Protein Structure Research Articles

Analysis of the SARS-CoV-2 inactivation mechanism using violet-blue light (405 nm).

The study evaluated the effects of violet-blue light (VBL) on cell viability and replication, carbonylation of three structural proteins (S, E, and N) and one non-structural protein (NSP13), and direct damage to the RNA of SARS-CoV-2. The virus was exposed to increasing doses of VBL along with influenza A and B viruses to compare their susceptibility. At the highest dose (21.6 J/cm2), SARS-CoV-2 was significantly more susceptible to VBL than the influenza viruses, with a reduction in viral titer of 2.33 log10. Viral RNA did not show significant changes after exposure to VBL, as demonstrated by next-generation sequencing and real-time PCR quantification, suggesting that the inactivation process does not involve direct nucleic acid damage. To exclude the role of the culture suspension in the inactivation process, virus viability experiments were performed using different dilutions of Dulbecco's modified Eagle's medium (DMEM) in phosphate-buffered saline (PBS). The results indicated that the suspension medium played a secondary role in virus inactivation, as viability did not increase with increasing DMEM dilution. Subsequent tests with three different antioxidants (NAC, AsA, and SOD) at different concentrations prevented viral inactivation, from 99.99% to 85.43% (with SOD 0.003 mM). Carbonylation of S and E proteins was more pronounced when viruses were suspended in DMEM rather than PBS, although the tests demonstrated that the intrinsic properties of the viral membrane were a crucial element to consider in relation to its susceptibility to VBL.IMPORTANCELight-based disinfection methods are often used in combination with other cleaning methods due to their non-invasive nature, versatility, and environmental benefits. VBL is an effective approach as it induces the production of reactive oxygen species that reduce microbial viability. In this study, lipid peroxidation was identified as an important factor affecting the structural integrity and function of the viral envelope, reducing its ability to interact with host cells and consequently its ability to be infectious. The lipid envelope of SARS-CoV-2, composed mainly of glycerophospholipids and lacking cholesterol and sphingolipids, appears to be the critical factor in its susceptibility, distinguishing it from influenza viruses, which have a lipid profile richer in components that protect against oxidative stress.

Protective effects and mechanisms of Saikosaponin A against myocardial ischemia based on network pharmacology, molecular docking, and experimental validation.

Saikosaponin A (SSA) is the primary component of Bupleuri radix, which has a variety of pharmacological properties. However, the potential mechanism of SSA's anti-myocardial ischemia (MI) effect has not yet been clarified. We investigated the exact effects and potential mechanisms of SSA on isoproterenol (ISO)-induced MI. A range of network pharmacology approaches have been applied to explore central targets and their underlying mechanisms. Molecular docking was used to identify the binding ability of the potential active components to the hub targets. A rat model of MI was established by subcutaneous injection of ISO (85mg/kg/day). The pathological myocardial morphology, myocardial enzymes, reactive oxygen species (ROS) production, myocardial mitochondrial structure, apoptosis level, and expression of key proteins in the apoptotic pathway were analyzed. Our animal studies revealed that SSA attenuated ISO-induced pathological cardiac injury and significantly reduced creatine kinase (CK), lactate dehydrogenase (LDH), creatine kinase isoenzyme (CK-MB) levels, ROS production, and damage to mitochondrial structures in the heart. In addition, SSA downregulated P53, Caspase-3, and BAX protein activities, upregulated BCL 2 protein activity, and attenuated cardiomyocyte apoptosis. Saikosaponin A alleviates ISO-induced MI by regulating the expression of proteins involved in the P53/BAX/Caspase-3 signaling pathway. Our data showed show that SSA can improve ISO-induced MI. In addition, the role of SSA may be related to its antioxidant stress, anti-apoptosis, and regulation of P53/BAX/Caspase-3 signaling pathway.

CABS-flex 3.0: an online tool for simulating protein structural flexibility and peptide modeling.

