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Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded subunits similar to bacterial RNA polymerases (RNAPs) stably bound to a set of nuclear-encoded PEP-associated proteins (PAPs). PAPs are essential to PEP activity and chloroplast biogenesis, but their roles are poorly defined. Here, we present cryoelectron microscopy (cryo-EM) structures of native 21-subunit PEP and a PEP transcription elongation complex from white mustard (Sinapis alba). We identify that PAPs encase the core polymerase, forming extensive interactions that likely promote complex assembly and stability. During elongation, PAPs interact with DNA downstream of the transcription bubble and with the nascent mRNA. The models reveal details of the superoxide dismutase, lysine methyltransferase, thioredoxin, and amino acid ligase enzymes that are subunits of PEP. Collectively, these data provide a foundation for the mechanistic understanding of chloroplast transcription and its role in plant growth and adaptation., Competing Interests: Declaration of interests The authors declare no competing interests., (Crown Copyright © 2024. Published by Elsevier Inc. All rights reserved.)

The emergence of non-precious metal-based robust and economic bifunctional oxygen electrocatalysts for both oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) is crucial for the rational design of commercial rechargeable Zn-air batteries (RZAB) with safe energy conversion and storage systems. Herein, a facile strategy to fabricate a cost-efficient, bifunctional oxygen electrocatalyst Fe 3 C/Fe decorated N doped carbon (FeC-700, the catalyst prepared at carbinization temperature of 700 °C) with a unique structure has been developed by carbonization of a single source precursor, tetrabutylammonium tetrachloroferrate(III) complex. The ORR and OER activity revealed excellent performance (ΔE=0.77 V) of the FeC-700 electrocatalyst, comparable to commercial Pt/C and RuO 2, respectively. The designed temperature-tuneable structure provided sufficiently accessible active sites for the continuous passage of electrons by shortening the mass transfer pathway, leading to extremely durable electrocatalysts with high ECSA and amazing charge transfer performance. Remarkably, the assembled Zn-air batteries with the FeC-700 catalyst as the bifunctional air electrode delivers gratifying charging-discharging ability with an impressive power density of 134 mW cm -2 with a long lifespan, demonstrating prodigious possibilities for practical application., (© 2024 Wiley-VCH GmbH.)

Methanol oxidation reaction (MOR) is a perfect alternative to the conventional oxygen evolution reaction (OER), generally utilized as the anode reaction for hydrogen generation via the electrochemical water splitting method. Moreover, MOR is also relevant to direct methanol fuel cells (DMFCs). These facts motivate the researchers to develop economical and efficient electrocatalysts for MOR. Herein, we have introduced an ethylene glycol-linked tetraphenyl porphyrin-based (EG-POR) covalent organic polymer (COP). The Ni(II)-incorporated EG-POR material Ni-EG-POR displayed excellent OER and MOR activities in an alkaline medium. The materials were thoroughly characterized using 13 C solid-state NMR, Fourier transform infrared spectroscopy (FT-IR), Brunauer-Emmett-Teller (BET) surface area analyzer, X-ray photoelectron spectroscopy (XPS), field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), thermogravimetric analyzer (TGA), and powder X-ray diffraction (PXRD) techniques. These organic-inorganic hybrid materials showed high chemical and thermal stability. Ni-EG-POR requires an overpotential of 400 mV (vs RHE) in OER and 190 mV (vs RHE) in MOR to achieve a current density of 10 mA cm -2 . In addition, the catalyst also showed excellent chronoamperometric and chronopotentiometric stability, indicating that the catalyst can provide stable current over a longer period and its potential as a non-noble metal MOR catalyst.

