Additional Intermediate States Research Articles

Buckling mediated by mobile localized elastic excitations.

Experiments reveal that structural transitions in thin sheets are mediated by the passage of transient and stable mobile localized elastic excitations. These "crumples" or "d-cones" nucleate, propagate, interact, annihilate, and escape. Much of the dynamics occurs on millisecond time scales. Nucleation sites correspond to regions where generators of the ideal unstretched surface converge. Additional stable intermediate states illustrate two forms of quasistatic inter-crumple interaction through ridges or valleys. These interactions create pairs from which extended patterns may be constructed in larger specimens. The onset of localized transient deformation with increasing sheet size is correlated with a characteristic stable crumple size, whose measured scaling with thickness is consistent with prior theory and experiment for localized elastic features in thin sheets. We offer a new theoretical justification of this scaling.

Revisiting the conformational transition model for the pH dependence of BSA structure using photoluminescence, circular dichroism, and ellipsometric Raman spectroscopy

Changes in pH affect metabolic pathways, primarily by modulating enzyme conformations, which is why a detailed analysis of pH-driven conformational transitions is required to understand the underlying biochemistry of diseases and biological organisms. In this work, we examined the pH-driven conformational dynamics of Bovine Serum Albumin (BSA), within the framework of the Foster Model. Circular Dichroism and Raman Optical Activity showed the conversion of helical into β-rich structures in the acid and basic regions, while an opening of BSA tertiary structure was shown by the upsurging of accessibility of ANS-BSA binding sites and the increasing of random contributions at regions F and B. We could then revisit the Foster Model by introducing two additional intermediate conformational states and structural reorganization at extreme pH values. This expanded model opens up new possibilities concerning protein-molecule interactions, promising far-reaching implications for fields such as drug design and biomaterials.

Dynamics and conformational propensities of staphylococcal CntA

Enzymes use transition metals as co-factors for catalytic roles in biological processes. Notably, manganese, iron, cobalt, nickel, copper and zinc are abundantly used. Staphylococcus aureus, a commensal bacterium asymptomatically, lies on the human body causing variety of infections. S. aureus is equipped by advanced virulence-regulatory circuits of metal acquisition like Cnt that acquires metals at infection sites by utilizing a nicotianamine-like metallophore staphylopine. Despite significant growth in structural studies, how CntA of Cnt system transmits conformational signal upon staphylopine recognition remains elusive. Here, we analyzed the structural changes adopted by CntA during close-to-open transition by computational approaches. CntA uses a bi-domain architectural form of domain II which performed 37° rigid body rotation and 1.1 Å translation assisted by inter-domain hinge cluster residues. Important clustered communities were found regulating the conformational changes in CntA where communities 4 and 5 are found crucial. Besides open and close states, the fluctuating regions sampled two additional intermediate states which were considered close or open previously. CntA prefers fluctuating the non-conserved regions rather than conserved where domain II turned out to be rigid and maintains a stable fold. Overall, the CntA system is a potential target for structural biologist to hamper such conformational behaviors at family level. Communicated by Ramaswamy H. Sarma

Quantum Dot Gate (QDG) Quantum Dot Channel (QDC) Multistate Logic Non-Volatile Memory (NVM) with High-K Dielectric HfO2 Barriers

This paper presents the theory, fabrication and experimental testing results for a multiple state Non-Volatile Memory (NVM), comprised of hafnium oxide high-k dielectric tunnel and gate barriers as well as a Silicon Quantum Dot Superlattice (QDSL) implemented for the floating gate and inversion channel (QDG) and (QDC) respectively. With the conclusion of Moore’s Law for conventional transistor fabrication, regarding the minimum gate size, current efforts in memory cell research and development are focused on bridging the gap between the conventions of the past sixty years and the future of computing. One method of continuing the increasing chip density is to create multistate devices capable of storing and processing additional logic states beyond 1 and 0. Replacing the silicon nitride floating gate of a conventional Flash NVM with QDSL gives rise to minibands that result in greater control over charge levels stored in the QDG and additional intermediate states. Utilizing Hot Carrier Injection (HCI) programming, for the realized device, various magnitudes of gate voltage pulses demonstrated the ability to accurately control the charge levels stored in the QDG. This corresponds to multiple threshold voltage shifts allowing detection of multiple states during read operations.

