Interaction Of Proteins Research Articles

The conserved protein adaptors CALM/AP180 and FCHo1/2 cooperatively recruit Eps15 to promote the initiation of clathrin-mediated endocytosis in yeast.

Clathrin-mediated endocytosis (CME) is a critical trafficking process that begins when an elaborate endocytic protein network is established at the plasma membrane. Interaction of early endocytic proteins with anionic phospholipids and/or cargo has been suggested to trigger CME initiation. However, the exact mechanism by which CME sites are initiated has not been fully elucidated. In the budding yeast Saccharomyces cerevisiae, higher levels of anionic phospholipids and cargo molecules exist in the newly formed daughter cell compared to the levels in the mother cell during polarized growth. Taking advantage of this asymmetry, we quantitatively compared CME proteins in S. cerevisiae mother versus daughter cells, observing differences in the dynamics and composition of key endocytic proteins. Our results show that CME site initiation occurs preferentially on regions of the plasma membrane with a relatively higher density of endocytic cargo and/or acidic phospholipids. Furthermore, our combined live cell-imaging and yeast genetics analysis provided evidence for a molecular mechanism in which CME sites are initiated when Yap1801 and Yap1802 (yeast CALM/AP180) and Syp1 (yeast FCHo1/2) coordinate with anionic phospholipids and cargo molecules to trigger Ede1 (yeast Eps15)-centric CME initiation complex assembly at the plasma membrane.

Importance of higher-order epistasis in large protein sequence-function relationships.

Epistasis complicates our understanding of protein sequence-function relationships and impedes our ability to build accurate predictive models for novel genotypes. Although pairwise epistasis has been extensively studied in proteins, the significance of higher-order epistasis for protein sequence-function relationships remains contentious, largely due to challenges in fitting higher-order epistatatic interactions for full-length proteins. Here, we introduce a novel transformer-based approach. The key feature of our method is that we can adjust the order of interactions fit by the model by changing the number of attention layers while also accounting for any global nonlinearity induced by the experimental conditions. This allows us to test if inclusion of higher-order interactions leads to enhanced model performance. Applying our method to 10 large protein sequence-function datasets, we found that the importance of higher-order epistasis differs substantially between proteins, accounting for up to 60% of the total variance attributed to epistasis. We also found that including higher-order epistasis is particularly important for generalizing locally sampled fitness data to distant regions of sequence space and for modeling an additional multipeak fitness landscape derived from combining mutagenesis data from 4 orthologous green fluorescencent proteins. Our findings suggest that higher-order epistasis often does play an important role in protein sequence-function relationships, and thus should be properly incorporated during protein engineering and evolutionary data analysis.

Protein persulfidation in plants: mechanisms and functions beyond a simple stress response

Abstract Posttranslational modifications (PTMs) can modulate the activity, localization and interactions of proteins and (re)define their biological function. Understanding how changing environments can alter cellular processes thus requires detailed knowledge about the dynamics of PTMs in time and space. A PTM that gained increasing attention in the last decades is protein persulfidation, where a cysteine thiol (-SH) is covalently bound to sulfane sulfur to form a persulfide (-SSH). The precise cellular mechanisms underlying the presumed persulfide signaling in plants are, however, only beginning to emerge. In the mitochondrial matrix, strict regulation of persulfidation and H2S homeostasis is of prime importance for maintaining mitochondrial bioenergetic processes because H2S is a highly potent poison for cytochrome c oxidase. This review summarizes the current knowledge about protein persulfidation and corresponding processes in mitochondria of the model plant Arabidopsis. These processes will be compared to the respective processes in non-plant models to underpin similarities or highlight apparent differences. We provide an overview of mitochondrial pathways that contribute to H2S and protein persulfide generation and mechanisms for H2S fixation and de-persulfidation. Based on current proteomic data, we compile a plant mitochondrial persulfidome and discuss how persulfidation may regulate protein function.

The Nucleolus and Its Interactions with Viral Proteins Required for Successful Infection.

