Single-File Protein Translocations through Graphene-MoS2 Heterostructure Nanopores

The Role of MXene Surface Terminations on Peptide Transportation in Nanopore Sensing

Nanopores with two-dimensional materials have various advantages in sensing, but the fast translocation of molecules hinders their scale-up applications. In this work, we investigate the influence of -F, -O, and -OH surface terminations on the translocation of peptides through MXene nanopores. We find that the longest dwell time always occurs when peptides pass through the Ti3C2O2 nanopores. This elongated dwell time is induced by the strongest interaction between peptides and the Ti3C2O2 membrane, in which the van der Waals interactions dominate. Compared to the other two MXene nanopores, the braking effect is indicated during the whole translocation process, which evidence the advantage of Ti3C2O2 in nanopore sensing. Our work demonstrates that membrane surface chemistry has a great influence on the translocation of peptides, which can be introduced in the design of nanopores for a better performance.

Protein Deceleration and Sequencing Using Si3N4-CNT Hybrid Nanopores

Protein sequencing is crucial for understanding the complex mechanisms driving biological functions and is of utmost importance in molecular diagnostics and medication development. Nanopores have become an effective tool for single molecule sensing, however, the weak charge and non-uniform charge distribution of protein make capturing and sensing very challenging, which poses a significant obstacle to the development of nanopore-based protein sequencing. In this study, to facilitate capturing of the unfolded protein, highly charged peptide was employed in our simulations, we found that the velocity of unfolded peptide translocating through a hybrid nanopore composed of silicon nitride membrane and carbon nanotube is much slower compared to bare silicon nitride nanopore, it is due to the significant interaction between amino acids and the surface of carbon nanotube. Moreover, by introducing variations in the charge states at the boundaries of carbon nanotube nanopores, the competition and combination of the electrophoretic and electroosmotic flows through the nanopores could be controlled, we then successfully regulated the translocation velocity of unfolded proteins through the hybrid nanopores. The proposed hybrid nanopore effectively retards the translocation velocity of protein through it, facilitates the acquisition of ample information for accurate amino acid identification.

Developing semi-empirical water model for efficiently simulating temperature-dependent chemisorption of CO2 in amine solvents

Classical molecular dynamics (MD) simulations without bond forming/breaking cannot be used to model chemical reactions (CRs) among small molecules. Although the first-principle MD simulation can adequately describe CRs with explicit water molecules, such simulation is normally too costly for most researchers to afford. Generally, water molecules in a solvent can exert hydrophobic forces on reacting molecules, which yields a so-called caging effect that cannot be ignored when constructing a free energy landscape for reacting molecules. Many recently developed semi-empirical methods (such as DFTB, PM6 and xTB) are highly efficient for modeling CRs, however none of them can be directly used to model bulk water properly. Here, we developed a modified xTB approach that enables the simulation of CRs in explicit water. Using the chemisorption of CO2 by amines in water as an example application, we demonstrate that our approach yielded results comparable with the first-principle ones, while only using a limited computing resource. Potentially, our proposed semi-empirical water model can be utilized for the computational study of any CR in water.

Protein Sequencing with Artificial Intelligence: Machine Learning Integrated Phosphorene Nanoslit

Achieving high throughput protein sequencing at single molecule resolution remains a daunting challenge. Herein, relying on a solid-state 2D phosphorene nanoslit device, an extraordinary biosensor to rapidly identify the key signatures of all twenty amino acids using an interpretable machine learning (ML) model is reported. The XGBoost regression algorithm allows the determination of the transmission function of all twenty amino acids with high accuracy. The resultant ML and DFT studies reveal that it is possible to identify individual amino acids through transmission and current signals readouts with high sensitivity and selectivity. Moreover, we thoroughly compared our results to those from graphene nanoslit and found that the phosphorene nanoslit device can be an ideal candidate for protein sequencing up to a 20-fold increase in transmission sensitivity. The present study facilitates high throughput screening of all twenty amino acids and can be further extended to other biomolecules for disease diagnosis and therapeutic decision making.

