Controlled Genetic Encoding of Unnatural Amino Acids in a Protein Nanopore

Conventional protein engineering methods for modifying protein nanopores are typically limited to 20 natural amino acids, which restrict the diversity of the nanopores in structure and function. To enrich the chemical environment inside the nanopore, we employed the genetic code expansion (GCE) technique to site-specifically incorporate the unnatural amino acid (UAA) into the sensing region of aerolysin nanopores. This approach leveraged the efficient pyrrolysine-based aminoacyl-tRNA synthetase-tRNA pair for a high yield of pore-forming protein. Both molecular dynamics (MD) simulations and single-molecule sensing experiments demonstrated that the conformation of UAA residues provided a favorable geometric orientation for the interactions of target molecules and the pore. This rationally designed chemical environment enabled the direct discrimination of multiple peptides containing hydrophobic amino acids. Our work provides a new framework for endowing nanopores with unique sensing properties that are difficult to achieve using classical protein engineering approaches.     

Ion transport and selectivity in nanopores with spatially inhomogeneous fixed charge distributions

Polymeric nanopores with fixed charges show ionic selectivity when immersed in aqueous electrolyte solutions. The understanding of the electrical interaction between these charges and the mobile ions confined in the inside nanopore solution is the key issue in the design of potential applications. The authors have theoretically described the effects that spatially inhomogeneous fixed charge distributions exert on the ionic transport and selectivity properties of the nanopore. A comprehensive set of one-dimensional distributions including the skin, core, cluster, and asymmetric cases are analyzed on the basis of the Nernst-Planck equations. Current-voltage curves, nanopore potentials, and transport numbers are calculated for the above distributions and compared with those obtained for a homogeneously charged nanopore with the same average fixed charge concentration. The authors have discussed if an appropriate design of the spatial fixed charge inhomogeneity can lead to an enhancement of the transport and selectivity with respect to the homogeneous nanopore case. Finally, they have compared the theoretical predictions with relevant experimental data.     

基于静电效应的石墨烯纳米孔选择性渗透特性

Two-dimensional graphene nanopores have proved to be a very effective molecular sieve with ultra-high molecular permeance due to the atomic thickness of graphene sheets. The mechanism of graphene nanopores for molecular sieving is generally the size-sieving effect of different molecules. However, high-selective molecular separation is difficult to realize based only on the size-sieving effect. Therefore, graphene nanopore-based membranes usually present high permeance but a moderate selectivity, such that the separation performance cannot far exceed those of traditional separation membranes. In this study, the effects of charges on graphene surfaces on the selective permeation of CO₂/N₂ mixtures through a graphene nanopore is studied using molecular dynamics simulations; its purpose to realize electrostatic effect-based selective molecular permeation through graphene nanopores and find a promising method to improve the selectivity of molecular separation. The simulation results show that graphene nanopores with negative charges have higher CO₂ permeance and lower N₂ permeance and, thus, present a high selectivity for the separation of the CO₂/N₂ mixtures. The graphene nanopore with positive charges, however, does not improve the selectivity. The electrostatic effect-based selectivity of graphene nanopores is related to the different molecular adsorption abilities on the graphene surface with charges. For negative charges, the adsorption ability of CO₂ molecules increases and the number of permeated molecules via surface mechanism increases and the experience time during the permeation process also increases; ultimately the CO₂ permeance increases with increasing the charge density. For the molecules permeated through the surface mechanism, they are firstly adsorbed onto the graphene surface and then diffuse to the pore region for the ultimate permeation; thus, their experience time is longer than that of the molecules permeated through a direct mechanism. Therefore, a longer experience time means a more significant contribution of the surface flux to the total flux. At high surface charge densities, the contribution of surface flux is dominated and thus the experience time is longer. For CO₂ molecules, the permeation rates increase with increasing the surface charge density. Namely, a higher experience time corresponds to a higher permeation rate for CO₂ molecules. A decrease of N₂ permeance with increasing the charge density is correlated to the increasing CO₂ permeance via the inhibition effects of non-permeating components on the permeation of permeating components. For positive charges, the adsorption abilities of CO₂ and N₂ molecules have no obvious variation with the charge density and their permeance is constant; therefore, the graphene nanopore still has no electrostatic effect-based selectivity.     

