ACS Central Science最新文献

The proximitome is defined as the entire collection of biomolecules spatially in the proximity of a biomolecule of interest. More broadly, the concept of the proximitome can be extended to the totality of cells proximal to a specific cell type. Since the spatial organization of biomolecules and cells is essential for almost all biological processes, proximitomics has recently emerged as an active area of scientific research. One of the growing strategies for proximitomics leverages reactive species─which are generated in situ and spatially confined, to chemically tag and capture proximal biomolecules and cells for systematic analysis. In this Outlook, we summarize different types of reactive species that have been exploited for proximitomics and discuss their pros and cons for specific applications. In addition, we discuss the current challenges and future directions of this exciting field.

Proximitomics leverages reactive species to chemically tag and capture proximal biomolecules and cells for systematic analysis, uncovering their interactions and spatial organizations in complex biological systems.

Chemical protein synthesis provides a powerful means to prepare novel modified proteins with precision down to the atomic level, enabling an unprecedented opportunity to understand fundamental biological processes. Of particular interest is the process of gene expression, orchestrated through the interactions between transcription factors (TFs) and DNA. Here, we combined chemical protein synthesis and high-throughput screening technology to decipher the role of post-translational modifications (PTMs), e.g., Lys-acetylation on the DNA binding activity of Max TF. We synthesized a focused library of singly, doubly, and triply modified Max variants including site-specifically acetylated and fluorescently tagged analogs. The resulting synthetic analogs were employed to decipher the molecular role of Lys-acetylation on the DNA binding activity and sequence specificity of Max. We provide evidence that the acetylation sites at Lys-31 and Lys-57 significantly inhibit the DNA binding activity of Max. Furthermore, by utilizing high-throughput binding measurements, we assessed the binding activities of the modified Max variants across diverse DNA sequences. Our results indicate that acetylation marks can alter the binding specificities of Max toward certain sequences flanking its consensus binding sites. Our work provides insight into the hidden molecular code of PTM-TFs and DNA interactions, paving the way to interpret gene expression regulation programs.

A focused library of site-specifically acetylated analogs of the transcription factor Max was chemically synthesized to dissect the molecular role of Lys-acetylation in the DNA binding activity of Max.

High capacity and long cycling often conflict with each other in electrode materials. Despite extensive efforts in structural design, it remains challenging to simultaneously achieve dual high electrochemical properties. In this study, we prepared brand-new completely uniform mesoporous cubic-cages assembled by large d-spacing Ni(OH)₂ coupled monolayers intercalated with VO₄^3– (NiCMCs) using a biomimetic approach. Such unique mesoporous structural configuration results in an almost full atomic exposure with an amazing specific surface area of 505 m²/g and atomic utilization efficiency close to the theoretical limit, which is the highest value and far surpasses all of the reported Ni(OH)₂. Thus, a breakthrough in simultaneously attaining high capacity approaching the 100% theoretical value and robust cycling of 10,000 cycles is achieved, setting a new precedent in achieving double-high attributes. When combined with high-performance Bi₂O₃ hexagonal nanotubes, the resulting aqueous battery exhibits an ultrahigh energy density of 115 Wh/kg and an outstanding power density of 9.5 kW/kg among the same kind. Characterizations and simulations reveal the important role of large interlayer spacing intercalation units and mesoporous cages for excellent electrochemical thermodynamics and kinetics. This work represents a milestone in developing “double-high” electrode materials, pointing in the direction for related research and paving the way for their practical application.

Mesoporous cubic nanocages, assembled from coupled monolayers with expanded interlayer spacing induced by intercalation, achieve nearly 100% theoretical capacity and robust cycling.

Templated synthesis of proteins containing non-natural amino acids (nnAAs) promises to expand the chemical space available to biological therapeutics and materials, but existing technologies are still limiting. Addressing these limitations requires a deeper understanding of the mechanism of protein synthesis and how it is perturbed by nnAAs. Here we examine the impact of nnAAs on the formation and ribosome utilization of the central elongation substrate: the ternary complex of native, aminoacylated tRNA, thermally unstable elongation factor, and GTP. By performing ensemble and single-molecule fluorescence resonance energy transfer measurements, we reveal that both the (R)- and (S)-β² isomers of phenylalanine (Phe) disrupt ternary complex formation to levels below in vitro detection limits, while (R)- and (S)-β³-Phe reduce ternary complex stability by 1 order of magnitude. Consistent with these findings, (R)- and (S)-β²-Phe-charged tRNAs were not utilized by the ribosome, while (R)- and (S)-β³-Phe stereoisomers were utilized inefficiently. (R)-β³-Phe but not (S)-β³-Phe also exhibited order of magnitude defects in the rate of translocation after mRNA decoding. We conclude from these findings that non-natural amino acids can negatively impact the translation mechanism on multiple fronts and that the bottlenecks for improvement must include the consideration of the efficiency and stability of ternary complex formation.