Scaling laws for single-file diffusion of adhesive particles

Single-file diffusion refers to the Brownian motion in narrow channels where particles cannot pass each other. In such processes, the diffusion of a tagged particle is typically normal at short times and becomes subdiffusive at long times. For hard-sphere interparticle interaction, the time-dependent mean squared displacement of a tracer is well understood. Here we develop a scaling theory for adhesive particles. It provides a full description of the time-dependent diffusive behavior with a scaling function that depends on an effective strength of adhesive interaction. Particle clustering induced by the adhesive interaction slows down the diffusion at short times, while it enhances subdiffusion at long times. The enhancement effect can be quantified in measurements irrespective of how tagged particles are injected into the system. Combined effects of pore structure and particle adhesiveness should speed up translocation of molecules through narrow pores.

Two Detection Modes of Nanoslit Sensing Based on Planar Heterostructure of Graphene/Hexagonal Boron Nitride

Solid-state nanopore sequencing is now confronted with problems of stochastic pore clogging and too fast speed during the DNA permeation through a nanopore, although this technique is revolutionary with long readability and high efficiency. These two problems are related to controlling molecular transportation during sequencing. To control the DNA motion and identify the four bases, we propose nanoslit sensing based on the planar heterostructure of two-dimensional graphene and hexagonal boron nitride. Molecular dynamics simulations are performed on investigating the motion of DNA molecules on the heterostructure with a nanoslit sensor. Results show that the DNA molecules are confined within the hexagonal boron nitride (HBN) domain of the heterostructure. And the confinement effects of the heterostructure can be optimized by tailoring the stripe length. Besides, there are two ways of DNA permeation through nanoslits: the DNA can cross or translocate the nanoslit under applied voltages along the y and z directions. The two detection modes are named cross-slit and trans-slit, respectively. In both modes, the ionic current drops can be observed when the nanoslit is occupied by the DNA. And the ionic currents and dwell times can be simultaneously detected to identify the four different DNA bases. This study can shed light on the sensing mechanism based on the nanoslit sensor of a planar heterostructure and provide theoretical guidance on designing devices controlling molecular transportation during nanopore sequencing.

Experimental study on single biomolecule sensing using MoS2-graphene heterostructure nanopores

Solid-state nanopores play an important role in sensing single-biomolecules such as DNA and proteins. However, an ultra-short translocation time hinders nanopores from acquiring more detailed information about biomolecules, and further applications such as sequencing and molecular structure analysis are limited. Related studies have shown that MoS₂ has no obvious impediment to biomolecule translocation while graphene may cause obstacles to this process. By combining these two-dimensional materials, nanopores might slow the biomolecule passage. Herein, we fabricated sub-10 nm ultra-thin MoS₂-graphene heterostructure nanopores with high stability and tested both dsDNA and native protein (BSA) at the single-molecule level in experiments for the first time. Some special signals with advanced order are observed, which may reflect the shape change of the BSA molecules during the slow translocation process. The results show that the translocation time of BSA is slowed down up to more than 100 ms and the signal length and form are determined by the extent of interaction between the BSA and the heterostructure nanopore. The weak interaction between the BSA and the MoS₂ layer increases the translocation probability, and meanwhile, the strong interaction of the graphene layer to BSA slows down the translocation and changes its structure. Therefore, our findings indicate the possibilities of slowing down the single-biomolecule translocation and the capability of acquiring more detailed information about biomolecules using MoS₂-graphene heterostructure nanopores.

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.

Solitons in Overdamped Brownian Dynamics

Solitons are commonly known as waves that propagate without dispersion. Here, we show that they can occur for driven overdamped Brownian dynamics of hard spheres in periodic potentials at high densities. The solitons manifest themselves as periodic sequences of different assemblies of particles moving in the limit of zero noise, where transport of single particles is not possible. They give rise to particle currents at even low temperature that appear in bandlike structures around certain hard-sphere diameters. At high temperatures, the bandlike structures are washed out by the noise, but the particle transport is still dominated by the solitons. All these predicted features should occur in a broad class of periodic systems and are amenable to experimental tests.

Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes

Two-dimensional (2D) nanomaterials such as graphene are increasingly used in research and industry for various biomedical applications. Extensive experimental and theoretical studies have revealed that 2D nanomaterials are promising drug delivery vehicles, yet certain materials exhibit toxicity under biological conditions. So far, it is known that 2D nanomaterials possess strong adsorption propensities for biomolecules. To mitigate potential toxicity and retain favorable physical and chemical properties of 2D nanomaterials, it is necessary to explore the underlying mechanisms of interactions between biomolecules and nanomaterials for the subsequent design of biocompatible 2D nanomaterials for nanomedicine. The purpose of this review is to integrate experimental findings with theoretical observations and facilitate the study of 2D nanomaterial interaction with biomolecules at the molecular level. We discuss the current understanding and progress of 2D nanomaterial interaction with proteins, lipid membranes, and DNA based on molecular dynamics (MD) simulation. In this review, we focus on the 2D graphene nanosheet and briefly discuss other 2D nanomaterials. With the ever-growing computing power, we can image nanoscale processes using MD simulation that are otherwise not observable in experiment. We expect that molecular characterization of the complex behavior between 2D nanomaterials and biomolecules will help fulfill the goal of designing effective 2D nanomaterials as drug delivery platforms.

Predicting biomolecule adsorption on MoS2 nanosheets with high structural fidelity

A new force field, MoSu-CHARMM, for the description of bio-interfacial structures at the aqueous MoS2 interface is developed, based on quantum chemical data. The force field describes non-covalent interactions between the MoS2 surface and a wide range of chemistries including hydrocarbon, alcohol, aldehyde, ketone, carboxylic acid, amine, thiol, and amino acid groups. Density functional theory (DFT), using the vdW-DF2 functional, is employed to create training and validation datasets, comprising 330 DFT binding energies for 21 organic compounds. Development of MoSu-CHARMM is guided by two criteria: (i) minimisation of energetic differences compared to target DFT data and (ii) preservation of the DFT energetic rankings of the different binding configurations. Force-field performance is validated against existing high-quality structural experimental data regarding adsorption of four 26-residue peptides at the aqueous MoS2 interface. Adsorption free energies for all twenty amino acids in liquid water are calculated to provide guidance for future peptide design, and interpret the properties of existing experimentally-identified MoS2-binding peptides. This force field will enable large-scale simulations of biological interactions with MoS2 surfaces in aqueous media where an emphasis on structural fidelity is prioritised.

Navigated Delivery of Peptide to the Nanopore Using In-Plane Heterostructures of MoS2 and SnS2 for Protein Sequencing

The impressive success of DNA sequencing using nanopores makes it possible to realize nanopore based protein sequencing. Well-controlled capture and linear movement of the protein are essential for accurate nanopore protein sequencing. Here, by taking advantage of different binding affinities of protein to two isomorphic materials, we theoretically designed a heterostructual platform for delivering the unfolded peptide to the nanopore sensing region. Due to the stronger binding between the peptide and SnS₂ compared to MoS₂, the peptide would adsorb to the SnS₂ nanostripe and keep its threadlike conformation in the MoS₂/SnS₂/MoS₂ heterostructure. Through switching the direction of the applied electric field in real time, the peptide was strategically driven to move along the designed path to the target nanopore. The ionic current blockades were also found to be different as the compositions of the peptide were changed, indicating the possibility for differentiating different peptides using this platform.

Fabrication of Nanopore in MoS2-Graphene vdW Heterostructure by Ion Beam Irradiation and the Mechanical Performance

Nanopore structure presents great application potential especially in the area of biosensing. The two-dimensional (2D) vdW heterostructure nanopore shows unique features, while research around its fabrication is very limited. This paper proposes for the first time the use of ion beam irradiation for creating nanopore structure in 2D vdW graphene-MoS2 heterostructures. The formation process of the heterostructure nanopore is discussed first. Then, the influence of ion irradiation parameters (ion energy and ion dose) is illustrated, based on which the optimal irradiation parameters are derived. In particular, the effect of stacking order of the heterostructure 2D layers on the induced phenomena and optimal parameters are taken into consideration. Finally, uniaxial tensile tests are conducted by taking the effect of irradiation parameters, nanopore size and stacking order into account to demonstrate the mechanical performance of the heterostructure for use under a loading condition. The results would be meaningful for expanding the applications of heterostructure nanopore structure, and can arouse more research interest in this area.

