Protein N-Terminal Acetylation: Structural Basis, Mechanism, Versatility, and Regulation.

N-terminal acetylation (NTA) is one of the most widespread protein modifications, which occurs on most eukaryotic proteins, but is significantly less common on bacterial and archaea proteins. This modification is carried out by a family of enzymes called N-terminal acetyltransferases (NATs). To date, 12 NATs have been identified, harboring different composition, substrate specificity, and in some cases, modes of regulation. Recent structural and biochemical analysis of NAT proteins allows for a comparison of their molecular mechanisms and modes of regulation, which are described here. Although sharing an evolutionarily conserved fold and related catalytic mechanism, each catalytic subunit uses unique elements to mediate substrate-specific activity, and use NAT-type specific auxiliary and regulatory subunits, for their cellular functions.

Recognition of centromere-specific histone Cse4 by the inner kinetochore Okp1-Ame1 complex.

Successful mitosis depends on the timely establishment of correct chromosomal attachments to microtubules. The kinetochore, a modular multiprotein complex, mediates this connection by recognizing specialized chromatin containing a histone H3 variant called Cse4 in budding yeast and CENP-A in vertebrates. Structural features of the kinetochore that enable discrimination between Cse4/CENP-A and H3 have been identified in several species. How and when these contribute to centromere recognition and how they relate to the overall structure of the inner kinetochore are unsettled questions. More generally, this molecular recognition ensures that only one kinetochore is built on each chromatid and that this happens at the right place on the chromatin fiber. We have determined the crystal structure of a Cse4 peptide bound to the essential inner kinetochore Okp1-Ame1 heterodimer from budding yeast. The structure and related experiments show in detail an essential point of Cse4 contact and provide information about the arrangement of the inner kinetochore.

Subnanometer Scale Mapping of Hydrogen Doping in Vanadium Dioxide.

Hydrogen donor doping of correlated electron systems such as vanadium dioxide (VO2) profoundly modifies the ground state properties. The electrical behavior of HxVO2 is strongly dependent on the hydrogen concentration; hence, atomic scale control of the doping process is necessary. It is however a nontrivial problem to quantitatively probe the hydrogen distribution in a solid matrix. As hydrogen transfers its sole electron to the material, the ionization mechanism is suppressed. In this study, a methodology mapping the doping distribution at subnanometer length scale is demonstrated across a HxVO2 thin film focusing on the oxygen-hydrogen bonds using electron energy loss spectroscopy (EELS) coupled with first-principles EELS calculations. The hydrogen distribution was revealed to be nonuniform along the growth direction and between different VO2 grains, calling for intricate hydrogenation mechanisms. Our study points to a powerful approach to quantitatively map dopant distribution in quantum materials relevant to energy and information sciences.

Semi-Synthetic CoA-α-Synuclein Constructs Trap N-Terminal Acetyltransferase NatB for Binding Mechanism Studies.

N-terminal acetylation is a chemical modification carried out by N-terminal acetyltransferases. A major member of this enzyme family, NatB, acts on much of the human proteome, including α-synuclein (αS), a synaptic protein that mediates vesicle trafficking. NatB acetylation of αS modulates its lipid vesicle binding properties and amyloid fibril formation, which underlies its role in the pathogenesis of Parkinson's disease. Although the molecular details of the interaction between human NatB (hNatB) and the N-terminus of αS have been resolved, whether the remainder of the protein plays a role in interacting with the enzyme is unknown. Here, we execute the first synthesis, by native chemical ligation, of a bisubstrate inhibitor of NatB consisting of coenzyme A and full-length human αS, additionally incorporating two fluorescent probes for studies of conformational dynamics. We use cryo-electron microscopy (cryo-EM) to characterize the structural features of the hNatB/inhibitor complex and show that, beyond the first few residues, αS remains disordered when in complex with hNatB. We further probe changes in the αS conformation by single molecule Förster resonance energy transfer (smFRET) to reveal that the C-terminus expands when bound to hNatB. Computational models based on the cryo-EM and smFRET data help to explain the conformational changes as well as their implications for hNatB substrate recognition and specific inhibition of the interaction with αS. Beyond the study of αS and NatB, these experiments illustrate valuable strategies for the study of challenging structural biology targets through a combination of protein semi-synthesis, cryo-EM, smFRET, and computational modeling.

