Laser-based temperature control to study the roles of entropy and enthalpy in polymer-nanopore interactions

Structure difference of Jack bean urease and Helicobacter pylori urease on binding interactions with quercetin

Urease catalyzes the hydrolysis of urea to carbamate and ammonia, leading to nitrogen loss, environmental pollution, and health issues, so numerous compounds have been screened for urease inhibition using Jack bean urease (JBU) and H. pylori urease (HPU) without consideration their structure difference. Previous studies have shown that the same inhibitor can exhibit distinct inhibitory effects on JBU and HPU, but limited papers focus on the effects mechanism. In this study, we systematically investigated the thermodynamic and kinetic properties of JBU and HPU binding with quercetin, focusing on the structural effects on both commonly studied ureases. The results revealed that quercetin inhibited both JBU and HPU activities, with IC50 values of 16.76 ± 0.77 μM and 36.17 ± 0.73 μM, respectively. Inhibition was identified as noncompetitive for JBU and mixed-competitive for HPU. Quercetin interacted with both JBU and HPU with quenching rate constants (Kq) of 3.72 ± 0.18 × 1013 M-1 s-1 for JBU and 0.28 ± 0.04 × 1013 M-1 s-1 for HPU. Molecular docking revealed that quercetin mainly bound to the flap region of JBU, inhibiting its function, and the JBU-quercetin complex had high binding stability and low binding free energy.

Photothermally Heated Asymmetric Thin Nanopores Suggest the Influence of Temperature on the Intermediate Conformational State of Cytochrome c in an Electric Field

Nanopore sensing is a label-free single-molecule technique that enables the study of the dynamical structural properties of proteins. Here, we detect the translocation of cytochrome c (Cyt c) through an asymmetric thin nanopore with photothermal heating to evaluate the influence of temperature on Cyt c conformation during its translocation in an electric field. Before Cyt c translocates through an asymmetric thin SiNx nanopore, ∼1 ms trapping events occur due to electric field-induced denaturation. These trapping events were corroborated by a control analysis with a transmission electron microscopy-drilled pore and denaturant buffer. Cyt c translocation events exhibited markedly greater broad current blockade when the pores were photothermally heated. Collectively, our molecular dynamics simulation predicted that an increased temperature facilitates denaturation of the α-helical structure of Cyt c, resulting in greater blockade current during Cyt c trapping. Our photothermal heating method can be used to study the influence of temperature on protein conformation at the single-molecule level in a label-free manner.

Harnessing Information Thermodynamics: Conversion of DNA Information into Mechanical Work in RNA Transcription and Nanopore Sequencing

Recent advancements in information thermodynamics have revealed that information can be directly converted into mechanical work. Specifically, RNA transcription and nanopore sequencing serve as prime examples of this conversion, by reading information from a DNA template. This paper introduces an information thermodynamic model in which these molecular motors can move along the DNA template by converting the information read from the template DNA into their own motion. This process is a stochastic one, characterized by significant fluctuations in forward movement and is described by the Fokker-Planck equation, based on drift velocity and diffusion coefficients. In the current study, it is hypothesized that by utilizing the sequence information of the template DNA as mutual information, the fluctuations can be reduced, thereby biasing the forward movement on DNA and, consequently, reducing reading errors. Further research into the conversion of biological information by molecular motors could unveil new applications, insights, and important findings regarding the characteristics of information processing in biology.

Nanomaterials in electrochemical nanobiosensors of miRNAs

Nanomaterial-based biosensors have received significant attention owing to their unique properties, especially enhanced sensitivity. Recent advancements in biomedical diagnosis have highlighted the role of microRNAs (miRNAs) as sensitive prognostic and diagnostic biomarkers for various diseases. Current diagnostics methods, however, need further improvements with regards to their sensitivity, mainly due to the low concentration levels of miRNAs in the body. The low limit of detection of nanomaterial-based biosensors has turned them into powerful tools for detecting and quantifying these biomarkers. Herein, we assemble an overview of recent developments in the application of different nanomaterials and nanostructures as miRNA electrochemical biosensing platforms, along with their pros and cons. The techniques are categorized based on the nanomaterial used.