Nuclear bodies are structures in eukaryotic cells that lack a plasma membrane and are considered protein condensates, DNA, or RNA molecules. Known nuclear bodies include the nucleolus, Cajal bodies, and promyelocytic leukemia nuclear bodies. These bodies are involved in the concentration, exclusion, sequestration, assembly, modification, and recycling of specific components involved in the regulation of ribosome biogenesis, RNA transcription, and RNA processing. Additionally, nuclear bodies have been shown to participate in cellular processes such as the regulation of transcription of the cell cycle, mitosis, apoptosis, and the cellular stress response. The dynamics and functions of these bodies depend on the state of the cell. It is now known that both DNA and RNA viruses can direct their proteins to nuclear bodies, causing alterations in their composition, dynamics, and functions. Although many of these mechanisms are still under investigation, it is well known that the interaction between viral and nuclear body proteins is necessary for the success of the viral infection cycle. In this review, we concisely describe the interaction between viral and nuclear body proteins. Furthermore, we focus on the role of the nucleolus in RNA virus infections. Finally, we discuss the possible implications of the interaction of viral proteins on cellular transcription and the formation/degradation of non-coding RNAs.

Abstract C110: The role of the S100 family signaling pathway proteins in Hispanic colorectal cancer disparities

Abstract Colorectal cancer (CRC) is a global health concern, ranking as the second deadliest and third most diagnosed cancer. In the United States alone, it is estimated that there will be 152,810 new cases of CRC in 2024. CRC has an overall survival rate of 90% when detected in its early stages (Stage I/II). However, due to low screening rates, only 39% of CRC patients in the U.S. are diagnosed during the early stage, particularly among the minority groups like Hispanics. This disparity can be attributed to various factors, including limited access to health care facilities and socio-economic barriers. Among Hispanics, CRC diagnosis and screening rate are lower, resulting in a higher incidence of late-stage (Stage III/IV) diagnosis compared to Non-Hispanic Whites (NHW). Only 33% of Hispanics receive timely diagnosis, and merely 49% undergo recommended screening protocols, in comparison to a diagnosis rate of 35% and screening rate of 58% in NHW. Addressing this health disparity emphasizes the urgent need for targeted interventions to improve early screening and diagnosis within the Hispanic population. We hypothesize that genetic factors across different ethnicities/races may influence gene expression patterns during various stages, thereby contributing to CRC tumorigenesis and progression. To enhance the chances of identifying markers for early detection and diagnosis among Hispanics, we aim to identify new ethnicity-specific transcriptomic profiles. RNA sequencing of Hispanic CRC, NHW CRC and their respective normal tissues adjacent to the tumor (NAT), revealed unique sets of differentially expressed genes (DEGs) with a log2 foldchange of ≥ 2.0 and ≤ -2.0 and p-adjusted value ≤ 0.05 in Hispanic (1831) and NHW (1225) CRC populations compared to their respective NATs. Further analysis identified DEGs specific to early (1012) and late (765) stages of CRC within the Hispanic population, as compared to the respective stages in the NHW. Ingenuity Pathway Analysis (IPA) was used to uncover significant DEGs associated with the S100 family signaling pathway in Hispanic CRC samples. Previous studies have indicated the involvement of the S100 family proteins and their signaling pathways in CRC development, progression, metastasis, and drug resistance through interactions with WNT/β-catenin, RAGE, MAPK and NF-κβ signaling pathways. Our investigation of DEGs within the S100 signaling pathway and their interaction with downstream effectors suggests differential expression of genes crucial in cellular processes, including matrix metallopeptidases (MMP), mitogen-activated protein kinases (MAP2K) and Wingless-related integration site (WNT) family proteins. Exploring these proteins and their downstream effectors in Hispanic CRC tissues and organoids would elucidate specific functional attributes influencing CRC progression. Understanding the interaction of proteins identified in this study may serve as potential ethnicity-specific biomarkers or targets for the development of novel therapeutic interventions for early-stage CRC diagnosis in Hispanics. Citation Format: Soumya Nair, Brian I Grajeda, Sourav Roy. The role of the S100 family signaling pathway proteins in Hispanic colorectal cancer disparities [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C110.