Simulating protein structure flexibility using classical methods is computationally demanding, especially for large proteins. To address this challenge, we have been developing the CABS-flex method, which enables fast simulations of protein structural flexibility by combining a coarse-grained simulation approach with all-atom detail. Previously available as the CABS-flex 2.0 web server, the method has now undergone a major upgrade with the release of CABS-flex 3.0. Key improvements include the introduction of intuitive flexibility modes that simplify the control of distance restraints and allow users to reflect known or expected dynamic regions; improved all-atom reconstruction for higher-quality model generation; a new feature for de novo peptide structure prediction, supporting both linear and cyclic peptides along with their conformational flexibility; and new tools for result analysis and visualization, facilitating deeper insights into structural flexibility. Additionally, AlphaFold pLDDT-derived restraints can be used as optional input for guiding simulations. The method accepts input as either a PDB/mmCIF structure or a sequence (for peptide modeling). Advanced options allow users to incorporate experimental or computational restraints. The CABS-flex 3.0 web server is available at https://lcbio.pl/cabsflex3. This website is free and open to all users, with no login requirement.

A single amino acid mutation in VP1 of coxsackievirus A6 determining efficiency of VP0 cleavage and proliferation.

CV-A6 is a major pathogen in the context of HFMD. The cost of treatment and hospitalization of children with HFMD may have a considerable financial impact on the families of patients. CV-A6 is a member of picornaviruses and forms infectious virion through maturation cleavage of VP0 into VP4 and VP2. Although it is well accepted that the autocatalytic process involves viral RNA, the detailed mechanism remains unclear. In this study, residues in VP1-143 were demonstrated to regulate the efficiency of VP0 cleavage and affect the ratio of provirion and virion. Glycine-to-arginine mutation was tolerant, not abolished, but affected the efficiency of VP0 cleavage. The results support a theory that residue mutations on a structural protein of a serotype/genotype within enteroviruses, not well-conserved across picornaviruses and far away from the VP0 cleavage site on the outside surface, regulate the efficiency of VP0 cleavage and render phenotypically different strains.

Phase behavior and dissociation kinetics of lamins in a polymer model of progeria.

One of the key structural proteins in the eukaryotic cell nucleus is lamin. Lamins can assemble into a two-dimensional protein meshwork at the nuclear periphery, known as the nuclear lamina, which provides rigidity and shape to the nucleus. Mutations in lamin proteins that alter the structure of the nuclear lamina underlie laminopathic diseases, including Hutchinson-Gilford Progeria Syndrome (HGPS). Experiments have shown that, compared to healthy cells, lamin supramolecular structures (e.g., protofilaments) assemble into a thicker lamina in HGPS, where they form highly stable nematic microdomains at the nuclear periphery, reminiscent of liquid crystals. This significantly alters the morphological and mechanical properties of the nucleus. In this study, we investigate the aggregation of lamin fibrous structures and their dissociation kinetics from the nuclear periphery by modeling them as coarse-grained, rod-like polymer chains confined within a rigid spherical shell. Our model reproduces the formation of multidirectional nematic domains at the nuclear surface and the reduced lamin dissociation observed in HGPS nuclei by adjusting lamin concentration, lamin-lamin (head-tail), and lamin-shell association strengths. While nematic phase formation requires relatively strong lamin-shell affinity under any non-vanishing inter-lamin attraction, the thickness of the lamina layer is primarily controlled by the head-tail association strength in the model. Furthermore, the unbinding kinetics of lamin chains from the lamina exhibit a concentration-dependent facilitated dissociation, suppressed by strong intra-lamin interactions, reminiscent of diseased nuclei. Overall, our calculations reveal the physical mechanisms by which mutations affecting native lamin interactions and concentration could lead to an abnormal nuclear lamina in laminopathic diseases.

SARS-CoV-2 virus lacking the envelope and membrane open-reading frames as a vaccine platform

To address the need for broadly protective SARS-CoV-2 vaccines, we developed an attenuated a SARS-CoV-2 vaccine virus that lacks the open reading frames of two viral structural proteins: the envelope (E) and membrane (M) proteins. This vaccine virus (ΔEM) replicates in a cell line stably expressing E and M but not in wild-type cells. Vaccination with ΔEM elicits a CD8 T-cell response against the viral spike and nucleocapsid proteins. Two vaccinations with ΔEM provide better protection of the lower respiratory tissues than a single dose against the Delta and Omicron XBB variants in hamsters. Moreover, ΔEM is effective as a booster in hamsters previously vaccinated with an mRNA-based vaccine, providing higher levels of protection in both respiratory tissues compared to the mRNA vaccine booster. Collectively, our data demonstrate the feasibility of a SARS-CoV-2 ΔEM vaccine candidate virus as a vaccine platform.