Scan-rate-dependent ion current rectification and rectification inversion in charged conical nanopores

Herein we report a theoretical study of diode-like behavior of negatively charged (e.g., glass or silica) nanopores at different potential scan rates (1-1000 V·s(-1)). Finite element simulations were used to determine current-voltage characteristics of conical nanopores at various electrolyte concentrations. This study demonstrates that significant changes in rectification behavior can be observed at high scan rates because the mass transport of ionic species appears sluggish on the time scale of the voltage scan. In particular, it explains the influence of the potential scan rate on the nanopore rectifying properties in the cases of classical rectification, rectification inversion, and the "transition" rectification domain where the rectification direction in the nanopore could be modulated according to the applied scan rate.     

Investigation of entrance effects on particle electrophoretic behavior near a nanopore for resistive pulse sensing

Resistive pulse sensing using solid-state nanopores provides a unique platform for detecting the structure and concentration of molecules of different types of analytes in an electrolyte solution. The capture of an entity into a nanopore is subject not only to the electrostatic force but also the effect of electroosmotic flow originating from the charged nanopore surface. In this study, we theoretically analyze spherical particle electrophoretic behavior near the entrance of a charged nanopore. By investigating the effects of pore size, particle–pore distance, and salt concentration on particle velocity, we summarize dominant mechanisms governing particle behavior for a range of conditions. In the literature, the Helmholtz–Smoluchowski equation is often adopted to evaluate particle translocation by considering the zeta potential difference between the particle and nanopore surfaces. We point out that, due to the difference of the electric field inside and outside the nanopore and the influence from the existence of the particle itself, the zeta potential of the particle, however, needs to be at least 30% higher than that of the nanopore to allow the particle to enter into the nanopore when its velocity is close to zero. Accordingly, we summarize the effective salt concentrations that enable successful particle capture and detection for different pore sizes, offering direct guidance for nanopore applications.     

Transmembrane potential across single conical nanopores and resulting memristive and memcapacitive ion transport

Memristive and memcapacitive behaviors are observed from ion transport through single conical nanopores in SiO(2) substrate. In i-V measurements, current is found to depend on not just the applied bias potential but also previous conditions in the transport-limiting region inside the nanopore (history-dependent, or memory effect). At different scan rates, a constant cross-point potential separates normal and negative hysteresis loops at low and high conductivity states, respectively. Memory effects are attributed to the finite mobility of ions as they redistribute within the negatively charged nanopore under applied potentials. A quantative correlation between the cross-point potential and electrolyte concentration is established.     

A nano-confined charged layer defies the principle of electrostatic interaction

The reactivity between two charged molecules and the activity of charged biomolecules are mainly governed by the principle of electrostatic interaction, i.e., like charges repel and opposite charges attract. In the present study it is shown that the principle of electrostatic interaction is violated in the nano-confined biomimetic environment. Thus a positively charged molecule shows more preference to a positively charged surface compared to a negatively charged surface.     

Quasi one-dimensional nanopores in single-wall carbon nanohorn colloids using grand canonical Monte Carlo simulation aided adsorption technique

The average interstitial nanopore structure of single-wall carbon nanohorn (SWNH) assemblies was determined using X-ray diffraction and grand canonical Monte Carlo (GCMC) simulation aided N(2) adsorption at 77 K. The interstitial nanopores of SWNH assemblies can be regarded as quasi one-dimensional pores due to the partial orientation of the SWNH particles; the average pore width of the interstitial pores is 0.6 nm. Good agreement between the GCMC simulation of a structural model with one-dimensional interstitial nanopores and an experimental adsorption isotherm below P/P(0) = 10(-4) is evidence of the quasi one-dimensionality of the interstitial nanopores. A snapshot from the GCMC simulation showed one-dimensional growth of adsorbed N(2) molecules.     