Solid-state and polymer nanopores for protein sensing: A review

In two decades, the solid state and polymer nanopores became attractive method for the protein sensing with high specificity and sensitivity. They also allow the characterization of conformational changes, unfolding, assembly and aggregation as well the following of enzymatic reaction. This review aims to provide an overview of the protein sensing regarding the technique of detection: the resistive pulse and ionic diodes. For each strategy, we report the most significant achievement regarding the detection of peptides and protein as well as the conformational change, protein-protein assembly and aggregation process. We discuss the limitations and the recent strategies to improve the nanopore resolution and accuracy. A focus is done about concomitant problematic such as protein adsorption and nanopore lifetime.

Revealing Topological Barriers against Knot Untying in Thermal and Mechanical Protein Unfolding by Molecular Dynamics Simulations

The knot is one of the most remarkable topological features identified in an increasing number of proteins with important functions. However, little is known about how the knot is formed during protein folding, and untied or maintained in protein unfolding. By means of all-atom molecular dynamics simulation, here we employ methyltransferase YbeA as the knotted protein model to analyze changes of the knotted conformation coupled with protein unfolding under thermal and mechanical denaturing conditions. Our results show that the trefoil knot in YbeA is occasionally untied via knot loosening rather than sliding under enhanced thermal fluctuations. Through correlating protein unfolding with changes in the knot position and size, several aspects of barriers that jointly suppress knot untying are revealed. In particular, protein unfolding is always prior to knot untying and starts preferentially from separation of two α-helices (α1 and α5), which protect the hydrophobic core consisting of β-sheets (β1-β4) from exposure to water. These β-sheets form a loop through which α5 is threaded to form the knot. Hydrophobic and hydrogen bonding interactions inside the core stabilize the loop against loosening. In addition, residues at N-terminal of α5 define a rigid turning to impede α5 from sliding out of the loop. Site mutations are designed to specifically eliminate these barriers, and easier knot untying is achieved under the same denaturing conditions. These results provide new molecular level insights into the folding/unfolding of knotted proteins.

Spontaneous DNA translocation through a van der Waals heterostructure nanopore for single-molecule detection

Solid-state nanopore detection and sequencing of a single molecule offers a new paradigm because of its several well-recognized features such as long reads, high throughput, high precision and direct analyses. However, several key technical challenges are yet to be addressed, especially the abilities to control the speed and direct the translocation of the target molecules. In this work, using molecular dynamics (MD) simulations, we found a spontaneous translocation of single-stranded DNA (ssDNA) through a van der Waals (vdW) heterostructure nanopore formed by stacking two graphenic materials, namely those of BC₃ and C₃N. Our results showed that, without using an external stimulus, ssDNA can be spontaneously transported through such a vdW nanopore from its BC₃ side to its C₃N side, with the C₃N surface demonstrating a stronger capability than the BC₃ surface to attract DNA bases. Thus, the distinct binding strengths of BC₃ and C₃N were concluded to drive the ssDNA translocation. The results indicated the vdW forces playing a leading role during the translocation process. Our simulations also showed, at the edges of the nanopore, a clear energy barrier for nucleotides, resulting in a translocation speed slowed to a value of 0.2 μs per base, i.e., twice as slow as that indicated for the latest published methods. The present findings provide a new architecture for biomolecule detection and sequencing, which may be considered some of the most important functions of nanomaterials in biological and chemical analyses.