Variational Forward-Backward Charge Transfer Analysis Based on Absolutely Localized Molecular Orbitals: Energetics and Molecular Properties.

To facilitate the understanding of charge-transfer (CT) effects in dative complexes, we propose a variational forward-backward (VFB) approach to decompose the overall CT stabilization energy into contributions from forward and backward donation in the framework of energy decomposition analysis based on absolutely localized molecular orbitals (ALMO-EDA). Such a decomposition is achieved by introducing two additional constrained intermediate states in which only one direction of CT is permitted. These two "one-way" CT states are variationally relaxed such that the associated nuclear forces can be readily obtained. This allows for a facile integration into the previously developed adiabatic EDA scheme, so that the molecular property changes arising from forward and back donation can be separately assigned. Using ALMO-EDA augmented by this VFB model, we investigate the energetic, geometric, and vibrational features of complexes composed of CO and main group Lewis acids (BH3, BeO/BeCO3) and complexes of the N2, CO, and BF isoelectronic series with [Ru(II)(NH3)5]2+. We identify that the shift in the stretching frequency of a diatomic π-acidic ligand (XY), such as CO, results from a superposition of the shifts induced by permanent electrostatics and backward CT: permanent electrostatics can cause an either red or blue shift depending on the alignment of the XY dipole in the dative complex, and this effect becomes more pronounced with a more polar XY ligand; the back-donation to the antibonding π orbital of XY always lowers the X-Y bond order and thus red-shifts its stretching frequency, and the strength of this interaction decays rapidly with the intermolecular distance. We also reveal that while σ forward donation contributes significantly to energetic stabilization, it affects the vibrational feature of XY mainly by shortening the intermolecular distance, which enhances both the electrostatic interaction and backward CT but in different rates. The synergistic effect of the forward and backward donations appears to be more significant in the transition-metal complexes, where the forward CT plays an essential role in overcoming the strong Pauli repulsion. These findings highlight that the shift in the XY stretching frequency is not a reliable metric for the strength of π back-donation. Overall, the VFB-augmented EDA scheme that we propose and apply in this work provides a useful tool to characterize the role played by each physical component that all together lead to the frequency shift observed.

Functional balance between Tcf21-Slug defines cellular plasticity and migratory modalities in high grade serous ovarian cancer cell lines.

Cellular plasticity and transitional phenotypes add to complexities of cancer metastasis that can be initiated by single cell epithelial to mesenchymal transition (EMT) or cooperative cell migration (CCM). Our study identifies novel regulatory cross-talks between Tcf21 and Slug in mediating phenotypic and migration plasticity in high-grade serous ovarian adenocarcinoma (HGSC). Differential expression and subcellular localization associate Tcf21, Slug with epithelial, mesenchymal phenotypes, respectively; however, gene manipulation approaches identify their association with additional intermediate phenotypic states, implying the existence of a multistep epithelial-mesenchymal transition program. Live imaging further associated distinct migratory modalities with the Tcf21/Slug status of cell systems and discerned proliferative/passive CCM, active CCM and EMT modes of migration. Tcf21-Slug balance identified across a phenotypic spectrum in HGSC cell lines, associated with microenvironment-induced transitions and the emergence of an epithelial phenotype following drug exposure. Phenotypic transitions and associated functionalities following drug exposure were affirmed to ensue from occupancy of Slug promoter E-box sequences by Tcf21. Our study effectively provides a framework for understanding the relevance of ovarian cancer plasticity as a function of two transcription factors.