β-Phe amino acids perturb several critical steps of the protein synthesis mechanism, revealing previously unappreciated bottlenecks that limit noncanonical amino acid incorporation into proteins.

A subset of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are encoded in their biosynthetic gene clusters (BGCs) with enzymes annotated as lantibiotic dehydratases. The functions of these putative lantibiotic dehydratases remain unknown. Here, we characterize an NRPS-PKS BGC with a putative lantibiotic dehydratase from the bacterium Stackebrandtia nassauensis (sna). Heterologous expression revealed several metabolites produced by the BGC, and the omission of selected biosynthetic enzymes revealed the biosynthetic pathway toward these compounds. The final product is a bisarginyl ureidopeptide with an enone electrophile. The putative lantibiotic dehydratase catalyzes peptide bond formation to a Thr that extends the peptide scaffold opposite to the NRPS and PKS biosynthetic direction. The condensation domain of the NRPS SnaA catalyzes the formation of a ureido group, and bioinformatics analysis revealed a distinct active site signature EHHXXHDG of ureido-generating condensation (C_urea) domains. This work demonstrates that the annotated lantibiotic dehydratase serves as a separate amide bond-forming machinery in addition to the NRPS, and that the lantibiotic dehydratase enzyme family possesses diverse catalytic activities in the biosynthesis of both ribosomal and nonribosomal natural products.

The discovery of threopeptin reveals the function of the putative lantibiotic dehydratases in nonribosomal peptide (NRP) BGCs and enables the bioinformatic prediction of ureido-containing NRPs.

Mitochondrial thermogenesis is a process in which heat is generated by mitochondrial respiration. In living organisms, the thermogenic mechanisms that maintain body temperature have been studied extensively in fat cells with little knowledge on how mitochondrial heat may act beyond energy expenditure. Here, we highlight that the exothermic oxygen reduction reaction (ΔH_f° = −286 kJ/mol) is the main source of the protonophore-induced mitochondrial thermogenesis, and this heat is conducted to other cellular organelles, including the nucleus. As a result, mitochondrial heat that reached the nucleus initiated the classical heat shock response, including the formation of nuclear stress granules and the localization of heat shock factor 1 (HSF1) to chromatin. Consequently, activated HSF1 increases the level of gene expression associated with the response to thermal stress in mammalian cells. Our results illustrate heat generated within the cells as a potential source of mitochondria-nucleus communication and expand our understanding of the biological functions of mitochondria in cell physiology.

Oxygen reduction reaction (ORR) is the exothermic reaction in mitochondria, and ORR-driven mitochondrial thermogenesis can induce the HSF1-mediated heat shock response in the nucleus.

Metalloporphyrins are widely used as homogeneous electrocatalysts for transformations relevant to clean energy and sustainable organic synthesis. Metalloporphyrins are well-known to aggregate due to π–π stacking, but surprisingly, the influence of aggregation on homogeneous electrocatalytic performance has not been investigated previously. Herein, we present three structurally related iron meso-phenylporphyrins whose aggregation properties are different in commonly used N,N-dimethylformamide (DMF) electrolyte. Both spectroscopy and light scattering provide evidence of extensive porphyrin aggregation under conventional electrocatalytic conditions. Using the electrocatalytic reduction of CO₂ to CO as a test reaction, cyclic voltammetry reveals an inverse dependence of the kinetics on the catalyst concentration. The inhibition extends to bulk performance, where up to 75% of the catalyst at 1 mM is inactive compared to at 0.25 mM. We additionally report how aggregation is perturbed by organic additives, axial ligands, and redox state. Periodic boundary calculations provide additional insights into aggregate stability as a function of metalloporphyrin structure. Finally, we generalize the aggregation phenomenon by surveying metalloporphyrins with different metals and substituents. This study demonstrates that homogeneous metalloporphyrins can aggregate severely in well-solubilizing organic electrolytes, that aggregation can be easily modulated through experimental conditions, and that the extent of aggregation must be considered for accurate catalytic benchmarking.

Solution aggregation of metalloporphyrins inhibits electrocatalysis. This complicates intrinsic activity comparisons but offers a new way to modulate activity by controlling aggregate speciation.