DNA Translocation through Vertically Stacked 2D Layers of Graphene and Hexagonal Boron Nitride Heterostructure Nanopore

Cost-effective, fast, and reliable DNA sequencing can be enabled by advances in nanopore-based methods, such as the use of atomically thin graphene membranes. However, strong interaction of DNA bases with graphene leads to undesirable effects such as sticking of DNA strands to the membrane surface. While surface functionalization is one way to counter this problem, here, we present another solution based on a heterostructure nanopore system, consisting of a monolayer of graphene and hexagonal boron nitride (hBN) each. Molecular dynamics studies of DNA translocation through this heterostructure nanopore revealed a surprising and crucial influence of the heterostructure layer order in controlling the base specific signal variability. Specifically, the heterostructure with graphene on top of hBN had nearly 3-10× lower signal variability than the one with hBN on top of graphene. Simulations point to the role of differential underside sticking of DNA bases as a possible reason for the observed influence of the layer order. Our studies can guide the development of experimental systems to study and exploit DNA translocation through two-dimensional heterostructure nanopores for single molecule sequencing and sensing applications.

Ångström- and Nano-scale Pore-Based Nucleic Acid Sequencing of Current and Emergent Pathogens

State-of-the-art nanopore sequencing enables rapid and real-time identification of novel pathogens, which has wide application in various research areas and is an emerging diagnostic tool for infectious diseases including COVID-19. Nanopore translocation enables de novo sequencing with long reads (> 10 kb) of novel genomes, which has advantages over existing short-read sequencing technologies. Biological nanopore sequencing has already achieved success as a technology platform but it is sensitive to empirical factors such as pH and temperature. Alternatively, ångström- and nano-scale solid-state nanopores, especially those based on two-dimensional (2D) membranes, are promising next-generation technologies as they can surpass biological nanopores in the variety of membrane materials, ease of defining pore morphology, higher nucleotide detection sensitivity, and facilitation of novel and hybrid sequencing modalities. Since the discovery of graphene, atomically-thin 2D materials have shown immense potential for the fabrication of nanopores with well-defined geometry, rendering them viable candidates for nanopore sequencing membranes. Here, we review recent progress and future development trends of 2D materials and their ångström- and nano-scale pore-based nucleic acid (NA) sequencing including fabrication techniques and current and emerging sequencing modalities. In addition, we discuss the current challenges of translocation-based nanopore sequencing and provide an outlook on promising future research directions.

Electrophoretic Transport of Single-Stranded DNA through a Two Dimensional Nanopore Patterned on an In-Plane Heterostructure

Recent advances in nanotechnology have facilitated fabrication of various solid state nanopores as a versatile alternative to biological nanopores; however, effective transport of a single-stranded DNA (ssDNA) molecule through solid state nanopores for sequencing has remained a challenge. In particular, the nonspecific interactions between the ssDNA and the engineered nanopore surface are known to impose difficulties on both transport and interrogation. Here, we show that a two-dimensional (2D) nanopore patterned on an in-plane heterostructure comprising both graphene and hexagonal boron nitride (hBN) can be utilized to transport the ssDNA electrophoretically. Energetically, a ssDNA molecule prefers to stay on the hBN domain than the graphene one since the former has a stronger van der Waals attraction with the ssDNA, as demonstrated in both classic molecular dynamics (MD) simulations and density functional theory (DFT) based calculations, which leads to the confinement of the ssDNA in the 2D nanopore. Therefore, this nanopore enables the manipulation of the conformation of a highly flexible ssDNA molecule on a flat 2D heterostructure surface, making it possible for sensing ssDNA bases using the high resolution atomic force microscopy (AFM) or scanning tunneling microscopy (STM) in the third dimension (perpendicular to the 2D surface).

Spontaneous Translocation of Single-Stranded DNA in Graphene-MoS2 Heterostructure Nanopores: Shape Effect

The appropriate translocation speed of a single-stranded DNA (ssDNA) through a solid-state nanopore is crucial for DNA sequencing technologies. By studying the geometry effect of graphene-MoS₂ hetero-nanopores with molecular dynamics simulations, we have found that the shape of these nanopores (circular, square, or triangular, with similar size) may have a significant effect on the spontaneous translocation of ssDNA, with the triangular nanopore showing the slowest translocation and the circular one the fastest. Further analyses reveal that such differences in the spontaneous ssDNA translocation arise from different electrostatic attractions between the positively charged Mo atoms exposed in the pore and the negatively charged phosphate groups (PO₄^-) in nucleotides; the "sharpness" and the total number of the exposed Mo atoms of the nanopores are responsible for different electrostatic attractions between ssDNA and the nanopore. Our findings suggest that graphene-MoS₂ heterostructure nanopores with lower symmetries (i.e., having sharper corners) are capable of slowing down the ssDNA translocation, which might help better facilitate the nucleotide sensing and DNA sequencing. The conclusion from these findings might also extend to other solid-state nanopores in designing appropriate shapes for better controlling of the translocation speed.