The TβRI promotes migration and metastasis through thrombospondin 1 and ITGAV in prostate cancer cells

AbstractTGFβ potently modifies the extracellular matrix (ECM), which is thought to favor tumor cell invasion. However, the mechanism whereby the cancer cells employ the ECM proteins to facilitate their motility is largely unknown. In this study we used RNA-seq and proteomic analysis to examine the proteins secreted by castration-resistant prostate cancer (CRPC) cells upon TGFβ treatment and found that thrombospondin 1 (THBS1) was observed to be one of the predominant proteins. The CRISPR Cas9, or siRNA techniques was used to downregulate TGFβ type I receptor (TβRI) to interfere with TGFβ signaling in various cancer cells in vitro. The interaction of ECM proteins with the TβRI in the migratory prostate cancer cells in response to TGFβ1 was demonstrated by several different techniques to reveal that THBS1 mediates cell migration by interacting with integrin subunit alpha V (ITGAV) and TβRI. Deletion of TβRI or THBS1 in cancer cells prevented their migration and invasion. THBS1 belongs to a group of tumorigenic ECM proteins induced via TGFβ signaling in CRPC cells, and high expression of THBS1 in human prostate cancer tissues correlated with the degree of malignancy. TGFβ-induced production of THBS1 through TβRI facilitates the invasion and metastasis of CRPC cells as shown in vivo xenograft animal experiments.

Spatial and signaling overlap of growth factor receptor systems at clathrin-coated sites.

Cellular communication is regulated at the plasma membrane by the interactions of receptor, adhesion, signaling, exocytic,and endocytic proteins. Yet, the composition and control of these complexes in response to external cues remain unclear. We use high-resolution and high-throughput fluorescence imaging to map the localization of growth factor receptors and related proteins at single clathrin-coated structures in human squamous HSC3 cells. We find distinct protein signatures between control cells and cells stimulated with growth factors. Clathrin sites at the plasma membrane are preloaded with some receptors but not others. Stimulation with epidermal growth factor induces capture and concentration of epidermal growth factor, fibroblast growth factor1, and low-density lipoprotein receptor (EGFR, FGFR1, and LDLR). Regulatory proteins including ubiquitin ligase Cbl, the scaffold Grb2, and the mechanoenzyme dynamin2 are also recruited. Disrupting FGFR1 or EGFR activity with drugs prevents the recruitment of both EGFR and FGFR1. EGF was able to activate FGFR1 phosphorylation. Our data reveal novel coclustering and activation of receptors and regulatory factors at clathrin-coated sites in response to stimulation by a single growth factor, EGF or FGF. This behavior integrates growth factor signaling and allows for complex responses to extracellular cues and drugs at the plasma membrane of human cells.

The signal that stimulates mammalian embryo development.

Embryo development is stimulated by calcium (Ca2+) signals that are generated in the egg cytoplasm by the fertilizing sperm. Eggs are formed via oogenesis. They go through a cell division known as meiosis, during which their diploid chromosome number is halved and new genetic combinations are created by crossing over. During formation the eggs also acquire cellular components that are necessary to produce the Ca2+ signal and also, to support development of the newly formed embryo. Ionized calcium is a universal second messenger used by cells in a plethora of biological processes and the eggs develop a "toolkit", a set of molecules needed for signaling. Meiosis stops twice and these arrests are controlled by a complex interaction of regulatory proteins. The first meiotic arrest lasts until after puberty, when a luteinizing hormone surge stimulates meiotic resumption. The cell cycle proceeds to stop again in the middle of the second meiotic division, right before ovulation. The union of the female and male gametes takes place in the oviduct. Following gamete fusion, the sperm triggers the release of Ca2+ from the egg's intracellular stores which in mammals is followed by repetitive Ca2+ spikes known as Ca2+ oscillations in the cytosol that last for several hours. Downstream sensor proteins help decoding the signal and stimulate other molecules whose actions are required for proper development including those that help to prevent the fusion of additional sperm cells to the egg and those that assist in the release from the second meiotic arrest, completion of meiosis and entering the first mitotic cell division. Here I review the major steps of egg formation, discuss the signaling toolkit that is essential to generate the Ca2+ signal and describe the steps of the signal transduction mechanism that activates the egg's developmental program and turns it into an embryo.