Thermostable direct hemolysin (TDH) is a ~19 kDa, hemolytic pore-forming toxin from the gram-negative marine bacterium Vibrio parahaemolyticus, one of the causative agents of seafood-borne acute gastroenteritis and septicemia. Previous studies have established that TDH exists as a tetrameric assembly in physiological state; however, there is limited knowledge regarding the molecular arrangement of its disordered N-terminal region (NTR)-the absence of which has been shown to compromise TDH's hemolytic and cytotoxic abilities. In our current study, we have employed single-particle cryo-electron microscopy to resolve the solution-state structures of wild-type TDH and a TDH construct with deletion of the NTR (NTD), in order to investigate structural aspects of NTR on the overall tetrameric architecture. We observed that both TDH and NTD electron density maps, resolved at global resolutions of 4.5 and 4.2 Å, respectively, showed good correlation in their respective oligomeric architecture. Additionally, we were able to locate extra densities near the pore opening of TDH which might correspond to the disordered NTR. Surprisingly, under cryogenic conditions, we were also able to observe novel supramolecular assemblies of TDH tetramers, which we were able to resolve to 4.3 Å. We further investigated the tetrameric and inter-tetrameric interaction interfaces to elaborate upon the key residues involved in both TDH tetramers and TDH super assemblies. Our current structural study will aid in understanding the mechanistic aspects of this pore-forming toxin and the role of its disordered NTR in membrane interaction., (© 2022 Wiley Periodicals LLC.)

Protein tertiary structure mimetics are valuable tools to target large protein-protein interaction interfaces. Here, we demonstrate a strategy for designing dimeric helix-hairpin motifs from a previously reported three-helix-bundle miniprotein that targets the receptor-binding domain (RBD) of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Through truncation of the third helix and optimization of the interhelical loop residues of the miniprotein, we developed a thermostable dimeric helix-hairpin. The dimeric four-helix bundle competes with the human angiotensin-converting enzyme 2 (ACE2) in binding to RBD with 2:2 stoichiometry. Cryogenic-electron microscopy revealed the formation of dimeric spike ectodomain trimer by the four-helix bundle, where all the three RBDs from either spike protein are attached head-to-head in an open conformation, revealing a novel mechanism for virus neutralization. The proteomimetic protects hamsters from high dose viral challenge with replicative SARS-CoV-2 viruses, demonstrating the promise of this class of peptides that inhibit protein-protein interaction through target dimerization., (© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Methionine and cysteine metabolisms are important for the survival and pathogenesis of Mycobacterium tuberculosis ( Mtb ). The transsulfuration pathway converts methionine to cysteine and represents an important link between antioxidant and methylation metabolism in diverse organisms. Using a combination of biochemistry and cryo-electron microscopy, we characterized the first enzyme of the transsulfuration pathway, cystathionine β-synthase ( Mtb Cbs) in Mtb . We demonstrated that Mtb Cbs is a heme-less, pyridoxal-5'-phosphate-containing enzyme, allosterically activated by S -adenosylmethionine (SAM). The atomic model of Mtb Cbs in its native and SAM-bound conformations revealed a unique mode of SAM-dependent allosteric activation. Further, SAM stabilized Mtb Cbs by sterically occluding proteasomal degradation, which was crucial for supporting methionine and redox metabolism in Mtb . Genetic deficiency of Mtb Cbs reduced Mtb survival upon homocysteine overload in vitro, inside macrophages, and in mice coinfected with HIV. Thus, the Mtb Cbs-SAM axis constitutes an important mechanism of coordinating sulfur metabolism in Mtb .

The receptor binding domain (RBD) of SARS-CoV-2 is the primary target of neutralizing antibodies. We designed a trimeric, highly thermotolerant glycan engineered RBD by fusion to a heterologous, poorly immunogenic disulfide linked trimerization domain derived from cartilage matrix protein. The protein expressed at a yield of ∼80-100 mg/L in transiently transfected Expi293 cells, as well as CHO and HEK293 stable cell lines and formed homogeneous disulfide-linked trimers. When lyophilized, these possessed remarkable functional stability to transient thermal stress of up to 100 °C and were stable to long-term storage of over 4 weeks at 37 °C unlike an alternative RBD-trimer with a different trimerization domain. Two intramuscular immunizations with a human-compatible SWE adjuvanted formulation elicited antibodies with pseudoviral neutralizing titers in guinea pigs and mice that were 25-250 fold higher than corresponding values in human convalescent sera. Against the beta (B.1.351) variant of concern (VOC), pseudoviral neutralization titers for RBD trimer were ∼3-fold lower than against wildtype B.1 virus. RBD was also displayed on a designed ferritin-like Msdps2 nanoparticle. This showed decreased yield and immunogenicity relative to trimeric RBD. Replicative virus neutralization assays using mouse sera demonstrated that antibodies induced by the trimers neutralized all four VOC to date, namely B.1.1.7, B.1.351, P.1, and B.1.617.2 without significant differences. Trimeric RBD immunized hamsters were protected from viral challenge. The excellent immunogenicity, thermotolerance, and high yield of these immunogens suggest that they are a promising modality to combat COVID-19, including all SARS-CoV-2 VOC to date.

