Structures of the Human HCN1 Hyperpolarization-Activated Channel.

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels underlie the control of rhythmic activity in cardiac and neuronal pacemaker cells. In HCN, the polarity of voltage dependence is uniquely reversed. Intracellular cyclic adenosine monophosphate (cAMP) levels tune the voltage response, enabling sympathetic nerve stimulation to increase the heart rate. We present cryo-electron microscopy structures of the human HCN channel in the absence and presence of cAMP at 3.5 Å resolution. HCN channels contain a K+ channel selectivity filter-forming sequence from which the amino acids create a unique structure that explains Na+ and K+ permeability. The voltage sensor adopts a depolarized conformation, and the pore is closed. An S4 helix of unprecedented length extends into the cytoplasm, contacts the C-linker, and twists the inner helical gate shut. cAMP binding rotates cytoplasmic domains to favor opening of the inner helical gate. These structures advance understanding of ion selectivity, reversed polarity gating, and cAMP regulation in HCN channels.

An Atomic Structure of the Human Spliceosome.

Mechanistic understanding of pre-mRNA splicing requires detailed structural information on various states of the spliceosome. Here we report the cryo electron microscopy (cryo-EM) structure of the human spliceosome just before exon ligation (the C∗ complex) at an average resolution of 3.76 Å. The splicing factor Prp17 stabilizes the active site conformation. The step II factor Slu7 adopts an extended conformation, binds Prp8 and Cwc22, and is poised for selection of the 3'-splice site. Remarkably, the intron lariat traverses through a positively charged central channel of RBM22; this unusual organization suggests mechanisms of intron recruitment, confinement, and release. The protein PRKRIP1 forms a 100-Å α helix linking the distant U2 snRNP to the catalytic center. A 35-residue fragment of the ATPase/helicase Prp22 latches onto Prp8, and the quaternary exon junction complex (EJC) recognizes upstream 5'-exon sequences and associates with Cwc22 and the GTPase Snu114. These structural features reveal important mechanistic insights into exon ligation.

Structure of the Post-catalytic Spliceosome from Saccharomyces cerevisiae.

Removal of an intron from a pre-mRNA by the spliceosome results in the ligation of two exons in the post-catalytic spliceosome (known as the P complex). Here, we present a cryo-EM structure of the P complex from Saccharomyces cerevisiae at an average resolution of 3.6 Å. The ligated exon is held in the active site through RNA-RNA contacts. Three bases at the 3' end of the 5' exon remain anchored to loop I of U5 small nuclear RNA, and the conserved AG nucleotides of the 3'-splice site (3'SS) are specifically recognized by the invariant adenine of the branch point sequence, the guanine base at the 5' end of the 5'SS, and an adenine base of U6 snRNA. The 3'SS is stabilized through an interaction with the 1585-loop of Prp8. The P complex structure provides a view on splice junction formation critical for understanding the complete splicing cycle.

Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator.

The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel evolved from the ATP-binding cassette (ABC) transporter family. In this study, we determined the structure of zebrafish CFTR in the absence of ATP by electron cryo-microscopy to 3.7 Å resolution. Human and zebrafish CFTR share 55% sequence identity, and 42 of the 46 cystic-fibrosis-causing missense mutational sites are identical. In CFTR, we observe a large anion conduction pathway lined by numerous positively charged residues. A single gate near the extracellular surface closes the channel. The regulatory domain, dephosphorylated, is located in the intracellular opening between the two nucleotide-binding domains (NBDs), preventing NBD dimerization and channel opening. The structure also reveals why many cystic-fibrosis-causing mutations would lead to defects either in folding, ion conduction, or gating and suggests new avenues for therapeutic intervention.

Molecular basis of multistep voltage activation in plant two-pore channel 1.

