular biology research and an essential pillar for the development and applications of molecular biology. Since 1977, when the first generation of sequencing technology opened the door to interpreting the genetic code, sequencing technology has been developing for three generations. It has applications in all aspects of life and scientific research, such as disease diagnosis, drug target discovery, pathological research, species protection, and SARS-CoV-2 detection. However, the first- and second-generation sequencing technology relied on fluorescence detection systems and DNA polymerization enzyme systems, which increased the cost of sequencing technology and limited its scope of applications. The third-generation sequencing technology performs PCR-free and single-molecule sequencing, but it still depends on the fluorescence detection device. To break through these limitations, researchers have made arduous efforts to develop a new advanced portable sequencing technology represented by nanopore sequencing. Nanopore technology has the advantages of small size and convenient portability, independent of biochemical reagents, and direct reading using physical methods. This paper reviews the research and development process of nanopore sequencing technology (NST) from the laboratory to commercially viable tools; discusses the main types of nanopore sequencing technologies and their various applications in solving a wide range of real-world problems. In addition, the paper collates the analysis tools necessary for performing different processing tasks in nanopore sequencing. Finally, we highlight the challenges of NST and its future research and application directions.

Machine Learning Prediction of the Transmission Function for Protein Sequencing with Graphene Nanoslit

Protein sequencing has rapidly changed the landscape of healthcare and life science by accelerating the growth of diagnostics and personalized medicines for a variety of fatal diseases. Next-generation nanopore/nanoslit sequencing is promising to achieve single-molecule resolution with chromosome-size-long readability. However, due to inherent complexity, high-throughput sequencing of all 20 amino acids demands different approaches. Aiming to accelerate the detection of amino acids, a general machine learning (ML) method has been developed for quick and accurate prediction of the transmission function for amino acid sequencing. Among the utilized ML models, the XGBoost regression model is found to be the most effective algorithm for fast prediction of the transmission function with a very low test root-mean-square error (RMSE ∼0.05). In addition, using the random forest ML classification technique, we are able to classify the neutral amino acids with a prediction accuracy of 100%. Therefore, our approach is an initiative for the prediction of the transmission function through ML and can provide a platform for the quick identification of amino acids with high accuracy.

Aerolysin nanopore-based identification of proteinogenic amino acids using a bipolar peptide probe

Nanopore technology has attracted extensive attention due to its rapid, highly sensitive, and label-free performance. In this study, we aimed to identify proteinogenic amino acids using a wild-type aerolysin nanopore. Specifically, bipolar peptide probes were synthesised by linking four aspartic acid residues to the N-terminal and five arginine residues to the C-terminal of individual amino acids. With the help of the bipolar peptide carrier, 9 proteinogenic amino acids were reliably recognised based on current blockade and dwell time using an aerolysin nanopore. Furthermore, by changing the charge of the peptide probe, two of the five unrecognized amino acids above mentioned were identified. These findings promoted the application of aerolysin nanopores in proteinogenic amino acid recognition.

Ab Initio Properties of Hybrid Cove-Edged Graphene Nanoribbons as Metallic Electrodes for Peptide Sequencing via Transverse Tunneling Current

Recently synthesized metallic cove-edged graphene nanoribbons are considered for use as one-dimensional (1D) electrodes for ideal atomistically resolved recognition of amino acids. To this purpose a narrow nanogap device is considered, and the transversal tunneling current flowing across it is calculated during the translocation of a model Gly homopeptide using the nonequilibrium Green function scheme, based on density functional theory. We show that the signal collected from the metallic spin states is characterized by a double peak per residue in analogy with the results obtained with 1D graphene nanoribbon template electrodes. The presented results pave the way for experimentally feasible atomistically resolved tunneling current recognition using metallic edge engineered graphene electrodes obtained by bottom-up fabrication strategies.

