Effects of Proline on Internal Friction in Simulated Folding Dynamics of Several Alanine-Based α-Helical Peptides.

We have studied in silico the effect of proline, a model cosolvent, on local and global friction coefficients in (un)folding of several typical alanine-based α-helical peptides. Local friction is related to dwell times of a single, ensemble-averaged hydrogen bond (HB) within each peptide. Global friction is related to energy dissipated in a series of configurational changes of each peptide experienced by increasing the number of HBs during folding. Both of these approaches are important in relation to future atomic force microscopic-based measurements of internal friction via force-clamp single-molecule force spectroscopy. Molecular dynamics (MD) simulations for six peptides, namely, ALA5, ALA8, ALA15, ALA21, (AAQAA)3, and H2N-GN(AAQAA)2G-COONH2, have been conducted at 2 and 5 M proline solutions in water. Using previously obtained MD data for these peptides in pure water as well as upgraded theoretical models, we obtained variations of local and global internal friction coefficients as a function of solution viscosity. The results showed the substantial role of proline in stabilizing the folded state and slowing the overall folding dynamics. Consequently, larger friction coefficients were obtained at larger viscosities. The local and global internal friction, i.e., respective, friction coefficients approximated to zero viscosity, was also obtained. The evolution of friction coefficients with viscosity was weakly dependent on the number of concurrent folding pathways but was rather dominated by a stabilizing effect of proline on the folded states. Obtained values of local and global internal friction showed qualitatively similar results and a clear dependency on the structure of the studied peptide.

Plasma Processing and Treatment of 2D Transition Metal Dichalcogenides: Tuning Properties and Defect Engineering.

Two-dimensional transition metal dichalcogenides (TMDs) offer fascinating opportunities for fundamental nanoscale science and various technological applications. They are a promising platform for next generation optoelectronics and energy harvesting devices due to their exceptional characteristics at the nanoscale, such as tunable bandgap and strong light-matter interactions. The performance of TMD-based devices is mainly governed by the structure, composition, size, defects, and the state of their interfaces. Many properties of TMDs are influenced by the method of synthesis so numerous studies have focused on processing high-quality TMDs with controlled physicochemical properties. Plasma-based methods are cost-effective, well controllable, and scalable techniques that have recently attracted researchers' interest in the synthesis and modification of 2D TMDs. TMDs' reactivity toward plasma offers numerous opportunities to modify the surface of TMDs, including functionalization, defect engineering, doping, oxidation, phase engineering, etching, healing, morphological changes, and altering the surface energy. Here we comprehensively review all roles of plasma in the realm of TMDs. The fundamental science behind plasma processing and modification of TMDs and their applications in different fields are presented and discussed. Future perspectives and challenges are highlighted to demonstrate the prominence of TMDs and the importance of surface engineering in next-generation optoelectronic applications.

A brief review on thermally induced oxidation and oxidative etching of thin MoS2 crystals.

Thin and single MoS2 flakes have already been employed in the world of flexible nanoelectronics, particularly in sensing, optoelectronics and energy harvesting. This review article briefly summarizes the recent advancements in the research on thermally induced oxidation and oxidative etching of such MoS2 crystals. Various temperature regimes are discussed along with the proposed mechanistic insights into respective oxidation and etching processes. The methods utilized to detect any surface-remaining minute amounts of Mo oxides are also mentioned.

GB1 hairpin kinetics: capturing the folding pathway with molecular dynamics, replica exchange and optimal dimensionality reduction.

We have performed molecular dynamics (MD) and replica-exchange (REMD) simulations of folding of the GB1 hairpin peptide in aqueous solution. REMD results were consistent with a cooperative zipper folding model. 120 µs MD trajectories at 320 K yielded relaxation times of 1.8 µs and 100 ns, with the slower assigned to global folding. The MD folding/unfolding transitions also followed the cooperative zipper model, specifying nucleation at the central turn followed by consecutive hydrogen bond formation. Formation of hydrogen bonds and hydrophobic contacts were highly correlated. Coarse-grained kinetic models constructed with the Optimal Dimensionality Reduction (ODR) approach found a folding time of 3.3 µs and unfolding time of 4.0 µs. Additionally, relaxation times in the 130-170 ns range could be assigned to formation of the transition state and off-path intermediates. The unfolded state was the most highly populated and, significantly, most heterogenous, assembling the largest number of microstates, primarily composed of extended and turn structures. The folded state was also heterogenous, but a to a lesser degree, involving the fully folded and partially folded in-register hairpins at early stages of the zipper pathway. The transition state corresponded to the nucleated hairpin, with central turn and first beta-sheet hydrogen bond, while the off-path intermediates were off-register partial hairpins. Our simulation results were in excellent agreement with experimental data on folded fraction, relaxation time and folding mechanism. The new findings from this work suggest a highly cooperative zipper folding mechanism, nascent hairpin transition state and ∼100 ns relaxation related to intermediate formation.Communicated by Ramaswamy H. Sarma.

