S-acylation of p62 promotes p62 droplet recruitment into autophagosomes in mammalian autophagy.

p62 is a well-characterized autophagy receptor that recognizes and sequesters specific cargoes into autophagosomes for degradation. p62 promotes the assembly and removal of ubiquitinated proteins by forming p62-liquid droplets. However, it remains unclear how autophagosomes efficiently sequester p62 droplets. Herein, we report that p62 undergoes reversible S-acylation in multiple human-, rat-, and mouse-derived cell lines, catalyzed by zinc-finger Asp-His-His-Cys S-acyltransferase 19 (ZDHHC19) and deacylated by acyl protein thioesterase 1 (APT1). S-acylation of p62 enhances the affinity of p62 for microtubule-associated protein 1 light chain 3 (LC3)-positive membranes and promotes autophagic membrane localization of p62 droplets, thereby leading to the production of small LC3-positive p62 droplets and efficient autophagic degradation of p62-cargo complexes. Specifically, increasing p62 acylation by upregulating ZDHHC19 or by genetic knockout of APT1 accelerates p62 degradation and p62-mediated autophagic clearance of ubiquitinated proteins. Thus, the protein S-acylation-deacylation cycle regulates p62 droplet recruitment to the autophagic membrane and selective autophagic flux, thereby contributing to the control of selective autophagic clearance of ubiquitinated proteins.

TOR-mediated Ypt1 phosphorylation regulates autophagy initiation complex assembly.

The regulation of autophagy initiation is a key step in autophagosome biogenesis. However, our understanding of the molecular mechanisms underlying the stepwise assembly of ATG proteins during this process remains incomplete. The Rab GTPase Ypt1/Rab1 is recognized as an essential autophagy regulator. Here, we identify Atg23 and Atg17 as binding partners of Ypt1, with their direct interaction proving crucial for the stepwise assembly of autophagy initiation complexes. Disruption of Ypt1-Atg23 binding results in significantly reduced Atg9 interactions with Atg11, Atg13, and Atg17, thus preventing the recruitment of Atg9 vesicles to the phagophore assembly site (PAS). Likewise, Ypt1-Atg17 binding contributes to the PAS recruitment of Ypt1 and Atg1. Importantly, we found that Ypt1 is phosphorylated by TOR at the Ser174 residue. Converting this residue to alanine blocks Ypt1 phosphorylation by TOR and enhances autophagy. Conversely, the Ypt1S174D phosphorylation mimic impairs both PAS recruitment and activation of Atg1, thus inhibiting subsequent autophagy. Thus, we propose TOR-mediated Ypt1 as a multifunctional assembly factor that controls autophagy initiation via its regulation of the stepwise assembly of ATG proteins.

Pacer Is a Mediator of mTORC1 and GSK3-TIP60 Signaling in Regulation of Autophagosome Maturation and Lipid Metabolism.

mTORC1 and GSK3 play critical roles in early stages of (macro)autophagy, but how they regulate late steps of autophagy remains poorly understood. Here we show that mTORC1 and GSK3-TIP60 signaling converge to modulate autophagosome maturation through Pacer, an autophagy regulator that was identified in our recent study. Hepatocyte-specific Pacer knockout in mice results in impaired autophagy flux, glycogen and lipid accumulation, and liver fibrosis. Under nutrient-rich conditions, mTORC1 phosphorylates Pacer at serine157 to disrupt the association of Pacer with Stx17 and the HOPS complex and thus abolishes Pacer-mediated autophagosome maturation. Importantly, dephosphorylation of Pacer under nutrient-deprived conditions promotes TIP60-mediated Pacer acetylation, which facilitates HOPS complex recruitment and is required for autophagosome maturation and lipid droplet clearance. This work not only identifies Pacer as a regulator in hepatic autophagy and liver homeostasis in vivo but also reveals a signal integration mechanism involved in late stages of autophagy and lipid metabolism.

Molecular architectures of iron complexes for oxygen reduction catalysis-Activity enhancement by hydroxide ions coupling.

