Surface-bound State Research Articles

The Pathway of a Transmembrane Helix Insertion into the Membrane Assisted by Sec61α Channel.

The significant inconsistency between the experimental and simulation results of the free energy for the translocon-assisted insertion of the transmembrane helix (TMH) has not been reasonably explained. Understanding the mechanism of TMH insertion through the translocon is the key to solving this problem. In this study, we performed a series of coarse-grained molecular dynamics simulations and calculated the potential mean forces (PMFs) for three insertion processes of a hydrophobic TMH. The simulations reveal the pathway of the TMH insertion assisted by a translocon. The results indicate that the TMH contacts the top of the lateral gate first and then inserts down the lateral gate, which agrees with the sliding model. The TMH begins to transfer laterally to the bilayer when it is blocked by the plug and reaches the exit of the lateral gate, where there is a free energy minimum point. We also found that the connecting section between TM2 and TM3 of Sec61α prevented TMH from leaving the lateral gate and directly transitioning to the surface-bound state. These findings provide insight into the mechanism of the insertion of TMH through the translocon.

Surface plasmon-cavity hybrid state and its graphene modulation at THz frequencies

Abstract Fabry–Pérot (F–P) cavity and metal hole array are classic photonic devices. Integrating F–P cavity with holey metal typically enhances interfacial reflection and dampens wave transmission. In this work, a hybrid bound surface state is found within rectangular metal holes on a silicon substrate by merging an extraordinary optical transmission (EOT) mode and a high-order F–P cavity mode both spatially and spectrally. Transmission, Q-factor, and bandwidth can be enhanced significantly with respect to the classical EOT and F–P interference by simply sweeping the cavity length. This state can provide EOT properties and ten times broader EOT bandwidth well below the effective plasma frequency of the periodic metal holes, where the metal holes typically show evanescent properties and do not support EOT in theory. Furthermore, a large modulation range of 25 % and 39 % is demonstrated with various graphene patterns for the transmittance of this hybrid state at 500 and 582 GHz, respectively.

Ligand-citric acid enhanced in-situ ROS generation by GBC@nZVI to promote the aerobic degradation of adsorbed 2,4-dichlorophenol

Nanoscale zero-valent iron (nZVI) can react with molecular oxygen to produce reactive oxygen species, but very low yield limits its widespread use. In this study, the effect of ligand-citric acid (CA) addition on the dissolved oxygen (DO) activation for in-situ generation of ROS and subsequent 2,4-DCP degradation by graphene carbon layer coated nZVI composites (GBC@nZVI) was systematically investigated. It was found that the introduction of CA significantly increased the ROS production and resulted in the generation of OH, O2− and 1O2 with values of 2.1, 2.3, and 1.5 times higher than that in systems without CA, respectively. Ligand CA could enhance the degradation of adsorbed 2,4-DCP over a wide pH range. The CA addition resulted in a significant increase in the degradation of 2,4-DCP from 40.8 % to 79.9 % and a significant decrease in the adsorption from 51.1 % to 19.1 % compared to the system without CA. This phenomenon can be attributed to the fact that the incorporation of CA promoted the efficient recycling of Fe(II)/Fe(III) in the surface-bound state from the iron oxide film on the GBC@nZVI which enhanced the generation of interfacial ROS using DO, and further facilitated the degradation of adsorbed 2,4-DCP rather than immobilization by adsorption alone. On the other hand, the formation of Fe(Ⅲ)-CA complexes with high stability provides enough soluble Fe(II) to produce more ROS in solution via the oxygen reduction. Furthermore, the graphene carbon layer is able to act as an electron conductor to promote the efficient transfer of electrons except to inhibiting the rapid oxidation of Fe0. The study not only reveals the promotion effect of ligand-CA addition on the in-situ generation of ROS from nZVI activated dissolved oxygen, but also provides a simple and green strategy for the removal of electron-rich aromatic pollutants from water pollution.