Current Rectification and Ionic Selectivity of α-Hemolysin: Coarse-Grained Molecular Dynamics Simulations

In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since they allow longer and faster simulations. We performed coarse-grained molecular dynamics of the ionic transport through the α-hemolysin protein nanopore, inserted into a lipid bilayer surrounded by solvent and ions. For this purpose, we used the MARTINI coarse-grained force field and its polarizable water solvent (PW). Moreover, the electric potential difference applied experimentally was mimicked by the application of an electric field to the system. We present, in this study, the results of 1.5 μs long-molecular dynamics simulations of 12 different systems for which different charged amino acids were neutralized, each of them in the presence of nine different electric fields ranging between ±0.04 V/nm (a total of around 100 simulations). We were able to observe several specific features of this pore, current asymmetry and anion selectivity, in agreement with previous studies and experiments, and we identified the charged amino acids responsible for these current behaviors, therefore validating our coarse-grain approach to study ionic transport through nanopores. We also propose a microscopic explanation of these ionic current features using ionic density maps.

Conical nanopores highlight the pro-aggregating effects of pyrimethanil fungicide on Aβ(1-42) peptides and dimeric splitting phenomena

The Aβ(1-42) aggregation is a key event in the physiopathology of Alzheimer's disease (AD). Exogenous factors such as environmental pollutants, and more particularly pesticides, can corrupt Aβ(1-42) assembly and could influence the occurrence and pathophysiology of AD. However, pesticide involvement in the early stages of Aβ(1-42) aggregation is still unknown. Here, we employed conical track-etched nanopore in order to analyse the Aβ(1-42) fibril formation in the presence of pyrimethanil, a widely used fungicide belonging to the anilinopyrimidine class. Our results evidenced a pro-aggregating effect of pyrimethanil on Aβ(1-42). Aβ(1-42) assemblies were successfully detected using conical nanopore coated with PEG. Using an analytical model, the large current blockades observed (>0.7) were assigned to species with size close to the sensing pore. The long dwell times (hundreds ms scale) were interpreted by the possible interactions amyloid/PEG using molecular dynamic simulation. Such interaction could leave until splitting phenomena of the dimer structure. Our work also evidences that the pyrimethanil induce an aggregation of Aβ(1-42) mechanism in two steps including the reorganization prior the elongation phase.

Nanopores in Graphene and Other 2D Materials: A Decade's Journey toward Sequencing

Nanopore techniques offer a low-cost, label-free, and high-throughput platform that could be used in single-molecule biosensing and in particular DNA sequencing. Since 2010, graphene and other two-dimensional (2D) materials have attracted considerable attention as membranes for producing nanopore devices, owing to their subnanometer thickness that can in theory provide the highest possible spatial resolution of detection. Moreover, 2D materials can be electrically conductive, which potentially enables alternative measurement schemes relying on the transverse current across the membrane material itself and thereby extends the technical capability of traditional ionic current-based nanopore devices. In this review, we discuss key advances in experimental and computational research into DNA sensing with nanopores built from 2D materials, focusing on both the ionic current and transverse current measurement schemes. Challenges associated with the development of 2D material nanopores toward DNA sequencing are further analyzed, concentrating on lowering the noise levels, slowing down DNA translocation, and inhibiting DNA fluctuations inside the pores. Finally, we overview future directions of research that may expedite the emergence of proof-of-concept DNA sequencing with 2D material nanopores.

Controlled movement of ssDNA conjugated peptide through Mycobacterium smegmatis porin A (MspA) nanopore by a helicase motor for peptide sequencing application

The lack of an efficient, low-cost sequencing method has long been a significant bottleneck in protein research and applications. In recent years, the nanopore platform has emerged as a fast and inexpensive method for single-molecule nucleic acid sequencing, but attempts to apply it to protein/peptide sequencing have resulted in limited success. Here we report a strategy to control peptide translocation through the MspA nanopore, which could serve as the first step toward strand peptide sequencing. By conjugating the target peptide to a helicase-regulated handle-ssDNA, we achieved a read length of up to 17 amino acids (aa) and demonstrated the feasibility of distinguishing between amino acid residues of different charges or between different phosphorylation sites. Further improvement of resolution may require engineering MspA-M2 to reduce its constriction zone's size and stretch the target peptide inside the nanopore to minimize random thermal motion. We believe that our method in this study can significantly accelerate the development and commercialization of nanopore-based peptide sequencing technologies.