MoS2 oxidative etching caught in the act: formation of single (MoO3) n molecules.

We report the presence of sub-nm MoO x clusters formed on basal planes of the 2H MoS2 crystals during thermal oxidative etching in air at a temperature of 370 °C. Using high resolution non-contact atomic force microscopy (AFM) we provide a histogram of their preferred heights. The AFM results combined with density functional theory (DFT) simulations show remarkably well that the MoO x clusters are predominantly single MoO3 molecules and their dimers at the sulfur vacancies. Additional Raman spectroscopy, and energy and wavelength dispersive X-ray spectroscopies as well as Kelvin probe AFM investigations confirmed the presence of the MoO3/MoO x species covering the MoS2 surface only sparsely. The X-ray absorption near edge spectroscopy data confirm the MoO3 stoichiometry. Taken together, our results show that oxidative etching and removal of Mo atoms at the atomic level follow predominantly via formation of single MoO3 molecules. Such findings confirm the previously only proposed oxidative etching stoichiometry.

Analytical Approaches for Deriving Friction Coefficients for Selected α-Helical Peptides Based Entirely on Molecular Dynamics Simulations.

In this paper we derive analytically from molecular dynamics (MD) simulations the friction coefficients related to conformational transitions within several model peptides with α-helical structures. We study a series of alanine peptides with various length from ALA5 to ALA21 as well as their two derivatives, the (AAQAA)3 peptide and a 13-residue KR1 peptide that is a derivative of the (AAQAA)2 peptide with the formula GN(AAQAA)2G. We use two kinds of approaches to derive their friction coefficients. In the local approach, friction associated with fluctuations of single hydrogen bonds are studied. In the second approach, friction coefficients associated with a folding transitions within the studied peptides are obtained. In both cases, the respective friction coefficients differentiated very well the subtle structural changes between studied peptides and compared favorably to experimentally available data.

Local Interactions of Atmospheric Oxygen with MoS2 Crystals.

Thin and single MoS2 flakes are envisioned to contribute to the flexible nanoelectronics, particularly in sensing, optoelectronics and energy harvesting. Thus, it is important to study their stability and local surface reactivity. Their most straightforward surface reactions in this context pertain to thermally induced interactions with atmospheric oxygen. This review focuses on local and thermally induced interactions of MoS2 crystals and single MoS2 flakes. First, experimentally observed data for oxygen-mediated thermally induced morphological and chemical changes of the MoS2 crystals and single MoS2 flakes are presented. Second, state-of-the-art mechanistic insight from computer simulations and arising open questions are discussed. Finally, the properties and fate of the Mo oxides arising from thermal oxidation are reviewed, and future directions into the research of the local MoS2/MoOx interface are provided.

Length Dependent Folding Kinetics of Alanine-Based Helical Peptides from Optimal Dimensionality Reduction.

We present a computer simulation study of helix folding in alanine homopeptides (ALA)n of length n = 5, 8, 15, and 21 residues. Based on multi-microsecond molecular dynamics simulations at room temperature, we found helix populations and relaxation times increasing from about 6% and ~2 ns for ALA5 to about 60% and ~500 ns for ALA21, and folding free energies decreasing linearly with the increasing number of residues. The helix folding was analyzed with the Optimal Dimensionality Reduction method, yielding coarse-grained kinetic models that provided a detailed representation of the folding process. The shorter peptides, ALA5 and ALA8, tended to convert directly from coil to helix, while ALA15 and ALA21 traveled through several intermediates. Coarse-grained aggregate states representing the helix, coil, and intermediates were heterogeneous, encompassing multiple peptide conformations. The folding involved multiple pathways and interesting intermediate states were present on the folding paths, with partially formed helices, turns, and compact coils. Statistically, helix initiation was favored at both termini, and the helix was most stable in the central region. Importantly, we found the presence of underlying universal local dynamics in helical peptides with correlated transitions for neighboring hydrogen bonds. Overall, the structural and dynamical parameters extracted from the trajectories are in good agreement with experimental observables, providing microscopic insights into the complex helix folding kinetics.

