Cryo-EM Structure of the Human Ribonuclease P Holoenzyme.

Ribonuclease (RNase) P is a ubiquitous ribozyme that cleaves the 5' leader from precursor tRNAs. Here, we report cryo-electron microscopy structures of the human nuclear RNase P alone and in complex with tRNAVal. Human RNase P is a large ribonucleoprotein complex that contains 10 protein components and one catalytic RNA. The protein components form an interlocked clamp that stabilizes the RNA in a conformation optimal for substrate binding. Human RNase P recognizes the tRNA using a double-anchor mechanism through both protein-RNA and RNA-RNA interactions. Structural comparison of the apo and tRNA-bound human RNase P reveals that binding of tRNA induces a local conformational change in the catalytic center, transforming the ribozyme into an active state. Our results also provide an evolutionary model depicting how auxiliary RNA elements in bacterial RNase P, essential for substrate binding, and catalysis, were replaced by the much more complex and multifunctional protein components in higher organisms.

Mechanistic insight into allosteric activation of human pyruvate carboxylase by acetyl-CoA.

Pyruvate carboxylase (PC) catalyzes the two-step carboxylation of pyruvate to produce oxaloacetate, playing a key role in the maintenance of metabolic homeostasis in cells. Given its involvement in multiple diseases, PC has been regarded as a potential therapeutic target for obesity, diabetes, and cancer. Albeit acetyl-CoA has been recognized as the allosteric regulator of PC for over 60 years, the underlying mechanism of how acetyl-CoA induces PC activation remains enigmatic. Herein, by using time-resolved cryo-electron microscopy, we have captured the snapshots of PC transitional states during its catalytic cycle. These structures and the biochemical studies reveal that acetyl-CoA stabilizes PC in a catalytically competent conformation, which triggers a cascade of events, including ATP hydrolysis and the long-distance communication between the two reactive centers. These findings provide an integrated picture for PC catalysis and unveil the unique allosteric mechanism of acetyl-CoA in an essential biochemical reaction in all kingdoms of life.

Coevolution of RNA and protein subunits in RNase P and RNase MRP, two RNA processing enzymes.

RNase P and RNase mitochondrial RNA processing (MRP) are ribonucleoproteins (RNPs) that consist of a catalytic RNA and a varying number of protein cofactors. RNase P is responsible for precursor tRNA maturation in all three domains of life, while RNase MRP, exclusive to eukaryotes, primarily functions in rRNA biogenesis. While eukaryotic RNase P is associated with more protein cofactors and has an RNA subunit with fewer auxiliary structural elements compared to its bacterial cousin, the double-anchor precursor tRNA recognition mechanism has remarkably been preserved during evolution. RNase MRP shares evolutionary and structural similarities with RNase P, preserving the catalytic core within the RNA moiety inherited from their common ancestor. By incorporating new protein cofactors and RNA elements, RNase MRP has established itself as a distinct RNP capable of processing ssRNA substrates. The structural information on RNase P and MRP helps build an evolutionary trajectory, depicting how emerging protein cofactors harmonize with the evolution of RNA to shape different functions for RNase P and MRP. Here, we outline the structural and functional relationship between RNase P and MRP to illustrate the coevolution of RNA and protein cofactors, a key driver for the extant, diverse RNP world.

Unveiling Nonsecular Collisional Dissipation of Molecular Alignment.

We conducted a joint theoretical and experimental study to investigate the collisional dissipation of molecular alignment. By comparing experimental measurements to the quantum simulations, the nonsecular effect in the collision dissipation of molecular alignment was unveiled from the gas-density-dependent decay rates of the molecular alignment revival signals. Different from the conventional perspective that the nonsecular collisional effect rapidly fades within the initial few picoseconds following laser excitation, our simulations of the time-dependent decoherence process demonstrated that this effect can last for tens of picoseconds in the low-pressure regime. This extended timescale allows for the distinct identification of the nonsecular effect from molecular alignment signals. Our findings present the pioneering evidence that nonsecular molecular collisional dissipation can endure over an extended temporal span, challenging established concepts and strengthening our understanding of molecular dynamics within dissipative environments.

Ultrafast Picometer-Resolved Molecular Structure Imaging by Laser-Induced High-Order Harmonics.