Developing cost-effective and high-performance electrocatalysts for oxygen reduction reaction (ORR) is critical for clean energy generation. Here, we propose an approach to the synthesis of iron phthalocyanine nanotubes (FePc NTs) as a highly active and selective electrocatalyst for ORR. The performance is significantly superior to FePc in randomly aggregated and molecularly dispersed states, as well as the commercial Pt/C catalyst. When FePc NTs are anchored on graphene, the resulting architecture shifts the ORR potentials above the redox potentials of Fe2+/3+ sites. This does not obey the redox-mediated mechanism operative on conventional FePc with a Fe2+-N moiety serving as the active sites. Pourbaix analysis shows that the redox of Fe2+/3+ sites couples with HO- ions transfer, forming a HO-Fe3+-N moiety serving as the ORR active sites under the turnover condition. The chemisorption of ORR intermediates is appropriately weakened on the HO-Fe3+-N moiety compared to the Fe2+-N state and thus is intrinsically more ORR active.

Mec1 regulates PAS recruitment of Atg13 via direct binding with Atg13 during glucose starvation-induced autophagy.

Mec1 is a DNA damage sensor, which performs an essential role in the DNA damage response pathway and glucose starvation-induced autophagy. However, the functions of Mec1 in autophagy remain unclear. In response to glucose starvation, Mec1 forms puncta, which are recruited to mitochondria through the adaptor protein Ggc1. Here, we show that Mec1 puncta also contact the phagophore assembly site (PAS) via direct binding with Atg13. Functional analysis of the Atg13-Mec1 interaction revealed two previously unrecognized protein regions, the Mec1-Binding Region (MBR) on Atg13 and the Atg13-Binding Region (ABR) on Mec1, which mediate their mutual association under glucose starvation conditions. Disruption of the MBR or ABR impairs the recruitment of Mec1 puncta and Atg13 to the PAS, consequently blocking glucose starvation-induced autophagy. Additionally, the MBR and ABR regions are also crucial for DNA damage-induced autophagy. We thus propose that Mec1 regulates glucose starvation-induced autophagy by controlling Atg13 recruitment to the PAS.

Pacer Mediates the Function of Class III PI3K and HOPS Complexes in Autophagosome Maturation by Engaging Stx17.

Class III PI3-kinase (PI3KC3) is essential for autophagy initiation, but whether PI3KC3 participates in other steps of autophagy remains unknown. The HOPS complex mediates the fusion of intracellular vesicles to lysosome, but how HOPS specifically tethers autophagosome to lysosome remains elusive. Here, we report Pacer (protein associated with UVRAG as autophagy enhancer) as a regulator of autophagy. Pacer localizes to autophagic structures and positively regulates autophagosome maturation. Mechanistically, Pacer antagonizes Rubicon to stimulate Vps34 kinase activity. Next, Pacer recruits PI3KC3 and HOPS complexes to the autophagosome for their site-specific activation by anchoring to the autophagosomal SNARE Stx17. Furthermore, Pacer is crucial for the degradation of hepatic lipid droplets, the suppression of Salmonella infection, and the clearance of protein aggregates. These results not only identify Pacer as a crucial multifunctional enhancer in autophagy but also uncover both the involvement of PI3KC3 and the mediators of HOPS's specific tethering activity in autophagosome maturation.

VPS34 Acetylation Controls Its Lipid Kinase Activity and the Initiation of Canonical and Non-canonical Autophagy.