Atomistic level characterisation of ssDNA translocation through the E. coli proteins CsgG and CsgF for nanopore sequencing

Two proteins of the Escherichia coli membrane protein complex, CsgG and CsgF, are studied as proteinaceous nanopores for DNA sequencing. It is highly desirable to control the DNA as it moves through the pores, this requires characterisation of DNA translocation and subsequent optimization of the pores. In order to inform protein engineering to improve the pores, we have conducted a series of molecular dynamics simulations to characterise the mechanical strength and conformational dynamics of CsgG and the CsgG-CsgF complex and how these impact ssDNA, water and ion movement. We find that the barrel of CsgG is more susceptible to damage from external electric fields compared to the protein vestibule. Furthermore, the presence of CsgF within the CsgG-CsgF complex enables the complex to withstand higher electric fields. We find that the eyelet loops of CsgG play a key role in both slowing the translocation rate of DNA and modulating the conductance of the pore. CsgF also impacts the DNA translocation rate, but to a lesser degree than CsgG.

In silico assessment of a novel single-molecule protein fingerprinting method employing fragmentation and nanopore detection

The identification of proteins at the single-molecule level would open exciting new venues in biological research and disease diagnostics. Previously, we proposed a nanopore-based method for protein identification called chop-n-drop fingerprinting, in which the fragmentation pattern induced and measured by a proteasome-nanopore construct is used to identify single proteins. In the simulation study presented here, we show that 97.1% of human proteome constituents are uniquely identified under close to ideal measuring circumstances, using a simple alignment-based classification method. We show that our method is robust against experimental error, as 69.4% can still be identified if the resolution is twice as low as currently attainable, and 10% of proteasome restriction sites and protein fragments are randomly ignored. Based on these results and our experimental proof of concept, we argue that chop-n-drop fingerprinting has the potential to make cost-effective single-molecule protein identification feasible in the near future.

Velocity control of protein translocation through a nanopore by tuning the fraction of benzenoid residues

Protein sequencing is essential to unveil the mechanism of cellular processes that govern the function of living organisms, and which play a crucial role in the field of drug design and molecular diagnostics. Nanopores have been proved to be effective tools in single molecule sensing, but the fast translocation speed of a peptide through a nanopore is one of the major obstacles that hinders the development of nanopore-based protein sequencing. In this work, by using molecular dynamics simulations (MDS) it is found that the peptide containing more hydrophobic residues permeates slower through a molybdenum disulfide nanopore, which originates from the strong interaction between the membrane surface and the hydrophobic residues. The binding affinity is remarkable especially for benzenoid residues as they contain a hydrophobic aromatic ring that is composed of relatively non-polar C-C and C-H bonds. By tuning the fraction of benzenoid residues of the peptide, the velocity of the protein translocation through the nanopore is well controlled. The peptide with all the hydrophobic residues being benzenoid residues is found to translocate through the nanopore almost ten times slower than the one without any benzenoid residues, which is beneficial for gathering adequate information for precise amino acid identification.

Is the Volume Exclusion Model Practicable for Nanopore Protein Sequencing?

The nanopore approach holds the possibility for achieving single-molecule protein sequencing. However, ongoing challenges still remain in the biological nanopore technology, which aims to identify 20 natural amino acids by reading the ionic current difference with the traditional current-sensing model. In this paper, taking aerolysin nanopores as an example, we calculate and compare the current blockage of each of 20 natural amino acids, which are all far from producing a detectable current blockage difference. Then, we propose a modified solution conductivity of σ' in the traditional volume exclusion model for nanopore sensing of a peptide. The σ' value describes the comprehensive result of ion mobility inside a nanopore, which is related to but not limited to nanopore-peptide interactions, and the positions, orientations, and conformations of peptides inside the nanopore. The nanopore experiments of a short peptide (VQIVYK) in wild type and mutant nanopores further demonstrate that the traditional volume exclusion model is not enough to fully explain the current blockage contribution and that many other factors such as enhanced nanopore-peptide interactions could contribute to a dominant part of the current change. This modified sensing model provides insights into the further development of nanopore protein sequencing methods.