Hydrogen-induced tunable remanent polarization in a perovskite nickelate.

Materials with field-tunable polarization are of broad interest to condensed matter sciences and solid-state device technologies. Here, using hydrogen (H) donor doping, we modify the room temperature metallic phase of a perovskite nickelate NdNiO3 into an insulating phase with both metastable dipolar polarization and space-charge polarization. We then demonstrate transient negative differential capacitance in thin film capacitors. The space-charge polarization caused by long-range movement and trapping of protons dominates when the electric field exceeds the threshold value. First-principles calculations suggest the polarization originates from the polar structure created by H doping. We find that polarization decays within ~1 second which is an interesting temporal regime for neuromorphic computing hardware design, and we implement the transient characteristics in a neural network to demonstrate unsupervised learning. These discoveries open new avenues for designing ferroelectric materials and electrets using light-ion doping.

Molecular role of NAA38 in thermostability and catalytic activity of the human NatC N-terminal acetyltransferase.

N-terminal acetylation occurs on over 80% of human proteins and is catalyzed by a family of N-terminal acetyltransferases (NATs). All NATs contain a small catalytic subunit, while some also contain a large auxiliary subunit that facilitates catalysis and ribosome targeting for co-translational acetylation. NatC is one of the major NATs containing an NAA30 catalytic subunit, but uniquely contains two auxiliary subunits, large NAA35 and small NAA38. Here, we report the cryo-EM structures of human NatC (hNatC) complexes with and without NAA38, together with biochemical studies, to reveal that NAA38 increases the thermostability and broadens the substrate-specificity profile of NatC by ordering an N-terminal segment of NAA35 and reorienting an NAA30 N-terminal peptide binding loop for optimal catalysis, respectively. We also note important differences in engagement with a stabilizing inositol hexaphosphate molecule between human and yeast NatC. These studies provide new insights for the function and evolution of the NatC complex.

Semi-synthetic CoA-α-Synuclein Constructs Trap N-terminal Acetyltransferase NatB for Binding Mechanism Studies.

N-terminal acetylation is a chemical modification carried out by N-terminal acetyltransferases (NATs). A major member of this enzyme family, NatB, acts on much of the human proteome, including α-synuclein (αS), a synaptic protein that mediates vesicle trafficking. NatB acetylation of αS modulates its lipid vesicle binding properties and amyloid fibril formation, which underlies its role in the pathogenesis of Parkinson's disease. Although the molecular details of the interaction between human NatB (hNatB) and the N-terminus of αS have been resolved, whether the remainder of the protein plays a role in interacting with the enzyme is unknown. Here we execute the first synthesis, by native chemical ligation, of a bisubstrate inhibitor of NatB consisting of coenzyme A and full-length human αS, additionally incorporating two fluorescent probes for studies of conformational dynamics. We use cryo-electron microscopy (cryo-EM) to characterize the structural features of the hNatB/inhibitor complex and show that, beyond the first few residues, αS remains disordered when in complex with hNatB. We further probe changes in the αS conformation by single molecule Förster resonance energy transfer (smFRET) to reveal that the C-terminus expands when bound to hNatB. Computational models based on the cryo-EM and smFRET data help to explain the conformational changes and their implications for hNatB substrate recognition and specific inhibition of the interaction with αS. Beyond the study of αS and NatB, these experiments illustrate valuable strategies for the study of challenging structural biology targets through a combination of protein semi-synthesis, cryo-EM, smFRET, and computational modeling.

Complex Oxides for Brain-Inspired Computing: A Review.

The fields of brain-inspired computing, robotics, and, more broadly, artificial intelligence (AI) seek to implement knowledge gleaned from the natural world into human-designed electronics and machines. In this review, the opportunities presented by complex oxides, a class of electronic ceramic materials whose properties can be elegantly tuned by doping, electron interactions, and a variety of external stimuli near room temperature, are discussed. The review begins with a discussion of natural intelligence at the elementary level in the nervous system, followed by collective intelligence and learning at the animal colony level mediated by social interactions. An important aspect highlighted is the vast spatial and temporal scales involved in learning and memory. The focus then turns to collective phenomena, such as metal-to-insulator transitions (MITs), ferroelectricity, and related examples, to highlight recent demonstrations of artificial neurons, synapses, and circuits and their learning. First-principles theoretical treatments of the electronic structure, and in situ synchrotron spectroscopy of operating devices are then discussed. The implementation of the experimental characteristics into neural networks and algorithm design is then revewed. Finally, outstanding materials challenges that require a microscopic understanding of the physical mechanisms, which will be essential for advancing the frontiers of neuromorphic computing, are highlighted.