Real-time visualization of molecular transformations is a captivating yet challenging frontier of ultrafast optical science and physical chemistry. While ultrafast x-ray and electron diffraction methods can achieve the needed subangstrom spatial resolution, their temporal resolution is still limited to hundreds of femtoseconds, much longer than the few femtoseconds required to probe real-time molecular dynamics. Here, we show that high-order harmonics generated by intense femtosecond lasers can be used to image molecules with few-ten-attosecond temporal resolution and few-picometer spatial resolution. This is achieved by exploiting the sensitive dependence of molecular recombination dipole moment to the geometry of the molecule at the time of harmonic emission. In a proof-of-principle experiment, we have applied this high-harmonic structure imaging (HHSI) method to monitor the structural rearrangement in NH_{3}, ND_{3}, and N_{2} from one to a few femtoseconds after the molecule is ionized by an intense laser. Our findings establish HHSI as an effective approach to resolve molecular dynamics with unprecedented spatiotemporal resolution, which can be extended to trace photochemical reactions in the future.

Computational simulations uncover enantioselective metabolism of chiral triazole fungicides by human CYP450 enzymes: A case study of tebuconazole.

Tebuconazole (TEB), a prominent chiral triazole fungicide, has been extensively utilized for plant pathogen control globally. Despite experimental evidence of TEB metabolism in mammals, the enantioselectivity in the biotransformation of R- and S-TEB enantiomers by specific CYP450s remains elusive. In this work, integrated in silico simulations were employed to unveil the binding interactions and enantioselective metabolic fate of TEB enantiomers within human CYP1A2, 2B6, 2E1, and 3A4. Molecular dynamics (MD) simulations clearly delineated the binding specificity of R- and S-TEB to the four CYP450s, crucially determining their differences in metabolic activity and enantioselectivity. The primary driving force for robust ligand binding was identified as van der Waals interactions with CYP450s, particularly involving the hydrophobic residues. Mechanistic insights derived from quantum mechanics/molecular mechanics (QM/MM) calculations established C2-methyl hydroxylation as the predominant route of R-/S-TEB metabolism, while C6-hydroxylation and triazol epoxidation were deemed kinetically infeasible pathways. Specifically, the resulting hydroxy-R-TEB metabolite primarily originates from R-TEB biotransformation by 1A2, 2E1 and 3A4, whereas hydroxy-S-TEB is preferentially produced by 2B6. These findings significantly contribute to our comprehension of the binding specificity and enantioselective metabolic fate of chiral TEB by CYP450s, potentially informing further research on human health risk assessment associated with TEB exposure.

High harmonic generation in solids: particle and wave perspectives.

High harmonic generation (HHG) from gas-phase atoms (or molecules) has opened up a new frontier in ultrafast optics, where attosecond time resolution and angstrom spatial resolution are accessible. The fundamental physical pictures of HHG are always explained by the laser-induced recollision of particle-like electron motion, which lay the foundation of attosecond spectroscopy. In recent years, HHG has also been observed in solids. One can expect the extension of attosecond spectroscopy to the condensed matter if a description capable of resolving the ultrafast dynamics is provided. Thus, a large number of theoretical studies have been proposed to understand the underlying physics of solid HHG. Here, we revisit the recollision picture in solid HHG and show some challenges of current particle-perspective methods, and present the recently developed wave-perspective Huygens-Fresnel picture for understanding dynamical systems within the ambit of strong-field physics.

m6Aminer: Predicting the m6Am Sites on mRNA by Fusing Multiple Sequence-Derived Features into a CatBoost-Based Classifier.

As one of the most important post-transcriptional modifications, m6Am plays a fairly important role in conferring mRNA stability and in the progression of cancers. The accurate identification of the m6Am sites is critical for explaining its biological significance and developing its application in the medical field. However, conventional experimental approaches are time-consuming and expensive, making them unsuitable for the large-scale identification of the m6Am sites. To address this challenge, we exploit a CatBoost-based method, m6Aminer, to identify the m6Am sites on mRNA. For feature extraction, nine different feature-encoding schemes (pseudo electron-ion interaction potential, hash decimal conversion method, dinucleotide binary encoding, nucleotide chemical properties, pseudo k-tuple composition, dinucleotide numerical mapping, K monomeric units, series correlation pseudo trinucleotide composition, and K-spaced nucleotide pair frequency) were utilized to form the initial feature space. To obtain the optimized feature subset, the ExtraTreesClassifier algorithm was adopted to perform feature importance ranking, and the top 300 features were selected as the optimal feature subset. With different performance assessment methods, 10-fold cross-validation and independent test, m6Aminer achieved average AUC of 0.913 and 0.754, demonstrating a competitive performance with the state-of-the-art models m6AmPred (0.905 and 0.735) and DLm6Am (0.897 and 0.730). The prediction model developed in this study can be used to identify the m6Am sites in the whole transcriptome, laying a foundation for the functional research of m6Am.