Edwardsiella ictaluri type III and type VI secretion system mutant strains as candidates for live attenuated vaccines.

Edwardsiella ictaluri, the causative agent of enteric septicemia of catfish, causes substantial economic losses to Channel Catfish Ictalurus punctatus producers in the United States. This study evaluates three E. ictaluri strains, each carrying a markerless deletion mutation in a type III or type VI secretion system gene, as candidates for a live attenuated vaccine against enteric septicemia of catfish in Channel Catfish. Replication in Channel Catfish cells, in vivo invasion and persistence, virulence, and the ability to provide single-dose protection against a wild-type E. ictaluri strain were evaluated for each mutant. In this study, three isogenic mutants were constructed that introduced deletions in esrC, eseG, and evpC. EsrC is a T3SS-encoded protein that regulates expression of multiple virulence genes, including the T3SS effector EseG and the T6SS structural protein EvpC. Each mutant strain was evaluated for its ability to replicate in Channel Catfish ovary cells and head-kidney-derived macrophage cells. Channel Catfish were also challenged with the mutant strains to evaluate if mutation affected invasion, colonization, or persistence within the head kidney, attenuated mortalities in Channel Catfish, or induced protection against disease following subsequent wild-type E. ictaluri exposure. Each mutant maintained the ability to replicate within head-kidney-derived macrophage cells and Channel Catfish ovary cells, as well as invade and colonize the head kidney. Although able to replicate intracellularly and successfully colonize catfish tissue, all three mutants were significantly attenuated in their ability to persist in tissues and cause mortality. A single immersion in mutant strains 28 d prior to exposure to wild-type E. ictaluri resulted in significantly lower mortality than fish immersed in sterile broth, with relative percent survival ranging from 95% to 100%. The findings demonstrate the potential for the development of live attenuated E. ictaluri vaccine strains through the targeted mutation of one or more E. ictaluri T3SS and T6SS genes.

Revealing arginine-cysteine and glycine-cysteine NOS linkages by a systematic re-evaluation of protein structures

Nitrogen-oxygen-sulfur (NOS) linkages act as allosteric redox switches, modulating enzymatic activity in response to redox fluctuations. While NOS linkages in proteins were once assumed to occur only between lysine and cysteine, our investigation shows that these bonds extend beyond the well–studied lysine-NOS-cysteine examples. By systematically analyzing over 86,000 high–resolution X-ray protein structures, we uncovered 69 additional NOS bonds, including arginine-NOS-cysteine and glycine-NOS-cysteine. Our pipeline integrates machine learning, quantum–mechanical calculations, and high-resolution X-ray crystallographic data to systematically detect these subtle covalent interactions and identify key predictive descriptors for their formation. The discovery of these previously unrecognized linkages broadens the scope of protein chemistry and may enable targeted modulation in drug design and protein engineering. Although our study focuses on NOS linkages, the flexibility of this methodology allows for the investigation of a wide range of chemical bonds and covalent modifications, including structurally resolvable posttranslational modifications (PTMs). By revisiting and re-examining well-established protein models, this work underscores how systematic data-driven approaches can uncover hidden aspects of protein chemistry and inspire deeper insights into protein function and stability.