Planar graphene/h-BN/graphene heterostructures for protein stretching and confinement

Protein stretching and confinement in nanochannels is critical for advancing single-molecule detection techniques. For standard nanochannels integrated with nano-sensors, reducing their cross-section is beneficial for reading highly localized signals with minimal error, but results in increasing difficulty for the initial capture of any chain molecules due to the entropy barrier. Using molecular dynamics simulations, we show that spontaneous protein stretching can be realized by a two-dimensional (2D) heterostructure composed of a hexagonal boron nitride (h-BN) nanoribbon stitched with two graphene (GRA) sheets (i.e., a sandwiched GRA/BN/GRA structure). Due to fast protein diffusion on its flat surface and adsorption potential difference between two 2D materials, this planar nanochannel permits effective capture and elongation of three representative intrinsically disordered proteins including amyloid-β (1-42), polyglutamine (42) and α-synuclein (61-95). Moreover, we found that the extremely narrow h-BN stripe can provide stronger confinement for a longer polyglutamine chain after being stretched. Our approach has the potential to facilitate the bona fide readout of single-molecule protein sequencing techniques.

Nanoconfined Fluids: What Can We Expect from Them?

Nanoconfined fluids (NCFs), which are confined in nanospaces, exhibit distinctive nanoscale effects, including surface effects, small-size effects, quantum effects, and others. The continuous medium hypothesis in fluid mechanics is not valid in this context because of the comparable characteristic length of spaces and molecular mean free path, and accordingly, the classical continuum theories developed for the bulk fluids usually cannot describe the mass and energy transport of NCFs. In this Perspective, we summarize the nanoscale effects on the thermodynamics, mass transport, flow dynamics, heat transfer, phase change, and energy transport of NCFs and highlight the related representative works. The applications of NCFs in the fields of membrane separation, oil and gas production, energy harvesting and storage, and biological engineering are especially indicated. Currently, the theoretical description framework of NCFs is still missing, and it is expected that this framework can be established by adopting the classical continuum theories with the consideration of nanoscale effects.

Potential interference with microtubule assembly by graphene: a tug-of-war

With the ever-increasing demand for graphene-based materials and their promising applications in numerous nanotechnologies, the biological effects of graphene on living systems have become crucial and ought to be well understood. Previously, both the cytotoxicity of graphene towards biological cells and its potential application as a nanomedicine have been revealed experimentally and theoretically. Besides many existing anticancer drugs that target microtubules, here we investigate the possibility of using graphene as a nanomedicine, which could alter the dynamic assembly and disassembly of a microtubule. We found that when a graphene nanosheet is at the hydrophilic interface of two neighboring heterodimers (containing α and β tubulins), it can pull one dimer away from the other through a "tug-of-war" mechanism, driven by the strong dispersive interaction exerted by the surface of the graphene nanosheet. This work demonstrates that based on the existing methods for mitigating graphene's cytotoxicity (already developed in this field), a graphene-based nanomedicine could be designed to target microtubules of cancer cells and induce cell apoptosis.

Lowering the Schottky barrier height of G/WSSe van der Waals heterostructures by changing the interlayer coupling and applying external biaxial strain

Graphene-based van der Waals (vdW) heterostructures composed of two-dimensional transition metal dichalcogenides (TMDs) and graphene show great potential in the design and manufacture of field effect transistors.

Beyond mass spectrometry, the next step in proteomics

Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do it. Here, we offer a survey that illuminates a few alternatives with the brightest prospects for identifying whole proteins and displacing MS for sequencing them. These alternatives all boast sensitivity superior to MS and promise to be scalable and seem to be adaptable to bioinformatics tools for calling the sequence of amino acids that constitute a protein.

