Stable Intermediate State Research Articles

The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models.

The process of RNA base fraying (i.e., the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA fraying and its sequence and direction dependence. In particular, we first introduce a method for determining biomolecular dynamics employing core-set Markov state models constructed using an advanced clustering technique. The method is validated on previously reported simulations. We then use the method to analyze extensive trajectories for four different RNA model duplexes. Results obtained using D. E. Shaw research and AMBER force fields are compared and discussed in detail and show a non-trivial interplay between the stability of intermediate states and the overall fraying kinetics.

Magnetization reversal in ferromagnetic Fibonacci nano-spirals

Abstract Nanostructured ferromagnetic materials are applicable in a broad range of technologies, especially in the areas of data storage and spintronics. In addition, special structures are of high interest in basic research, aiming at understanding magnetization reversal processes on the nano-scale and thus possibly creating new applications. The strong influence of the shape anisotropy in magnetic nanoparticles enables tailoring magnetization reversal processes by the shape of such a particle. Typically, symmetrical structures are investigated, such as nano-dots, doughnuts, squares, rectangles, etc. Here we report on spiral nano-structures with constantly varying bending radii, modelled according to the Fibonacci spiral which is well-known from diverse plants and biological processes and also related to many mathematical problems. The magnetic Fibonacci nano-spirals with a thicker and a thinner lateral structure size as well as a mirrored form, building a heart-like shape, show large numbers of steps in the hysteresis loops, corresponding to stable intermediate states, due to nucleation and annihilation of domains which do not propagate along the spirals. The numbers of these stable intermediate states which could be utilized for data storage as well as the coercive fields depend strongly on the spiral dimensions and the orientation of the external magnetic field. Simulating minor loops showed the high stability of the intermediate states and thus underlined the possibility to use such structures for data storage.

Localization trajectory and Chern-Simons axion coupling for bilayer quantum anomalous Hall systems

Quantum anomalous Hall (QAH) multilayers provide a platform of topological materials with high Chern numbers. We investigate the localization routes of bilayer QAH systems with Chern number C = 2 under strong disorder, by numerical simulations on their quantum transport properties and the Chern-Simons axion coupling. Compared to the single layer counterpart with C = 2, the localization trajectories present much richer behaviors, for example, the existence of the stable intermediate state with C = 1 can be tuned by model parameters. This state was always unstable in the single layer case. Furthermore, the two parameter scaling trajectories also exhibit multiple patterns, some of which were not captured by the standard Pruisken picture. During the process towards localization, the Chern-Simons axion coupling shows a surprisingly remarkable peak which is even higher and sharper in the large size limit. Therefore the disordered bilayer QAH system can be a good candidate for this nontrivial magnetoelectric coupling mediated by orbital motions.

Effect of ethanol on insulin dimer dissociation.

Insulin-dimer dissociation is an essential biochemical process required for the activity of the hormone. We investigate this dissociation process at the molecular level in water and at the same time, in 5% and 10% water-ethanol mixtures. We compute the free energy surface of the protein dissociation processes by employing biased molecular dynamics simulation. In the presence of ethanol (EtOH), we observe a marked lowering in the free energy barrier of activation of dimer dissociation from that in the neat water, by as much as ∼50%, even in the 5% water-ethanol solution. In addition, ethanol is found to induce significant changes in the dissociation pathway. We extract the most probable conformations of the intermediate states along the minimum energy pathway in the case of all the three concentrations (EtOH mole fractions 0, 5, and 10). We explore the change in microscopic structures that occur in the presence of ethanol. Interestingly, we discover a stable intermediate state in the water-ethanol binary mixture where the centers of the monomers are separated by about 3 nm and the contact order parameter is close to zero. This intermediate is stabilized by the wetting of the interface between the two monomers by the preferential distribution of ethanol and water molecules. This wetting serves to reduce the free energy barrier significantly and thus results in an increase in the rate of dimer dissociation. We also analyze the solvation of the two monomers during the dissociation and both the proteins' departure from the native state configuration to obtain valuable insights into the dimer dissociation processes.