First Insight into Lignin Valorization as a Promising Biopolymer for the Modulation of the Physicochemical Properties of Port Wine.

Lignosulfonate (LS), kraft lignin (KL), and organosolv lignin (OL) were evaluated as potential modulating agents of the physicochemical properties of Port wine at two different concentrations for 7 and 30 days. KL and LS demonstrated the ability to remove proteins and potentiate the anthocyanin concentration. LS reduced the tannin content and the interaction of salivary acidic proline-rich proteins with wine phenolic compounds. None of the lignin promoted a perceptible color change; however, the yellowish color of KL and OL at 100 g/hL contributed to an increase in the yellow tones of wines. Lignin improved wine aroma by reducing the amount of unwanted volatiles by 30% and increasing the content of ethyl esters associated with fruity aromas by up to 60%. The results suggest that lignin, especially LS, can be employed as a modulating agent, positively impacting wine's physicochemical properties. This valorization of a byproduct opens up new opportunities for the wine industry.

MBPathNCP: A Metabolic Pathway Prediction Model for Chemicals and Enzymes Based on Network Consistency Projection

Background: Metabolic pathway is an important biological pathway in living organisms as it produces necessary energy to maintain vital movement. Although main part of metabolic pathway has been uncovered by the great efforts in recent years, its completeness is still a problem. The undetected chemical reactions in metabolic pathway have become a hinder for better understanding on its mechanism. Prediction of metabolic pathways that a chemical or enzyme can participate in is the first step to remove this hinder. Objective: This study aimed to design an effective computational method to predict the metabolic pathways of chemicals and enzymes. Methods: A new computational model was proposed to predict the metabolic pathways of chemicals and enzymes, which was called MBPathNCP. The kernels for chemicals/enzymes and pathways were constructed using the interactions of chemicals and proteins, and the validated associations between chemicals/enzymes and pathways. The network consistency projection was applied to the kernels and association adjacency matrix to yield the association score for each pair of chemicals/ enzymes and pathways. Results: Cross-validation results on this model shown its good performance. The further tests indicated the reasonability of the entire architecture and its superiority when the negative samples were much than positive samples. Conclusion: The proposed model MBPathNCP was efficient to predict the metabolic pathways of chemicals and enzymes and can be a latent useful tool to investigate metabolic pathway system.

Preparation of Polyclonal Antibodies to Barley Granule-Bound Amylopectin Synthase Ia and Their Application in the Characterization of Interacting Proteins

The production of amylose is facilitated by granule-bound starch synthase (GBSS). Despite its importance, the specific protein interactions involving barley grain-bound starch synthase Ia (HvGBSSIa) remain poorly understood. To elucidate this, we engineered a pET-32a-HvGBSSIa prokaryotic expression vector for specific expression in E. coli Rosetta cells. A rabbit anti-HvGBSSIa polyclonal antibody was generated and employed to enrich HvGBSSIa-binding proteins from barley grains through immunoprecipitation. The isolated complexes were then resolved through SDS-PAGE, and the constituent proteins were identified using mass spectrometry coupled with database searches. Our results confirmed the successful preparation of a highly specific polyclonal antibody against HvGBSSI. Furthermore, differential expression of HvGBSSIa was assessed across various barley tissues and developmental stages of the grain, revealing peak expression at 25 days post-flowering. Proteins interacting with HvGBSSIa, including sucrose synthase and starch branching enzyme, were identified through co-immunoprecipitation. This study lays the groundwork for further detailed analyses of the HvGBSSIa protein complex in barley.