Single-molecule analysis of interaction between p53TAD and MDM2 using aerolysin nanopores

Protein–protein interactions (PPIs) are regarded as important, but undruggable targets. Intrinsically disordered p53 transactivation domain (p53TAD) mediates PPI with mouse double minute 2 (MDM2), which is an attractive anticancer target for therapeutic intervention. Here, using aerolysin nanopores, we probed the p53TAD peptide/MDM2 interaction and its modulation by small-molecule PPI inhibitors or p53TAD phosphorylation. Although the p53TAD peptide showed short-lived (<100 ms) translocation, the protein complex induced the characteristic extraordinarily long-lived (0.1 s ∼ tens of min) current blockage, indicating that the MDM2 recruitment by p53TAD peptide almost fully occludes the pore. Simultaneously, the protein complex formation substantially reduced the event frequency of short-lived peptide translocation. Notably, the addition of small-molecule PPI inhibitors, Nutlin-3 and AMG232, or Thr18 phosphorylation of p53TAD peptide, were able to diminish the extraordinarily long-lived events and restore the short-lived translocation of the peptide rescued from the complex. Taken together, our results elucidate a novel mechanism of single-molecule sensing for analyzing PPIs and their inhibitors using aerolysin nanopores. This novel methodology may contribute to remarkable improvements in drug discovery targeted against undruggable PPIs.

Using aerolysin nanopores, we probed protein–protein interaction (PPI) between p53TAD and MDM2 and its modulation by small-molecule PPI inhibitors and p53TAD phosphorylation.     

Ion channels of N-terminally linked alamethicin dimers: enhancement of cation-selectivity by substitution of Glu for Gln at position 7

Alamethicin forms voltage-gated ion channels that have moderate cation-selectivity. The enhancement of the cation-selectivity by introducing negatively charged residues at positions 7 and 18 has been studied using the tethered homodimers of alamethicin with Q7 and E18 (di-alm-Q7E18) and its analog with E7 and Q18 (di-alm-E7Q18). In the dimeric peptides, monomer peptides are linked at the N-termini by a disulfide bond. Both the peptides formed long lasting ion channels at cis-positive voltages when added to the cis-side membrane. Their long open duration enabled us to obtain current-voltage (I-V(m)) relations and reversal potentials at the single-channel level by applying a voltage ramp during the channel opening. The reversal potentials measured in asymmetric KCl solutions indicated that ionized E7 provided strong cation-selectivity, whereas ionized E18 little influenced the charge selectivity. This was also the case for the macroscopic charge selectivity determined from the reversal potentials obtained by the macroscopic I-V(m) measurements. The results are accounted for by stronger electrostatic interactions between permeant ions and negatively charged residues at the narrowest part of the pore than at the pore mouth.     

Modulating ion current rectification generating high energy output in a single glass conical nanopore channel by concentration gradient

Inspired by biological systems that have the inherent skill to generate considerable bioelectricity from the salt content in fluids with highly selective ion channels and pumps on cell membranes,herein,a fully abiotic,single glass conical nanopores energy-harvesting is demonstrated.Ion current rectification(ICR)in negatively charged glass conical nanopores is shown to be controlled by the electrolyte concentration gradient depending on the direction of ion diffusion.The degree of ICR is enhanced with the increasing forward concentration difference.An unusual rectification inversion is observed when the concentration gradient is reversely applied.The maximum power output with the individual nanopore approaches10~4pW.This facile and cost-efficient energy-harvesting system has the potential to power tiny biomedical devices or construct future clean-energy recovery plants.     

Optimized polymer-enzyme electrostatic interactions significantly improve penicillin G amidase efficiency in charged PEGA polymers

Hydrolytic yields as high as 80% were obtained by using penicillin G amidase (PGA) on substrates anchored on optimized positively charged PEGA polymers. By increasing the amount of permanent charges inside the polymer, electrostatic interactions between the positively charged PEGA⁺ and the negatively charged PGA (pI=5.2-5.4) were strengthened, thus favouring the accessibility of the bulky enzyme (MW=88 kDa) inside the pores. The effect of different amounts of charges on polymer swelling and protein retention inside the polymer was investigated and correlated to the enzyme efficiency demonstrating that electrostatic interactions predominate over swelling properties in determining enzyme accessibility.     