Rotational echo spectroscopy for accurate measurement of molecular alignment.

We measure the molecular alignment induced in gas using molecular rotational echo spectroscopy. Our results show that the echo intensity and the time interval between the local extremas of the echo responses depend sensitively on the pump intensities and the initial molecular rotational temperature, respectively. This allows us to accurately extract these experimental parameters from the echo signals and then further determine the molecular alignment in experiments. The accuracy of our method has been verified by comparing the simulation with the extracted parameters from the molecular alignment experiment performed with a femtosecond pump pulse.

Fingerprint of the Interbond Electron Hopping in Second-Order Harmonic Generation.

We experimentally explore the fingerprint of the microscopic electron dynamics in second-order harmonic generation (SHG). It is shown that the interbond electron hopping induces a novel source of nonlinear polarization and plays an important role even when the driving laser intensity is 2 orders of magnitude lower than the characteristic atomic field. Our model predicts anomalous anisotropic structures of the SHG yield contributed by the interbond electron hopping, which is identified in our experiments with ZnO crystals. Moreover, a generalized second-order susceptibility with an explicit form is proposed, which provides a unified description in both the weak and strong field regimes. Our work reveals the nonlinear responses of materials at the electron scale and extends the nonlinear optics to a previously unexplored regime, where the nonlinearity related to the interbond electron hopping becomes dominant. It paves the way for realizing controllable nonlinearity on an ultrafast time scale.

Enhancement of the photocurrents injected in gapped graphene by the orthogonally polarized two-color laser field.

We theoretically investigate the photocurrents injected in gapped graphene by the orthogonally polarized two-color laser field. Depending on the relative phase, the photocurrents can be coherently controlled by deforming the electron trajectory in the reciprocal space. Under the same field strength, the peak photocurrent in the orthogonally polarized two-color field is about 20 times larger than that for linearly polarized light, and about 3.6 times for elliptically polarized light. The enhancement of the photocurrent can be attributed to an obvious asymmetric distribution of the real population in the reciprocal space, which is sensitive to the waveform of the laser field and related to the quantum interference between the electron trajectories. Our work provides a noncontact method to effectively enhance the injected current in graphene.

Multilevel quantum interference in the formation of high-order fractional molecular alignment echoes.

We theoretically investigate the formation of the high-order fractional alignment echo in OCS molecule and systematically study the dependence of echo intensity on the intensities and time delay of the two excitation pulses. Our simulations reveal an intricate dependence of the intensity of high-order fractional alignment echo on the laser conditions. Based on the analysis with rotational density matrix, this intricate dependence is further demonstrated to arise from the interference of multiple quantum pathways that involve multilevel rotational transitions. Our result provides a comprehensive multilevel picture of the quantum dynamics of high-order fractional alignment echo in molecular ensembles, which will facilitate the development of "rotational echo spectroscopy."

Huygens-Fresnel Picture for High Harmonic Generation in Solids.

High harmonic generation (HHG) is usually described by the laser-induced recollision of particlelike electrons, which lies at the heart of attosecond physics and also inspires numerous attosecond spectroscopic methods. Here, we demonstrate that the wavelike behavior of electrons plays an important role in solid HHG. By taking an analogy to the Huygens-Fresnel principle, an electron wave perspective on solid HHG is proposed by using the wavelet stationary-phase method. From this perspective, we have explained the deviation between the cutoff law predicted by the particlelike recollision model and the numerical simulation of semiconductor Bloch equations. Moreover, the emission times of HHG can be well predicted with our method involving the wave property of electrons. However, in contrast, the prediction with the particlelike recollision model shows obvious deviations compared to the semiconductor Bloch equations simulation. The wavelike properties of the electron motion can also be revealed by the HHG in a two-color field.

Dynamic Core Polarization in High Harmonic Generation from Solids: The Example of MgO Crystals.

Previously, the strong field processes in solids have always been explained by the single-active-electron (SAE) model with a frozen core excluding the fluctuation of background electrons. In this work, we demonstrate the strong field induced dynamic core polarization effect and propose a model for revealing its role in high harmonic generation (HHG) from solids. We show that the polarized core induces an additional polarization current beyond the SAE model based on the frozen cores. It gives a new mechanism for HHG and leads to new anisotropic structures, which are experimentally observed with MgO. Our experiments indicate that the influences of dynamic core polarization on HHG are obvious for both linearly and elliptically polarized laser fields. Our work establishes the bridge between the HHG and the dynamic changes of the effective many-electron interaction in solids, which paves the way to probe the ultrafast electron dynamics.