Evolution of Pt and Pd species in functionalized UiO-67 metal-organic frameworks

Abstract Functionalization of metal-organic frameworks (MOFs) with noble metals is a promising way for producing new versatile catalysts that will combine the outstanding porosity and specific surface area of MOFs with high catalytic activity of metals. Here, we present a comparative study of two metal-organic frameworks with UiO-67 topology, functionalized with palladium and platinum moieties. The initial structure of all studied samples contained palladium or platinum atoms grafted into MCl2bpydc (M = Pd, Pt) linkers of MOFs. The materials were further activated by heating in inert and H2-containing atmospheres. Both Pd- and Pt- functionalized materials exhibited high thermal stability upon heating in these atmospheres. The evolution of Pt and Pd species during the activation procedure was monitored by in situ time-resolved X-ray absorption near-edge structure (XANES) spectroscopy. We applied multivariate curve resolution alternating least squares (MCR-ALS) approach to XANES to unravel the intermediates which can be formed during the activation procedure. For UiO-67-Pd, only simple one-step transformation from PdCl2bpydc to Pd nanoparticles (NPs) was observed. For UiO-67-Pt, two additional intermediate states were observed, which behave differently depending on the activation procedure. Theoretical calculation of XANES spectra allowed us to suggest the 3D-atomic structures corresponding to each of the pure spectra determined by MCR-ALS. In addition, reaction enthalpies for different possible reaction routes were calculated within a density functional theory approach. Based on the experimental and theoretical results showed that Pd nanoparticles (NPs) tend to be formed in UiO-67-Pd samples irrespective of the activation procedure, while either Pt NPs or isolated PtII active sites, grafted in the MOF framework may be formed in UiO-67-Pt samples depending on the activation temperature and atmosphere.

Energy Efficiency and Renewable Energy Management with Multi-State Power-Down Systems

A power-down system has an on-state, an off-state, and a finite or infinite number of intermediate states. In the off-state, the system uses no energy and in the on-state energy it is used fully. Intermediate states consume only some fraction of energy but switching back to the on-state comes at a cost. Previous work has mainly focused on asymptotic results for systems with a large number of states. In contrast, the authors study problems with a few states as well as systems with one continuous state. Such systems play a role in energy-efficiency for information technology but are especially important in the management of renewable energy. The authors analyze power-down problems in the framework of online competitive analysis as to obtain performance guarantees in the absence of reliable forecasting. In a discrete case, the authors give detailed results for the case of three and five states, which corresponds to a system with on-off states and three additional intermediate states “power save”, “suspend”, and “hibernate”. The authors use a novel balancing technique to obtain optimally competitive solutions. With this, the authors show that the overall best competitive ratio for three-state systems is 9 5 and the authors obtain optimal ratios for various five state systems. For the continuous case, the authors develop various strategies, namely linear, optimal-following, progressive and exponential. The authors show that the best competitive strategies are those that follow the offline schedule in an accelerated manner. Strategy “progressive” consistently produces competitive ratios significantly better than 2.

Characterization of the Search Complex and Recognition Mechanism of the AlkD-DNA Glycosylase.

DNA damage is a routine problem for cells, and pathways such as base excision repair have evolved to protect the genome by using DNA glycosylases to first recognize and excise lesions. The search mechanism of these enzymes is of particular interest due to the seemingly intractable problem of probing the billions of base pairs in the genome for potential damage. It has been hypothesized that glycosylases form multiple protein-DNA conformational states to efficiently search and recognize DNA lesions, ultimately only flipping out the damaged substrate into the active site. A unique DNA glycosylase, the Bacillus cereus AlkD enzyme, has been shown to excise damaged DNA without flipping the nucleobase into a protein binding pocket following lesion recognition. Here, we use microsecond-scale all-atom molecular dynamics simulations to characterize the AlkD recognition mechanism, putting it in perspective with other DNA glycosylases. We first identify and describe two distinct enzyme-DNA conformations of AlkD: the search complex (SC) and excision complex (EC). The SC is distinguished by the linearity of DNA, changes in four helical parameters in the vicinity of the lesion, and changes in distance between active site residues and the DNA. Free DNA simulations are used to demonstrate that the DNA structural deviations and increased active site interactions present in the EC are initiated by the recognition of a methylation-induced signal in the rises both 5' to the methylation and opposing this base. Our results support the hypothesis that subtle geometric distortions in DNA are recognized by AlkD and are consequently probed to initiate concerted protein and DNA conformational changes which prime excise without additional intermediate states. This mechanism is shown to be consistent among the three methylated DNA sequences that have been crystallized bound to AlkD.