Selective Molecular Sieving through a Large Graphene Nanopore with Surface Charges

The precise control of the pore sizes at an atomic level has proved to be the biggest challenge of all for nanoporous graphene membranes for gas separation. Here, we propose a simple method to realize the selective molecular sieving through originally nonselective graphene nanopores by adding charges on the graphene surfaces. Molecular dynamic simulations show that the CO₂/N₂ selectivity of the graphene nanopore with a diameter of 0.52 nm increases up to 22.78 for a surface charge density of only -5.934 e/nm². The selectivity improvement is related to the distinctive adsorption intensities of CO₂ and N₂ molecules on the charge-loaded graphene surfaces. This work points toward a promising road to tune the selectivity of graphene nanopores and therefore promotes the realization of porous graphene membranes and other two-dimensional porous membranes by accepting the pores with a wide size distribution and reducing the requirements in the control of pore sizes.

Parameterization of Molybdenum Disulfide Interacting with Water Using the Free Energy Perturbation Method

Water contact angles (WCA) are often used to parametrize force field parameters of novel 2D nanomaterials, such as molybdenum disulfide (MoS₂), which has emerged as a promising nanomaterial in many biomedical applications due to its unique and impressive properties. However, there is a wide range of water-MoS₂ contact angles in the literature depending on the aging process on the surface of a MoS₂ nanosheet and/or substrate material. In this study, we revisit and optimize existing parameters for the basal plane of MoS₂ with two popular water models, TIP3P and SPC/E, using the wide range of WCAs from various experiments. We develop and deploy the free energy perturbation method for parametrizing MoS₂ with experimentally determined WCAs for both fresh and aged surfaces. Energy decomposition analysis on the simulation trajectories reveals that MoS₂-water interaction is dominated by van der Waals interaction, which mainly comes from the top layer of MoS₂. We conclude that to describe both fresh and aged MoS₂ surfaces it is convenient to only adjust the Lennard-Jones parameter ε_S (the depth of the potential well of a sulfur atom), which displays a surprisingly linear correlation with WCAs.

Estimation of Shape, Volume, and Dipole Moment of Individual Proteins Freely Transiting a Synthetic Nanopore

This paper demonstrates that high-bandwidth current recordings in combination with low-noise silicon nitride nanopores make it possible to determine the molecular volume, approximate shape, and dipole moment of single native proteins in solution without the need for labeling, tethering, or other chemical modifications of these proteins. The analysis is based on current modulations caused by the translation and rotation of single proteins through a uniform electric field inside of a nanopore. We applied this technique to nine proteins and show that the measured protein parameters agree well with reference values but only if the nanopore walls were coated with a nonstick fluid lipid bilayer. One potential challenge with this approach is that an untethered protein is able to diffuse laterally while transiting a nanopore, which generates increasingly asymmetric disruptions in the electric field as it approaches the nanopore walls. These "off-axis" effects add an additional noise-like element to the electrical recordings, which can be exacerbated by nonspecific interactions with pore walls that are not coated by a fluid lipid bilayer. We performed finite element simulations to quantify the influence of these effects on subsequent analyses. Examining the size, approximate shape, and dipole moment of unperturbed, native proteins in aqueous solution on a single-molecule level in real time while they translocate through a nanopore may enable applications such as identifying or characterizing proteins in a mixture, or monitoring the assembly or disassembly of transient protein complexes based on their shape, volume, or dipole moment.

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

Single molecule protein sequencing would represent a disruptive burst in proteomic research with important biomedical impacts. Due to their success in DNA sequencing, nanopore based devices have been recently proposed as possible tools for the sequencing of peptide chains. One of the open questions in nanopore protein sequencing concerns the ability of such devices to provide different signals for all the 20 standard amino acids. Here, using equilibrium all-atom molecular dynamics simulations, we estimated the pore clogging in α-Hemolysin nanopore associated to 20 different homopeptides, one for each standard amino acid. Our results show that pore clogging is affected by amino acid volume, hydrophobicity and net charge. The equilibrium estimations are also supported by non-equilibrium runs for calculating the current blockades for selected homopeptides. Finally, we discuss the possibility to modify the α-Hemolysin nanopore, cutting a portion of the barrel region close to the trans side, to reduce spurious signals and, hence, to enhance the sensitivity of the nanopore.