Surface Characterization of MoS2 Atomic Layers Mechanically Exfoliated on a Si Substrate.

Mo disulfide overlayers with the thickness exceeding 1.77 nm were obtained on Si substrates through mechanical exfoliation. The resulting Mo disulfide flakes were then analyzed ex situ using combination of Auger electron spectroscopy (AES), elastic-peak electron spectroscopy (EPES) and scanning electron microscopy (SEM) in order to characterize their surface chemical composition, electron transport phenomena and surface morphology. Prior to EPES measurements, the Mo disulfide surface was sputter-cleaned and amorphized by 3 kV argon ions, and the resulting S/Mo atomic ratio varied in the range 1.80-1.88, as found from AES measurements. The SEM images revealed single crystalline small-area (up to 15 µm in lateral size) Mo disulfide flakes having polygonal or near-triangular shapes. Such irregular-edged flakes exhibited high crystal quality and thickness uniformity. The inelastic mean free path (IMFP), characterizing electron transport, was evaluated from the relative EPES using Au reference material for electron energies E = 0.5-2 keV. Experimental IMFPs, λ, determined for the AES-measured surface compositions were approximated by the simple function λ = kEp, where k = 0.0289 and p = 0.946 were fitted parameters. Additionally, these IMFPs were compared with IMFPs resulting from the two methods: (i) present calculations based on the formalism of the Oswald et al. model; (ii) the predictive equation of Tanuma et al. (TPP-2M) for the measured Mo0.293S0.551C0.156 surface composition (S/Mo = 1.88), and also for stoichiometric MoS2 composition. The fitted function was found to be reasonably consistent with the measured, calculated and predicted IMFPs. We concluded that the measured IMFP value at 0.5 keV was only slightly affected by residual carbon contamination at the Mo disulfide surface.

Surface-Bound and Volatile Mo Oxides Produced During Oxidation of Single MoS2 Crystals in Air and High Relative Humidity.

We report on the MoO3 oxides and their derivatives on microscopic 2H MoS2 flakes oxidized in air and high relative humidity at a moderate temperature range below 410 °C. We combine XPS and AFM measurements such as topography, friction, creation of nanoscale ripples and scratches on the MoS2 flakes deposited on Si substrates. We detect MoO3 oxides mostly by measuring selected nanomechanical properties of the MoO3 layer, such as its compressive mechanical stress at the plastic yield. We discuss basal surface coverage of the single MoS2 flakes by the MoO3 oxides. We discuss conditions for appearance of all possible MoO3 oxide derivatives, such as molybdenum(VI) hydroxyoxides and MoO3 hydrates. Our findings agree with an expected mechanistic switch in thermal oxidation in water vapors vs. air.

Visualization of the internal structure of Didymosphenia geminata frustules using nano X-ray tomography.

For the first time, the three-dimensional (3D) internal structure of naturally produced Didymosphenia geminata frustules were nondestructively visualized at sub-100 nm resolution. The well-optimized hierarchical structures of these natural organisms provide insight that is needed to design novel, environmentally friendly functional materials. Diatoms, which are widely distributed in freshwater, seawater and wet soils, are well known for their intricate, siliceous cell walls called 'frustules'. Each type of diatom has a specific morphology with various pores, ribs, minute spines, marginal ridges and elevations. In this paper, the visualization is performed using nondestructive nano X-ray computed tomography (nano-XCT). Arbitrary cross-sections through the frustules, which can be extracted from the nano-XCT 3D data set for each direction, are validated via the destructive focused ion beam (FIB) cross-sectioning of regions of interest (ROIs) and subsequent observation by scanning electron microscopy (SEM). These 3D data are essential for understanding the functionality and potential applications of diatom cells.

Microstructure and nanomechanical properties of single stalks from diatom Didymosphenia geminata and their change due to adsorption of selected metal ions.

