Pre-transition State Research Articles

A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis.

Myosin motors use the energy of ATP to produce force and directed movement on actin by a swing of the lever-arm. ATP is hydrolysed during the off-actin re-priming transition termed recovery stroke. To provide an understanding of chemo-mechanical transduction by myosin, it is critical to determine how the reverse swing of the lever-arm and ATP hydrolysis are coupled. Previous studies concluded that the recovery stroke of myosin II is initiated by closure of the Switch II loop in the nucleotide-binding site. Recently, we proposed that the recovery stroke of myosin VI starts with the spontaneous re-priming of the converter domain to a putative pre-transition state (PTS) intermediate that precedes Switch II closing and ATPase activation. Here, we investigate the transition from the pre-recovery, post-rigor (PR) state to PTS in myosin VI using geometric free energy simulations and the string method. First, our calculations rediscover the PTS state agnostically and show that it is accessible from PR via a low free energy transition path. Second, separate path calculations using the string method illuminate the mechanism of the PR to PTS transition with atomic resolution. In this mechanism, the initiating event is a large movement of the converter/lever-arm region that triggers rearrangements in the Relay-SH1 region and the formation of the kink in the Relay helix with no coupling to the active site. Analysis of the free-energy barriers along the path suggests that the converter-initiated mechanism is much faster than the one initiated by Switch II closure, which supports the biological relevance of PTS as a major on-pathway intermediate of the recovery stroke in myosin VI. Our analysis suggests that lever-arm re-priming and ATP hydrolysis are only weakly coupled, so that the myosin recovery stroke is initiated by thermal fluctuations and stabilised by nucleotide consumption via a ratchet-like mechanism.

Microcalorimetry reveals multi-state thermal denaturation of G. stearothermophilus tryptophanyl-tRNA synthetase.

Mechanistic studies of Geobacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford an unusually detailed description-the escapement mechanism-for the distinct steps coupling catalysis to domain motion, efficiently converting the free energy of ATP hydrolysis into biologically useful alternative forms of information and work. Further elucidation of the escapement mechanism requires understanding thermodynamic linkages between domain configuration and conformational stability. To that end, we compare experimental thermal melting of fully liganded and apo TrpRS with a computational simulation of the melting of its fully liganded form. The simulation also provides important structural cameos at successively higher temperatures, enabling more confident interpretation. Experimental and simulated melting both proceed through a succession of three transitions at successively higher temperature. The low-temperature transition occurs at approximately the growth temperature of the organism and so may be functionally relevant but remains too subtle to characterize structurally. Structural metrics from the simulation imply that the two higher-temperature transitions entail forming a molten globular state followed by unfolding of secondary structures. Ligands that stabilize the enzyme in a pre-transition (PreTS) state compress the temperature range over which these transitions occur and sharpen the transitions to the molten globule and fully denatured states, while broadening the low-temperature transition. The experimental enthalpy changes provide a key parameter necessary to convert changes in melting temperature of combinatorial mutants into mutationally induced conformational free energy changes. The TrpRS urzyme, an excerpted model representing an early ancestral form, containing virtually the entire catalytic apparatus, remains largely intact at the highest simulated temperatures.

Transition Metal Catalyzed Remote C-H Activation: A New Direction Towards Site-Selective Chemical Reactions

Transition metal catalyzed remote C-H activation offers a powerful tool to modify architecture of organic molecules. Remote or distal C-H activation of aromatic and aliphatic compounds presents more challenge than proximal sites due to the inaccessibility of these sites in formation of energetically favorable organometallic pre-transition states. Nonetheless, recent years have witnessed remarkable progress in reaching out and functionalizing distal C-H bonds. With the advancement of this field, synthetic modifications of organic molecules have become more step and atom economical, and have shown great promise to revolutionize synthetic organic chemistry.

Characterization of a novel mutant with inhibition of storage root formation in sweet potato.

Sweet potato is a widely cultivated crop with storage roots. Although many studies have been conducted on the mechanism of its storage root formation, the details have not been fully elucidated. We screened mutant lines with inhibition of storage root formation to clarify parts of the mechanism. In this study, the process of storage root formation in one of the mutant lines, C20-8-1, was investigated. The inhibition of storage root formation was observed during the early stages of growth. The roots in C20-8-1 did not show histological differences compared to those in wild type. The transition from fibrous roots to pencil roots, which are the developmental stages prior to mature storage root formation, was delayed or inhibited in C20-8-1. The upregulation of starch biosynthesis-related genes and downregulation of lignin biosynthesis genes with storage root swelling were not confirmed in the root of C20-8-1 during the developmental transition stage, suggesting that most of the roots in C20-8-1 are in the pre-transition state toward the storage root swelling. C20-8-1 showed a mutant phenotype during the critical period of storage root swelling initiation, and further clarification of this mutation is expected to provide new insights into storage root formation.