Generation of isolated circularly polarized attosecond pulses by three-color laser field mixing.

We propose and theoretically demonstrate a method to generate the circularly polarized supercontinuum with three-color electric fields. The three-color field is synthesized from an orthogonally polarized two-color (OTC) laser field and an infrared gating field. All driving pulse durations are extended to 40 fs. We demonstrate that the three-color field imposes curved trajectories for ionized electrons and extends the time interval between each harmonic emitting. Through adjusting intensity ratios among three components of the driving field, a nearly circular isolated attosecond pulse can be generated.

Measuring the rotational temperature and pump intensity in molecular alignment experiments via high harmonic generation.

We demonstrate a method to simultaneously measure the rotational temperature and pump intensity in laser-induced molecular alignment by the time-resolved high harmonic spectroscopy (HHS). It relies on the sensitive dependence of the arising times of the local minima and maxima of the harmonic yields at the rotational revivals on the pump intensity and rotational temperature. By measuring the arising times of these local extrema from the time-resolved harmonic signals, the rotational temperature and pump intensity can be accurately measured. We have demonstrated our method using N2 molecules. The validity and robustness of our method are tested with different harmonic orders and by changing the gas pressures as well as the distance between the gas exit and the optical axis. Moreover, we have also demonstrated the versatility of our method by applying it to CO2 molecules.

Determination of Electron Band Structure using Temporal Interferometry.

We propose an all-optical method to directly reconstruct the band structure of semiconductors. Our scheme is based on the temporal Young's interferometer realized by high harmonic generation with a few-cycle laser pulse. As a time-energy domain interferometer, temporal interference encodes the band structure into the fringe in the energy domain. The relation between the band structure and the emitted harmonic frequencies is established. This enables us to retrieve the band structure from the spectrum of high harmonic generation with a single-shot measurement. Our scheme paves the way to study matters under ambient conditions and to track the ultrafast modification of band structures.

Channel-closing effects of electronic excitation in solids.

We investigate the electronic excitation of solids in strong fields by solving the time-dependent Schrödinger equation. The excitation probability exhibits a strong modulation as a function of laser intensity when the initial states fill in the whole valence band. To have a clear insight into the modulation, we further study the electronic excitation from a single eigenstate in solids. A series of resonance-like enhancements of excitation probability are produced by changing the laser intensity and wavelength. We attribute the resonance-like enhancements to the channel-closing effects in solids. It is shown that the excitation probability exhibits enhancements when the value of channel is odd for intracycle interference and an integer for intercycle interference. This is different from the atom that the enhancement occur in the integer channels. We also reveal that the channel-closing effects can be observed by solid high-order harmonic generation.

All-optical measurement of high-order fractional molecular echoes by high-order harmonic generation.

An all-optical measurement of high-order fractional molecular echoes is demonstrated by using high-order harmonic generation (HHG). Excited by a pair of time-delayed short laser pulses, the signatures of full and high order fractional (1/2 and 1/3) alignment echoes are observed in the HHG signals measured from CO 2 molecules at various time delays of the probe pulse. By increasing the time delay of the pump pulses, much higher order fractional (1/4) alignment echo is also observed in N 2O molecules. With an analytic model based on the impulsive approximation, the spatiotemporal dynamics of the echo process are retrieved from the experiment. Compared to the typical molecular alignment revivals, high-order fractional molecular echoes are demonstrated to dephase more rapidly, which will open a new route towards the ultrashort-time measurement. The proposed HHG method paves an efficient way for accessing the high-order fractional echoes in molecules.

Reciprocal-Space-Trajectory Perspective on High-Harmonic Generation in Solids.

We revisit the mechanism of high-harmonic generation (HHG) from solids by comparing HHG in laser fields with different ellipticities but a constant maximum amplitude. It is shown that the cutoff of HHG is strongly extended in a circularly polarized field. Moreover, the harmonic yield with large ellipticity is comparable to or even higher than that in the linearly polarized field. To understand the underlying physics, we develop a reciprocal-space-trajectory method, which explains HHG in solids by a trajectory ensemble from different ionization times and different initial states in the reciprocal space. We show that the cutoff extension is related to an additional preacceleration step prior to ionization, which has been overlooked in solids. By analyzing the trajectories and the time-frequency spectrogram, we show that the HHG in solids cannot be interpreted in terms of the classical recollision picture alone. Instead, the radiation should be described by the electron-hole interband polarization, which leads to the unusual ellipticity dependence. We propose a new four-step model to understand the mechanism of HHG in solids.