Voltage-gated ion channels confer excitability to biological membranes, initiating and propagating electrical signals across large distances on short timescales. Membrane excitation requires channels that respond to changes in electric field and couple the transmembrane voltage to gating of a central pore. To address the mechanism of this process in a voltage-gated ion channel, we determined structures of the plant two-pore channel 1 at different stages along its activation coordinate. These high-resolution structures of activation intermediates, when compared with the resting-state structure, portray a mechanism in which the voltage-sensing domain undergoes dilation and in-membrane plane rotation about the gating charge-bearing helix, followed by charge translocation across the charge transfer seal. These structures, in concert with patch-clamp electrophysiology, show that residues in the pore mouth sense inhibitory Ca2+ and are allosterically coupled to the voltage sensor. These conformational changes provide insight into the mechanism of voltage-sensor domain activation in which activation occurs vectorially over a series of elementary steps.

Resolving Multielement Semiconductor Nanocrystals at the Atomic Level: Complete Deciphering of Domains and Order in Complex CuαZnßSnγSeδ (CZTSe) Tetrapods.

Semiconductor nanocrystals (NCs) with high elemental and structural complexity can be engineered to tailor for electronic, photovoltaic, thermoelectric, and battery applications etc. However, this greater complexity causes ambiguity in the atomic structure understanding. This in turn hinders the mechanistic studies of nucleation and growth, the theoretical calculations of functional properties, and the capability to extend functional design across complementary semiconductor nanocrystals. Herein, we successfully deciphered the atomic arrangements of 4 different nanocrystal domains in CuαZnßSnγSeδ (CZTSe) nanocrystals using crucial zone axis analysis on multiple crystals in different orientations. The results show that the essence of crystallographic progression from binary to multielemental semiconductors is actually the change of theoretical periodicity. This transition is caused by decreased symmetry in the crystal instead of previously assumed crystal deformation. We further reveal that these highly complex crystalline entities have highly ordered element arrangements as opposed to the previous understanding that their elemental orderings are random.

Unveiling Variations in Electronic and Atomic Structures Due to Nanoscale Wurtzite and Zinc Blende Phase Separation in GaAs Nanowires.

Phase separation is an intriguing phenomenon often found in III-V nanostructures, but its effect on the atomic and electronic structures of III-V nanomaterials is still not fully understood. Here we study the variations in atomic arrangement and band structure due to the coexistence of wurtzite (WZ) and zinc blende (ZB) phases in single GaAs nanowires by using scanning transmission electron microscopy and monochromated electron energy loss spectroscopy. The WZ lattice distances are found to be larger (by ∼1%), along both the nanowire length direction and the perpendicular direction, than the ZB lattice. The band gap of the WZ phase is ∼20 meV smaller than that of the ZB phase. A shift of ∼70 meV in the conduction band edge between the two phases is also found. The direct and local measurements in single GaAs nanowires reveal important effects of phase separation on the properties of individual III-V nanostructures.

Say Cheese: Structure of the Cardiac Electrical Engine Is Captured.

Voltage-gated sodium channel (Nav)1.5 is the predominantly expressed sodium channel in the myocardium. Mutations in the gene encoding Nav1.5 are associated with several types of cardiac arrhythmias. In their recent study, Jiang et al. provide a detailed structure of the rat Nav1.5, with major implications regarding its physiology, pharmacology, and pathophysiology.

ABC2A: A Straightforward and Fast Method for the Accurate Backmapping of RNA Coarse-Grained Models to All-Atom Structures.

RNAs play crucial roles in various essential biological functions, including catalysis and gene regulation. Despite the widespread use of coarse-grained (CG) models/simulations to study RNA 3D structures and dynamics, their direct application is challenging due to the lack of atomic detail. Therefore, the reconstruction of full atomic structures is desirable. In this study, we introduced a straightforward method called ABC2A for reconstructing all-atom structures from RNA CG models. ABC2A utilizes diverse nucleotide fragments from known structures to assemble full atomic structures based on the CG atoms. The diversification of assembly fragments beyond standard A-form ones, commonly used in other programs, combined with a highly simplified structure refinement process, ensures that ABC2A achieves both high accuracy and rapid speed. Tests on a recent large dataset of 361 RNA experimental structures (30-692 nt) indicate that ABC2A can reconstruct full atomic structures from three-bead CG models with a mean RMSD of ~0.34 Å from experimental structures and an average runtime of ~0.5 s (maximum runtime < 2.5 s). Compared to the state-of-the-art Arena, ABC2A achieves a ~25% improvement in accuracy and is five times faster in speed.