Modeling the selective partitioning of cations into negatively charged nanopores in water

Partitioning and transport of water and small solutes into and through nanopores are important to a variety of chemical and biological processes and applications. Here we study water structure in negatively charged model cylindrical [carbon nanotube (CNT)-like] nanopores, as well as the partitioning of positive ions of increasing size (Na+, K+, and Cs+) into the pore interior using extensive molecular dynamics simulations. Despite the simplicity of the simulation system-containing a short CNT-like nanopore in water carrying a uniformly distributed charge of qpore=-ne surrounded by n (=0,...,8) cations, making the overall system charge neutral-the results provide new and useful insights on both the pore hydration and ion partitioning. For n=0, that is, for a neutral nanopore, water molecules partition into the pore and form single-file hydrogen-bonded wire spanning the pore length. With increasing n, water molecules enter the pore from both ends with preferred orientations, resulting in a mutual repulsion between oriented water molecules at the pore center and creating a cavity-like low density region at the center. For low negative charge densities on the pore, the driving force for partitioning of positive ions into the pore is weak, and no partitioning is observed. Increasing the pore charge gradually leads to partitioning of positive ions into the pore. Interestingly, over a range of intermediate negative charge densities, nanopores display both thermodynamic as well as kinetic selectivity toward partitioning of the larger K+ and Cs+ ions into their interior over the smaller Na+ ions. Specifically, the driving force is in the order K+>Cs+>Na+, and K+ and Cs+ ions enter the pore much more rapidly than Na+ ions. At higher charge densities, the driving force for partitioning increases for all cations-it is highest for K+ ions-and becomes similar for Na+ and Cs+ ions. The variation of thermodynamic driving force and the average partitioning time with the pore charge density together suggest the presence of free energy barriers in the partitioning process. We discuss the role of ion hydration in the bulk and in the pore interior as well as of the pore hydration in determining the barrier heights for ion partitioning and the observed thermodynamic and kinetic selectivities.     

The role of electrostatic interactions on the rejection of organic solutes in aqueous solutions with nanofiltration

The effects of electrostatic interactions on the rejection of organic solutes with nanofiltration membranes were investigated. For two different membranes, the rejection of selected organic acids, positively and negatively charged pharmaceuticals and neutral pharmaceuticals was investigated at different feed water chemistries (different ionic strengths and pH conditions, with and without the presence of NOM and divalent cations). It was concluded that for negatively charged membranes, electrostatic repulsion leads to an increase of the rejection of negatively charged solutes and electrostatic attraction leads to a decrease of the rejection of positively charged solutes, compared to neutral solutes. Neutral and positively charged solutes engage in hydrophobic interactions with negatively charged membranes, whereas negatively charged solutes do not engage in hydrophobic interactions since they cannot approach the membrane surface. This provides proof for the theory of an increased concentration of positively charged organic solutes and a decreased concentration of negatively charged organic solutes at the membrane surface compared to the bulk fluid. This concept may be denoted as “charge concentration polarisation”. The concept was further used as a modelling tool to predict the effects of electrostatic interactions on the rejection of trace organic solutes.     

Scalable synthesis and coupling of quaternary α-arylated amino acids: α-aryl substituents are tolerated in α-helical peptides

Quaternary amino acids are important tools for the modification and stabilisation of peptide secondary structures. Here we describe a practical and scalable synthesis applicable to quaternary alpha-arylated amino acids (Q4As), and the development of solid-phase synthesis conditions for their incorporation into peptides. Monomeric and dimeric α-helical peptides are synthesised with varying degrees of Q4A substitution and their structures examined using biophysical methods. Both enantiomers of the Q4As are tolerated in folded monomeric and oligomeric α-helical peptides, with the (R)-enantiomer slightly more so than the (S).

Both R and S enantiomers of Fmoc-protected amino acids bearing α-aryl substituents may be made on gram scale. Solid-phase synthesis leads to helical peptides unperturbed by the presence of these additional α-aryl groups.     