Tristate ferroelectric memory and strain memory in Bi1/2Na1/2TiO3-based relaxor ferroelectrics

Tristate ferroelectric memory and strain memory of Bi1/2Na1/2TiO3 (BNT)-based relaxor ferroelectrics are proposed. These memory effects can be realized in BNT-based materials with double-like P-E hysteresis loops and obvious non-zero remanent polarization. An underlying triple-well free-energy landscape, in which the relaxor state serves as an intermediate stable state between two ferroelectric remanent states, is thought to be responsible for such a ferroelectric behavior and provides the basis for the tristate ferroelectric memory effect. Besides, the strain memory effect utilizes the inherent strain difference between relaxor and ferroelectric states. Experimental verifications on Bi1/2(Na0.8K0.2)1/2(Ti0.955Fe0.030Nb0.015)O3 ceramics show that the tristate ferroelectric memory and the strain memory can be operated as proposed, and the programmability and the retention ability of both effects are fairly good. The present study provides a facile approach to the multistate ferroelectric memory and shape memory piezoelectric actuator applications.

Magnetic properties of perovskite Ca1−xSrxFeO3

We synthesized Ca1−xSrxFeO3 containing tetravalent iron Fe4+ with high valence by low temperature heat treatment along with ozone oxidization. We investigated the magnetic properties of perovskite Ca1−xSrxFeO3. The charge disproportionation transition temperature (TCD) of Ca1−xSrxFeO3 was observed from x = 0.0 to 0.6 in the magnetic susceptibility measurements. The decrease in TCD occurs is attributed to deformation of the crystal structure. The metamagnetic transitions with hysteresis were observed in the magnetization curves of all the compositions. The metamagnetic behavior is due to helical magnetism, which means that there are intermediate stable states before magnetization is saturated. In the Sr-rich region with x = 0.8 and 1.0, the saturation magnetization shows forced ferromagnetic order with a value of ∼3.2 μB at high magnetic field, H ∼ 60 T.

Mechanical Unfolding Pathway of the High-Potential Iron–Sulfur Protein Revealed by Single-Molecule Atomic Force Microscopy: Toward a General Unfolding Mechanism for Iron–sulfur Proteins

High-potential iron-sulfur proteins (HiPIPs) are an important class of metalloproteins with a [4Fe-4S] cluster coordinated by four cysteine residues. Distinct from other iron-sulfur proteins, the cluster in HiPIP has a high reduction potential, making it an essential electron carrier in bacterial photosynthesis. Here, we combined single-molecule atomic force microscopy and protein engineering techniques to investigate the mechanical unfolding mechanism of HiPIP from Chromatium tepidum (cHiPIP). We found that cHiPIP unfolds in a two-step fashion with the protein sequence sequestered by the iron-sulfur center as a stable unfolding intermediate state. The rupture of the iron-sulfur center of cHiPIP proceeds in two distinct parallel pathways; one pathway involves the concurrent rupture of multiple iron-thiolate bonds, and the other one involves the sequential rupture of the iron-thiolate bonds. This mechanistic information was further confirmed by mutational studies. We found that the rupture of the iron-thiolate bonds in reduced and oxidized cHiPIP occurred in the range of 150-180 pN at a pulling speed of 400 nm/s, similar to that measured for iron-thiolate bonds in rubredoxin and ferredoxin. Our results may have important implications for understanding the general unfolding mechanism governing iron-sulfur proteins, as well as the mechanism governing the mechanical rupture of the iron-sulfur center.

Predicting Cotranscriptional Folding Kinetics For Riboswitch.

On the basis of a helix-based transition rate model, we developed a new method for sampling cotranscriptional RNA conformational ensemble and the prediction of cotranscriptional folding kinetics. Applications to E. coli. SRP RNA and pbuE riboswitch indicate that the model may provide reliable predictions for the cotranscriptional folding pathways and population kinetics. For E. coli. SRP RNA, the predicted population kinetics and the folding pathway are consistent with the SHAPE profiles in the recent cotranscriptional SHAPE-seq experiments. For the pbuE riboswitch, the model predicts the transcriptional termination efficiency as a function of the force. The theoretical results show (a) a force-induced transition from the aptamer (antiterminator) to the terminator structure and (b) the different folding pathways for the riboswitch with and without the ligand (adenine). More specifically, without adenine, the aptamer structure emerges as a short-lived kinetic transient state instead of a thermodynamically stable intermediate state. Furthermore, from the predicted extension-time curves, the model identifies a series of conformational switches in the pulling process, where the predicted relative residence times for the different structures are in accordance with the experimental data. The model may provide a new tool for quantitative predictions of cotranscriptional folding kinetics, and results can offer useful insights into cotranscriptional folding-related RNA functions such as regulation of gene expression with riboswitches.