Identifying the critical state of complex biological systems by the directed-network rank score method.

Catastrophic transitions are ubiquitous in the dynamic progression of complex biological systems; that is, a critical transition at which complex systems suddenly shift from one stable state to another occurs. Identifying such a critical point or tipping point is essential for revealing the underlying mechanism of complex biological systems. However, it is difficult to identify the tipping point since few significant differences in the critical state are detected in terms of traditional static measurements. In this study, by exploring the dynamic changes in gene cooperative effects between the before-transition and critical states, we presented a model-free approach, the directed-network rank score (DNRS), to detect the early-warning signal of critical transition in complex biological systems. The proposed method is applicable to both bulk and single-cell RNA-sequencing (scRNA-seq) data. This computational method was validated by the successful identification of the critical or pre-transition state for both simulated and six real datasets, including three scRNA-seq datasets of embryonic development and three tumor datasets. In addition, the functional and pathway enrichment analyses suggested that the corresponding DNRS signaling biomarkers were involved in key biological processes. The source code is freely available at https://github.com/zhongjiayuan/DNRS. Supplementary data are available at Bioinformatics online.

Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip

To correctly aminoacylate tRNALeu, leucyl-tRNA synthetase (LeuRS) catalyzes three reactions: activation of leucine by ATP to form leucyl-adenylate (Leu-AMP), transfer of this amino acid to tRNALeu and post-transfer editing of any mischarged product. Although LeuRS has been well characterized biochemically, detailed structural information is currently only available for the latter two stages of catalysis. We have solved crystal structures for all enzymatic states of Neisseria gonorrhoeae LeuRS during Leu-AMP formation. These show a cycle of dramatic conformational changes, involving multiple domains, and correlate with an energetically unfavorable peptide-plane flip observed in the active site of the pre-transition state structure. Biochemical analyses, combined with mutant structural studies, reveal that this backbone distortion acts as a trigger, temporally compartmentalizing the first two catalytic steps. These results unveil the remarkable effect of this small structural alteration on the global dynamics and activity of the enzyme.

Enantioselective oxa-Diels-Alder Sequences of Dendralenes.

Diene-transmissive hetero-Diels-Alder sequences involving carbonyl dienophiles are reported for the first time. High enantioselectivities are achieved in the reaction of phenylglyoxal with a broad range of dendralene structures, through the optimization of a Pd2+ catalyst system. The initial catalyst-controlled enantioselective oxa-Diels-Alder (ODA) cycloaddition to a [3]dendralene generates a dihydropyran carrying a semicyclic diene. This participates in a subsequent catalyst or substrate-controlled Diels-Alder reaction to generate sp3 -rich fused polycyclic systems containing both heterocycles and carbocycles. Computational investigations reveal a concerted asynchronous mechanism. π-Complexation of a diene C=C bond to Pd2+ occurs in both the pre-transition state (TS) complex and in cycloaddition TSs, controlling stereoselectivity. A formal enantioselective [4+2]cycloaddition of a CO2 dienophile is demonstrated.

Molecular dynamics simulations of ultralow hysteretic behavior in super-elastic shape memory alloys

Shape memory alloys (SMAs) that exhibit superelasticity with large recoverable strain and small hysteresis are in demand for practical applications, although their synthesis remains a challenge. We introduce metastable engineering to dope conventional SMA solid-solution atoms of relatively high concentration with "weak" local lattice distortion to realize ultralow hysteretic superelasticity. Large-scale molecular dynamic (MD) simulations of NiTi-based SMAs are performed to demonstrate how the presence of 2 ∼ 4 at.% Nb dopants lead to a stress-induced transition from a metastable pretransitional state to a strain-glass state. This is facilitated by a macroscopically homogeneous and continuous phase transformation in the course of superelastic loading and unloading. This spinodal decomposition-like phase transformation process endows SMAs with anhysteretic superelasticity that is insensitive to loading direction and grain size (below 15 nm). These findings show promise of achieving ultralow hysteretic superelasticity with large recoverable strain for SMAs.