Modulation of electrophoresis, electroosmosis and diffusion for electrical transport of proteins through a solid-state nanopore

Nanopore probing of molecular level transport of proteins is strongly influenced by electrolyte type, concentration, and solution pH. As a result, electrolyte chemistry and applied voltage are critical for protein transport and impact, for example, capture rate (C_R), transport mechanism (i.e., electrophoresis, electroosmosis or diffusion), and 3D conformation (e.g., chaotropic vs. kosmotropic effects). In this study, we explored these using 0.5–4 M LiCl and KCl electrolytes with holo-human serum transferrin (hSTf) protein as the model protein in both low (±50 mV) and high (±400 mV) electric field regimes. Unlike in KCl, where events were purely electrophoretic, the transport in LiCl transitioned from electrophoretic to electroosmotic with decreasing salt concentration while intermediate concentrations (i.e., 2 M and 2.5 M) were influenced by diffusion. Segregating diffusion-limited capture rate (R_diff) into electrophoretic (R_diff,EP) and electroosmotic (R_diff,EO) components provided an approach to calculate the zeta-potential of hSTf (ζ_hSTf) with the aid of C_R and zeta potential of the nanopore surface (ζ_pore) with (ζ_pore–ζ_hSTf) governing the transport mechanism. Scrutinization of the conventional excluded volume model revealed its shortcomings in capturing surface contributions and a new model was then developed to fit the translocation characteristics of proteins.

Figure shows hSTf protein translocating through a solid-state nanopore under an applied electric field and the resulting current traces. The transport mechanism is determined by the interplay of electrophoretic and electroosmotic force.

Free energy and kinetics of cAMP permeation through connexin26 via applied voltage and milestoning

The connexin family is a diverse group of highly regulated wide-pore channels permeable to biological signaling molecules. Despite the critical roles of connexins in mediating selective molecular signaling in health and disease, the basis of molecular permeation through these pores remains unclear. Here, we report the thermodynamics and kinetics of binding and transport of a second messenger, adenosine-3',5'-cyclophosphate (cAMP), through a connexin26 hemichannel (Cx26). First, inward and outward fluxes of cAMP molecules solvated in KCl solution were obtained from 4 μs of ± 200 mV simulations. These fluxes data yielded a single-channel permeability of cAMP and cAMP/K⁺ permeability ratio consistent with experimentally measured values. The results from voltage simulations were then compared with the potential of mean force (PMF) and the mean first passage times (MFPTs) of a single cAMP without voltage, obtained from a total of 16.5 μs of Voronoi-tessellated Markovian milestoning simulations. Both the voltage simulations and the milestoning simulations revealed two cAMP-binding sites, for which the binding constants K_D and dissociation rates k_off were computed from PMF and MFPTs. The protein dipole inside the pore produces an asymmetric PMF, reflected in unequal cAMP MFPTs in each direction once within the pore. The free energy profiles under opposite voltages were derived from the milestoning PMF and revealed the interplay between voltage and channel polarity on the total free energy. In addition, we show how these factors influence the cAMP dipole vector during permeation, and how cAMP affects the local and nonlocal pore diameter in a position-dependent manner.

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.

Simultaneous Sensing of Force and Current Signals to Recognize Proteinogenic Amino Acids at a Single-Molecule Level

The identification ability of nanopore sequencing is severely hindered by the diversity of amino acids in a protein. To tackle this problem, a graphene nanoslit sensor is adopted to collect force and current signals to distinguish 20 residues. Extensive molecular dynamics simulations are performed on sequencing peptides under pulling force and applied electric field. Results show that the signals of force and current can be simultaneously collected. Tailoring the geometry of the nanoslit sensor optimizes signal differences between tyrosine and alanine residues. Using the tailored geometry, the characteristic signals of 20 types of residues are detected, enabling excellent distinguishability so that the residues are well-grouped by their properties and signals. The signals reveal a trend in which the larger amino acids have larger pulling forces and lower ionic currents. Generally, the graphene nanoslit sensor can be employed to simultaneously sense two signals, thereby enhancing the identification ability and providing an effective mode of nanopore protein sequencing.

