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

Stimuli-Responsive Ion Transport Regulation in Nanochannels by Adhesion-Induced Functionalization of Macroscopic Outer Surface

Responsive regulation of ion transport through nanochannels is crucial in the design of smart nanofluidic devices for sequencing, sensing, and water-energy nexus. Functionalization of the inner wall of the nanochannel enhances interaction with ions and fluid but restricts versatile chemical approaches and accurate characterizations of fluidic interfaces. Herein, we reveal a responsive regulating mechanism of ion transport through nanochannels by polydopamine (PDA)-induced functionalization on the macroscopic outer surface of nanochannels. Responsive molecules were codeposited with PDA on the outer surface of nanochannels and formed a valve of nanometer thickness to manually manipulate ion transport by changing its gap spacing, surface charge, and wettability under external stimulus. The response ratio can be up to 100-fold by maximizing the proportion of responsive molecules on the outer surface. Laminating the codepositions of different responsive molecules with PDA on the channel's outer surface produces multiple responses. A nearly universal adhesion of PDA with responsive molecules on the open outer surface induces nanochannels responsive to different external stimuli with variable response ratios and arbitrary combinations. The results challenge the primary role of functionalization on the nanoconfined interface of nanofluidics and open opportunities for developing new-style nanofluidic devices through the functionalization of macroscopic interface.

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.

Biohybrid Membrane Formation by Directed Insertion of Aquaporin into a Solid-State Nanopore

Biohybrid nanopores combine the durability of solid-state nanopores with the precise structure and function of biological nanopores. Particular care must be taken to control how biological nanopores adapt to their surroundings once they come into contact with the solid-state nanopores. Two major challenges are to precisely control this adaptability under dynamic conditions and provide predesigned functionalities that can be manipulated for engineering applications. In this work, we report on the computational design of a distinctive class of biohybrid active membrane layers, built from the directed-insertion of an aquaporin-incorporated lipid nanodisc into a model alkyl-functionalized silica pore. We show that in an aqueous environment when a pressure difference exists between the two sides of the solid-state nanopore, the preferential interactions between the hydrocarbon tail of the lipid molecules that surround the aquaporin protein and the alkyl group functionalizing the interior surface of the silica nanopore enable the insertion of the aquaporin-incorporated lipid shell into the nanopore by forcing out the water molecules. The same preferential interactions are responsible for the structural stability of the inserted aquaporin-incorporated lipid shell as well as the water sealing properties of the lipid-alkyl interface. We further show that the aquaporin protein stabilized in the alkyl-functionalized silica nanopore preserves its biological structure and function in both pure and saline water, and, remarkably, its water permeability is equal to the one measured in the biological environment. The designed biohybrid membrane could pave the way for the development of durable transformative devices for water filtration.

ProtSeq: Toward high-throughput, single-molecule protein sequencing via amino acid conversion into DNA barcodes

We demonstrate early progress toward constructing a high-throughput, single-molecule protein sequencing technology utilizing barcoded DNA aptamers (binders) to recognize terminal amino acids of peptides (targets) tethered on a next-generation sequencing chip. DNA binders deposit unique, amino acid-identifying barcodes on the chip. The end goal is that, over multiple binding cycles, a sequential chain of DNA barcodes will identify the amino acid sequence of a peptide. Toward this, we demonstrate successful target identification with two sets of target-binder pairs: DNA-DNA and Peptide-Protein. For DNA-DNA binding, we show assembly and sequencing of DNA barcodes over six consecutive binding cycles. Intriguingly, our computational simulation predicts that a small set of semi-selective DNA binders offers significant coverage of the human proteome. Toward this end, we introduce a binder discovery pipeline that ultimately could merge with the chip assay into a technology called ProtSeq, for future high-throughput, single-molecule protein sequencing.

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Designed ProtSeq protein sequencing method compatible with widely used NGS technology

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Built Target-Switch SELEX to isolate aptamers specific to N-terminal amino acids (AAs)

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Showed binding, ligation, cleavage, and NGS of six DNA binders in ordered barcode chain

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Developed pipeline to deconvolve AAs from DNA barcodes to identify putative proteins

On the chirality-dependent adsorption behavior of volatile organic compounds on carbon nanotubes

The capture and removal of volatile organic compounds (VOCs) have received extensive attention due to their toxicity and carcinogenicity. In order to extend the applications of carbon nanotubes (CNTs) in this field, a deep understanding of the interaction mechanism between VOCs and CNTs is crucial. In this article, molecular dynamics simulations are performed to systematically investigate the multi-molecule adsorption behavior of four representative VOC species on CNTs with a variety of chirality indices. Simulation results reveal that different VOC species exhibit significantly different adsorption preferences on CNTs. For both zigzag and armchair CNTs, the adsorption affinity is positively correlated with the hydrophobicity of VOC molecules and follows the order of toluene > ether > acetone > methanol. This adsorption preference is supported by the binding free energy calculations resulting from the umbrella sampling algorithm. Moreover, the adsorption affinity increases with the diameter of both zigzag and armchair CNTs. Furthermore, the effects of diameter become more significant for those VOC species possessing higher hydrophobicity. As for the effects of chirality, zigzag CNTs show greater adsorption affinity than armchair ones with similar diameters. However, simulation results also indicate that the adsorption affinity does not vary monotonically from zigzag to armchair orientations, leading to additional complexities of harvesting and elimination of VOC molecules in terms of CNTs. Results and data analysis presented in this work suggest that CNT chirality is an important factor for controlling the adsorption of harmful VOC molecules on CNT surfaces.

Mapping the morphological identifiers of distinct conformations via the protein translocation current in nanopores

Conformational changes of proteins play a vital role in implementing their functions and revealing the underlying mechanisms in various biological processes. It is still challenging to monitor protein conformations with temporal fingerprints of current-resistance pulses in the nanopore technique. Here the low-resolution morphologies of different conformations of a typical integrin, α_xβ₂, were estimated via relative blockade currents simulated from all-atom molecular dynamics (MD). Distinct conformational states of α_xβ₂ were directly explained by the volume and shape identifiers. Protein modulation in ionic current was analyzed from the conductivity distribution inside the protein-blocked nanopore. Combining a discrete model with spheroidal approximation, a MD-based approach was developed to theoretically predict the volume and shape of the nanopore for sensing α_xβ₂. This method was also applicable in specifying morphological identifiers of six other proteins, and the theoretical predictions are in good agreement with the experimental measurements. These results potentiated the validity of this method for the conformational identification of proteins in nanopores.