Decoding collagen’s thermally induced unfolding and refolding pathways

Collagen has been evolutionarily selected as the preferred building block of extracellular structures. Despite inherent thermodynamic instability of individual proteins at body temperature, collagen manages to assemble into higher-order structures that provide mechanical support to tissues. Sequence features that enhance collagen stability have been deduced primarily from studies of collagen-mimetic peptides, as collagen's large size has precluded high-resolution studies of its structure. Thus, methods are needed to analyze the structure and mechanics of full-length collagen proteins. In this study, we used AFM imaging to investigate the thermal response of collagen type IV, a key component of basement membranes. We observed a time-dependent loss of folded structures upon exposure to body temperature, with structural destabilization along the collagenous domain reflected by shorter contour lengths (seen also for collagens type I and III). We characterized the sequence-dependent bending stiffness profile of collagen IV as a function of temperature and identified a putative initiation site for thermally induced unfolding. Interchain disulfide bonds in collagen IV were shown to enhance thermal stability and serve as primary nucleation sites for in vitro refolding. In contrast to the canonical C-to-N-terminal folding direction, we found an interchain cystine knot to enable folding in the opposite direction. A multiple sequence alignment revealed that this cystine knot is evolutionarily conserved across metazoan phyla, highlighting its significance in the stabilization of early collagen IV structures. Our findings provide mechanistic insight into the unfolding and refolding pathways of collagen IV, and how its heterogeneous sequence influences stability and mechanics.

Further delineation of defects in MRPS2 causing human OXPHOS deficiency and early developmental abnormalities in zebrafish.

Mitochondrial ribosomal protein-small 2 (MRPS2) encodes a vital structural protein essential for assembling mitoribosomal small subunit and thus mitochondrial translation. Any defect in mitochondrial translation impacts OXPHOS activity and cellular respiration. Defects in MRPS2 have been implicated recently in four families with combined oxidative phosphorylation deficiency-36 (MIM# 617950). We herein describe two individuals from two unrelated families with variable phenotypes of acute onset severe metabolic decompensation and symptomatic hypoglycemia. Exome sequencing identified bi-allelic variants in MRPS2 (NM_016034.5) in the affected individuals: P1: c.490 G > A p.(Glu164Lys); and P2: c.413 G > A p.(Arg138His). Further evaluation of the variant c.490 G > A p.(Glu164Lys) in patient-derived skin fibroblasts revealed decreased expression of MRPS2 transcript and protein levels of MRPS2 along with expression of complex I and IV proteins. Proteomics analysis revealed decreased expression of small subunit proteins and increased expression of large subunit proteins. Also, reduced complex I and IV enzyme activities, mitochondrial respiration (OCR), and altered mitochondrial morphology on confocal imaging were observed. Additionally, mrps2 knockout zebrafish larvae demonstrated an abnormal developmental phenotype and reduced Complex IV activity. With these findings, we identify additional families with variants in MRPS2, illustrating the variable clinical spectrum and validate the pathogenicity of defects in MRPS2 through in-vitro and in-vivo assays.

Prediction of Temperature Factors in Proteins: Effect of Data Pre-Processing and Experimental Conditions

The B-factor or temperature factor is one of the most important parameters in addition to the atomic coordinates, and which is refined during the determination of the protein structure and stored in the Protein Data Bank. It reflects the uncertainty of the atomic positions and is closely linked to atomic flexibility. By using graphlet degree vectors as feature descriptors in a linear model—together with appropriate data transformation and consideration of various experimental factors—the model provides better prediction results. For example, the inclusion of crystal contacts in the linear model significantly improves the prediction accuracy. Since the distributions of the B-factors typically follow an inverse gamma distribution, applying a logarithmic transformation further improves the performance of the model. It has also been shown that large ligands, such as those found in protein–DNA complexes, have a significant impact on the quality of the prediction. A linear model based on graphlet degree vectors proves to be effective not only for the prediction of B-factors and the validation of deposited protein structures but also for the qualitative estimation of root-mean-square fluctuations derived from molecular dynamics.