Selective area doping for Mott neuromorphic electronics.

The cointegration of artificial neuronal and synaptic devices with homotypic materials and structures can greatly simplify the fabrication of neuromorphic hardware. We demonstrate experimental realization of vanadium dioxide (VO2) artificial neurons and synapses on the same substrate through selective area carrier doping. By locally configuring pairs of catalytic and inert electrodes that enable nanoscale control over carrier density, volatility or nonvolatility can be appropriately assigned to each two-terminal Mott memory device per lithographic design, and both neuron- and synapse-like devices are successfully integrated on a single chip. Feedforward excitation and inhibition neural motifs are demonstrated at hardware level, followed by simulation of network-level handwritten digit and fashion product recognition tasks with experimental characteristics. Spatially selective electron doping opens up previously unidentified avenues for integration of emerging correlated semiconductors in electronic device technologies.

Molecular mechanism of N-terminal acetylation by the ternary NatC complex.

Protein N-terminal acetylation is predominantly a ribosome-associated modification, with NatA-E serving as the major enzymes. NatC is the most unusual of these enzymes, containing one Naa30 catalytic subunit and two auxiliary subunits, Naa35 and Naa38; and substrate selectivity profile that overlaps with NatE. Here, we report the cryoelectron microscopy structure of S. pombe NatC with a NatE/C-type bisubstrate analog and inositol hexaphosphate (IP6), and associated biochemistry studies. We find that the presence of three subunits is a prerequisite for normal NatC acetylation activity in yeast and that IP6 binds tightly to NatC to stabilize the complex. We also describe the molecular basis for IP6-mediated NatC complex stabilization and the overlapping yet distinct substrate profiles of NatC and NatE.

Novel Bisubstrate Inhibitors for Protein N-Terminal Acetyltransferase D.

Protein N-terminal acetyltransferase D (NatD, NAA40) that specifically acetylates the alpha-N-terminus of histone H4 and H2A has been implicated in various diseases, but no inhibitor has been reported for this important enzyme. Based on the acetyl transfer mechanism of NatD, we designed and prepared a series of highly potent NatD bisubstrate inhibitors by covalently linking coenzyme A to different peptide substrates via an acetyl or propionyl spacer. The most potent bisubstrate inhibitor displayed an apparent Ki value of 1.0 nM. Biochemical studies indicated that bisubstrate inhibitors are competitive to the peptide substrate and noncompetitive to the cofactor, suggesting that NatD undergoes an ordered Bi-Bi mechanism. We also demonstrated that these inhibitors are highly specific toward NatD, displaying about 1000-fold selectivity over other closely related acetyltransferases. High-resolution crystal structures of NatD bound to two of these inhibitors revealed the molecular basis for their selectivity and inhibition mechanism, providing a rational path for future inhibitor development.

Menin-regulated Pbk controls high fat diet-induced compensatory beta cell proliferation.

Pancreatic beta cells undergo compensatory proliferation in the early phase of type 2 diabetes. While pathways such as FoxM1 are involved in regulating compensatory beta cell proliferation, given the lack of therapeutics effectively targeting beta cell proliferation, other targetable pathways need to be identified. Herein, we show that Pbk, a serine/threonine protein kinase, is essential for high fat diet (HFD)-induced beta cell proliferation in vivo using a Pbk kinase deficiency knock-in mouse model. Mechanistically, JunD recruits menin and HDAC3 complex to the Pbk promoter to reduce histone H3 acetylation, leading to epigenetic repression of Pbk expression. Moreover, menin inhibitor (MI) disrupts the menin-JunD interaction and augments Pbk transcription. Importantly, MI administration increases beta cell proliferation, ameliorating hyperglycemia, and impaired glucose tolerance (IGT) in HFD-induced diabetic mice. Notably, Pbk is required for the MI-induced beta cell proliferation and improvement of IGT. Together, these results demonstrate the repressive role of the menin/JunD/Pbk axis in regulating HFD-induced compensatory beta cell proliferation and pharmacologically regulating this axis may serve as a novel strategy for type 2 diabetes therapy.

Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK.

The human N-terminal acetyltransferase E (NatE) contains NAA10 and NAA50 catalytic, and NAA15 auxiliary subunits and associates with HYPK, a protein with intrinsic NAA10 inhibitory activity. NatE co-translationally acetylates the N-terminus of half the proteome to mediate diverse biological processes, including protein half-life, localization, and interaction. The molecular basis for how NatE and HYPK cooperate is unknown. Here, we report the cryo-EM structures of human NatE and NatE/HYPK complexes and associated biochemistry. We reveal that NAA50 and HYPK exhibit negative cooperative binding to NAA15 in vitro and in human cells by inducing NAA15 shifts in opposing directions. NAA50 and HYPK each contribute to NAA10 activity inhibition through structural alteration of the NAA10 substrate-binding site. NAA50 activity is increased through NAA15 tethering, but is inhibited by HYPK through structural alteration of the NatE substrate-binding site. These studies reveal the molecular basis for coordinated N-terminal acetylation by NatE and HYPK.

Molecular basis for N-terminal alpha-synuclein acetylation by human NatB.

NatB is one of three major N-terminal acetyltransferase (NAT) complexes (NatA-NatC), which co-translationally acetylate the N-termini of eukaryotic proteins. Its substrates account for about 21% of the human proteome, including well known proteins such as actin, tropomyosin, CDK2, and α-synuclein (αSyn). Human NatB (hNatB) mediated N-terminal acetylation of αSyn has been demonstrated to play key roles in the pathogenesis of Parkinson's disease and as a potential therapeutic target for hepatocellular carcinoma. Here we report the cryo-EM structure of hNatB bound to a CoA-αSyn conjugate, together with structure-guided analysis of mutational effects on catalysis. This analysis reveals functionally important differences with human NatA and Candida albicans NatB, resolves key hNatB protein determinants for αSyn N-terminal acetylation, and identifies important residues for substrate-specific recognition and acetylation by NatB enzymes. These studies have implications for developing small molecule NatB probes and for understanding the mode of substrate selection by NAT enzymes.

Introducing Ion Migration and Light-Induced Secondary Ion Redistribution for Phase-Stable and High-Efficiency Inorganic Perovskite Solar Cells.

Inorganic halide perovskites have been demonstrated as a promising alternative for light absorption because of their improved thermal stability compared with organic-inorganic halide perovskites. However, low power conversion efficiency and phase instability are major hindrances to their application. Here, a straightforward approach, by adding a layer of CsBr on the top of CsPbI3, is reported for high-efficiency and phase-stable CsPbI3-based solar cells. Characterizations demonstrate that the bromide ion can migrate from the surface into the bulk of CsPbI3, mitigating the nonuniform depth distribution of iodide in the CsPbI3 absorber and passivating the bulk defects. Impressively, the light illumination can induce secondary-ion redistribution, which is identified as a crucial process to further enhance the carrier extraction efficiency, strengthen the lattice stability, and improve the film homogenization. Accordingly, a high efficiency of 17% is obtained for the CsPbI3-based solar cell. Moreover, the unencapsulated device exhibits remarkable phase stability, maintaining 93% of its initial efficiency under room temperature after being stored in the nitrogen glovebox for over 5000 h.

Structure and Mechanism of Acetylation by the N-Terminal Dual Enzyme NatA/Naa50 Complex.

NatA co-translationally acetylates the N termini of over 40% of eukaryotic proteins and can associate with another catalytic subunit, Naa50, to form a ternary NatA/Naa50 dual enzyme complex (also called NatE). The molecular basis of association between Naa50 and NatA and the mechanism for how their association affects their catalytic activities in yeast and human are poorly understood. Here, we determined the X-ray crystal structure of yeast NatA/Naa50 as a scaffold to understand coregulation of NatA/Naa50 activity in both yeast and human. We find that Naa50 makes evolutionarily conserved contacts to both the Naa10 and Naa15 subunits of NatA. These interactions promote catalytic crosstalk within the human complex, but do so to a lesser extent in the yeast complex, where Naa50 activity is compromised. These studies have implications for understanding the role of the NatA/Naa50 complex in modulating the majority of the N-terminal acetylome in diverse species.