We present topographical and nanomechanical characterization of single Didymosphenia geminata stalk. We compared the samples before and after adsorption of metal ions from freshwater samples. Transmission electron microscopy studies of single stalk cross-sections have shown three distinct layers and an additional thin extra coat on the external layer (called "EL"). Using scanning electron microscopy and atomic force microscopy (AFM), we found that topography of single stalks after ionic adsorption differed significantly from topography of pristine stalks. AFM nanoindentation studies in ambient conditions yielded elastic moduli of 214 ± 170 MPa for pristine stalks and 294 ± 108 MPa for stalks after ionic adsorption. Statistical tests showed that those results were significantly different. We conducted only preliminary comparisons between ionic adsorption of several stalks in air and in water. While the stalks with ions were on average stiffer than the pristine stalks in air, they became more compliant than the pristine stalks in water. We also heated the stalks and detected EL softening at 50°C ± 15°C. AFM nanoindentation in air on the softened samples yielded elastic moduli of 26 ± 9 MPa for pristine samples and 43 ± 22 MPa for stalks with absorbed metal ions. Substantial decrease of the EL elastic moduli after heating was expected. Significantly different elastic moduli for the samples after ionic adsorption in both cases (i.e., for heated and nonheated samples), as well as behavior of the stalks immersed in water, point to permanent structural EL changes due to ions.

Branched amphiphilic cationic oligopeptides form peptiplexes with DNA: a study of their biophysical properties and transfection efficiency.

Over the past decade, peptides have emerged as a new family of potential carriers in gene therapy. Peptides are easy to synthesize and quite stable. Additionally, sequences shared by the host proteome are not expected to be immunogenic or trigger inflammatory responses, which are commonly observed with viral approaches. We recently reported on a new class of branched amphiphilic peptide capsules (BAPCs) that self-assemble into extremely stable nanospheres. These capsules are capable of retaining and delivering alpha-emitting radionuclides to cells. Here we report that, in the presence of double stranded plasmid DNA, BAPCs are unable to form. Instead, depending of the peptide/DNA ratios, the peptides either coat the plasmid surface forming nanofibers (high peptide to DNA ratio) or condense the plasmid into nanometer-sized compacted structures (at low peptide to DNA ratios). Different gene delivery efficiencies are observed for the two types of assemblies. The compacted nanometer-sized structures display much higher transfection efficiencies in HeLa cells. This level of transfection is greater than that observed for a lipid-based reagent when the total number of viable transfected cells is taken into account.

Single molecule studies of force-induced S2 site exposure in the mammalian Notch negative regulatory domain.

Notch signaling in metazoans is responsible for key cellular processes related to embryonic development and tissue homeostasis. Proteolitic cleavage of the S2 site within an extracellular NRR domain of Notch is a key early event in Notch signaling. We use single molecule force-extension (FX) atomic force microscopy (AFM) to study force-induced exposure of the S2 site in the NRR domain from mouse Notch 1. Our FX AFM measurements yield a histogram of N-to-C termini lengths, which we relate to conformational transitions within the NRR domain. We detect four classes of such conformational transitions. From our steered molecular dynamics (SMD) results, we associate first three classes of such events with the S2 site exposure. AFM experiments yield their mean unfolding forces as 69 ± 42, 79 ± 45, and 90 ± 50 pN, respectively, at 400 nm/s AFM pulling speeds. These forces are matched by the SMD results recalibrated to the AFM force loading rates. Next, we provide a conditional probability analysis of the AFM data to support the hypothesis that a whole sequence of conformational transitions within those three clases is the most probable pathway for the force-induced S2 site exposure. Our results support the hypothesis that force-induced Notch activation requires ligand binding to exert mechanical force not in random but in several strokes and over a substantial period of time.

Changes of protein stiffness during folding detect protein folding intermediates.

Single-molecule force-quench atomic force microscopy (FQ-AFM) is used to detect folding intermediates of a simple protein by detecting changes of molecular stiffness of the protein during its folding process. Those stiffness changes are obtained from shape and peaks of an autocorrelation of fluctuations in end-to-end length of the folding molecule. The results are supported by predictions of the equipartition theorem and agree with existing Langevin dynamics simulations of a simplified model of a protein folding. In the light of the Langevin simulations the experimental data probe an ensemble of random-coiled collapsed states of the protein, which are present both in the force-quench and thermal-quench folding pathways.

Single-molecule studies of disulfide bond reduction pathways used by human thioredoxin.