Synergism Interactions of Plant-Based Proteins: Their Effect on Emulsifying Properties in Oil/Water-Type Model Emulsions

This study investigated the synergistic effects of three protein concentrates from legumes (pea, lentil, and lima bean) as emulsifiers and stabilizers of oil-in-water (O/W) emulsions using a simplex-centroid mixture design. The aim was to check whether proteins combined in different proportions have better emulsifying properties than isolated proteins. During this study, each protein concentrate was characterized by different evaluated parameters: emulsifying activity, emulsion stability, accelerated stability test, thermal coagulation time, stability to coalescence, and others. After statistical analysis mixture optimization, it was found that the best formulation for stabilizing O/W emulsion under the tested conditions (2% total protein; 3% sunflower oil) was the protein blend containing 21.21% pea, 32.78% lentil, and 46.01% fava bean. This blend exhibited better emulsification properties compared to the individual proteins.

Resistance of estrogen receptor function to BET bromodomain inhibition is mediated by transcriptional coactivator cooperativity.

The bromodomain and extraterminal domain (BET) family of proteins are critical chromatin readers that bind to acetylated histones through their bromodomains to activate transcription. Here, we reveal that bromodomain inhibition fails to repress oncogenic targets of estrogen receptor because of an intrinsic transcriptional mechanism. While bromodomains are necessary for the transcription of many genes, bromodomain-containing protein 4 (BRD4) binds to estrogen receptor binding sites and activates transcription of critical oncogenes such as MYC, independently of its bromodomains. BRD4 associates with the Mediator complex and disruption of Mediator reduces BRD4's enhancer occupancy. Profiling changes of the post-initiation RNA polymerase II (Pol II)-associated factors revealed that BET proteins regulate interactions between Pol II and elongation factors SPT5, SPT6 and the polymerase-associated factor 1 complex, which associate with BET proteins independently of their bromodomains and mediate their transcription elongation effect. Our findings highlight the importance of bromodomain-independent functions and interactions of BET proteins in the development of future therapeutic strategies.

Tyrobp deficiency blocks NLRP3-mediated inflammation and pyroptosis to alleviate myocardial ischemia-reperfusion injury through regulating Syk

PurposeThe present study aims to investigate the biological function of Tyrobp in myocardial ischemia-reperfusion injury (MIRI) and to clarify its potential reaction mechanisms. MethodsAC16 cells were induced by oxygen-glucose deprivation/reoxygenation (OGD/R) to simulate the MIRI in vitro. The cell transfection technology was used to downregulate Tyrobp, followed by assessment of cell damage, apoptosis and cytokines production via Cell Counting Kit (CCK)-8 assay, lactate dehydrogenase (LDH) release assay, TUNEL and ELISA assays, respectively. Immunofluorescence assay was performed to assess GSDMD. Corresponding proteins were detected via western blotting, and Co-immunoprecipitation (Co-IP) assay was used to validate proteins interaction. ResultsTyrobp was upregulated in OGD/R-exposed AC16 cells, and Tyrobp deficiency significantly alleviated OGD/R-caused cell viability loss, LDH release and cell apoptosis in AC16 cells. Meanwhile, Tyrobp deficiency inhibited the activation of NLRP3 inflammasome, reduced the production of cytokines and inhibited GSDMD intensity and GSDMD-N expression. Additionally, Tyrobp could interact with Syk and regulate Syk/NF-κB signaling. The rescue experiments showed that the above effects of Tyrobp deficiency on OGD/R-exposed AC16 cells were partly weakened by Syk overexpression. ConclusionTyrobp deficiency alleviated MIRI by inhibiting NLRP3-mediated inflammation and pyroptosis through regulating Syk, providing a novel target for the treatment of MIRI.

Exploring the Knowledge of an Outstanding Protein to Protein Interaction Transformer.