The class III phosphoinositide 3-kinase VPS34 plays a key role in the regulation of vesicular trafficking and macroautophagy. So far, we know little about the molecular mechanism of VPS34 activation besides its interaction with regulatory proteins to form complexes. Here, we report that VPS34 is specifically acetylated by the acetyltransferase p300, and p300-mediated acetylation represses VPS34 activity. Acetylation at K771 directly diminishes the affinity of VPS34 for its substrate PI, while acetylation at K29 hinders the VPS34-Beclin 1 core complex formation. Inactivation of p300 induces VPS34 deacetylation, PI3P production, and autophagy, even in AMPK-/-, TSC2-/-, or ULK1-/- cells. In fasting mice, liver autophagy correlates well with p300 inactivation/VPS34 deacetylation, which facilitates the clearance of lipid droplets in hepatocytes. Thus, p300-dependent VPS34 acetylation/deacetylation is the physiological key to VPS34 activation, which controls the initiation of canonical autophagy and of non-canonical autophagy in which the upstream kinases of VPS34 can be bypassed.

Tricoordinated Single-Atom Cobalt in Zeolite Boosting Propane Dehydrogenation.

Propane dehydrogenation (PDH) reaction has emerged as one of the most promising propylene production routes due to its high selectivity for propylene and good economic benefits. However, the commercial PDH processes usually rely on expensive platinum-based and poisonous chromium oxide based catalysts. The exploration of cost-effective and ecofriendly PDH catalysts with excellent catalytic activity, propylene selectivity, and stability is of great significance yet remains challenging. Here, we discovered a new active center, i.e., an unsaturated tricoordinated cobalt unit (≡Si-O)CoO(O-Mo) in a molybdenum-doped silicalite-1 zeolite, which afforded an unprecedentedly high propylene formation rate of 22.6 molC3H6 gCo-1 h-1 and apparent rate coefficient of 130 molC3H6 gCo-1 h-1 bar-1 with >99% of propylene selectivity at 550 °C. Such activity is nearly one magnitude higher than that of previously reported Co-based catalysts in which cobalt atoms are commonly tetracoordinated, and even superior to that of most of Pt-based catalysts under similar operating conditions. Density functional theory calculations combined with the state-of-the-art characterizations unravel the role of the unsaturated tricoordinated Co unit in facilitating the C-H bond-breaking of propane and propylene desorption. The present work opens new opportunities for future large-scale industrial PDH production based on inexpensive non-noble metal catalysts.

FAM134B oligomerization drives endoplasmic reticulum membrane scission for ER-phagy.

Degradation of endoplasmic reticulum (ER) by selective autophagy (ER-phagy) is crucial for ER homeostasis. However, it remains unclear how ER scission is regulated for subsequent autophagosomal sequestration and lysosomal degradation. Here, we show that oligomerization of ER-phagy receptor FAM134B (also referred to as reticulophagy regulator 1 or RETREG1) through its reticulon-homology domain is required for membrane fragmentation in vitro and ER-phagy in vivo. Under ER-stress conditions, activated CAMK2B phosphorylates the reticulon-homology domain of FAM134B, which enhances FAM134B oligomerization and activity in membrane fragmentation to accommodate high demand for ER-phagy. Unexpectedly, FAM134B G216R, a variant derived from a type II hereditary sensory and autonomic neuropathy (HSAN) patient, exhibits gain-of-function defects, such as hyperactive self-association and membrane scission, which results in excessive ER-phagy and sensory neuron death. Therefore, this study reveals a mechanism of ER membrane fragmentation in ER-phagy, along with a signaling pathway in regulating ER turnover, and suggests a potential implication of excessive selective autophagy in human diseases.

The updates in Libcint 6: More integrals, API refinements, and SIMD optimization techniques.

Libcint is a library designed for the evaluation of analytical integrals for Gaussian type orbitals. It prioritizes simplicity, ease of use, and efficiency for the development of quantum chemistry programs. In the release of version 6.0, Libcint supports the computation of integrals for various operators, such as overlap, Coulomb, Gaunt, Breit, attenuated Coulomb, Slater-type geminals, and Yukawa potential, as well as arbitrary orders of derivatives for these operators. To enhance the usability of the library, Libcint provides a uniform function signature for all integral functions. A code generator is included to automate the implementation of new integrals. To achieve better performance on modern central processing unit architectures, the library employs explicit single instruction multiple data parallelization in the code implementation.