Cluster-Enhanced Nanopore Sensing of Ovarian Cancer Marker Peptides in Urine

The development of novel methodologies that can detect biomarkers from cancer or other diseases is both a challenge and a need for clinical applications. This partly motivates efforts related to nanopore-based peptide sensing. Recent work has focused on the use of gold nanoparticles for selective detection of cysteine-containing peptides. Specifically, tiopronin-capped gold nanoparticles, trapped in the cis-side of a wild-type α-hemolysin nanopore, provide a suitable anchor for the attachment of cysteine-containing peptides. It was recently shown that the attachment of these peptides onto a nanoparticle yields unique current signatures that can be used to identify the peptide. In this article, we apply this technique to the detection of ovarian cancer marker peptides ranging in length from 8 to 23 amino acid residues. It is found that sequence variability complicates the detection of low-molecular-weight peptides (<10 amino acid residues), but higher-molecular-weight peptides yield complex, high-frequency current fluctuations. These fluctuations are characterized with chi-squared and autocorrelation analyses that yield significantly improved selectivity when compared to traditional open-pore analysis. We demonstrate that the technique is capable of detecting the only two cysteine-containing peptides from LRG-1, an emerging protein biomarker, that are uniquely present in the urine of ovarian cancer patients. We further demonstrate the detection of one of these LRG-1 peptides spiked into a sample of human female urine.

Narrowing Signal Distribution by Adamantane Derivatization for Amino Acid Identification Using an α-Hemolysin Nanopore

The rapid progress in nanopore sensing has sparked interest in protein sequencing. Despite recent notable advancements in amino acid recognition using nanopores, chemical modifications usually employed in this process still need further refinements. One of the challenges is to enhance the chemical specificity to avoid downstream misidentification of amino acids. By employing adamantane to label proteinogenic amino acids, we developed an approach to fingerprint individual amino acids using the wild-type α-hemolysin nanopore. The unique structure of adamantane-labeled amino acids (ALAAs) improved the spatial resolution, resulting in distinctive current signals. Various nanopore parameters were explored using a machine-learning algorithm and achieved a validation accuracy of 81.3% for distinguishing nine selected amino acids. Our results not only advance the effort in single-molecule protein characterization using nanopores but also offer a potential platform for studying intrinsic and variant structures of individual molecules.

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.

Decoration of Ultramicrotome-Cut Polymers with Silver Nanoparticles: Effect of Post-Deposition Laser Treatment

Today, ultramicrotome cutting is a practical tool, which is frequently applied in the preparation of thin polymeric films. One of the advantages of such a technique is the decrease in surface roughness, which enables an effective recording of further morphological changes of polymeric surfaces during their processing. In view of this, we report on ultramicrotome-cut polymers (PET, PEEK) modified by a KrF excimer laser with simultaneous decoration by AgNPs. The samples were immersed into AgNP colloid, in which they were exposed to polarized laser light. As a result, both polymers changed their surface morphology while simultaneously being decorated with AgNPs. KrF laser irradiation of the samples resulted in the formation of ripple-like structures on the surface of PET and worm-like ones in the case of PEEK. Both polymers were homogeneously covered by AgNPs. The selected area of the samples was then irradiated by a violet semiconductor laser from the confocal laser scanning microscope with direct control of the irradiated area. Various techniques, such as AFM, FEGSEM, and CLSM were used to visualize the irradiated area. After irradiation, the reverse pyramid was formed for both types of polymers. PET samples exhibited thicker transparent reverse pyramids, whereas PEEK samples showed thinner brownish ones. We believe that his technique can be effectively used for direct polymer writing or the preparation of stimuli-responsive nanoporous membranes.

Localized Nanopore Fabrication via Controlled Breakdown

Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.

