Molecular Dynamics Investigation of Polylysine Peptide Translocation through MoS2 Nanopores

Orientation dependence of current blockade in single amino acid translocation through a graphene nanopore

After the successful commercialization of DNA sequencing using biological nanopores, the next frontier for nanopore technology is protein sequencing, a significantly more complex task. Molecules passing through the solid-state nanopores produce current blockades that correlate linearly with their volume in the simplest model. As thinner membranes provide better volume sensitivity, 2D materials such as graphene and MoS2 membranes have been explored. Molecular dynamics studies have primarily focused on the translocation of the homogeneous polypeptide chains through 2D membranes. In this study, we investigated the translocation of 20 single amino acids through the monolayer and bilayer graphene nanopores using the all-atom molecular dynamics. These studies were motivated by the fact that single amino acids, as fundamental units of peptide chains, provide a simpler model for understanding pore-molecule interactions during translocations by eliminating the neighbour effects found in chains. Herein, it is shown that the correlation between the ionic current blockade and the volume of single amino acids is strongly affected by their orientation at the pore, especially when the molecule is static at the pore. We explained this phenomenon by the fact that with increasing vdW volume, the amino acid in a particular orientation has a longer projection along the perpendicular direction of the pore plane. We demonstrated distinctive current and force signals for different amino-acid translocations. We observed that some of the smaller amino acids with low molecular volume produced disproportionately high current blockades in a particular orientation due to their lower structural fluctuations during translocation. We investigated how the dipole moment (of the translocating amino acids) and its alignment with the electric field in the pores were linked with our observations.

Molecular Dynamics of Peptide Sequencing through MoS2 Solid-State Nanopores for Binary Encoding Applications

Biological peptides have emerged as promising candidates for data storage applications due to their versatility and programmability. Recent advances in peptide synthesis and sequencing technologies have enabled the development of peptide-based data storage systems for realizing novel information storage technologies with enhanced capacity, durability, and data access speeds. In this study, we performed coarse-grained peptide sequencing of 12 distinct sequences through single-layer MoS2 solid-state nanopores (SSNs) using molecular dynamics (MD). Peptide sequences were composed of 1 positively charged, 1 negatively charged, and 4 neutral amino acids, with the position of amino acids in the sequence being shuffled to generate all possible configurations. From MD, the goal was to evaluate the efficiency of these peptide sequences to encode binary information based on ionic current traces monitored during their passage through the SSNs. Classification approaches using LightGBM were trained and tested to analyze different sequence factors such as the position of amino acids or the spacing between charged amino acids in the sequences. Our findings reveal the presence of two distinct groups of sequences determined by the relative position of the positively charged amino acid compared to the negatively charged amino acid. Furthermore, we observe a strong correlation between discrimination accuracy and the separation in the sequence between charged amino acids, depending on the number of adjacent neutral amino acids between them. Finally, MD allowed us to establish the nonlinear relationship between amino acid positions inside the pore (called sequence motifs) and fluctuations in ionic current traces to discriminate false positives and to enable effective training of machine learning classification algorithms. These very promising results emphasized the best approaches to design peptide sequences as building blocks for molecular data storage. Finally, this study highlights the potential of the proposed approach for designing peptide sequence combinations that could help the development of efficient, scalable, and reliable molecular data storage solutions, with future research focused on encoding longer binary chains to enhance storage capacity and support the goal of stable, energy-free biological systems.

Nanopore Identification of Polyglutamine Length via Cross-Slit Sensing

Nanopore sensing is now reshaping analytical proteomics with its simplicity, convenience, and high sensitivity. Determining the length of polyglutamine (polyQ) is crucial for the rapid screening of Huntington's disease. In this computational study, we present a cross-nanoslit detection approach to determine the polyQ length, where the nanoslit is carved within a two-dimensional (2D) in-plane heterostructure of graphene (GRA) and hexagonal boron nitride (hBN). We designed a heterostructure with an hBN strip embedded in the graphene sheet. With such a design, polyQ peptides can spontaneously and linearly stretch out on the hBN stripe. By tuning the strength of an external in-plane electric field, molecular transportation of polyQ peptides along the hBN stripe can be effectively regulated. Subsequent cross-nanoslit motion can be applied to record time-dependent electric signals. The signal features are then utilized to train the machine learning classification models. The machine-learning-assisted recognition enables accurate determination of the protein's length. This nanoslit-sensing method may offer theoretical guidance on 2D heterostructure design for the detection of polyQ peptide lengths and rapid screening of protein-related diseases.

Evolution of nanopores in hexagonal boron nitride

The engineering of atomically-precise nanopores in two-dimensional materials presents exciting opportunities for both fundamental science studies as well as applications in energy, DNA sequencing, and quantum information technologies. The exceptional chemical and thermal stability of hexagonal boron nitride (h-BN) suggest that exposed h-BN nanopores will retain their atomic structure even when subjected to extended periods of time in gas or liquid environments. Here we employ transmission electron microscopy to examine the time evolution of h-BN nanopores in vacuum and in air and find, even at room temperature, dramatic geometry changes due to atom motion and edge contamination adsorption, for timescales ranging from one hour to one week. The discovery of nanopore evolution contrasts with general expectations and has profound implications for nanopore applications of two-dimensional materials.

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.