Key Residues Affecting Transglycosylation Activity in Family 18 Chitinases: Insights into Donor and Acceptor Subsites.

Understanding features that determine transglycosylation (TG) activity in glycoside hydrolases is important because it would allow the construction of enzymes that can catalyze controlled synthesis of oligosaccharides. To increase TG activity in two family 18 chitinases, chitinase D from Serratia proteamaculans ( SpChiD) and chitinase A from Serratia marcescens ( SmChiA), we have mutated residues important for stabilizing the reaction intermediate and substrate binding in both donor and acceptor sites. To help mutant design, the crystal structure of the inactive SpChiD-E153Q mutant in complex with chitobiose was determined. We identified three mutations with a beneficial effect on TG activity: Y28A (affecting the -1 subsite and the intermediate), Y222A (affecting the intermediate), and Y226W (affecting the +2 subsite). Furthermore, exchange of D151, the middle residue in the catalytically important DXDXE motif, to asparagine reduced hydrolytic activity ≤99% with a concomitant increase in apparent TG activity. The combination of mutations yielded even higher degrees of TG activity. Reactions with the best mutant, SpChiD-D151N/Y226W/Y222A, led to rapid accumulation of high levels of TG products that remained stable over time. Importantly, the introduction of analogous mutations at the same positions in SmChiA (Y163A equal to Y28A and Y390F similar to Y222A) had similar effects on TG efficiency. Thus, the combination of the decreasing hydrolytic power, subsite affinity, and stability of intermediate states provides a powerful, general strategy for creating hypertransglycosylating mutants of retaining glycoside hydrolases.

Mean first-passage time in a delayed tristable system driven by correlated multiplicative and additive white noises

This paper investigates the mean first-passage times (MFPTs) of a delayed tristable system driven by correlated multiplicative and additive noises. The results suggest that the correlation between the multiplicative and additive noises can induce symmetry-breaking in the delayed tristable system. The noise-induced dynamics, such as the noise enhanced stability (NES) and the resonant activation (RA), can be observed with considering the combined influences of correlated noises and intermediate stable state. The time delay plays an important role in the MFPTs. For example, with respect to the middle well, the increase of time delay results in the weakening of the stability of the two lateral wells; thus, all the MFPTs are decreased notably. Moreover, a law of MFPTs is established for three different potential wells. That is, the MFPT T(s1 → s3) (between the left and right wells) is equal to the sum of T(s1 → s2) (from left well to middle one) and T(s2 → s3) (from middle well to right one). However, this change regulation can be first broken with an increase in time delay, and then restored with the increase of correlation between noises.

Elucidation of the structural stability and dynamics of heterogeneous intermediate ensembles in unfolding pathway of the N-terminal domain of TDP-43.

The N-terminal domain of the RNA binding protein TDP-43 (NTD) is essential to both physiology and proteinopathy; however, elucidation of its folding/unfolding still remains a major quest. In this study, we have investigated the biophysical behavior of intermediate ensembles employing all-atom molecular dynamics simulations in 8 M urea accelerated with high temperatures to achieve unfolded states in a confined computation time. The cumulative results of the 2.75 μs simulations show that unfolding of the NTD at 350 K evolves through different stable and meta-stable intermediate states. The free-energy landscape reveals two meta-stable intermediates (IN and IU) stabilized by non-native interactions, which are largely hydrophilic and highly energetically frustrated. A single buried tryptophan residue, W80, undergoes solvent exposure to different extents during unfolding; this suggests a structurally heterogeneous population of intermediate ensembles. Furthermore, the structure properties of the IN state show a resemblance to the molten globule (MG) state with most of the secondary structures intact. The unfolding of the NTD is initiated by the loss of β-strands, and the unfolded (U) states exhibit a population of non-native α-helices. These non-native unfolded intermediate ensembles may mediate protein oligomerization, leading to the formation of pathological, irreversible aggregates, characteristics of disease pathogenesis.