Dynamics of Simultaneous, Single Ion Transport through Two Single-Walled Carbon Nanotubes: Observation of a Three-State System

The ability to actively manipulate and transport single molecules in solution has the potential to revolutionize chemical synthesis and catalysis. In previous work, we developed a nanopore platform using the interior of a single-walled carbon nanotube (diameter = 1.5 nm) for the Coulter detection of single cations of Li(+), K(+), and Na(+). We demonstrate that as a result of their fabrication, such systems have electrostatic barriers present at their ends that are generally asymmetric, allowing for the trapping of ions. We show that above this threshold bias, traversing the nanopore end is not rate-limiting and that the pore-blocking behavior of two parallel nanotubes follows an idealized Markov process with the electrical potential. Such nanopores may allow for high-throughput linear processing of molecules as new catalysts and separation devices.     

Alpha-helix-inducing dimerization of synthetic polypeptide scaffolds on gold

Designed, synthetic polypeptides that assemble into four-helix bundles upon dimerization in solution were studied with respect to folding on planar gold surfaces. A model system with controllable dimerization properties was employed, consisting of negatively and positively charged peptides. Circular dichroism spectroscopy and surface plasmon resonance based measurements showed that at neutral pH, the peptides were able to form heterodimers in solution, but unfavorable electrostatic interactions prevented the formation of homodimers. The dimerization propensity was found to be both pH- and buffer-dependent. A series of infrared absorption-reflection spectroscopy experiments of the polypeptides attached to planar gold surfaces revealed that if the negatively charged peptide was immobilized from a loading solution where it was folded, its structure was retained on the surface provided it had a cysteine residue available for anchoring to gold. If it was immobilized as random coil, it remained unstructured on the surface but was able to fold through heterodimerization if subsequently exposed to a positively charged polypeptide. When the positively charged peptide was immobilized as random coil, heterodimerization could not be induced, probably because of high-affinity interactions between the charged primary amine groups and the gold surface. These observations are intended to pave the way for future engineering of functional surfaces based on polypeptide scaffolds where folding is known to be crucial for function.     

Effect of crown ether on ion currents through synthetic membranes containing a single conically shaped nanopore

Ion-current measurements were made on synthetic polymer membranes that contained a single conically shaped nanopore. This entailed placing an electrolyte solution on either side of the membrane, using an electrode placed in each solution to control the transmembrane potential, and measuring the resulting transmembrane ion current. The effect of the crown ether commonly called 18-crown-6 (18C6) on the measured ion current was investigated. Adding 18C6 to the electrolyte solution on one side of a conical nanopore membrane provides a way to rectify the ion current flowing through the nanopore. This chemical rectification is observed only when the cation of the electrolyte is complexed by 18C6 (e.g., K+), and when the mouth diameter of the conical nanopore is of molecular dimensions, in this case approximately 1.5 nm. This chemical rectification can either augment or diminish the inherent electrostatic rectification observed with these small mouth-diameter nanopores. We have interpreted these results using a model based on the formation of a junction potential at the membrane-solution interface. This junction potential arises because the transference number for the K+-18C6 complex in bulk solution is larger than its transference number in the mouth of the conical nanopore.     

Designed alpha-helical barrels for charge-selective peptide translocation

Synthetic alpha-helix based pores for selective sensing of peptides have not been characterized previously. Here, we report large transmembrane pores, pPorA formed from short synthetic alpha-helical peptides of tunable conductance and selectivity for single-molecule sensing of peptides. We quantified the selective translocation kinetics of differently charged cationic and anionic peptides through these synthetic pores at single-molecule resolution. The charged peptides are electrophoretically pulled into the pores resulting in an increase in the dissociation rate with the voltage indicating successful translocation of peptides. More specifically, we elucidated the charge pattern lining the pore lumen and the orientation of the pores in the membrane based on the asymmetry in the peptide-binding kinetics. The salt and pH-dependent measurements confirm the electrostatic dominance and charge selectivity in controlling target peptide interaction with the pores. Remarkably, we tuned the selectivity of the pores to charged peptides by modifying the charge composition of the pores, thus establishing the molecular and electrostatic basis of peptide translocation. We suggest that these synthetic pores that selectively conduct specific ions and biomolecules are advantageous for nanopore proteomics analysis and synthetic nanobiotechnology applications.

Synthetic alpha-helix based pores for selective sensing of peptides have not been characterized previously.