Single-Entity Detection With TEM-Fabricated Nanopores

Nanopore-based single-entity detection shows immense potential in sensing and sequencing technologies. Solid-state nanopores permit unprecedented detail while preserving mechanical robustness, reusability, adjustable pore size, and stability in different physical and chemical environments. The transmission electron microscope (TEM) has evolved into a powerful tool for fabricating and characterizing nanometer-sized pores within a solid-state ultrathin membrane. By detecting differences in the ionic current signals due to single-entity translocation through the nanopore, solid-state nanopores can enable gene sequencing and single molecule/nanoparticle detection with high sensitivity, improved acquisition speed, and low cost. Here we briefly discuss the recent progress in the modification and characterization of TEM-fabricated nanopores. Moreover, we highlight some key applications of these nanopores in nucleic acids, protein, and nanoparticle detection. Additionally, we discuss the future of computer simulations in DNA and protein sequencing strategies. We also attempt to identify the challenges and discuss the future development of nanopore-detection technology aiming to promote the next-generation sequencing technology.

Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?

A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.

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.

Single nucleotide detection using bilayer MoS2 nanopores with high efficiency

Single nucleotide detection is important for early detection of diseases and for DNA sequencing. Monolayer (ML) MoS₂ nanopores have been used to identify and distinguish single nucleotides with good signal-to-noise ratio in the recent past. Here, we use a bilayer (BL) MoS₂ nanopore (∼1.3 nm thick) to detect distinct single nucleotides with high spatial resolution and longer dwell time. In this study, the performance of similar sized (<3 nm) ML and BL MoS₂ nanopores for detection of a single nucleotide has been compared. Both single nucleotide and single stranded DNA translocations through them are studied. For single nucleotide detection, we observe that BL MoS₂ nanopores demonstrate twice the dwell time as compared to ML MoS₂ nanopores with 95% confidence. Single nucleotide detection rate for BL MoS₂ nanopores (50–60 nucleotides per s) is five-fold higher as compared to ML MoS₂ nanopores (10–15 nucleotides per s) in 10 pM analyte concentration. For single stranded DNA, we observe 89% (for 60 DNA molecules detected) single nucleotide detection efficiency with BL MoS₂ nanopores as compared to 85% for ML MoS₂. The DNA sequencing efficiency through BL MoS₂ nanopores is also found to be 8–10% better than through ML MoS₂ nanopores, irrespective of DNA sequencing orientation. Thus, owing to improved analyte/nanopore charge interaction BL MoS₂ nanopores can be used for single nucleotide detection with high resolution due to longer dwell time, detection rate and efficiency. This study demonstrates the improved ability of BL MoS₂ nanopores in sequencing DNA with 8–10% higher efficiency, two-times temporally resolved single-nucleotide current signatures and five-times higher detection rate, compared to ML MoS₂ nanopores.

Bilayer MoS₂ nanopores are suitable for fast and high-efficiency single nucleotide detection and DNA sequencing due to fast analyte capture and improved dwell time.

Microscopic Detection Analysis of Single Molecules in MoS2 Membrane Nanopores

A systematic microscopic analysis of the various resistive effects involved in the electronic detection of single biomolecules in a nanopore of a MoS₂ nanoribbon is presented. The variations of the transverse electronic current along the two-dimensional (2D) membrane due to the translocation of DNA and protein molecules through the pore are obtained by model calculations based on molecular dynamics (MD) and Boltzmann transport formalism, which achieved good agreement with the experimental data. Our analysis points to a self-consistent interaction among ions, charge carriers around the pore rim, and biomolecules. It provides a comprehensive understanding of the effects of the electrolyte concentration, pore size, nanoribbon geometry, and also the doping polarity of the nanoribbon on the electrical sensitivity of the nanopore in detecting biomolecules. These results can be utilized for fine-tuning the design parameters in the fabrication of highly sensitive 2D nanopore biosensors.

Nanopore sensing of single-biomolecules: a new procedure to identify protein sequence motifs from molecular dynamics

Solid-state nanopores have emerged as one of the most versatile tools for single-biomolecule detection and characterization. Nanopore sensing is based on the measurement of variations in ionic current as charged biomolecules immersed in an electrolyte translocate through nanometer-sized channels, in response to an external voltage applied across the membrane. The passage of a biomolecule through a pore yields information about its structure and chemical properties, as demonstrated experimentally with sub-microsecond temporal resolution. However, extracting the sequence of a biomolecule without the information about its position remains challenging due to the fact there is a large variability of sensing events recorded. In this paper, we performed microsecond time scale all-atom non-equilibrium Molecular Dynamics (MD) simulations of peptide translocation (motifs of alpha-synuclein, associated with Parkinson's disease) through single-layer MoS2 nanopores. First, we present an analysis based on the current threshold to extract and characterize meaningful sensing events from ionic current time series computed from MD. Second, a mechanism of translocation is established, for which side chains of each amino acid are oriented parallel to the electric field when they are translocating through the pore and perpendicular otherwise. Third, a new procedure based on the permutation entropy (PE) algorithm is detailed to identify protein sequence motifs related to ionic current drop speed. PE is a technique used to quantify the complexity of a given time series and it allows the detection of regular patterns. Here, PE patterns were associated with protein sequence motifs composed of 1, 2 or 3 amino acids. Finally, we demonstrate that this very promising procedure allows the detection of biological mutations and could be tested experimentally, despite the fact that reconstructing the sequence information remains unachievable at this time.

Biomolecular Material Recognition in Two Dimensions: Peptide Binding to Graphene, h-BN, and MoS2 Nanosheets as Unique Bioconjugates

Two-dimensional nanosheet-based materials such as graphene, hexagonal boron nitride, and MoS₂ represent intriguing structures for a variety of biological applications ranging from biosensing to nanomedicine. Recent advances have demonstrated that peptides can be identified with affinity for these three materials, thus generating a highly unique bioconjugate interfacial system. This Review focuses on recent advances in the formation of bioconjugates of these types, paying particular attention to the structure/function relationship of the peptide overlayer. This is achieved through the amino acid composition of the nanosheet binding peptides, thus allowing for precise control over the properties of the final materials. Such bioconjugate systems offer rapid advances via direct property control that remain difficult to achieve for biological applications using nonbiological approaches.