Direct Oxygen-Oxygen Cleavage through Optimizing Interatomic Distances in Dual Single-atom Electrocatalysts for Efficient Oxygen Reduction Reaction.

The oxygen reduction reaction (ORR) on transition single-atom catalysts (SACs) is sustainable in energy-conversion devices. However, the atomically controllable fabrication of single-atom sites and the sluggish kinetics of ORR have remained challenging. Here, we accelerate the kinetics of acid ORR through a direct O-O cleavage pathway through using a bi-functional ligand-assisted strategy to pre-control the distance of hetero-metal atoms. Concretely, the as-synthesized Fe-Zn diatomic pairs on carbon substrates exhibited an outstanding ORR performance with the ultrahigh half-wave potential of 0.86 V vs. RHE in acid electrolyte. Experimental evidence and density functional theory calculations confirmed that the Fe-Zn diatomic pairs with a specific distance range of around 3 Å, which is the key to their ultrahigh activity, average the interaction between hetero-diatomic active sites and oxygen molecules. This work offers new insight into atomically controllable SACs synthesis and addresses the limitations of the ORR dissociative mechanism.

Understanding Alkaline Hydrogen Oxidation Reaction on PdNiRuIrRh High-Entropy-Alloy by Machine Learning Potential.

High-entropy alloy (HEA) catalysts have been widely studied in electrocatalysis. However, identifying atomic structure of HEA with complex atomic arrangement is challenging, which seriously hinders the fundamental understanding of catalytic mechanism. Here, we report a HEA-PdNiRuIrRh catalyst with remarkable mass activity of 3.25 mA µg-1 for alkaline hydrogen oxidation reaction (HOR), which is 8-fold enhancement compared to that of commercial Pt/C. Through machine learning potential-based Monte Carlo simulation, we reveal that the dominant Pd-Pd-Ni/Pd-Pd-Pd bonding environments and Ni/Ru oxophilic sites on HEA surface are beneficial to the optimized adsorption/desorption of *H and enhanced *OH adsorption, contributing to the excellent HOR activity and stability. This work provides significant insights into atomic structure and catalytic mechanism for HEA and offers novel prospects for developing advanced HOR electrocatalysts.

Recent Developments of Microscopic Study for Lanthanide and Manganese Doped Luminescent Materials.

Luminescent materials are indispensable for applications in lighting, displays and photovoltaics, which can transfer, absorb, store and utilize light energy. Their performance is closely related with their size and morphologies, exact atomic arrangement, and local configuration about photofunctional centers. Advanced electron microscopy-based techniques have enabled the possibility to study nanostructures with atomic resolution. Especially, with the advanced micro-electro-mechanical systems, it is able to characterize the luminescent materials at the atomic scale under various environments, providing a deep understanding of the luminescent mechanism. Accordingly, this review summarizes the recent achievements of microscopic study to directly image the microstructure and local environment of activators in lanthanide and manganese (Ln/Mn2+ )-doped luminescent materials, including: 1) bulk materials, the typical systems are nitride/oxynitride phosphors; and 2) nanomaterials, such as nanocrystals (hexagonal-phase NaLnF4 and perovskite) and 2D nanosheets (Ca2 Ta3 O10 and MoS2 ). Finally, the challenges and limitations are highlighted, and some possible solutions to facilitate the developments of advanced luminescent materials are provided.

Theoretical Predictions, Experimental Modulation Strategies, and Applications of MXene-Supported Atomically Dispersed Metal Sites.

Atomically dispersed metal sites (ADMSs) attract immense attention because they can be used in the fields of energy and environmental protection as they are characterized by high atomic utilization efficiency and exhibit high activity. Various supports for anchoring isolated metal atoms are developed to construct ADMSs characterized by highly stable and well-defined structures. This can be achieved by increasing the number of anchoring sites and reinforcing metal-support interactions. MXenes, a new series of 2D nanomaterials, exhibit promising potential in stabilizing isolated metal atoms because of their large specific surface areas and unique surface properties. The high conductivity and hydrophilicity of MXenes can be attributed to the nature of surface functionalization and the properties of tunable structures of the materials. Benefiting from these excellent properties, MXenes can find their applications in various fields. Herein, the precise characterization methods that can be followed to study ADMSs, the construction of MXene-supported ADMSs using theoretical predictions, and experimental modulation strategies are summarized, and their corresponding applications in electrocatalysis, organocatalysis, and advanced battery systems are systematically illustrated. It is hoped that this review will provide insights that can be used for the further development of MXene-supported ADMSs.