Protein-to-protein interaction (PPI) prediction aims to predict whether two given proteins interact or not. Compared with traditional experimental methods of high cost and low efficiency, the current deep learning based approach makes it possible to discover massive potential PPIs from large-scale databases. However, deep PPI prediction models perform poorly on unseen species, as their proteins are not in the training set. Targetting on this issue, the paper first proposes PPITrans, a Transformer based PPI prediction model that exploits a language model pre-trained on proteins to conduct binary PPI prediction. To validate the effectiveness on unseen species, PPITrans is trained with Human PPIs and tested on PPIs of other species. Experimental results show that PPITrans significantly outperforms the previous state-of-the-art on various metrics, especially on PPIs of unseen species. For example, the AUPR improves 0.339 absolutely on Fly PPIs. Aiming to explore the knowledge learned by PPITrans from PPI data, this paper also designs a series of probes belonging to three categories. Their results reveal several interesting findings, like that although PPITrans cannot capture the spatial structure of proteins, it can obtain knowledge of PPI type and binding affinity, learning more than binary PPI.

Genipin 1-O-β-D-gentiobioside ameliorates CUMS-induced prefrontal cortex neuron neuronal apoptosis by modulating HIPK2 SUMOylation

BackgroundDepression is a common mental illness with more than 280 million sufferers worldwide. Inflammation, particularly the c-Jun amino-terminal kinase (JNK) pathway, contributes to depression development and neuronal apoptosis. Gardenia is a herb with therapeutic effects on depression that has been shown to inhibit neuronal apoptosis. However, one of the components in gardenia, Genipin 1-O-β-D-gentiobioside(GG), has been less studied for its mechanism on depression. Thus, in the current study, we investigate how Genipin 1-O-β-D-gentiobioside improves depression and elucidate its possible mechanism of action. MethodsIn this investigation, we utilize a chronic unpredictable mild stress (CUMS) mouse model and corticosterone-induced primary cortical neurons to examine the role of GG in ameliorating depressive symptoms and neuronal apoptosis. TUNEL staining and flow cytometry assessed the effects of GG on neuronal apoptosis. Western Blot analyses and immunofluorescence assays apoptosis-related proteins in the prefrontal cortex and primary neurons. The site of action of GG in regulating homeodomain interacting protein kinase 2 (HIPK2) SUMOylation was further explored in primary neurons. We constructed siRNA-SUMO1 vectors to transfect primary neuronal cells with intracellular SUMO1 knockdown. Proximity ligation assay (PLA) experiments were performed on primary neurons according to the instructions of the assay kit to observe the physical relationship between HIPK2 and SUMO1. We predicted the HIPK2 SUMOylation modification site by an online database and constructed vectors to target and site-directed mutagenesis, then to transfected primary neuronal cells. ResultsThe results showed that GG effectively alleviated depressive-like behaviours, down-regulated apoptosis-related proteins (p-JNK, Bax, Cleaved-Caspase-3), and inhibited neuronal apoptosis in CUMS-induced depressed mice and corticosterone-induced primary cortical neurons. We reveal a complex mechanism underlying the link between GG, SUMOylation of HIPK2, and complex pathways of neuronal apoptosis regulation. K326 and K1189 are the key SUMOylation sites regulated by GG in intricate interactions of apoptosis-related proteins. ConclusionOur study demonstrated that GG exerts antidepressant-like actions through neuroprotective effects by inhibiting the apoptosis of prefrontal cortex neurons, revealing the mechanism of GG inhibition of JNK phosphorylation by enhancing HIPK2 SUMOylation.

Influence of synergistic/competitive interactions of nonionic emulsifiers and proteins on the foam stability of whole egg liquids: Based on air-water and oil-water dual interface perspectives

Nonionic emulsifiers (NE) are widely used in sponge cakes because they can effectively improve the foaming properties of whole egg liquids (WEL). The WEL are rich in protein, lipids and water, forming air-water and oil-water interface during whipping and foaming. However, different NE plays different roles in the interface. No systematic study has been conducted on the stabilization mechanism of WEL by NE. This study first investigated the effect of different NE on the foaming properties of WEL. It was found that WEL with sucrose ester-9 (SE-9) had the highest foam stability (FS) (92.52%), while that with Tween 80 had the lowest (75.55%). It was found that this was related to the higher interfacial protein substitution ability of Tween 80. Next, free triglyceride content and CLSM analysis confirmed that NE promoted the formation of more oil-water interfaces in the foam. Moreover, NE could improve FS by reducing droplet size and increasing viscosity. Finally, the higher surface activity of NE than proteins was demonstrated by interfacial adsorption kinetics and dilatation rheology. SE-9 interacted with proteins at the air-water interface to enhance interfacial rigidity, whereas adsorption of Tween 80 led to a decrease in the rearrangement rate. The results also showed that the formation of oil-water interfacial films was dominated by the adsorption of NE. This study illustrated how different NE stabilized air-water and oil-water interfaces, and the effect of synergistic/competitive interactions with proteins on the stability of the interfaces. This will provide new insights into the stability regulation of WEL foam.