Pretransition state and apo structures of the filament-forming enzyme SgrAI elucidate mechanisms of activation and substrate specificity

Enzyme filamentation is a widespread phenomenon that mediates enzyme regulation and function. For the filament-forming sequence-specific DNA endonuclease SgrAI, the process of filamentation both accelerates its DNA cleavage activity and expands its DNA sequence specificity, thus allowing for many additional DNA sequences to be rapidly cleaved. Both outcomes—the acceleration of DNA cleavage and the expansion of sequence specificity—are proposed to regulate critical processes in bacterial innate immunity. However, the mechanistic bases underlying these events remain unclear. Herein, we describe two new structures of the SgrAI enzyme that shed light on its catalytic function. First, we present the cryo-EM structure of filamentous SgrAI bound to intact primary site DNA and Ca2+ resolved to ∼2.5 Å within the catalytic center, which represents the trapped enzyme–DNA complex prior to the DNA cleavage reaction. This structure reveals important conformational changes that contribute to the catalytic mechanism and the binding of a second divalent cation in the enzyme active site, which is expected to contribute to increased DNA cleavage activity of SgrAI in the filamentous state. Second, we present an X-ray crystal structure of DNA-free (apo) SgrAI resolved to 2.0 Å resolution, which reveals a disordered loop involved in DNA recognition. Collectively, these multiple new observations clarify the mechanism of expansion of DNA sequence specificity of SgrAI, including the indirect readout of sequence-dependent DNA structure, changes in protein–DNA interactions, and the disorder-to-order transition of a crucial DNA recognition element.

Ambimodal Pericyclic Rearrangements of Dialkenyl-Bullvalenes Give Tetrahydro-1,8-ethenoheptalenes.

The fluxional structure of bullvalene is expanded by the discovery of a [5,5]-sigmatropic rearrangement of dialkenyl substituted derivatives. This gives rise to tetrahydro-1,8-ethenoheptalenes (THEH), representing the first examples of this tricyclic scaffold. Variation of the substitution pattern alters the product distribution, including one thermodynamically balanced between THEH and bullvalene isomers. DFT calculations are used to explore the thermodynamic landscape and reaction mechanism revealing a pretransition state bifurcation leading to a concerted ambimodal rearrangement pathway.

Influence of Composition on the Evolution of Dislocation Substructure in the Low-Stability State Polycrystalline Cu-Al Alloys under Plastic Deformation

New concepts of dislocation physics of plasticity and strength are considered using quantitative methods of transmission diffraction electron microscopy. New concepts of dislocation physics of plasticity and strength are considered using quantitative methods of transmission diffraction electron microscopy. The analysis of changes in the parameters of the dislocation substructure (DSS) is given on the example of alloys Cu-0.5 and 14 аt. % Al and the influence of these parameters on the change in the substructure of the material at a temperature T=293 K is considered. It is shown that at each stage of deformation, there are usually two substructures ("old" and "new"). The blurring of the transition from stage to stage is associated with the presence of weakly stable pre-transition structural-phase States at certain degrees of deformation of several types of substructures simultaneously, i.e., a weakly stable structural-phase state of the system. Against the background of the "old" substructure, a "new" one is born, which in the process of deformation becomes the main one, and then the "old" one, in the depths of which another substructure is formed. Experimental evidence of this regularity is obtained for FCC alloys. The presence of grain boundaries complicates the diagrams: a third substructure is formed near the grain boundaries, which corresponds to the following substructures (later) in the sequence of DSS transformations.

Mechanism and dynamics of [formula omitted] + CCl4 halophilic reaction

In halophilic reactions, the nucleophile attacks the halogen moiety of the substrate instead of the carbon atom and displaces a carbanion as the leaving group. We report here a detailed ab initio and DFT study of the mechanism and dynamics of the reaction between CCl4 and CH2NO2− in the gas phase. The potential energy profiles for the reaction were mapped using DFT, MP2, and CCSD(T) methods considering the bimolecular halophilic (SN2X), SN2, and H/Cl exchange pathways. The SN2X pathway results in the products CCl3− + CH2ClNO2, while the H/Cl exchange pathway gives CHCl3 + CHClNO2−. The H/Cl exchange products were also possible by a sequential pathway that involved the SN2X reaction followed by a proton transfer from CH2ClNO2 to CCl3−. The SN2X and the sequential H/Cl exchange pathways were found to be barrierless and energetically feasible. The atomic-level mechanisms followed in the reaction was investigated by on-the-fly classical trajectory simulations at the B3LYP/6-311++G∗∗ level of theory. The trajectory simulations support the formation of both the halophilic and H/Cl exchange products. The halophilic reaction was found to largely follow non-IRC dynamical pathway that avoids the pre-transition state complex. In addition, the dynamics of the reaction was found to be nonstatistical with the trajectories showing recrossing behavior and nonexponential lifetimes for the post-transition state complex that leads to the halophilic products.