Influence of the Distance between Nanoparticles in Clusters on the Magnetization Reversal Process

Fourfold magnetic nanoparticles, created from nanowires or in the form of an open square, offer the possibility of creating quaternary memory devices with four unambiguously distinguishable stable states at remanence. This feature, however, has been simulated for single magnetic nanoparticles or clusters with interparticle distances similar to the nanoparticle dimensions. For the possible use in bit-patterned media, it is important to understand the scaling behavior of the stability of the additional intermediate states with the interparticle distance. The paper investigates exemplarily nanoparticles of two shapes which were found to be optimum to gain four states at remanence. For clusters of these particles, the probability of reaching the additional intermediate states in all particles in the same field region is strongly reduced with decreased interparticle distance. The differences between both shapes indicate possible solutions for this problem in the form of new nanoparticle shapes.

N-Terminal Domain of Luciferase Controls Misfolding Avoidance

The proteomes of all forms of life are predominated by large proteins. In contrast to small, one-domain proteins, little is known about folding pathways of large multidomain proteins. In this report we study Firefly (Photinus pyralis) luciferase as a model for investigating the mechanical folding and refolding of large, multidomain proteins. Using AFM-based single molecule force spectroscopy, our results indicate that Luciferase unfolds mechanically in three distinct unfolding stages. This unfolding pathway is unique as it produces additional intermediate states when the protein is extended in the presence of a single cofactor, ATP, or the pair of cofactors, D-(-)-luciferin and ATP. The modulation of the force-extension curve by ligands and denaturing chemicals, aided by computer simulations and crystallography structures, allowed us to interpret that force-extension profile as the sequential unfolding of Luciferase from the C-terminus to the N-terminus. Our results from mechanical unfolding suggest that Luciferase unfolds in a multiple-step process and that the N-terminal domain is the most stable. Interestingly, our results from single-molecule refolding experiments show that complete unfolding causes Luciferase to get trapped in non-native configurations that prevent refolding. In addition, however, these experiments show how partial unfolding of the C-terminal residues of Luciferase - with the N-terminal domain remaining folded - allow the entire protein to robustly refold, which is a novel feature of Luciferase. This feature of refolding indicates that the N-terminal domain of Luciferase may directly be involved in preventing folding into kinetic traps and provides insight on why it has evolved to fold co-translationally. These results represent an important step in understanding the folding landscapes of large proteins and have applications in drug targeting strategies and force-sensing technologies.

A simple three-dimensional-focusing, continuous-flow mixer for the study of fast protein dynamics

We present a simple, yet flexible microfluidic mixer with a demonstrated mixing time as short as 80 μs that is widely accessible because it is made of commercially available parts. To simplify the study of fast protein dynamics, we have developed an inexpensive continuous-flow microfluidic mixer, requiring no specialized equipment or techniques. The mixer uses three-dimensional, hydrodynamic focusing of a protein sample stream by a surrounding sheath solution to achieve rapid diffusional mixing between the sample and sheath. Mixing initiates the reaction of interest. Reactions can be spatially observed by fluorescence or absorbance spectroscopy. We characterized the pixel-to-time calibration and diffusional mixing experimentally. We achieved a mixing time as short as 80 μs. We studied the kinetics of horse apomyoglobin (apoMb) unfolding from the intermediate (I) state to its completely unfolded (U) state, induced by a pH jump from the initial pH of 4.5 in the sample stream to a final pH of 2.0 in the sheath solution. The reaction time was probed using the fluorescence of 1-anilinonaphthalene-8-sulfonate (1,8-ANS) bound to the folded protein. We observed unfolding of apoMb within 760 μs, without populating additional intermediate states under these conditions. We also studied the reaction kinetics of the conversion of pyruvate to lactate catalyzed by lactate dehydrogenase using the intrinsic tryptophan emission of the enzyme. We observe sub-millisecond kinetics that we attribute to Michaelis complex formation and loop domain closure. These results demonstrate the utility of the three-dimensional focusing mixer for biophysical studies of protein dynamics.

Intermediate states during mRNA–tRNA translocation

Recent studies support the notion that the pre-translocation (PRE) ribosomal complex functions, at least in part, as a Brownian machine, stochastically fluctuating among multiple conformations and transfer RNA (tRNA) binding configurations. Apart from the relatively more energetically stable conformational states of the PRE complex, termed macrostate I (MS I) and macrostate II (MS II), several additional intermediate states have been recently discovered. Structural and kinetic analyses of these states, made possible by cryogenic-electron microscopy (cryo-EM), X-ray crystallography, and single-molecule fluorescence resonance energy transfer (smFRET), have provided important insights into the translocation process, which is now understood to proceed, at least in the first step of the process, as a Brownian machine that is transiently stabilized in the 'productive' MS II conformation by the binding of the translocase elongation factor G (EF-G).