Cobalt-Promoted Noble-Metal Catalysts for Efficient Hydrogen Generation from Ammonia Borane Hydrolysis.

Ammonia borane (AB) has been regarded as a promising material for chemical hydrogen storage. However, the development of efficient, cost-effective, and stable catalysts for H2 generation from AB hydrolysis remains a bottleneck for realizing its practical application. Herein, a step-by-step reduction strategy has been developed to synthesize a series of bimetallic species with small sizes and high dispersions onto various metal oxide supports. Superior to other non-noble metal species, the introduction of Co species can remarkably and universally promote the catalytic activity of various noble metals (e.g., Pt, Rh, Ru, and Pd) in AB hydrolysis reactions. The optimized Pt0.1%Co3%/TiO2 catalyst exhibits a superhigh H2 generation rate from AB hydrolysis, showing a turnover frequency (TOF) value of 2250 molH2 molPt-1 min-1 at 298 K. Such a TOF value is about 10 and 15 times higher than that of the monometal Pt/TiO2 and commercial Pt/C catalysts, respectively. The density functional theory (DFT) calculation reveals that the synergy between Pt and CoO species can remarkably promote the chemisorption and dissociation of water molecules, accelerating the H2 evolution from AB hydrolysis. Significantly, the representative Pt0.25%Co3%/TiO2 catalyst exhibits excellent stability, achieving a record-high turnover number of up to 215,236 at room temperature. The excellent catalytic performance, superior stability, and low cost of the designed catalysts create new prospects for their practical application in chemical hydrogen storage.

Construction of a Novel Cascade Electrolysis-Heterocatalysis System by Using Zeolite-Encaged Ultrasmall Palladium Catalysts for H2 O2 Generation.

In situ generation of hydrogen peroxide (H2 O2 ) has attracted extensive attention, especially in water treatment. However, traditional anthraquinones can only produce high-concentration H2 O2 and its transportation and storage are not convenient and dangerous. Herein, an in situ and on-demand strategy to produce H2 O2 by using a cascade water electrolysis together with a heterocatalysis system is provided. Beginning with water, H2, and O2 can be generated via electrolysis and then react with each other to produce H2 O2 immediately on efficient zeolite-encaged ultrasmall Pd catalysts. Significantly, the H2 O2 generation rate in the optimized cascade system reaches up to 0.85 mol L-1 h-1 gPd -1 , overcoming most of the state-of-the-art catalysts in previous literature. The confinement effect of zeolites is not only beneficial to the formation of highly dispersed metal species, promoting the H2 O2 generation, but also inhibits the H2 O2 decomposition, enhancing the production yield of H2 O2 . In addition, the effect of electrolytes, sizes of Pd species, as well as zeolite acidity are also systematically studied. This work provides a new avenue for H2 O2 generation via a highly efficient cascade electrolysis-heterocatalysis system by using zeolite-supported metal catalysts. The high catalytic efficiency and green process for H2 O2 generation make it very promising for further practical applications.

Hybrid digital-analog FSO fronthaul system with channel-adaptive insertion of analog bandwidth.

With the arrival of the 5th generation mobile network, the number of user devices is increasing exponentially, and thus it is necessary to expand the capacity of transmission systems. In order to further improve the system spectral efficiency on the basis of existing mobile fronthaul devices, we propose a hybrid digital-analog fronthaul transmission system with adaptive insertion of analog bandwidth, which can dynamically change the position of inserted analog bandwidth based on the state information of free space optical (FSO) channel. We consider the effects of atmospheric attenuation and turbulence on the FSO channel and derive an analytical expression for the maximum analog signal bandwidth that can be inserted into the first null of the digital signal spectrum to meet BER requirement of 3.8 × 10-3. Through a comprehensive simulation, it is verified that the analog bandwidth is obtained by this expression can exactly represent the lower bound of the simulation results under weak turbulence condition. The obtained results show that the maximum insertable analog bandwidth beyond the spectral null of the digital signal can reach 10% of the digital signal bandwidth, even in the FSO link with a transmission distance of 0.5 km and attenuation factor of 8 dB/km.