Genome-Wide Identification of the PHR Gene Family in Six Cucurbitaceae Species and Its Expression Analysis in Cucurbita moschata

Phosphorus, as an essential nutrient, plays an important role in plant growth and development. Although Phosphate Starvation Response 1 (PHR1) or PHR1-like have been recognized as central regulators of phosphorus (Pi) homeostasis in several plants, they have not been systematically studied in Cucurbitaceae. In this study, 11, 10, 8, 12, 12, and 22 PHR genes were identified in cucumber, melon, bottle gourd, watermelon, wax gourd, and pumpkin, respectively, by genome-wide analysis. Phylogenetic analysis showed that the Cucurbitaceae PHR genes were divided into seven distinct subfamilies. These genes were further phylogenetically analyzed for their chromosomal localization, gene structure, protein structure, and synteny. Genomic homology analysis showed that many PHR genes existed in the corresponding homology blocks of six Cucurbitaceae species. qRT-PCR analysis showed that the CmoPHR genes exhibited differential expression under different concentrations of phosphate treatment. Transcriptional self-activation assays showed that CmoPHR2, CmoPHR9, CmoPHR16, and CmoPHR17 proteins had transcriptional self-activating activity. The results of this study provide a basis for the further cloning and functional validation of genes related to the phosphate regulatory network in pumpkin.

Laryngeal Cancer in the Modern Era: Evolving Trends in Diagnosis, Treatment, and Survival Outcomes

Background/Objectives: Laryngeal cancer (LC), predominantly squamous cell carcinoma (SCC), represents a considerable health burden worldwide. Tumour subsite heterogeneity (supraglottic, glottic, subglottic) influences clinical behavior and outcomes. This review synthesizes current knowledge on epidemiology, risk factors, diagnostics, histological variants, biomarkers, treatment modalities, and survival. Results: This narrative review synthesizes current literature on the epidemiology, risk factors, diagnosis, histological variants, biomarkers, and prognosis of LC. The review highlights the critical influence of tumour sites (supraglottic, glottic, subglottic) on metastatic patterns and survival. Key risk factors of LC include tobacco and alcohol use, human papillomavirus (HPV) infection, and occupational exposures. The diagnostic process encompasses clinical examination, endoscopy, biopsy, and imaging. Several biomarkers that aid in diagnosis, treatment plan determination, and prognosis prediction have been established. These biomarkers include long noncoding RNAs, cell cycle regulators, apoptosis regulators, oncogenes, tumour suppressor genes, growth factor pathway components, angiogenic factors, structural proteins, sex hormone receptors, and immunological markers. Current treatment modalities range from organ-preserving surgery and radiotherapy to combined chemoradiotherapy and total laryngectomy. Finally, survival data are presented and stratified by stage and subsite. Conclusions: The review underscores the need for a multidisciplinary approach to LC management, integrating clinical, pathological, and molecular information to optimize patient outcomes.

SARS-CoV-2 ORF3a drives dynamic dense body formation for optimal viral infectivity

SARS-CoV-2 hijacks multiple organelles for virion assembly, of which the mechanisms have not been fully understood. Here, we identified a SARS-CoV-2-driven membrane structure named the 3a dense body (3DB). 3DBs are unusual electron-dense and dynamic structures driven by the accessory protein ORF3a via remodeling a specific subset of the trans-Golgi network (TGN) and early endosomal membrane. 3DB formation is conserved in related bat and pangolin coronaviruses but was lost during the evolution to SARS-CoV. During SARS-CoV-2 infection, 3DB recruits the viral structural proteins spike (S) and membrane (M) and undergoes dynamic fusion/fission to maintain the optimal unprocessed-to-processed ratio of S on assembled virions. Disruption of 3DB formation resulted in virions assembled with an abnormal S processing rate, leading to a dramatic reduction in viral entry efficiency. Our study uncovers the crucial role of 3DB in maintaining maximal SARS-CoV-2 infectivity and highlights its potential as a target for COVID-19 prophylactics and therapeutics.