Drastically different restructuring of airborne and surface-anchored soot aggregates

Combustion soot particles are fractal aggregates of hydrophobic spherules. Mixing of soot particles with other chemicals during atmospheric processing may partially offset their hydrophobicity, promoting water uptake and structural compaction. We investigated morphological changes in fractal soot particles coated by sulfuric acid and then humidified, both in airborne and surface-bound states. Airborne soot was probed by tandem differential mobility analysis. Surface-bound soot was studied in a controlled microenvironment of a closed cell, using environmental transmission electron microscopy. After humidification, the airborne particles became fully compact, but the deposited particles showed only minor morphological changes despite significant water uptake. Although minor, those changes were detected during both water condensation and evaporation, indicating that condensation-evaporation cycles play an important role in atmospheric soot compaction. Lesser restructuring of deposited aggregates was caused by surface anchoring and coating loss, making anchoring an indispensable tool for preserving morphology of aggregates against changing experimental environment.

Photoemission Spectroscopy Using Virtual Photons Emitted by Positron Sticking: A Complementary Probe for Top-Layer Surface Electronic Structures.

We present a spectroscopic method which utilizes virtual photons to selectively measure the electronic structure of the topmost atomic layer. These virtual photons are created when incident positrons transition from vacuum states to bound surface states on the sample surface and can transfer sufficient energy to excite electrons into the vacuum. The short interaction range of the virtual photons restricts the penetration depth to approximately the Thomas-Fermi screening length. Measurements and analysis of the kinetic energies of the emitted electrons made on a single layer of graphene deposited on Cu and on the clean Cu substrate show that the ejected electrons originate exclusively from the topmost atomic layer. Moreover, we find that the kinetic energies of the emitted electrons reflect the density of states at the surface. These results demonstrate that this technique will be a complementary tool to existing spectroscopic techniques in determining the electronic structure of 2D materials and fragile systems due to the absence of subsurface contributions and probe-induced surface damage.

Enhancing effects of dissolved and media surface-bound organic matter on titanium dioxide nanoparticles transport in iron oxide-coated porous media under acidic conditions

Natural organic matter (NOM) and iron oxides have been proved to be crucial factors controlling the behaviors of nanoparticles in heterogenous environment. Here, we conducted experimental and modeling study on the transport of titanium dioxide nanoparticles (TiO2 NPs) in iron oxide-coated quartz in the presence of NOM under acidic conditions. Results showed the antagonistic effects of iron oxides and NOM on TiO2 NPs mobility. The inhibition of iron oxides coated on quartz was crystal form-dependent other than quantity-dependent. Amorphous ferric oxyhydroxide with higher specific surface area brought more positive charge and favorable deposition sites onto quartz, and induced more retention of nanoparticles than two crystalline iron oxides, goethite and hematite. Dissolved organic matter (DOM) facilitated TiO2 NPs transport in iron oxide-coated quartz. In comparation with the limited enhancing effects of DOM, the NOM coatings on media surface partially or largely offset the inhibition of goethite on nanoparticles mobility through direct occupation of attachment sites and sites screening due to the steric repulsion of the macromolecules. Owing to the higher steric hindrance, humic acid, both in dissolved and media surface-bound states, exerted stronger facilitating effects on TiO2 NPs mobility relative to fulvic acid.

Thermopower and thermophase in a d -wave superconductor

In an unconventional superconductor, the interplay of scattering off impurities and Andreev processes may lead to different scattering times for electronlike and holelike quasiparticles. Such electron-hole asymmetry appears when the impurity scattering phase shift is intermediate between the Born and unitary limits and leads to an expectation for large thermoelectric effects. Here, we examine the thermoelectric response of a $d$-wave superconductor connected to normal-metal reservoirs under a temperature bias using a fully self-consistent quasiclassical theory. The thermoelectrically induced quasiparticle current is cancelled by superflow in an open circuit setup, but at the cost of a charge imbalance induced at the contacts and extending across the structure. We investigate the resulting thermopower and thermophase and their dependencies on scattering phase shift, mean free path, and interface transparency. For crystal-axis orientations such that surface-bound zero-energy Andreev states are formed, the thermoelectric effect is reduced as a result of locally reduced electron-hole asymmetry. For a semiballistic superconductor with good contacts, we find thermopowers of order several ${\mu}V/K$, suggesting a thermovoltage measurement as a promising path to investigate thermoelectricity in unconventional superconductors.