Structure diagram and dynamics of formation of hexagonal boron nitride in phase-field crystal model.

The phase-field crystal (PFC-model) is a powerful tool for modelling of the crystallization in colloidal and metallic systems. In the present work, the modified hyperbolic phase-field crystal model for binary systems is presented. This model takes into account slow and fast dynamics of moving interfaces for both concentration and relative atomic number density (which were taken as order parameters). The model also includes specific mobilities for each dynamical field and correlated noise terms. The dynamics of chemical segregation with origination of mixed pseudo-hexagonal binary phase (the so-called 'triangle phase') is used as a benchmark in two spatial dimensions for the developing model. Using the free energy functional and specific lattice vectors for hexagonal crystal, the structure diagram of co-existence of liquid and three-dimensional hexagonal phase for the binary PFC-model was carried out. Parameters of the crystal lattice correspond to the hexagonal boron nitride (BN) crystal, the values of which have been taken from the literature. The paper shows the qualitative agreement between the developed structure diagram of the PFC model and the previously known equilibrium diagram for BN constructed using thermodynamic functions. This article is part of the theme issue 'Transport phenomena in complex systems (part 2)'.

Unraveling the Complexity of Nano-Dispersoids in the Oxide Dispersion Strengthened Alloy 617.

Nanocrystalline oxides are mainly responsible for Ni-base oxide dispersion strengthened (ODS) superalloys excellent thermo-mechanical properties. To establish the microstructural correlations between the metallic matrix and various oxide dispersoids, we report here the atomic-scale structure and chemistry of the complex nano-oxide dispersoids. Ultrahigh-resolution Cs-aberration-corrected scanning transmission electron microscopy (STEM) based techniques have been used to resolve nano-dispersoids in the Alloy 617 ODS. These nano-oxides, interestingly, possess a variety of high-angle annular dark-field (HAADF) contrasts, that is, bright, dark, and bi-phases. Both the light and heavy atoms have been found to be present in Y­Al­O complex-oxide nanostructures in varying quantities and forming a characteristic interface with the metallic matrix. In overcoming the limitation of conventional STEM-HAADF imaging, the integrated differential phase-contrast imaging technique was employed to investigate the oxygen atoms along with other elements in the dispersoids and its interface with the matrix. The most intriguing aspect of the study is the discovery of a few atoms thick Al2O3 interlayer (shell) around a monoclinic Y­Al­O core in the Ni-matrix. On the other hand, when the dispersoid is a hexagonal type Y­Al­O complex, the interface energy is already low, maintaining a semi-coherent interface and it was devoid of a shell.

Correlating 3D Surface Atomic Structure and Catalytic Activities of Pt Nanocrystals.

Active sites and catalytic activity of heterogeneous catalysts is determined by their surface atomic structures. However, probing the surface structure at an atomic resolution is difficult, especially for solution ensembles of catalytic nanocrystals, which consist of heterogeneous particles with irregular shapes and surfaces. Here, we constructed 3D maps of the coordination number (CN) and generalized CN (CN_) for individual surface atoms of sub-3 nm Pt nanocrystals. Our results reveal that the synthesized Pt nanocrystals are enclosed by islands of atoms with nonuniform shapes that lead to complex surface structures, including a high ratio of low-coordination surface atoms, reduced domain size of low-index facets, and various types of exposed high-index facets. 3D maps of CN_ are directly correlated to catalytic activities assigned to individual surface atoms with distinct local coordination structures, which explains the origin of high catalytic performance of small Pt nanocrystals in important reactions such as oxygen reduction reactions and CO electro-oxidation.