Spike (S) glycoprotein of SARS-CoV2 exists chiefly in two conformations, open and closed. Most previous structural studies on S protein have been conducted at pH 8.0, but knowledge of the conformational propensities under both physiological and endosomal pH conditions is important to inform vaccine development. Our current study employed single-particle cryoelectron microscopy to visualize multiple states of open and closed conformations of S protein at physiological pH 7.4 and near-physiological pH 6.5 and pH 8.0. Propensities of open and closed conformations were found to differ with pH changes, whereby around 68% of S protein exists in open conformation at pH 7.4. Furthermore, we noticed a continuous movement in the N-terminal domain, receptor-binding domain (RBD), S2 domain, and stalk domain of S protein conformations at various pH values. Several key residues involving RBD-neutralizing epitopes are differentially exposed in each conformation. This study will assist in developing novel therapeutic measures against SARS-CoV2., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Virtually all SARS-CoV-2 vaccines currently in clinical testing are stored in a refrigerated or frozen state prior to use. This is a major impediment to deployment in resource-poor settings. Furthermore, several of them use viral vectors or mRNA. In contrast to protein subunit vaccines, there is limited manufacturing expertise for these nucleic-acid-based modalities, especially in the developing world. Neutralizing antibodies, the clearest known correlate of protection against SARS-CoV-2, are primarily directed against the receptor-binding domain (RBD) of the viral spike protein, suggesting that a suitable RBD construct might serve as a more accessible vaccine ingredient. We describe a monomeric, glycan-engineered RBD protein fragment that is expressed at a purified yield of 214 mg/l in unoptimized, mammalian cell culture and, in contrast to a stabilized spike ectodomain, is tolerant of exposure to temperatures as high as 100 °C when lyophilized, up to 70 °C in solution and stable for over 4 weeks at 37 °C. In prime:boost guinea pig immunizations, when formulated with the MF59-like adjuvant AddaVax, the RBD derivative elicited neutralizing antibodies with an endpoint geometric mean titer of ∼415 against replicative virus, comparing favorably with several vaccine formulations currently in the clinic. These features of high yield, extreme thermotolerance, and satisfactory immunogenicity suggest that such RBD subunit vaccine formulations hold great promise to combat COVID-19., Competing Interests: Conflict of interest A provisional patent application has been filed for the RBD formulations described in this article. S. K. M, S. A., R. V, S. P, R. S are inventors. G. N., R. V. are founders of Mynvax, and S. P., R. S., N. G., A. U., and P. R. are employees of Mynvax Private Limited., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Stabilization of the metastable envelope glycoprotein (Env) of HIV-1 is hypothesized to improve induction of broadly neutralizing antibodies. We improved the expression yield and stability of the HIV-1 envelope glycoprotein BG505SOSIP.664 gp140 by means of a previously described automated sequence and structure-guided computational thermostabilization approach, PROSS. This combines sequence conservation information with computational assessment of mutant stabilization, thus taking advantage of the extensive natural sequence variation present in HIV-1 Env. PROSS is used to design three gp140 variants with 17-45 mutations relative to the parental construct. One of the designs is experimentally observed to have a fourfold improvement in yield and a 4 °C increment in thermostability. In addition, the designed immunogens have similar antigenicity profiles to the native flexible linker version of wild type, BG505SOSIP.664 gp140 (NFL Wt) to major epitopes targeted by broadly neutralizing antibodies. PROSS eliminates the laborious process of screening many variants for stability and functionality, providing a proof of principle of the method for stabilization and improvement of yield without compromising antigenicity for next generation complex, highly glycosylated vaccine candidates., Competing Interests: Declaration of Competing Interest None declared