Elucidation of stable intermediates in urea-induced unfolding pathway of human carbonic anhydrase IX

Human carbonic anhydrase IX (CAIX) has evolved as a promising biomarker for cancer prognosis, due to its overexpression in various cancers and restricted expression in normal tissue. However, limited information is available on its biophysical behavior. The unfolding of CAIX in aqueous urea solution was studied using all-atom molecular dynamics simulation approach. The results of this study revealed a stable intermediate state along the unfolding pathway of CAIX. At intermediate concentrations of urea (2.0–4.0 M), the protein displays a native-like structure with a large population of its secondary structure and hydrophobic contacts remaining intact in addition to small confined overall motions. Beyond 4.0 M urea, the unfolding is more gradual and at 8.0 M urea the structure is largely collapsed due to the solvent effect. The hydrophobic contact analysis suggests that the contact in terminal α-helices is separated initially which propagates in the loss of contacts from centrally located β-sheets. The reduction of 60–65% tertiary contacts in 7.0–8.0 M urea suggested the presence of residual structure in unfolded state and is confirmed with structural snap shot. Free energy landscape analysis suggested that unfolding of CAIX exists through the different intermediate states.

Accelerating Dynamics of H on Graphene by Coadsorbates.

There are several factors that affect the dynamics of adsorbed hydrogen atoms on a carbon surface. Using density functional calculations we show that coadsorption can be a highly influential factor. The diffusion of hydrogen adsorbed on graphene is explored in the presence of H-containing molecules. Without coadsorbates the diffusion barrier of H on graphene is 0.94 eV, while with water/ammonia it is 0.85/0.12 eV. The low barrier in the case of ammonia is attributed to the formation of a stable intermediate state NH4, while such a stable state is not found in the case of water. In addition, hydrogen fluoride, hydrogen sulfide, arsine, and phosphine were also considered. We found that stronger hydrogen-hydride bonds lead to lower diffusion barriers of H on graphene.

Ternary Resistance Switching Memory Behavior Based on Graphene Oxide Embedded in a Polystyrene Polymer Layer

Nonvolatile ternary memory devices were fabricated using the composite of polystyrene (PS) and graphene oxide(GO) as active layers, which have an reliable intermediate state. The current-voltage (I-V) curves of the indium tin oxide (ITO)/PS+GO/Al device under the external applied voltages exhibited current tri-stability with three conductivity states, which clearly revealed ternary memory performance. Under the stimulus of the external voltage, a stable intermediate conductivity state was observed. In the write-read-erase-read test, the ITO/PS+GO/Al device exhibited rewritable, nonvolatile, ternary memory properties. The resistance as functions of the time indicated that three conductivity states held for 2 × 105 s, suggesting that the good stability of the ITO/PS+GO/Al devices. HRTEM and XPS observation indicated that the Al top electrode reacted with oxygen within in GO.

Understanding the contribution of disulfide bridges to the folding and misfolding of an anti-Aβ scFv.

ScFv-h3D6 is a single chain variable fragment that precludes Aβ peptide-induced cytotoxicity by withdrawing Aβ oligomers from the amyloid pathway to the worm-like pathway. Production of scFv molecules is not a straightforward procedure because of the occurrence of disulfide scrambled conformations generated in the refolding process. Here, we separately removed the disulfide bond of each domain and solved the scrambling problem; and then, we intended to compensate the loss of thermodynamic stability by adding three C-terminal elongation mutations, previously described to stabilize the native fold of scFv-h3D6. Such stabilization occurred through stabilization of the intermediate state in the folding pathway and destabilization of a different, β-rich, intermediate state driving to worm-like fibrils. Elimination of the disulfide bridge of the less stable domain, VL , deeply compromised the yield and increased the aggregation tendency, but elimination of the disulfide bridge of the more stable domain, VH , solved the scrambling problem and doubled the production yield. Notably, it also changed the aggregation pathway from the protective worm-like morphology to an amyloid one. This was so because a partially unfolded intermediate driving to amyloid aggregation was present, instead of the β-rich intermediate driving to worm-like fibrils. When combining with the elongation mutants, stabilization of the partially unfolded intermediate driving to amyloid fibrils was the only effect observed. Therefore, the same mutations drove to completely different scenarios depending on the presence of disulfide bridges and this illustrates the relevance of such linkages in the stability of different intermediate states for folding and misfolding.