State dynamics of a double sandbar system

A 9.3-year dataset of low-tide time-exposure images from Surfers Paradise, Northern Gold Coast, Australia was used to characterise the state dynamics of a double sandbar system. The morphology of the nearshore sandbars was described by means of the sequential bar state classification scheme of Wright and Short [1984. Morphodynamic variability of surf zones and beaches: a synthesis. Marine Geology 56, 93–118]. Besides the two end members (the dissipative (D) and the reflective (R) states) and the four intermediate states (longshore bar and trough (LBT), rhythmic bar and beach (RBB), transverse bar and rip (TBR) and low tide terrace (LTT)), we identified two additional intermediate bar states. The erosive transverse bar and rip (eTBR) state related to the dominant oblique angle of wave incidence at the study site and the rhythmic low tide terrace (rLTT) related to the multiple bar setting. Using the alongshore barline variability and alongshore trough continuity as morphological indicators enabled the objective classification of the inner and outer bar states from the images. The outer bar was mostly in the TBR state and generally advanced sequentially through the states LBT–RBB–TBR–eTBR–LBT, with occasional transitions to the D state. Wave events led to abrupt state transitions of the outer bar, but, in contrast to expectations, did not necessarily correspond to upstate transitions. Instead, upstate (downstate) transitions coincided with angles of wave incidence θ larger (smaller) than 30°. The upstate TBR–eTBR–LBT sequence during high-angle events highlights the role of alongshore currents in bar straightening. The outer bar was found to govern the state of the inner bar to a large extent. Two types of inner bar behaviour were distinguished, based on the outer bar state. For intermediate outer bar states, the alongshore variability of the dominant inner rLTT state (52% in time) mainly related to that of the outer bar, implying some sort of morphological coupling. For dissipative outer bar states, however, the more upstate inner bar frequently separated from the shoreline and persistently developed rip channels as TBR became the most frequent state (60% in time).

Theory of ultrafast nonresonant multiphoton transitions in polyatomic molecules: Basics and application to optimal control theory

A systematic approach is presented to describe nonresonant multiphoton transitions, i.e., transitions between two electronic states without the presence of additional intermediate states resonant with the single-photon energy. The method is well suited to describe femtosecond spectroscopic experiments and, in particular, attempts to achieve laser pulse control of molecular dynamics. The obtained effective time-dependent Schrodinger equation includes effective couplings to the radiation field which combine powers of the field strength and effective transition dipole operators between the initial and final states. To arrive at time-local equations our derivation combines the well-known rotating wave approximation with the approximation of slowly varying amplitudes. Under these terms, the optimal control formalism can be readily extended to also account for nonresonant multiphoton events. Exemplary, nonresonant two- and three-photon processes, similar to those occurring in the recent femtosecond pulse-shaping experiments on CpMn(CO)(3), are treated using related ab initio potential energy surfaces.

Role of the Substrate Field Inhomogeneities in Coherent Resonant Raman Scattering

The peculiar role of the substrate field on the nonlinear optical response of a molecular adsorbate experiencing a resonant Raman scattering process is analyzed. The description of the internal dynamics is done in terms of the renormalized normal mode coordinates that account for the conformational changes induced in the adsorbate by the substrate field. This analytical description, well-adapted to weak substrate fields, points out the underlying mechanisms that are responsible for the enhancement of the resonant Raman signal observed in some molecules. They involve elementary processes bringing additional intermediate vibrational states into play, depending on the nature of the field inhomogeneities. Also, according to the relative values of the unperturbed equilibrium positions of the modes, their displacements, and frequency changes due to the substrate field, enhancement as well as decrease of the signal can possibly be observed and are evaluated. Of course, for a strong substrate field, the number of intermediate vibrational levels participating in the Raman process becomes very large, and a complete numerical evaluation is required.

Dynamics of EF-G interaction with the ribosome explored by classification of a heterogeneous cryo-EM dataset

A method of supervised classification using two available structure templates was applied to investigate the possible heterogeneity existing in a large cryo-EM dataset of an Escherichia coli 70S ribosome–EF-G complex. Two subpopulations showing the ribosome in distinct conformational states, related by a ratchet-like rotation of the 30S subunit with respect to the 50S subunit, were extracted from the original dataset. The possible presence of additional intermediate states is discussed.