Disulfide bond reduction pathways used by human thioredoxin (hTrx) are studied at the single molecule level using a recombinant protein (I27SS)8. (I27SS)8 contains eight tandem repeats of identical immunoglobulin-like modules with one disulfide bond in each module. Single (I27SS)8 molecules are stretched at constant force applied by a cantilever in a force-clamp mode of atomic force microscopy (FC-AFM). Disulfide reduction events are accurately detected from stepwise increases in the end-to-end length of (I27SS)8. Earlier FC-AFM studies observed one disulfide reduction pathway used by hTrx and suggested an additional electron tunneling mechanism. Here, a very large set of unbiased FC-AFM data is collected in a range of clamping forces. By analyzing the data using exponential fits and dwell time histograms two disulfide reduction pathways used by hTrx are resolved. Based on previous studies one of these pathways is attributed to force-dependent Michaelis-Menten catalysis. The latter reduction pathway is weakly force-inhibited and occurs sporadically. Bimolecular nucleophilic substitutions (SN2) and electron tunneling (ET) mechanisms are discussed to explain the second pathway. Direct SN2 and ET mechanisms cannot be discounted, but a hypothetical E2-SN2 mechanism involving a hydride reducing a disulfide bond provides an interesting alternative, which needs to be verified in future experiments.

Local thermomechanical analysis of a microphase-separated thin lamellar PS-b-PEO film.

We use atomic force microscopy (AFM) and hot tip AFM (HT-AFM) to thermophysically characterize a 30 nm thick film of poly(styrene-block-ethylene oxide), PS-b-PEO, and to modify its lamellar patterns having spacing of 39 ± 3 nm. AFM tip scans of the polymer film induce either abrasive surface patterns or nanoscale ripples, which depend upon the tip force, temperature, and number of scans. The evolution of the lamellar patterns is explained by the polymer film molecular structure and mode I crack propagation in the polymer combined with the stick-and-slip behavior of the AFM tip. The HT-AFM measurements at various tip-sample temperatures and scanning speeds yield several thermophysical quantities: the PEO melting temperature of 54 ± 12 °C, the PS glass transition temperature of 54 ± 12 °C, the PS-b-PEO specific heat of 3.6 ± 2.7 J g(-1) K(-1), the PEO melting enthalpy of 111 ± 88 J g(-1), and the free energy of Helmholtz for PEO unfolding (and melting) of 10(-20) J nm(-2). These quantities are obtained for PS-b-PEO volumes of 30,000 nm(3), which correspond to 30 ag of the polymer.

Complete noise analysis of a simple force spectroscopy AFM setup and its applications to study nanomechanics of mammalian Notch 1 protein.

We describe a complete noise analysis and application of a custom made AFM force spectroscopy setup on pulling a recombinant protein with an NRR domain of mouse Notch 1. Our table top AFM setup is affordable, has an open architecture, and is easily transferable to other laboratories. Its calculated noise characteristics are dominated by the Brownian noise with 2% non-Brownian components integrated over the first thermally induced resonance of a typical cantilever. For a typical SiN cantilever with a force constant of ~15 pN nm(-1) and in water the force sensitivity and resolution are less than 10 pN, and the corresponding deflection sensitivities are less than 100 pm Hz(-1/2). Also, we obtain a sub-ms time resolution in detecting the protein length change, and only few ms cantilever response times as measured in the force clamp mode on a well-known protein standard. Using this setup we investigate force-induced conformational transitions in the NRR region of a mouse Notch 1. Notch is an important protein related to leukemia and breast cancers in humans. We demonstrate that it is feasible to develop AFM-based studies of the force-induced conformational transitions in Notch. Our results match recent steered molecular dynamics simulations of the NRR unfolding and constitute a first step towards a detailed study of Notch activation with AFM.

Force-activated reactivity switch in a bimolecular chemical reaction.

The effect of mechanical force on the free-energy surface that governs a chemical reaction is largely unknown. The combination of protein engineering with single-molecule force-clamp spectroscopy allows us to study the influence of mechanical force on the rate at which a protein disulfide bond is reduced by nucleophiles in a bimolecular substitution reaction (S(N)2). We found that cleavage of a protein disulfide bond by hydroxide anions exhibits an abrupt reactivity 'switch' at ∼500 pN, after which the accelerating effect of force on the rate of an S(N)2 chemical reaction greatly diminishes. We propose that an abrupt force-induced conformational change of the protein disulfide bond shifts its ground state, drastically changing its reactivity in S(N)2 chemical reactions. Our experiments directly demonstrate the action of a force-activated switch in the chemical reactivity of a single molecule.