Actin, which plays a crucial role in cellular structure and function, interacts with various binding proteins, notably myosin. In mammals, actin is composed of six isoforms that exhibit high levels of sequence conservation and structural similarity overall. As a result, the selection of actin isoforms was considered unimportant in structural studies of their binding with myosin. However, recent high-resolution structural research discovered subtle structural differences in the N-terminus of actin isoforms, suggesting the possibility that each actin isoform may engage in specific interactions with myosin isoforms. In this study, we aimed to explore this possibility, particularly by understanding the influence of different actin isoforms on the interaction with myosin 7A. First, we compared the reported actomyosin structures utilizing the same type of actin isoforms as the high-resolution filamentous skeletal α-actin (3.5 Å) structure elucidated using cryo-EM. Through this comparison, we confirmed that the diversity of myosin isoforms leads to differences in interaction with the actin N-terminus, and that loop 2 of the myosin actin-binding sites directly interacts with the actin N-terminus. Subsequently, with the aid of multiple sequence alignment, we observed significant variations in the length of loop 2 across different myosin isoforms. We predicted that these length differences in loop 2 would likely result in structural variations that would affect the interaction with the actin N-terminus. For myosin 7A, loop 2 was found to be very short, and protein complex predictions using skeletal α-actin confirmed an interaction between loop 2 and the actin N-terminus. The prediction indicated that the positively charged residues present in loop 2 electrostatically interact with the acidic patch residues D24 and D25 of actin subdomain 1, whereas interaction with the actin N-terminus beyond this was not observed. Additionally, analyses of the actomyosin-7A prediction models generated using various actin isoforms consistently yielded the same results regardless of the type of actin isoform employed. The results of this study suggest that the subtle structural differences in the N-terminus of actin isoforms are unlikely to influence the binding structure with short loop 2 myosin 7A. Our findings are expected to provide a deeper understanding for future high-resolution structural binding studies of actin and myosin.

Myosin, a superfamily of motor proteins, obtain the energy they require for movement from ATP hydrolysis to perform various functions by binding to actin filaments. Extensive studies have clarified the diverse functions performed by the different isoforms of myosin. However, the unavailability of resolved structures has made it difficult to understand the way in which their mechanochemical cycle and structural diversity give rise to distinct functional properties. With this study, we seek to further our understanding of the structural organization of the myosin 7A motor domain by modeling the tertiary structure of myosin 7A based on its primary sequence. Multiple sequence alignment and a comparison of the models of different myosin isoforms and myosin 7A not only enabled us to identify highly conserved nucleotide binding sites but also to predict actin binding sites. In addition, the actomyosin-7A complex was predicted from the protein–protein interaction model, from which the core interface sites of actin and the myosin 7A motor domain were defined. Finally, sequence alignment and the comparison of models were used to suggest the possibility of a pliant region existing between the converter domain and lever arm of myosin 7A. The results of this study provide insights into the structure of myosin 7A that could serve as a framework for higher resolution studies in future.

Rocaglamide (Roc-A), a natural phytochemical isolated from Aglaia species, is known to exert anticancer effects. Allergic inflammation can enhance the tumorigenic potential of cancer cells. We hypothesized that Roc-A could regulate allergic inflammation. Roc-A prevented an antigen from increasing the hallmarks of allergic reactions in vitro. Roc-A suppressed passive cutaneous anaphylaxis (PCA) and passive systemic anaphylaxis (PSA). RNA sequencing analysis showed that Roc-A prevented the antigen from increasing the expression of IL-4 in RBL2H3 cells. Roc-A also prevented the antigen from increasing the expression of interleukin-4 receptor (IL-4R). Roc-A was found to form a hydrogen-bonding network with residues N92 and L64 of IL-4R in a molecular docking simulation. Roc-A prevented the antigen from inducing the binding of IL-4R to JAK1. Chromatin immunoprecipitation (ChIP) assays showed that C-Jun could bind to promoter sequences of IL-4 and IL-4R. Mouse recombinant IL-4 protein increased β-hexosaminidase activity, IL-4R expression, and the hallmarks of allergic inflammation in the antigen-independent manner. Mouse recombinant IL-4 protein increased the expressions of CD163 and arghinase-1 and markers of M2 macrophages, but decreased the expression of iNOS, a marker of M1 macrophages in lung macrophages. Roc-A regulated the effects of a culture medium of antigen-stimulated RBL2H3 cells on the expressions of iNOS and arginase-1 in RAW264.7 macrophages. The blocking of IL-4 or downregulation of IL-4R exerted negative effects on the hallmarks of allergic reactions in vitro. The blocking of IL-4 or downregulation of IL-4R also exerted negative effects on PCA, and the downregulation of IL-4R exerted negative effects on PSA. An miR-34a mimic exerted negative effects on allergic reactions in vitro. The downregulation of IL-4R prevented the antigen from decreasing the expression of miR-34a in RBL2H3 cells. We identified chemicals that could bind to IL-4R via molecular docking analysis. The IL-4R docking chemical 1536801 prevented the antigen from increasing β-hexosaminidase activity and the hallmarks of allergic reactions. The IL-4R docking chemical 1536801 also exerted a negative effect on PCA. TargetScan analysis predicted miR-34a as a negative regulator of IL-4R. We found that the anti-allergic effect of Roc-A and its mechanisms were associated with miR-34a. Taken together, our results show that understanding IL-4R-mediated allergic reactions can provide clues for the development of anti-allergy therapeutics.