Two‐Photon Absorption via Deep Local Levels as Virtual Intermediate States in Semiconductors

AbstractThe enhancement of the coherent nonlinear losses are observed in ZnO and ZnSe crystals within the whole range of the interband two‐photon absorption (TPA) spectra. The effect is explained theoretically in terms of nonresonant participation of the deep local levels (DL) of impurities and native defects in the forbidden gap as additional intermediate virtual states of TPA. Calculations of interband TPA via DL including the influence of the momentum indeterminacy in local states are presented. The role of spatial interference of virtual contributions of the localized intermediate states in the momentum conservation is revealed. The possibility of the technological control of the additional nonlinearities is shown experimentally. The place of these phenomena among the widely investigated processes of coherent TPA via band states and the incoherent two‐step absorption through DL are discussed.

The ATPase mechanism of skeletal and smooth muscle acto-subfragment 1.

The transient and steady-state kinetic parameters for the ATPase cycle of the complex of skeletal muscle actin with smooth or skeletal muscle subfragment 1 (S-1) were determined over a wide range of actin concentrations from measurements of protein tryptophan fluorescence, the transient hydrolysis step, and the steady-state rate. The properties of the completely associated system were determined by using S-1 covalently cross-linking to actin. A four-state model was found to provide a good approximation to the kinetic and steady-state behavior: (sequence; see text) where T, D, and Pi refer to ATP, ADP, and inorganic phosphate, respectively. The formation of AM1T and M1T occurs by a rapid equilibrium binding of T followed by a very fast step. Actin is in rapid equilibrium with M1T and M2.DPi, with association constants K2 and K4. The three rate constants k1, k-1, and k5 were obtained by fitting observed rate constants from transient state measurements and VM to the model using values of k3 and k-3 determined for S-1 alone. To fit the data for skeletal or smooth muscle acto-S-1, the calculated rate constant of the hydrolysis step k1 and the equilibrium constant K1 had to be 2-3 times smaller than the corresponding parameters (k3, K3) for S-1. The calculated effective rate constant for product release must be large for striated muscle (85 s-1 at 20 degrees C, low ionic strength) and relatively small for smooth muscle (3 s-1). The difference in the actin-concentration dependence of association and of steady-state ATPase activity was predicted correctly from the rate constants fitted to the transient evidence. While the proposed mechanism does not exclude the possibility of additional ATP or product intermediate states, the properties of such states cannot be deduced from the kinetic evidence.

Infrared Absorption inp-Type GaP

Infrared absorption measurements have been performed on Zn-doped GaP at 300 and 90 \ifmmode^\circ\else\textdegree\fi{}K. The absorption observed at 300 \ifmmode^\circ\else\textdegree\fi{}K between 1 and 12 \ensuremath{\mu} is attributed to a combination of intraband free-carrier absorption (FCA) and direct interband absorption arising from transitions between the ${\ensuremath{\Gamma}}_{8}$ and ${\ensuremath{\Gamma}}_{7}$ (splitoff) valence bands. The absorption at 90 \ifmmode^\circ\else\textdegree\fi{}K is identified as photoionization of holes from the Zn acceptor levels to the ${\ensuremath{\Gamma}}_{8}$ and ${\ensuremath{\Gamma}}_{7}$ valence bands. Because of the small spin-orbit splitting (82 meV) and strong nonparabolicity of the valence bands in GaP, both the interband and intraband absorption are qualitatively different from similar absorption in other III-V compounds. The interband transitions give rise to extremely broad overlapping absorption bands while the FCA exhibits an unusually large magnitude. We propose a model for FCA in $p\ensuremath{-}\mathrm{GaP}$ which includes the effect of virtual intermediate states in the light-hole and splitoff valence bands. It is shown, on the basis of this model, that FCA in $p\ensuremath{-}\mathrm{GaP}$ should have a wavelength dependence which depends on the scattering mechanism in the usual way, but whose magnitude is enhanced by the additional intermediate states. In agreement with transport measurements, we find that holes are scattered principally by acoustic and nonpolar optical phonons.