Feasible Route for a Large Area Few-Layer MoS2 with Magnetron Sputtering.

In this article, we report continuous and large-area molybdenum disulfide (MoS2) growth on a SiO2/Si substrate by radio frequency magnetron sputtering (RFMS) combined with sulfurization. The MoS2 film was synthesized using a two-step method. In the first step, a thin MoS2 film was deposited by radio frequency (RF) magnetron sputtering at 400 °C with different sputtering powers. Following, the as-sputtered MoS2 film was further subjected to the sulfurization process at 600 °C for 60 min. Sputtering combined with sulfurization is a viable route for large-area few-layer MoS2 by controlling the radio-frequency magnetron sputtering power. A relatively simple growth strategy is demonstrated here that simultaneously enhances thin film quality physically and chemically. Few-layers of MoS2 are established using Raman spectroscopy, X-ray diffractometer, high-resolution field emission transmission electron microscope, and X-ray photoelectron spectroscopy measurements. Spectroscopic and microscopic results reveal that these MoS2 layers are of low disorder and well crystallized. Moreover, high quality few-layered MoS2 on a large-area can be achieved by controlling the radio-frequency magnetron sputtering power.

Probing the interaction between NatA and the ribosome for co-translational protein acetylation.

N-terminal acetylation is among the most abundant protein modifications in eukaryotic cells. Over the last decade, significant progress has been made in elucidating the function of N-terminal acetylation for a number of diverse systems, involved in a wide variety of biological processes. The enzymes responsible for the modification are the N-terminal acetyltransferases (NATs). The NATs are a highly conserved group of enzymes in eukaryotes, which are responsible for acetylating over 80% of the soluble proteome in human cells. Importantly, many of these NATs act co-translationally; they interact with the ribosome near the exit tunnel and acetylate the nascent protein chain as it is being translated. While the structures of many of the NATs have been determined, the molecular basis for the interaction with ribosome is not known. Here, using purified ribosomes and NatA, a very well-studied NAT, we show that NatA forms a stable complex with the ribosome in the absence of other stabilizing factors and through two conserved regions; primarily through an N-terminal domain and an internal basic helix. These regions may orient the active site of the NatA to face the peptide emerging from the exit tunnel. This work provides a framework for understanding how NatA and potentially other NATs interact with the ribosome for co-translational protein acetylation and sets the foundation for future studies to decouple N-terminal acetyltransferase activity from ribosome association.

Controlling gold nanoparticle seeded growth in thermophilic ferritin protein templates.

Ferritin protein cages provide templates for inorganic nanoparticle synthesis in more environmentally-friendly conditions. Thermophilic ferritin from Archaeoglobus fulgidus (AfFtn) has been shown to encapsulate pre-formed 6-nm gold nanoparticles (AuNPs) and template their further growth within its 8-nm cavity. In this study, we explore whether using a gold complex with electrostatic complementarity to the anionic ferritin cavity can promote efficient seeded nanoparticle growth. We also compare wt AfFtn and a closed pore mutant AfFtn to explore whether the ferritin pores influence final AuNP size.

Overcoming the Limitations of Sputtered Nickel Oxide for High-Efficiency and Large-Area Perovskite Solar Cells.

Perovskite solar cells (PSCs) are one of the promising photovoltaic technologies for solar electricity generation. NiO x is an inorganic p-type semiconductor widely used to address the stability issue of PSCs. Although high efficiency is obtained for the devices employing NiO x as the hole transport layer, the fabrication methods have yet to be demonstrated for industrially relevant manufacturing of large-area and high-performance devices. Here, it is shown that these requirements can be satisfied by using the magnetron sputtering, which is well established in the industry. The limitations of low fill factor and short-circuit current commonly observed in sputtered NiO x -derived PSCs can be overcome through magnesium doping and low oxygen partial pressure deposition. The fabricated PSCs show a high power conversion efficiency of up to 18.5%, along with negligible hysteresis, improved ambient stability, and high reproducibility. In addition, good uniformity is also demonstrated over an area of 100 cm2. The simple and well-established approach constitutes a reliable and scale method paving the way for the commercialization of PSCs.