Thermoelectric Transport in a Correlated Electron System on the Surface of Liquid Helium.

We report on the direct observation of the thermoelectric transport in a nondegenerate electron system trapped on the surface of liquid helium. The microwave-induced excitation of the vertical transitions of electrons between the surface-bound states results in their lateral flow, which we were able to detect by employing a segmented electrode configuration. We show that this flow of electrons arises due to the Seebeck effect. Our experimental results are in good agreement with the theoretical calculations based on kinetic equations. This demonstrates the importance of the fast electron-electron collisions, which, in particular, leads to the violation of the Wiedemann-Franz law in this system.

Activation of Cytochrome C Peroxidase Function Through Coordinated Foldon Loop Dynamics upon Interaction with Anionic Lipids

Cardiolipin (CL) is a mitochondrial anionic lipid that plays important roles in the regulation and signaling of mitochondrial apoptosis. CL peroxidation catalyzed by the assembly of CL-cytochrome c (cyt c) complexes at the inner mitochondrial membrane is a critical checkpoint. The structural changes in the protein, associated with peroxidase activation by CL and different anionic lipids, are not known at a molecular level. To better understand these peripheral protein-lipid interactions, we compare how phosphatidylglycerol (PG) and CL lipids trigger cyt c peroxidase activation, and correlate functional differences to structural and motional changes in membrane-associated cyt c. Structural and motional studies of the bound protein are enabled by magic angle spinning solid state NMR spectroscopy, while lipid peroxidase activity is assayed by mass spectrometry. PG binding results in a surface-bound state that preserves a nativelike fold, which nonetheless allows for significant peroxidase activity, though at a lower level than binding its native substrate CL. Lipid-specific differences in peroxidase activation are found to correlate to corresponding differences in lipid-induced protein mobility, affecting specific protein segments. The dynamics of omega loops C and D are upregulated by CL binding, in a way that is remarkably controlled by the protein:lipid stoichiometry. In contrast to complete chemical denaturation, membrane-induced protein destabilization reflects a destabilization of select cyt c foldons, while the energetically most stable helices are preserved. Our studies illuminate the interplay of protein and lipid dynamics in the creation of lipid peroxidase-active proteolipid complexes implicated in early stages of mitochondrial apoptosis.

Motional quantum states of surface electrons on liquid helium in a tilted magnetic field

The Jaynes-Cummings model (JCM), one of the paradigms of quantum electrodynamics, was introduced to describe interaction between light and a fictitious two-level atom. Recently it was suggested that the JCM Hamiltonian can be invoked to describe the motional states of electrons trapped on the surface of liquid helium and subjected to a constant uniform magnetic field tilted with respect to the surface [Yunusova et al. Phys. Rev. Lett. 122, 176802 (2019)]. In this case, the surface-bound (Rydberg) states of an electron are coupled to the electron cyclotron motion by the in-plane component of tilted field. Here we investigate, both theoretically and experimentally, the spectroscopic properties of surface electrons in a tilted magnetic field and demonstrate that such a system exhibits a variety of phenomena common to the light dressed states of atomic and molecular systems. This shows that electrons on helium realize a prototypical atomic system where interaction between components can be engineered and controlled by simple means and with high accuracy, and which therefore can be potentially used as a new flexible platform for quantum experiments. Our work introduces a pure condensed-matter system of electrons on helium into the context of atomic, molecular and optical physics.

How Lipids Mobilise Membrane-Bound Cytochrome C Seen by Solid-State NMR

Reactive oxygen species (ROS) in mitochondria are associated with various disease conditions, ranging from cancer to neurodegeneration. ROS-mediated oxidative damage of proteins, DNA and lipids plays an important role in downstream pathogenic processes. Remarkably, the mitochondrial heme protein cytochrome c even specifically catalyzes the reaction between ROS and polyunsaturated anionic lipids, including in particular cardiolipin. The products of this enzymatic reaction act as subsequent triggers of apoptosis. We have employed solid-state NMR spectroscopy as a unique tool to gain insight into the protein-lipid nanocomplex of lipid-bound cytochrome c, in order to understand how lipid binding regulates its pro-apoptotic lipid peroxidase activity. I discuss how our published and unpublished studies reveal new information about the structure and dynamics of the peripheral membrane protein as it interacts with lipid bilayers containing different lipid species. Magic angle spinning NMR is applied to the membrane-bound protein to probe its structure and dynamics, but also its mode of interaction with the lipids and solvent. While the protein retains much of its native fold in its surface-bound state, it also undergoes localised mobilisation. The latter process is essential for the lipid peroxidase activity, with the level of activity (and mobility) regulated by the characteristics of the bound lipid membrane, protein/lipid stoichiometry and other factors.