Copper Site Motion Promotes Catalytic NOx Reduction under Zeolite Confinement.

Ammonia-mediated selective catalytic reduction (NH3-SCR) is currently the key approach to abate nitrogen oxides (NOx) emitted from heavy-duty lean-burn vehicles. The state-of-art NH3-SCR catalysts, namely, copper ion-exchanged chabazite (Cu-CHA) zeolites, perform rather poorly at low temperatures (below 200 °C) and are thus incapable of eliminating effectively NOx emissions under cold-start conditions. Here, we demonstrate a significant promotion of low-temperature NOx reduction by reinforcing the dynamic motion of zeolite-confined Cu sites during NH3-SCR. Combining complex impedance-based in situ spectroscopy (IS) and extended density-functional tight-binding molecular dynamics simulation, we revealed an environment- and temperature-dependent nature of the dynamic Cu motion within the zeolite lattice. Further coupling in situ IS with infrared spectroscopy allows us to unravel the critical role of monovalent Cu in the overall Cu mobility at a molecular level. Based on these mechanistic understandings, we elicit a boost of NOx reduction below 200 °C by reinforcing the dynamic Cu motion in various Cu-zeolites (Cu-CHA, Cu-ZSM-5, Cu-Beta, etc.) via facile postsynthesis treatments, either in a reductive mixture at low temperatures (below 250 °C) or in a nonoxidative atmosphere at high temperatures (above 450 °C).

Exact exchange with range-separated algorithm for thermodynamic limit of periodic Hartree-Fock theory.

The expensive cost of computing exact exchange in periodic systems limits the application range of density functional theory with hybrid functionals. To reduce the computational cost of exact change, we present a range-separated algorithm to compute electron repulsion integrals for Gaussian-type crystal basis. The algorithm splits the full-range Coulomb interactions into short-range and long-range parts, which are, respectively, computed in real and reciprocal space. This approach significantly reduces the overall computational cost, as integrals can be efficiently computed in both regions. The algorithm can efficiently handle large numbers of k points with limited central processing unit (CPU) and memory resources. As a demonstration, we performed an all-electron k-point Hartree-Fock calculation for LiH crystal with one million Gaussian basis functions, which was completed on a desktop computer in 1400 CPU hours.

Efficient Hartree-Fock exchange algorithm with Coulomb range separation and long-range density fitting.

Separating the Coulomb potential into short-range and long-range components enables the use of different electron repulsion integral algorithms for each component. The short-range part can be efficiently computed using the analytical algorithm due to the locality in both the Gaussian-type orbital basis and the short-range Coulomb potentials. The integrals for the long-range Coulomb potential can be approximated with the density fitting method. A very small auxiliary basis is sufficient for the density fitting method to accurately approximate the long-range integrals. This feature significantly reduces the computational efforts associated with the N4 scaling in density fitting algorithms. For large molecules, the range separation and long-range density fitting method outperforms the conventional analytical integral evaluation scheme employed in Hartree-Fock calculations and provides more than twice the overall performance. In addition, this method offers a higher accuracy compared to conventional density fitting methods. The error in the Hartree-Fock energy can be easily reduced to 0.1 µEh per atom or smaller.

Scalar Breit interaction for molecular calculations.

Variational treatment of the Dirac-Coulomb-Gaunt or Dirac-Coulomb-Breit two-electron interaction at the Dirac-Hartree-Fock level is the starting point of high-accuracy four-component calculations of atomic and molecular systems. In this work, we introduce, for the first time, the scalar Hamiltonians derived from the Dirac-Coulomb-Gaunt and Dirac-Coulomb-Breit operators based on spin separation in the Pauli quaternion basis. While the widely used spin-free Dirac-Coulomb Hamiltonian includes only the direct Coulomb and exchange terms that resemble nonrelativistic two-electron interactions, the scalar Gaunt operator adds a scalar spin-spin term. The spin separation of the gauge operator gives rise to an additional scalar orbit-orbit interaction in the scalar Breit Hamiltonian. Benchmark calculations of Aun (n = 2-8) show that the scalar Dirac-Coulomb-Breit Hamiltonian can capture 99.99% of the total energy with only 10% of the computational cost when real-valued arithmetic is used, compared to the full Dirac-Coulomb-Breit Hamiltonian. The scalar relativistic formulation developed in this work lays the theoretical foundation for the development of high-accuracy, low-cost correlated variational relativistic many-body theory.