Ectopic Expression of Mouse Melanopsin in Drosophila Photoreceptors Reveals Fast Response Kinetics and Persistent Dark Excitation

The intrinsically photosensitive M1 retinal ganglion cells (ipRGC) initiate non-image-forming light-dependent activities and express the melanopsin (OPN4) photopigment. Several features of ipRGC photosensitivity are characteristic of fly photoreceptors. However, the light response kinetics of ipRGC is much slower due to unknown reasons. Here we used transgenic Drosophila, in which the mouse OPN4 replaced the native Rh1 photopigment of Drosophila R1-6 photoreceptors, resulting in deformed rhabdomeric structure. Immunocytochemistry revealed OPN4 expression at the base of the rhabdomeres, mainly at the rhabdomeral stalk. Measurements of the early receptor current, a linear manifestation of photopigment activation, indicated large expression of OPN4 in the plasma membrane. Comparing the early receptor current amplitude and action spectra between WT and the Opn4-expressing Drosophila further indicated that large quantities of a blue absorbing photopigment were expressed, having a dark stable blue intermediate state. Strikingly, the light-induced current of the Opn4-expressing fly photoreceptors was ∼40-fold faster than that of ipRGC. Furthermore, an intense white flash induced a small amplitude prolonged dark current composed of discrete unitary currents similar to the Drosophila single photon responses. The induction of prolonged dark currents by intense blue light could be suppressed by a following intense green light, suggesting induction and suppression of prolonged depolarizing afterpotential. This is the first demonstration of heterologous functional expression of mammalian OPN4 in the genetically emendable Drosophila photoreceptors. Moreover, the fast OPN4-activated ionic current of Drosophila photoreceptors relative to that of mouse ipRGC, indicates that the slow light response of ipRGC does not arise from an intrinsic property of melanopsin.

Magnetization Reversal in Ferromagnetic Nanorings of Fourfold Symmetries

Magnetic nanoparticles offer a broad spectrum of magnetization reversal processes and respective magnetic states, such as onion, horseshoe, or vortex states as well as various states including domain walls. These states can be correlated with stable intermediate states at remanence, enabling new quaternary memory devices storing two bits in one particle. The stability of these intermediated states was tested with respect to shape modifications, variations in the anisotropy axes, and rotations and fluctuations of the external magnetic field. In our micromagnetic simulations, 6 different stable intermediate states were observed at vanishing magnetic field in addition to the remanence state. The angular region of approx. 5°–12° between nanoring and external magnetic field was identified as being most stable with respect to all modifications, with an onion state as technologically best accessible intermediate state to create quaternary memory devices.

Square nano-magnets as bit-patterned media with doubled possible data density

Due to their possible applications in magneto-electronic devices, nanostructured magnetic particles are one of the most important topics in recent research. In such low-dimensional systems, the shape anisotropy can significantly be increased, compared with magneto-crystalline and magneto-elastic anisotropies – and thus allows for tailoring magnetic properties by shape design. Especially square nanowire objects which can lead to stable intermediate states are of technical relevance. Such systems could be used as quaternary memory cells, i.e. for storing 2 bits per storage position, expanding the possible limits of Moore’s law. Recent experimental investigations have revealed the influence of lateral dimensions, wall thicknesses, corner shapes, etc. on magnetization reversal mechanisms and corresponding hysteresis loop shapes, supported by micromagnetic simulations of such systems. The article provides an overview of previous theoretical and experimental results and gives an outlook to possible implementation of these nano-particles in novel hard-disk or MRAM technology.

Investigating the Structural Change in Protein Aqueous Solution Using Temperature-Dependent Near-Infrared Spectroscopy and Continuous Wavelet Transform.