Recent advances in cryo-electron microscopy (cryo-EM) have facilitated the high-resolution structural determination of macromolecular complexes in their native states, providing valuable insights into their dynamic behaviors. However, insufficient understanding or experience with the cryo-EM image processing parameters can result in the loss of biological meaning. In this paper, we investigate the dihydrolipoyl acetyltransferase (E2) inner core complex of the pyruvate dehydrogenase complex (PDC) and reconstruct the 3D maps using five different symmetry parameters. The results demonstrate that the reconstructions yield structurally identical 3D models even at a near-atomic structure. This finding underscores a crucial message for researchers engaging in single-particle analysis (SPA) with relatively user-friendly and convenient image processing software. This approach helps reduce the risk of missing critical biological details, such as the dynamic properties of macromolecules.

Bacillus cereus is a significant foodborne pathogen that presents a critical challenge in food safety due to its ability to form resistant spores and produce various toxins. The potential for severe food poisoning makes rapid and accurate identification of this pathogen essential. Conventional microbiological methods for B. cereus identification rely on morphological characteristics and biochemical tests, requiring extensive time and labor. However, even automated biochemical systems like VITEK2, while providing reliable results, still require up to 16 h for analysis and complex sample preparation procedures. MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry utilizes laser-induced ionization of bacterial proteins and subsequent time-of-flight analysis to generate unique mass spectral patterns. This established analytical technique for bacterial identification offers exceptional speed and simplicity through direct protein profiling. In this study, we optimized MALDI-TOF analysis conditions for B. cereus identification by examining various cultivation times. Our results demonstrated complete species-level identification accuracy with MALDI-TOF scores ≥ 2.0 with 12-h cultures, matching the reliability of VITEK2 while significantly reducing processing time. The identification rates decreased significantly from 100% at 12 h to 73.3% at 24 h and 50% at 48 h of incubation, correlating directly with increased spore formation. Detailed analysis at 4-h intervals revealed that high identification rates (93.3%) were maintained during 16 h of cultivation before declining significantly. This study establishes MALDI-TOF as a reliable and efficient tool for rapid B. cereus identification, representing a significant advancement in food safety diagnostics with potential time savings of more than 50% compared to conventional methods.

The chirality of a chemical differentiates it from its mirror-image counterpart. This unique property has significant implications in chemistry, biology, and drug discovery, where chiral chemicals display high selectivity and activity in achieving target specificity and reducing attrition rates in drug development. Stress granules (SGs) are dynamic assemblies of proteins and RNA that form in the cytoplasm of cells under stress conditions. Modulating their formation or disassembly could offer a novel approach to treating a wide range of diseases. This has led to significant interest in SGs as potential therapeutic targets. This study examined the NTF2-like domain of G3BP1 as a possible target for SG modulation. Molecular docking was used to simulate the interactions of compounds with the domain, and a potential candidate with a chiral structure was identified. The experiments showed that the compound induced the formation of SG-like granules. Importantly, the ability of this compound to modulate SG offers valuable insights into a new mechanism underlying the dynamics and promoting the assembly of SGs, and this new mechanism, in turn, holds potential for the development of drugs with diverse mechanisms of action and potentially synergistic effects.