Analytical Model for Particle Capture in Nanopores Elucidates Competition among Electrophoresis, Electroosmosis, and Dielectrophoresis

The interaction between nanoparticles dispersed in a fluid and nanopores is governed by the interplay of hydrodynamical, electrical, and chemical effects. We developed a theory for particle capture in nanopores and derived analytical expressions for the capture rate under the concurrent action of electrical forces, fluid advection, and Brownian motion. Our approach naturally splits the average capture time in two terms, an approaching time due to the migration of particles from the bulk to the pore mouth and an entrance time associated with a free-energy barrier at the pore entrance. Within this theoretical framework, we described the standard experimental condition where a particle concentration is driven into the pore by an applied voltage, with specific focus on different capture mechanisms: under pure electrophoretic force, in the presence of a competition between electrophoresis and electroosmosis, and finally under dielectrophoretic reorientation of dipolar particles. Our theory predicts that dielectrophoresis is able to induce capture for both positive and negative voltages. We performed a dedicated experiment involving a biological nanopore (α-hemolysin) and a rigid dipolar dumbbell (realized with a β-hairpin peptide) that confirms the theoretically proposed capture mechanism.

Enabling nanopore technology for sensing individual amino acids by a derivatization strategy

Nanopore technology holds remarkable promise for sequencing proteins and peptides. To achieve this, it is necessary to establish a characteristic profile for each individual amino acid through the statistical description of its translocation process. However, the subtle molecular differences among all twenty amino acids along with their unpredictable conformational changes at the nanopore sensing region result in very low distinguishability. Here we report the electrical sensing of individual amino acids using an α-hemolysin nanopore based on a derivatization strategy. Using derivatized amino acids as detection surrogates not only prolongs their interactions with the sensing region, but also improves their conformational variation. Furthermore, we show that distinct characteristics including current blockades and dwell times can be observed among all three classes of amino acids after 2,3-naphthalenedicarboxaldehyde (NDA)- and 2-naphthylisothiocyanate (NITC)-derivatization, respectively. These observable characteristics were applied towards the identification and differentiation of 9 of the 20 natural amino acids using their NITC derivatives. The method demonstrated herein will pave the way for the identification of all amino acids and further protein and peptide sequencing.

N-Terminal Derivatization-Assisted Identification of Individual Amino Acids Using a Biological Nanopore Sensor

Nanopore technology has been employed as a powerful tool for DNA sequencing and analysis. To extend this method to peptide sequencing, a necessary step is to profile individual amino acids (AAs) through their nanopore stochastic signals, which remains a great challenge because of the low signal-to-noise ratio and unpredictable conformational changes of AAs during their translocation through nanopores. We showed that the combination of an N-terminal derivatization strategy of AAs with nanopore technology could lead to effective in situ differentiation of AAs. Four different derivatization reactions have been tested with five selected AAs: Ala, Phe, Tyr, His, and Asp. Using an α-hemolysin nanopore, we demonstrated the feasibility of derivatization-assisted identification of AAs regardless of their charge composition and polarity. The method was further applied to discriminate each individual AA in testing data sets using their established nanopore profiles from training data sets. We envision that this proof-of-concept study will not only pave a way for identification of individual AAs but also lead to future applications in protein/peptide sequencing using the nanopore technology.

Analytical techniques for multiplex analysis of protein biomarkers

INTRODUCTION

The importance of biomarkers for pharmaceutical drug development and clinical diagnostics is more significant than ever in the current shift toward personalized medicine. Biomarkers have taken a central position either as companion markers to support drug development and patient selection, or as indicators aiming to detect the earliest perturbations indicative of disease, minimizing therapeutic intervention or even enabling disease reversal. Protein biomarkers are of particular interest given their central role in biochemical pathways. Hence, capabilities to analyze multiple protein biomarkers in one assay are highly interesting for biomedical research.

AREAS COVERED

We here review multiple methods that are suitable for robust, high throughput, standardized, and affordable analysis of protein biomarkers in a multiplex format. We describe innovative developments in immunoassays, the vanguard of methods in clinical laboratories, and mass spectrometry, increasingly implemented for protein biomarker analysis. Moreover, emerging techniques are discussed with potentially improved protein capture, separation, and detection that will further boost multiplex analyses.

EXPERT COMMENTARY

The development of clinically applied multiplex protein biomarker assays is essential as multi-protein signatures provide more comprehensive information about biological systems than single biomarkers, leading to improved insights in mechanisms of disease, diagnostics, and the effect of personalized medicine.