Electrochemically Tagging Elastin-like Polymers-Modified Au Surfaces

We are exploring Elastin-like-Polymer (ELP) as a transducing enhancement element for biosensors. While previous work in our lab has investigated surface-bound ELP conformational state with electrochemical impedance spectroscopy to understand its stimuli-response, we would like to use ELP as an electrically active transducer in sensor applications. To achieve this, we must understand how much of the ELP is covalently attached to the electrode and functionalize the electrochemically-inert ELP with a faradaic tag. We present a proof-of-concept model for modifying the C-terminus of the ELP with Toluidine Blue O, an electrically active phenothiazine compound. Our system uses simple and accessible conjugation chemistry for this purpose and is conducted in aqueous solution. Further, reducing the thiol bonds will remove the covalently-bound ELP from the electrode surface to obtain an estimate of the ELP surface coverageThus far, we have successful decoupled the thiol-gold bond using the cyclic voltammetry reduction technique.. Electrochemical impedance spectroscopy confirmed that the modified electrode after thiol desorption returned to a similar state compared to a bare electrode. Additionally, we successfully measured an electrochemical signal attributed to the Toluidine Blue O tag conjugated to ELP based on its redox properties (Figure 1). We intend to further expand this work by refining the conjugation protocol, comparing various tags and conjugation chemistries, and relating surface coverage to desorption amounts of covalently bound ELP. Acknowledgements: The authors would like to acknowledge the financial support from the College of Medicine at Drexel University, NSF (CBET 1638896), the Collaborative Research Excellence Initiative Pilot Research Program at the University of New Hampshire, and the Hamel Center of Undergraduate Research at the University of New Hampshire. The authors also would like to acknowledge the assistance of Dr. Balog’s laboratory and Dr. Halpern’s laboratory.

Experimental and Computational Study of Molecular Water Interactions with Condensed Nopinone Surfaces Under Atmospherically Relevant Conditions.

Water and organics are omnipresent in the atmosphere, and their interactions influence the properties and lifetime of both aerosols and clouds. Nopinone is one of the major reaction products formed from β-pinene oxidation, a compound emitted by coniferous trees, and it has been found in both gas and particle phases in the atmosphere. Here, we investigate the interactions between water molecules and nopinone surfaces by combining environmental molecular beam (EMB) experiments and molecular dynamics (MD) simulations. The EMB method enables detailed studies of the dynamics and kinetics of water interacting with solid nopinone at 170-240 K and graphite coated with a molecularly thin nopinone layer at 200-270 K. MD simulations that mimic the experimental conditions have been performed to add insights into the molecular-level processes. Water molecules impinging on nopinone surfaces are efficiently trapped (≥97%), and only a minor fraction scatters inelastically while maintaining 35-65% of their incident kinetic energy (23.2 ± 1.0 kJ mol-1). A large fraction (60-80%) of the trapped molecules desorbs rapidly, whereas a small fraction (20-40%) remains on the surface for more than 10 ms. The MD calculations confirm both rapid water desorption and the occurrence of strongly bound surface states. A comparison of the experimental and computational results suggests that the formation of surface-bound water clusters enhances water uptake on the investigated surfaces.