The circulatory protein, human serum albumin (HSA), is widely used as a model protein for the study of protein structure. In this work, the structures of human serum albumin in aqueous solutions are studied using temperature-dependent near-infrared (NIR) spectroscopy with the aid of continuous wavelet transform (CWT). Near-infrared spectra of human serum albumin solutions with different concentrations were measured over a temperature range of 30-85 ℃. Then, continuous wavelet transform was performed on the spectra to enhance the resolution. As a result of the resolution enhancement, spectral bands around 4361, 4521, 4600 and 4260 cm-1 were extracted from the overlapping low-resolution signals. The four bands can be assigned to the protein structures of α-helix, β-sheet, an intermediate state and side chains, respectively. The variations in intensity of the bands around 4361 and 4521 cm-1 with temperature show that the increase of temperature leads to the loss of α-helical structure but the formation of β-sheet, and the denaturation temperature of human serum albumin is about 55 ℃. The variation of the band around 4600 cm-1 indicates that the temperature-induced unfolding process of human serum albumin occurs through a stable intermediate state, and a significant change in the microenvironment of the side chains about 63 ℃ is observed from the variation of the band around 4260 cm-1. On the other hand, the transformed spectra in the region of 8000-5600 cm-1 provide an explicit evidence for the structural changes of water during the process of protein denaturation, and the unfolding process of HSA can be reflected by these changes.

Probing the Enhancement Mechanism of Catalyst-Assisted Nonaqueous Oxygen Evolution Reaction in Lithium-Oxygen Batteries

Introduction Rational catalyst design for Li-O2 recharge (i.e. oxygen evolution reaction, OER) has been hindered by a large large discrepancy on whether solid catalysts are effective in evolving O2 via decomposing solid lithium peroxide (Li2O2). One school of thought reported pronounced catalyst influence on improving the oxidation kinetics of Li2O2.1-3 Another school of thought reported that applying catalysts leads no improvement in the Li2O2-oxidation kinetics due to lacking of soluble species derived from Li2O2-oxidation.4These discrepancies and open questions preclude rational design of efficient catalysts for non-aqueous OER. Results and Discussion By using online electrochemical mass spectrometry (OEMS), we show that solid catalysts (e.g. ruthenium) effectively promote Li2O2-oxidation kinetics to evolve O2 in a solid-state environment.5 We select a widely-investigated solid catalyst, ruthenium (Ru),5, 6 as an example to study whether and how the solid-solid catalysis reaction kinetics was promoted. Figure 1 shows the efficacy of the solid Ru catalyst in solid-state and liquid-based Li-O2 cells using Vulcan carbon (VC) and Ru supported on VC (VC+Ru).5 First, the Ru catalyst reduces the overpotential of the Li-OER over the entire charge capacity (450 mV lower compared to pure VC) with the similar O2 evolution efficiency in liquid-based Li-O2 cell indicating that the solid catalysts could promote the Li2O2 decomposition kinetics. Second, in solid-state environment where no soluble species were available, the Ru catalyst also shows apparent effectiveness with higher OER efficiency (0.872 O2/2e-) compared to that of VC (0.650 O2/2e-).5 Based on these observations, we propose that the role of the solid catalyst for Li2O2-oxidation is to reduce the energy of the reaction intermediate states such as Li2-xO2 by forming a stable intermediate state i.e. Li2-xO2 (solid)-Ru, from which to decrease the overpotential needed for Li-extraction from Li2O2.5Further studies using operando UV-vis spectroscopy, X-ray absorption spectroscopy and X-ray photoelectron spectroscopy will be discussed to examine the proposed enhancement mechanism. Figure caption: Fig. 1. The efficacy of solid catalyst Ru on Li2O2 oxidation in solid-state and liquid-based cell. Galvanostatic voltage profiles of VC and VC+Ru in solid-state cell (a) and liquid-based cell (b), in-situ O2 evolution analysis by OEMS in solid-state cell (c) and liquid-based cell (d).5 Acknowledgements This work is partially supported by a grant from the Research Grants Council (RGC) of the Hong Kong Special Administrative Region (HK SAR), China, under Theme-based Research Scheme through Project No. T23-407/13-N, and partially supported by a RGC project No. CUHK14200615.