Structural and Energy Characteristics of NiAl Alloys with Deviations from Stoichiometric Composition. Part 2

The analysis of the atomic and phase structure confirmed the difference between the structural-phase states at the heating and cooling stages. Based on the analysis of the influence of the deviation of the atomic composition from the stoichiometric condition of the intermetallic compound during cooling, it is established that the deviation is a significant factor in the area of low-stability pre-transitional structural-phase states before the transformation. The behavior of the long-range parameter temperature dependence curves during the cooling of alloys of non-stoichiometric compositions differs significantly from the behavior of the corresponding alloy curve of a stoichiometric composition alloy. It is shown that in the case of cooling of alloys of non-stoichiometric compositions, a significant supercooling is required to establish a long-range order, and the appearance of ordered phases occurs at significantly lower temperatures. It is found that the temperature dependence curve of the long-range parameter of the Ni45Al55 alloy is significantly lower than the corresponding curve of the Ni55Al45 alloy. This indicates different mechanisms for establishing the long-range order of alloys with non-stoichiometric compositions. It is noted that the deviation of the system composition from the stoichiometric one causes a significant reduction of ordered and disordered regions. This article is a continuation of the work published earlier in the journal Izvestiya AltGU. 2020. №1 (111).

Structural and Energy Characteristics of NiAl Alloys with Deviations from Stoichiometric Composition. General Provisions. Part 1

The research results are presented in two parts. The first part presents data describing the general state of the problem of low-stability pre-transitional structural phase states in intermetallides of the Ni-Al system. Physical interpretations of low-stability structural phase states in condensed systems are described along with the applied physical-mathematical model based on a calculated block of 32x32x32 elementary cells (65536 atoms) of an ordered BCC structure (superstructure B2, Pearson symbol cP2). The study is carried out by Monte Carlo methods using the Metropolis algorithm for an intermetallic NiAl sample of stoichiometric composition (used as an example). It is found out that a kind of hysteresis is observed during thermal cycling. The presence of such hysteresis indicates the irreversibility of the occurring processes. This implies a difference in the structural phase states at the heating and cooling stages.
 The second part of the paper will demonstrate the results of a computer simulation of changes in structural phase states. The focus will be made on the low-stability pre-transitional structural phase states and energy characteristics of intermetallides образом with deviations from the stoichiometric composition of Ni45Al55 and Ni55Al45.

High-pressure phase stability and elasticity of ammonia hydrate

Abstract Phase stability and elasticity of ammonia hydrate have been studied using Raman spectroscopy and Brillion scattering in diamond-anvil cells up to 53 GPa at 300 K. Here we have established the high-pressure phase diagram of ammonia hydrate in three different compositions, including ammonia monohydrate (AMH, NH3·H2O), dihydrate (ADH, NH3·2H2O), and trihydrate (ATH, NH3·3H2O). In contrast to previous experimental results, our Raman and Brillouin measurements at 300 K have shown that all three ammonia hydrates start to dehydrate at 2.1–2.2 GPa. Dehydration of the ammonia hydrate leads to the formation of single-crystal ice-VII and an increase in the concentration of NH3 in the residual liquid. The residual liquid finally turns into solid ammonia hemihydrate phase II (AHH-II) at 4–4.6 GPa, leading to a 28% jump in the compressional-wave velocity (VP). Considering a 10–15 vol% NH3 in the mantle of ice giants, AHH should thus be the dominant form of NH3 coexisting with H2O-ice in the ice giants. Further Brillouin measurements provide crucial constraints on the VP of AHH and the single-crystal elasticity of ice-VII at high pressures and 300 K. VP of AHH increases smoothly with pressure. No anomalous change in VP of AHH was identified up to 39 GPa, although a solid to solid phase transition was noted to occur at ~18 GPa by Raman measurements. In addition, the elasticity of single-crystal ice-VII, which was the dehydration product of ammonia hydrate, has been determined up to 53 GPa at 300 K. The deviation of C12 from C44 observed at 11.4 and 14.6 GPa could be caused by the hydrogen bond symmetrizations or the ordering of dipole of single-crystal ice-VII. An abnormal softening in the elastic moduli C11, C12, and the adiabatic moduli KS together with stiffening in C44 was observed between 42 and 53 GPa, which should be caused by the transition from ice-VII to its pre-transitional state. Of particular interest is the dramatic increase in the anisotropy of ice-VII with increasing pressure. Combining the sound velocity of AHH and ice-VII, we have modeled the VP of ice giants with a volume ratio of 20% AHH and 80% ice-VII in the mantle. The obtained high-pressure phase diagram and elastic properties of ammonia hydrate could contribute to understanding the structure of the mantle in the ice giants and satellites.