Terminal charges modulate the pore forming activity of cationic amphipathic helices

KIA peptides are a series of designer-made cationic amphipathic α-helical antimicrobial peptides of different lengths, based on the repetitive sequence [KIAGKIA]. They can form toroidal pores in membranes, wherein the helices are aligned in a transmembrane orientation. Solid-state 15N NMR is used here to differentiate between the surface-bound and transmembrane states. We find that the pore-forming activity increases when the peptides carry a positive charge (Lys residue) at the N-terminus, compared to a hydrophobic Ile-Ala N-terminal motif. In contrast, a positive charge at the C-terminus gives a lower membrane activity compared to C-terminal Ile-Ala. For peptides with otherwise identical sequence, a more than ten-fold difference in vesicle leakage can be observed, depending on which terminus carries the charge. This difference is attributed to a shift in the equilibrium between peptide helices oriented on the membrane surface and those inserted into the membrane in a pore-forming state. We show that the 3D hydrophobic moment can be used to predict which peptide sequence is more prone to form pores and will thereby show a higher membranolytic activity.

Selectivity in Electron Attachment to Water Clusters

Electron attachment onto water clusters to form water cluster anions is studied by varying the point of electron attachment along a molecular beam axis and probing the produced cluster anions using photoelectron spectroscopy. The results show that the point of electron attachment has a clear effect on the final distribution of isomers for a cluster containing 78 water molecules, with isomer I formed preferentially near the start of the expansion and isomer II formed preferentially once the molecular beam has progressed for several millimeters. These changes can be accounted for by the cluster growth rate along the beam. Near the start of the expansion, cluster growth is proceeding rapidly with condensing water molecules solvating the electron, while further along the expansion, the growth has terminated and electrons are attached to large and cold preformed clusters, leading to the isomer associated with a loosely bound surface state.

Peptide conformation and oligomerization characteristics of surface-mediated assemblies revealed by molecular dynamics simulations and scanning tunneling microscopy.

The characteristics of peptide conformations in both solution and surface-bound states, using poly-glycine as a model structure, are analyzed by using molecular dynamics (MD) simulations. The clustering analysis revealed significant linearization effect on the peptide conformations as a result of adsorption to surface, accompanied by varied adsorption kinetics and energetics. Depending on the inter-peptide interaction characteristics, distinctively different surface-mediated oligomerization modalities, such as antiparallel conformations, can be identified in MD and confirmed by scanning tunneling microscopy (STM) analysis of the assembly structures. These observations are beneficial for obtaining molecular insights of assembling propensity relating to peptide-surface and peptide–peptide interactions.

Cholesterol and phosphatidylethanolamine lipids exert opposite effects on membrane modulations caused by the M2 amphipathic helix

Membrane curvature remodeling induced by amphipathic helices (AHs) is essential in many biological processes. Here we studied a model amphipathic peptide, M2AH, derived from influenza A M2. We are interested in how M2AH may promote membrane curvature by altering membrane physical properties. We used atomic force microscopy (AFM) to examine changes in membrane topographic and mechanical properties. We used electron paramagnetic resonance (EPR) spectroscopy to explore changes in lipid chain mobility and chain orientational order. We found that M2AH perturbed lipid bilayers by generating nanoscale pits. The structural data are consistent with lateral expansion of lipid chain packing, resulting in a mechanically weaker bilayer. Our EPR spectroscopy showed that M2AH reduced lipid chain mobility and had a minimal effect on lipid chain orientational order. The EPR data are consistent with the surface-bound state of M2AH that acts as a chain mobility inhibitor. By comparing results from different lipid bilayers, we found that cholesterol enhanced the activity of M2AH in inducing bilayer pits and altering lipid chain mobility. The results were explained by considering specific M2AH-cholesterol recognition and/or cholesterol-induced expansion of interlipid distance. Both AFM and EPR experiments revealed a modest effect of anionic lipids. This highlights that membrane interaction of M2AH is mainly driven by hydrophobic forces. Lastly, we found that phosphatidylethanolamine (PE) lipids inhibited the activity of M2AH. We explained our data by considering interlipid hydrogen-bonding that can stabilize bilayer organization. Our results of lipid-dependent membrane modulations are likely relevant to M2AH-induced membrane restructuring.