Production and purification of recombinant proteins VP2 and VP3 of the <i>Alongshan</i> virus of the <i>Jingmenvirus</i> group and evaluation of their immunochemical properties

Introduction. Alongshan virus is a representative of the unclassified group of Jingmenviruses (Flaviviridae), which is detected in Ixodes persulcatus, Ixodes ricinus ticks and various mosquito species in Russia, China, Finland and France. Unlike traditional orthoflaviviruses, the Alongshan virus genome is represented by 4 positive-sense RNA segments. The first and third segments of the genome encode proteins homologous to proteins of the replicative machinery of orthoflaviviruses, the remaining segments encode putative structural proteins that have no known homologues: segment 2 — VP1a (envelope protein), VP1b and NuORF; segment 4 — VP2 (capsid) and VP3 (membrane). Human cases of Alongshan virus-associated disease have been described. The aim of this study is to develop a system for expression and purification of recombinant VP2 and hydrophilic site VP3 proteins to test their antigenic properties. Materials and methods. Miass527 strain of Alongshan virus was used to produce hyperimmune mouse sera and recombinant proteins in a bacterial expression system. Bioinformatic analysis of sequences encoding target proteins and genetically engineered cloning were carried out in this study. Western blotting and enzyme immunoassay (ELISA) were performed to control the results. Results. Recombinant proteins of Alongshan virus have been used in a laboratory diagnostic test system to determine the presence of antibodies to the virus. The obtained recombinant VP2 protein is able to detect antibodies in all tested sera of infected mice, as well as antibodies in human sera both in Western blotting and in enzyme immunoassay. At the same time, antibodies to the recombinant region of VP3 protein were detected irregularly in antiviral immune sera. Conclusion. The detection of antibodies to Alongshan virus in patients confirms the necessity for further investigation of this group of viruses.

Crystal structure of a recombinant Agaricus bisporus mushroom mannose-binding protein with a longer C-terminal region.

A lectin-like protein was discovered in Agaricus bisporus as part of the mushroom tyrosinase complex. The protein has a β-trefoil fold, which is typical of the ricin B-like-type lectin family. The structure of the recombinant protein has been elucidated, and its specific sugar-binding affinity towards mannose and mannitol has also been reported; therefore, the protein was named A. bisporus mannose-binding protein (Abmb). Although the sugar-binding site of Abmb is predicted to be close to the C-terminus, the sugar-binding site has not yet been determined. In this study, a variant of recombinant Abmb with a longer C-terminal region including a 6×His-tag was constructed and its structure was solved at 1.51 and 2.34 Å resolution in an orthorhombic and a monoclinic space group, respectively. The overall structure showed a β-trefoil fold as previously reported; however, several surface loop regions including the C-terminal region showed high flexibility. In addition, a glycan-search assay of this variant showed weak binding affinity towards β-D-galactose but no affinity towards α-D-mannose. The plasticity of the C-terminal tail could be related to the differences in the carbohydrate-binding affinity of Abmb.

The repressor PrtR1 and the global H-NS-like regulators MvaT and MvaV enable the fine-tuning of R-tailocin expression in Pseudomonas protegens

BackgroundBacteria rely on an arsenal of weapons to challenge their opponents in highly competitive environments. To specifically counter closely related bacteria, specialized weapons with a narrow activity spectrum are deployed, particularly contractile phage tail-like particles or R-tailocins. Their production leads to the lysis of the producing cells, indicating that their expression must be carefully orchestrated so that only a small percentage of cells produce R-tailocins for the benefit of the entire population.ResultsIn this study, we set out to better understand how the production of these phage tail-like weapons is regulated in environmental pseudomonads using the competitive plant root colonizer and environmental model strain Pseudomonas protegens CHA0. Using an RNA sequencing (RNA-seq) approach, we found that genes involved in DNA repair, particularly the SOS response program, are upregulated following exposure of the pseudomonad to the DNA-damaging agents mitomycin C and hydrogen peroxide, while genes involved in cell division and primary metabolism are downregulated. The R-tailocin and prophage gene clusters were also upregulated in response to these DNA damaging agents. By combining reverse genetics, transcriptional reporters and chromatin immunoprecipitation sequencing (ChIP-seq), we show that the R-tailocin locus-specific LexA-like regulator PrtR1 represses R-tailocin gene expression by binding directly to the promoter region of the cluster, while the histone-like nucleoid structuring (H-NS) proteins MvaT and MvaV act as master regulators that indirectly regulate R-tailocin cluster expression.ConclusionOur results suggest that at least these three regulators operate in concert to ensure tight control of R-tailocin expression and cell lytic release in environmental Pseudomonas protegens strains.