Investigation of the molecular motor of muscle: from generating life in a test tube to myosin structure over beers.

This article traces 60 years of investigation of the molecular motor of skeletal muscle from the 1940s through the 1990s. It started with the discovery that myosin interaction with actin in the presence of ATP caused shortening of threads of actin and myosin. In 1957, structures protruding from myosin filaments were seen for the first time and called "cross bridges." A combination of techniques led to the proposal in 1969 of the "swinging-tilting cross bridge" model of contraction. In the early 1980s, a major problem arose when it was shown that a probe attached to the cross bridges did not move during contraction. A spectacular breakthrough came when it was discovered that only the cross bridge was required to support movement in an in vitro motility assay. Next it was determined that single myosin molecules caused the movement of actin filaments in 10-nm steps. The atomic structure of the cross bridge was published in 1993, and this discovery supercharged the muscle field. The cross bridge contained a globular head or motor domain that bound actin and ATP. But the most striking feature was the long tail of the cross bridge surrounded by two subunits of the myosin molecule. This structure suggested that the tail might act as a lever arm magnifying head movement. Consistent with this proposal, genetic techniques that lengthened the lever arm resulted in larger myosin steps. Thus the molecular motor of muscle operated not by the tilting of the globular head of myosin but by tilting of the lever arm generating the driving force for contraction.

Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions.

We present Simu-D, a software suite for the simulation and successive identification of local structures of atomistic systems, based on polymers, under extreme conditions, in the bulk, on surfaces, and at interfaces. The protocol is built around various types of Monte Carlo algorithms, which include localized, chain-connectivity-altering, identity-exchange, and cluster-based moves. The approach focuses on alleviating one of the main disadvantages of Monte Carlo algorithms, which is the general applicability under a wide range of conditions. Present applications include polymer-based nanocomposites with nanofillers in the form of cylinders and spheres of varied concentration and size, extremely confined and maximally packed assemblies in two and three dimensions, and terminally grafted macromolecules. The main simulator is accompanied by a descriptor that identifies the similarity of computer-generated configurations with respect to reference crystals in two or three dimensions. The Simu-D simulator-descriptor can be an especially useful tool in the modeling studies of the entropy- and energy-driven phase transition, adsorption, and self-organization of polymer-based systems under a variety of conditions.

Approximate Atomic Green Functions.

In atomic and many-particle physics, Green functions often occur as propagators to formally represent the (integration over the) complete spectrum of the underlying Hamiltonian. However, while these functions are very crucial to describing many second- and higher-order perturbation processes, they have hardly been considered and classified for complex atoms. Here, we show how relativistic (many-electron) Green functions can be approximated and systematically improved for few- and many-electron atoms and ions. The representation of these functions is based on classes of virtual excitations, or so-called excitation schemes, with regard to given bound-state reference configurations, and by applying a multi-configuration Dirac-Hartree-Fock expansion of all atomic states involved. A first implementation of these approximate Green functions has been realized in the framework of Jac, the Jena Atomic Calculator, and will facilitate the study of various multi-photon and/or multiple electron (emission) processes.

Giant Thickness-Tunable Bandgap and Robust Air Stability of 2D Palladium Diselenide.

Uncovering the thickness-dependent electronic property and environmental stability for 2D materials are crucial issues for promoting their applications in high-performance electronic and optoelectronic devices. Herein, the extrahigh air stability and giant tunable electronic bandgap of chemical vapor deposition (CVD)-derived few-layer PdSe2 on Au foils, by using scanning tunneling microscope/spectroscopy (STM/STS), are reported. The robust stability of 2D PdSe2 is uncovered by the observation of nearly defect/adsorption-free atomic lattices on long-time air-exposed samples. A one-to-one correspondence between the electronic bandgap (from ≈1.15 to ≈0 eV) and thickness of PdSe2 /Au (from bilayer to bulk) is established. It is also revealed that few-layer semiconducting PdSe2 flakes present zero-gap edges, induced by hybridization of Pd 4d and Se 4p orbitals. This work hereby provides straightforward evidence for the thickness-tunable electronic property and air stability of 2D semiconductors, thus shedding light on their applications in next-generation electronic devices.