Electrophysiological interrogation of asymmetric droplet interface bilayers reveals surface-bound alamethicin induces lipid flip-flop

The droplet interface bilayer (DIB) method offers simple control over initial leaflet compositions in model membranes, enabling an experimental path to filling gaps in our knowledge about the interplay between compositional lipid asymmetry, membrane properties, and the behaviors of membrane-active species. Yet, the stability of lipid leaflet asymmetry in DIBs has received very little attention, particularly in the presence of peptides and ion channels that are often studied in DIBs. Herein, we demonstrate for the first time parallel, capacitance-based measurements of intramembrane potential with arrays of asymmetric DIBs assembled in a microfluidic device to characterize the stability of leaflet asymmetry over many hours in the presence and absence of membrane-active peptides. DIBs assembled from opposing monolayers of the ester (DPhPC) and ether (DOPhPC) forms of diphytanoyl-phosphatidylcholine yielded asymmetric bilayers with leaflet compositions that were stable for at least 18 h as indicated by a stable |137 mV| intramembrane potential. In contrast, the addition of surface-bound alamethicin peptides caused a gradual, concentration-dependent decrease in the magnitude of the dipole potential difference. Intermittent current-voltage measurements revealed that alamethicin in asymmetric DIBs also shifts the threshold voltage required to drive peptide insertion and ion channel formation. These outcomes take place over the course of 1 to 5 h after membrane formation, and suggest that alamethicin peptides promote lipid flip-flop, even in the un-inserted, surface-bound state, by disordering lipids in the monolayer to which they bind. Moreover, this methodology establishes the use of parallel electrophysiology for efficiently studying membrane asymmetry in arrays of DIBs.

Binding of Cytotoxic Aβ25-35 Peptide to the Dimyristoylphosphatidylcholine Lipid Bilayer.

Aβ25-35 is a short, cytotoxic, and naturally occurring fragment of the Alzheimer's Aβ peptide. To map the molecular mechanism of Aβ25-35 binding to the zwitterionic dimyristoylphosphatidylcholine (DMPC) bilayer, we have performed replica exchange with solute tempering molecular dynamics simulations using all-atom explicit membrane and water models. Consequences of sequence truncation on the binding mechanism have been measured by utilizing as a control our previous simulations probing binding of the longer peptide Aβ10-40 to the same bilayer. The most intriguing feature of Aβ25-35 binding to the DMPC bilayer is a coexistence of two bound states with strikingly different characteristics: a dominant surface-bound state and a less stable inserted state. In the surface-bound state, the peptide samples extended conformations, in which its unbound C-terminal is pointed away from the bilayer. In contrast, in the inserted state, the C-terminal resides deep in the bilayer hydrophobic core. In both states, the N-terminal remains anchored to the bilayer. Free energy landscape analysis reveals that the two states are separated by a moderate barrier, suggesting that Aβ25-35 monomer may frequently interconvert between them. The net effect of Aβ25-35 binding is a minor impact on the bilayer structure, which contrasts with the considerable bilayer perturbations induced by a longer Aβ10-40 peptide penetrating deep into the bilayer core. Therefore, we conclude that the binding mechanisms of Aβ25-35 and Aβ10-40 peptides are different. Potential implications of our results for Aβ25-35 cytotoxicity are discussed. A comparison of experimental data with our findings reveals a good agreement.

Electronic confining effects in Sierpiński triangle fractals

Electron confinement in fractal Sierpi\ifmmode \acute{n}\else \'{n}\fi{}ski triangles (STs) on Ag(111) is investigated using scanning tunneling spectroscopy and theoretically simulated by employing an improved two-dimensional (2D) multiple scattering theory in which the energy-dependent phase shifts are explicitly calculated from the electrostatic potentials of the molecular building block of STs. Well-defined bound surface states are observed in three kinds of triangular cavities with their sides changing at a scale factor of 2. The decrease in length of the cavities results in an upshift of the resonances that deviates from an expected inverse quadratic dependence on the cavity length due to the less efficient confinement of smaller triangular cavities. Differential conductance maps at some specific biases present a series of alternative bright and dark rounded triangles preserving the symmetry of the boundary. Our improved 2D multiple scattering model reproduces the characteristics of the standing wave patterns and all features in the differential conductance spectra measured in experiments, illustrating that the elastic loss boundary scattering dominates the resonance broadening in these ST quantum corrals. Moreover, the self-similar structure of STs, that a larger central cavity is surrounded by three smaller ones with a half side length, gives rise to interactions of surface states confined in neighboring cavities, which are helpful for the suppression of the linewidth in differential conductance spectra.