The Influence of Grain Size on Low-Stability Pre-Transitional Structural-Phase States of NiAl Intermetallide

Using the Monte Carlo method, the influence of grain size (model cell dimensions) on the peculiarities of pretransitional, low-stability structural-phase states of NiAl intermetallide in the region of structural-phase transformations is investigated during thermal cycling (heating and cooling). An analysis of the temperature dependences of the long-range order parameters shows that during heating the maximal long-range order is observed in an alloy with the maximal grain size, while the minimal – in the alloy with the smallest grain size. In order to achieve disordering of the alloy by increasing its grain size, it has to be increasingly overheated. Under cooling, long-range order primarily appears in a fine-grained alloy. The larger the grain size, the wider the temperature interval of the structural-phase transformation. The peculiarities of formation of the structural-phase states in the course of cooling as a function of the grain size (model cell dimensions) indicate that the first ordered regions appear in the fine-grained alloy. As the grain size increases, the temperature at which long-range order appears becomes lower, in other words, a still higher overcooling is required for the system's atomically-ordered states to be formed.

The Influence of Variations in Atomic Composition on Low-Stability Pretransitional Structural-Phase States of a NiAl Intermetallic Compound

An analysis of the influence of a deviation of atomic composition from stoichiometry performed by the Monte Carlo method using a NiAl intermetallide as an example in the course of its cooling demonstrates that such deviation is an important factor in the region of pretransitional low-stability structural-phase states preceding transformation. The short-range order parameter values in non-stoichiometric alloys in their absolute values are essentially lower than those of a stoichiometric intermetallide; hence the tendency towards atomic ordering in non-stoichiometric intermetallics is noticeably lower than that in the stoichiometric alloys. The behavior of the temperature plots of the long-range order parameter in non-stoichiometric alloys during their cooling is considerably different from that of a stoichiometric intermetallide. In the case of cooling of non-stoichiometric alloys, a considerable degree of overcooling is required for the long-range order to set, and the formation of ordered phases occurs at much lower temperatures. Moreover, the temperature plot of long-range parameter of the Ni45Al55 alloy lies somewhat lower than that of the Ni55Al45 alloy, which implies that setting of the longrange order in these non-stoichiometric alloys occurs in different ways. It is underlined that a deviation of the system’s composition from stoichiometry gives rise to an essential refinement of the ordered and disordered regions.

The Influence of Vacancy Concentration of Low-Stability Pre-Transitional Structural-Phase States and Energy Characteristics of NiAl Intermetallide

Using the Monte Carlo method, the influence of vacancy concentration on the structural-phase states and energy characteristics is investigated by the example of an intermetallic compound NiAl in the course of its heating and cooling. According to the analysis, the availability and concentration of vacancies are important factors in the pre-transitional low-stability structural-phase states prior to transformation. On the one hand, neither the vacancies nor their concentration affect the temperature ranges of structural-phase transformations, on the other hand, they essentially influence both the pre-transitional low-stability structural-phase states and the rate of diffusion processes. The temperature behavior of the short-range order parameter suggests that the higher the vacancy concentration (i.e., system’s defectiveness), the higher the temperatures at which the tendencies for increasing atomic ordering would be manifested due to intensified diffusion. This, in turn, evidences of a higher starting structural transformation temperature with an increase in the number of defects in the alloy during cooling. An analysis of the temperature curves of the long-range order parameter of the NiAl intermetallide allows making a conclusion that an increased vacancy concentration (i.e., the alloy’s defectiveness) gives rise to a logical result – decreased long-range ordering in the system in the region of low-stability pre-transitional states and increased starting transformation temperature.

Влияние размера зерна на слабоустойчивые предпереходные структурно-фазовые состояния интерметаллида NiAl

Влияние размера зерна на слабоустойчивые предпереходные структурно-фазовые состояния интерметаллида NiAl

Solvent and Substituent Effects on the Phosphine + CO2 Reaction

A theoretical study of the substituent and solvent effects on the reaction of phosphines with CO2 has been carried out by means of Møller-Plesset (MP2) computational level calculations and continuum polarizable method (PCM) solvent models. Three stationary points along the reaction coordinate have been characterized, a pre-transition state (TS) assembly in which a pnicogen bond or tetrel bond is established between the phosphine and the CO2 molecule, followed by a transition state, and leading finally to the adduct in which the P–C bond has been formed. The solvent effects on the stability and geometry of the stationary points are different. Thus, the pnicogen bonded complexes are destabilized as the dielectric constant of the solvent increases while the opposite happens within the adducts with the P–C bond and the TSs trend. A combination of the substituents and solvents can be used to control the most stable minimum.