Coarse-grained molecular dynamics study of wettability influence on protein translocation through solid nanopores

Protein translocation through nanopores is widely involved in molecular sensing and analyzing devices, whereby nanopore surface properties are crucial. However, fundamental understanding of how these properties affect protein motion inside nanopores remains lacking. In this work, we study the influence of nanopore surface wettability on voltage-driven protein translocation through nanopores with coarse-grained molecular dynamics simulations. The results show that the electrophoretic mobility of protein translocation increases as the contact angle of nanopore surface increases from 0° to 90°, but becomes almost constant as the contact angle is above 90°. This observation can be attributed to the variation of the friction coefficient of protein translocation through the nanopores with different nanopore contact angles. We further show that the interaction between nanopore and water, rather than that between the nanopore and protein, dominates the protein transport in nanopores. These findings provide new insights into protein translocation dynamics across nanopores and will be beneficial to the design of high-efficiency nanopore devices for single molecule protein sensing.

Perforating Freestanding Molybdenum Disulfide Monolayers with Highly Charged Ions

Porous single-layer molybdenum disulfide (MoS₂) is a promising material for applications such as DNA sequencing and water desalination. In this work, we introduce irradiation with highly charged ions (HCIs) as a new technique to fabricate well-defined pores in MoS₂. Surprisingly, we find a linear increase of the pore creation efficiency over a broad range of potential energies. Comparison to atomistic simulations reveals the critical role of energy deposition from the ion to the material through electronic excitation in the defect creation process and suggests an enrichment in molybdenum in the vicinity of the pore edges at least for ions with low potential energies. Analysis of the irradiated samples with atomic resolution scanning transmission electron microscopy reveals a clear dependence of the pore size on the potential energy of the projectiles, establishing irradiation with highly charged ions as an effective method to create pores with narrow size distributions and radii between ca. 0.3 and 3 nm.

FraC nanopores with adjustable diameter identify the mass of opposite-charge peptides with 44 dalton resolution

A high throughput single-molecule method for identifying peptides and sequencing proteins based on nanopores could reduce costs and increase speeds of sequencing, allow the fabrication of portable home-diagnostic devices, and permit the characterization of low abundance proteins and heterogeneity in post-translational modifications. Here we engineer the size of Fragaceatoxin C (FraC) biological nanopore to allow the analysis of a wide range of peptide lengths. Ionic blockades through engineered nanopores distinguish a variety of peptides, including two peptides differing only by the substitution of alanine with glutamate. We also find that at pH 3.8 the depth of the peptide current blockades scales with the mass of the peptides irrespectively of the chemical composition of the analyte. Hence, this work shows that FraC nanopores allow direct readout of the mass of single peptide in solution, which is a crucial step towards the developing of a real-time and single-molecule protein sequencing device.

Atomic-Scale Fluidic Diodes Based on Triangular Nanopores in Bilayer Hexagonal Boron Nitride

Nanofluidic diodes based on nanochannels have been studied theoretically and experimentally for applications such as biosensors and logic gates. However, when analyzing attoliter-scale samples or enabling high-density integration of lab-on-a-chip devices, it is beneficial to miniaturize the size of a nanofluidic channel. Using molecular dynamics simulations, we investigate conductance of nanopores in bilayer hexagonal boron nitride (h-BN). Remarkably, we found that triangular nanopores possess excellent rectifications of ionic currents while hexagonal ones do not. It is worth highlighting that the pore length is only about 0.7 nm, which is about the atomic limit for a bipolar diode. We determined scaling relations between ionic currents I and pore sizes L for small nanopores, that are I ∼ L¹ in a forward biasing voltage and I ∼ L² in a reverse biasing voltage. Simulation results qualitatively agree with analytical ones derived from the one-dimensional Poisson-Nerst-Planck equations.