Investigation of Co-Assembly of Peanut Protein and Rice Protein: Effects on Protein Conformation and Immunoglobulin E Binding Capacity

Reducing the allergenicity of food components through processing is attracting great attention in the food industry. This study investigated the structure and allergenicity of complexes formed from peanut protein (PP) and rice protein (RP) using the pH-driven method. The properties of the PP–RP complexes were investigated using morphological analysis, multi-spectroscopic characterization, IgE binding capacity analysis, and in vitro digestibility studies. Morphological analysis showed that the complexes lost their particulate structures after pH-driven treatment. Spectroscopic analysis showed that the pH-driven treatment promoted protein structural changes, making them more susceptible to degradation. There were also changes in the tertiary structures of the proteins in the complexes following the pH-driven treatment. The IgE binding capacity and digestibility studies suggested that the pH-driven treatment reduced the potential allergenicity of PP by altering its structure under gastrointestinal conditions. This study provides a promising approach for producing hypoallergenic peanut protein ingredients for use in the food industry.

Carotenoids in Skin Photoaging: Unveiling Protective Effects, Molecular Insights, and Safety and Bioavailability Frontiers

Skin photoaging, driven primarily by ultraviolet radiation, remains a critical dermatological concern. Carotenoids, a class of natural pigments with potent antioxidant properties, have emerged as promising agents for preventing and mitigating photoaging. This review comprehensively integrates current understanding regarding the triggers of skin photoaging, oxidative stress and their associated signal pathways, the photoprotective roles and mechanisms of carotenoids, as well as their bioavailability. Common C40 carotenoids, such as β-carotene, lycopene, astaxanthin, lutein, and zeaxanthin demonstrate remarkable antioxidant activity, primarily attributed to their conjugated double bond structures. Many studies have demonstrated that both oral and topical administration of these C40 carotenoids can effectively alleviate skin photoaging. Specifically, they play a crucial role in promoting the formation of a new skin barrier and enhancing the production of collagen and elastin, key structural proteins essential for maintaining skin integrity and elasticity. Mechanistically, these carotenoids combat photoaging by effectively scavenging reactive oxygen species and modulating oxidative stress responsive signal pathways, including MAPK, Nrf2, and NF-κB. Notably, we also anticipate the anti-photoaging potential of novel carotenoids, with a particular emphasis on bacterioruberin, a C50 carotenoid derived from halophilic archaea. Bacterioruberin exhibits a superior radical scavenging capacity, outperforming the conventional C40 carotenoids. Furthermore, when considering the application of carotenoids, aspects such as safe dosage, bioavailability, and possible long term usage issues, including allergies and pigmentation disorders, must be taken into account. This review underscores the anti-photoaging mechanism of carotenoids, providing strategies and theoretical basis for the prevention and treatment of photoaging.

Designer artificial environments for membrane protein synthesis

Protein synthesis in natural cells involves intricate interactions between chemical environments, protein-protein interactions, and protein machinery. Replicating such interactions in artificial and cell-free environments can control the precision of protein synthesis, elucidate complex cellular mechanisms, create synthetic cells, and discover new therapeutics. Yet, creating artificial synthesis environments, particularly for membrane proteins, is challenging due to the poorly defined chemical-protein-lipid interactions. Here, we introduce MEMPLEX (Membrane Protein Learning and Expression), which utilizes machine learning and a fluorescent reporter to rapidly design artificial synthesis environments of membrane proteins. MEMPLEX generates over 20,000 different artificial chemical-protein environments spanning 28 membrane proteins. It captures the interdependent impact of lipid types, chemical environments, chaperone proteins, and protein structures on membrane protein synthesis. As a result, MEMPLEX creates new artificial environments that successfully synthesize membrane proteins of broad interest but previously intractable. In addition, we identify a quantitative metric, based on the hydrophobicity of the membrane-contacting amino acids, that predicts membrane protein synthesis in artificial environments. Our work allows others to rapidly study and resolve the “dark” proteome using predictive generation of artificial chemical-protein environments. Furthermore, the results represent a new frontier in artificial intelligence-guided approaches to creating synthetic environments for protein synthesis.