Nanopore Analysis as a Tool for Studying Rapid Holliday Junction Dynamics and Analyte Binding

Holliday junctions (HJs) are an important class of nucleic acid structure utilized in DNA break repair processes. As such, these structures have great importance as therapeutic targets and for understanding the onset and development of various diseases. Single-molecule fluorescence resonance energy transfer (smFRET) has been used to study HJ structure-fluctuation kinetics, but given the rapid time scales associated with these kinetics (approximately sub-milliseconds) and the limited bandwidth of smFRET, these studies typically require one to slow down the structure fluctuations using divalent ions (e.g., Mg²⁺). This modification limits the ability to understand and model the underlying kinetics associated with HJ fluctuations. We address this here by utilizing nanopore sensing in a gating configuration to monitor DNA structure fluctuations without divalent ions. A nanopore analysis shows that HJ fluctuations occur on the order of 0.1-10 ms and that the HJ remains locked in a single conformation with short-lived transitions to a second conformation. It is not clear what role the nanopore plays in affecting these kinetics, but the time scales observed indicate that HJs are capable of undergoing rapid transitions that are not detectable with lower bandwidth measurement techniques. In addition to monitoring rapid HJ fluctuations, we also report on the use of nanopore sensing to develop a highly selective sensor capable of clear and rapid detection of short oligo DNA strands that bind to various HJ targets.

Probing Protein Nanopores with Poly(ethylene glycol)s

Neutral water-soluble poly(ethylene glycol)s (PEGs) have been extensively explored in protein nanopore research for the past several decades. The principal use of PEGs is to investigate the membrane protein ion channel physical characteristics and transport properties. In addition, protein nanopores are used to study polymer-protein interactions and polymer physicochemical properties. In this review, we focus on the biophysical studies on probing protein ion channels with PEGs, specifically on nanopore sizing by PEG partitioning. We discuss the fluctuation analysis of ion channel currents in response to the PEGs moving within their confined geometries. The advantages, limitations, and recent developments of the approach are also addressed. This article is protected by copyright. All rights reserved.

Voltage-activated complexation of α-synuclein with three diverse β-barrel channels: VDAC, MspA, and α-hemolysin

Voltage-activated complexation is the process by which a transmembrane potential drives complex formation between a membrane-embedded channel and a soluble or membrane-peripheral target protein. Metabolite and calcium flux across the mitochondrial outer membrane was shown to be regulated by voltage-activated complexation of the voltage-dependent anion channel (VDAC) and either dimeric tubulin or α-synuclein (αSyn). However, the roles played by VDAC's characteristic attributes-its anion selectivity and voltage gating behavior-have remained unclear. Here, we compare in vitro measurements of voltage-activated complexation of αSyn with three well-characterized β-barrel channels-VDAC, MspA, and α-hemolysin-that differ widely in their organism of origin, structure, geometry, charge density distribution, and voltage gating behavior. The voltage dependences of the complexation dynamics for the different channels are observed to differ quantitatively but have similar qualitative features. In each case, energy landscape modeling describes the complexation dynamics in a manner consistent with the known properties of the individual channels, while voltage gating does not appear to play a role. The reaction free energy landscapes thus calculated reveal a non-trivial dependence of the αSyn/channel complex stability on the surface density of αSyn.

Protein identification by nanopore peptide profiling

Nanopores are single-molecule sensors used in nucleic acid analysis, whereas their applicability towards full protein identification has yet to be demonstrated. Here, we show that an engineered Fragaceatoxin C nanopore is capable of identifying individual proteins by measuring peptide spectra that are produced from hydrolyzed proteins. Using model proteins, we show that the spectra resulting from nanopore experiments and mass spectrometry share similar profiles, hence allowing protein fingerprinting. The intensity of individual peaks provides information on the concentration of individual peptides, indicating that this approach is quantitative. Our work shows the potential of a low-cost, portable nanopore-based analyzer for protein identification.

Peptide mass fingerprinting is a traditional approach for protein identification by mass spectrometry. Here, the authors provide evidence that peptide mass fingerprinting is also feasible using FraC nanopores, demonstrating protein identification based on nanopore measurements of digested peptides.

Nanopore sensing: A physical-chemical approach

Protein nanopores have emerged as an important class of sensors for the understanding of biophysical processes, such as molecular transport across membranes, and for the detection and characterization of biopolymers. Here, we trace the development of these sensors from the Coulter counter and squid axon studies to the modern applications including exquisite detection of small volume changes and molecular reactions at the single molecule (or reactant) scale. This review focuses on the chemistry of biological pores, and how that influences the physical chemistry of molecular detection.