MLL1 is regulated by KSHV LANA and is important for virus latency.

Mixed lineage leukemia 1 (MLL1) is a histone methyltransferase. Kaposi's sarcoma-associated herpesvirus (KSHV) is a leading cause of malignancy in AIDS. KSHV latently infects tumor cells and its genome is decorated with epigenetic marks. Here, we show that KSHV latency-associated nuclear antigen (LANA) recruits MLL1 to viral DNA where it establishes H3K4me3 modifications at the extensive KSHV terminal repeat elements during primary infection. LANA interacts with MLL1 complex members, including WDR5, integrates into the MLL1 complex, and regulates MLL1 activity. We describe the 1.5-Å crystal structure of N-terminal LANA peptide complexed with MLL1 complex member WDR5, which reveals a potential regulatory mechanism. Disruption of MLL1 expression rendered KSHV latency establishment highly deficient. This deficiency was rescued by MLL1 but not by catalytically inactive MLL1. Therefore, MLL1 is LANA regulable and exerts a central role in virus infection. These results suggest broad potential for MLL1 regulation, including by non-host factors.

Entropy Confinement Promotes Hydrogenolysis Activity for Polyethylene Upcycling.

Chemical upcycling that catalyzes waste plastics back to high-purity chemicals holds great promise in end-of-life plastics valorization. One of the main challenges in this process is the thermodynamic limitations imposed by the high intrinsic entropy of polymer chains, which makes their adsorption on catalysts unfavorable and the transition state unstable. Here, we overcome this challenge by inducing the catalytic reaction inside mesoporous channels, which possess a strong confined ability to polymer chains, allowing for stabilization of the transition state. This approach involves the synthesis of p-Ru/SBA catalysts, in which Ru nanoparticles are uniformly distributed within the channels of an SBA-15 support, using a precise impregnation method. The unique design of the p-Ru/SBA catalyst has demonstrated significant improvements in catalytic performance for the conversion of polyethylene into high-value liquid fuels, particularly diesel. The catalyst achieved a high solid conversion rate of 1106 g ⋅ gRu -1 ⋅ h-1 at 230 °C. Comparatively, this catalytic activity is 4.9 times higher than that of a control catalyst, Ru/SiO2 , and 14.0 times higher than that of a commercial catalyst, Ru/C, at 240 °C. This remarkable catalytic activity opens up immense opportunities for the chemical upcycling of waste plastics.

Efficient evaluation of the Breit operator in the Pauli spinor basis.

The frequency-independent Coulomb-Breit operator gives rise to the most accurate treatment of two-electron interaction in the non-quantum-electrodynamics regime. The Breit interaction in the Coulomb gauge consists of magnetic and gauge contributions. The high computational cost of the gauge term limits the application of the Breit interaction in relativistic molecular calculations. In this work, we apply the Pauli component integral-density matrix contraction scheme for gauge interaction with a maximum spin- and component separation scheme. We also present two different computational algorithms for evaluating gauge integrals. One is the generalized Obara-Saika algorithm, where the Laplace transformation is used to transform the gauge operator into Gaussian functions and the Obara-Saika recursion is used for reducing the angular momentum. The other algorithm is the second derivative of Coulomb interaction evaluated with Rys-quadrature. This work improves the efficiency of performing Dirac-Hartree-Fock with the variational treatment of Breit interaction for molecular systems. We use this formalism to examine relativistic trends in the Periodic Table and analyze the relativistic two-electron interaction contributions in heavy-element complexes.