Native-state fingerprint on the ubiquitin translocation across a nanopore

We study the translocation of the ubiquitin molecule (Ubq) across a channel with a double section which constitutes a general feature of several transmembrane nanopores such as the α-hemolysin (αHL). Our purpose is to establish the structure-dependent character of the Ubq translocation pathway. This implies to find the correspondence, if any, between the translocational unfolding steps and the Ubq native state. For this reason, it is convenient to apply a coarse-grained computational approach, where the protein is described only by the backbone and the force field only exploits the information contained in the native state (in the spirit of Gō-like models, or native-centric models). The αHL-like pore is portrayed as two coaxial confining cylinders: a larger one for the vestibule and a narrower one for the barrel (or stem). Such simplified approach allows a large number of translocation events to be collected by limited computational resources. The co-translocational unfolding of Ubq is described via a few collective variables that characterize the translocation progress. We find two translocation intermediates (stalled conformations) that can be associated with specific unfolding stages. In particular, in the earliest step, the strand S5 unfolds and enters the pore. This step splits the native conformation into two structural clusters packing against each other in the Ubq fold. A second stall occurs when the hairpin of the N terminal engages the stem region.

Polynucleotide differentiation using hybrid solid-state nanopore functionalizing with α-hemolysin

We report results from full atomistic molecular dynamics simulations on the properties of biomimetic nanopores. This latter result was obtained through the direct insertion of an α-hemolysin protein inside a hydrophobic solid-state nanopore. Upon translocation of different DNA strands, we demonstrate here that the theoretical system presents the same discrimination properties as the experimental one obtained previously. This opens an interesting way to promote the stability of a specific protein inside a solid nanopore to develop further biomimetic applications for DNA or protein sequencing.

Vibration assisted electron tunneling through nano-gaps in graphene nano-ribbons for amino-acid and peptide bond recognition

Peptide bond and amino-acid recognition by tunneling current flowing across nano-gaps of graphene nano-ribbons has been recently discussed. Theoretical predictions of the tunneling current signals were used in the elastic regime showing peculiar fingerprints. However, inelastic scattering due to vibrations is expected to play an important role. Then, the proposed strategy for peptide sequencing and amino-acid recognition is revised in the light of such inelastic scattering phenomena. Phonon and local vibrational mode assisted current tunneling is calculated by treating electron-phonon scattering in the context of the lowest order expansion of the self-consistent Born approximation. We study Gly and Ala homo-peptides as an example of very similar, small and neutral amino-acids that would be indistinguishable by means of standard techniques, such as the ionic blockade current, in real peptides. We show that all the inelastic contributions to the tunneling current are in the bias range 0 V ≤ V ≤ 0.5 V and that they can be classified, from an atomistic point of view, in terms of energy sub-ranges that they belong to. Peculiar fingerprints can be found for the typical configurations that have been recently found for peptide bond recognition by tunneling current.

Simultaneous single-molecule discrimination of cysteine and homocysteine with a protein nanopore

Discrimination between cysteine and homocysteine at the single-molecule level is achieved within a K238Q mutant aerolysin nanopore, which provides a confined space for high spatial resolution to identify the amino acid difference with a 5'-benzaldehyde poly(dA)₄ probe. Our strategy allows potential detection and characterization of various amino acids and their modifications, and provides a crucial step towards developing nanopore protein sequencing devices.

Translocation intermediates of ubiquitin through an α-hemolysin nanopore: implications for detection of post-translational modifications

Nanopore based sensors constitute a promising approach to single molecule protein characterization being able, in principle, to detect sequences, structural elements and folding states of proteins and polypeptide chains. In narrow nanopores, one of the open issues concerns the coupling between unfolding and translocation. Here, we studied the ubiquitin translocation in an α-hemolysin nanopore, the most widely used pore for nanopore sensing, via all-atom molecular dynamics simulations. We completely characterize the co-translocational unfolding pathway finding that robust translocation intermediates are associated with the rearrangement of secondary structural elements, as also confirmed by coarse grained simulations. An interesting recurrent pattern is the clogging of the α-hemolysin constriction by an N-terminal β-hairpin. This region of ubiquitin is the target of several post-translational modifications. We propose a strategy to detect post-translational modifications at the N-terminal using the α-hemolysin nanopore based on the comparison of the co-translocational unfolding signals associated with modified and unmodified proteins.