Strain-Dependent Adhesion Variations of Shouchella clausii Isolated from Healthy Human Volunteers: A Study on Cell Surface Properties and Potential Probiotic Benefits.

The probiotic potential of Shouchella clausii is widely recognized, but little is known about its adhesive properties. Hence, this study aims to investigate the adhesion potential and cell surface properties of four human-origin S. clausii strains (B619/R, B603/Nb, B106, and B637/Nm). We evaluated epithelial adhesion, Extracellular Matrix (ECM) binding, aggregation ability, and cell surface hydrophobicity and used genome analysis for validation. Our results demonstrate that adhesion capability is a strain-specific attribute, with significant variations observed among the four strains. B619/R, B603/Nb, and B106 displayed stronger adhesion properties than B637/Nm. Supplementary adhesion assays showed that B637/Nm displayed high hydrophobicity, significant auto-aggregation, and significant mucin-binding abilities. Conversely, B619/R, B603/Nb, and B106 had mildly hydrophobic surfaces and low aggregation abilities. Genome annotation revealed the presence of various adhesion proteins in four strains. Notably, the reduced adhesion potential of B637/Nm was supported by the absence of the cell wall surface anchor family protein (LPxTG motif), which is crucial for interactions with intestinal epithelial cells or mucus components. Further, docking studies provided insights into the interaction of adhesion proteins with gut mucins. These findings contribute to a better understanding of how S. clausii strains interact with the gut environment, facilitating the development of probiotic formulations tailored for improved gut health and well-being.

Formation mechanism and stability of egg white fluid gels under ultrahigh-pressure homogenization pretreatment and synergistic heating effect

The thermal sterilization process of protein beverages inevitably leads to the formation of insoluble thermal aggregates, greatly reducing the texture and taste of protein beverages. In this study, homogenized egg white (HEW) was obtained by ultrahigh-high-pressure (UHP) homogenization pretreatment of egg white (EW), and then a special egg white fluid gel (EWFG) was prepared by water bath heating. The results showed that the optimal conditions for preparing EWFG were three cycles at 20 MPa homogenizing pressure and heating in a water bath at 72℃ for 10 min. Under these conditions, the EWFG was a milky-white homogeneous liquid with an average particle size of about 560 nm. Measurements of the physicochemical properties of HEW and EWFG showed that the UHP homogenization treatment reduced the viscosity of HEW, decreased the particle size of protein aggregates, and increased the zeta potential, which altered the interactions of proteins during the subsequent heating process and facilitated the formation of homogeneous and dispersed EWFG. EWFG showed good stability at pH 6–10 and in low-concentration saline and medium-concentration sucrose solutions. The EWFG obtained by the present treatment is more suitable for factory-scale production and has great potential for protein beverage applications.

Self-assembled superstructure alleviates air-water interface effect in cryo-EM

Cryo-electron microscopy (cryo-EM) has been widely used to reveal the structures of proteins at atomic resolution. One key challenge is that almost all proteins are predominantly adsorbed to the air-water interface during standard cryo-EM specimen preparation. The interaction of proteins with air-water interface will significantly impede the success of reconstruction and achievable resolution. Here, we highlight the critical role of impenetrable surfactant monolayers in passivating the air-water interface problems, and develop a robust effective method for high-resolution cryo-EM analysis, by using the superstructure GSAMs which comprises surfactant self-assembled monolayers (SAMs) and graphene membrane. The GSAMs works well in enriching the orientations and improving particle utilization ratio of multiple proteins, facilitating the 3.3-Å resolution reconstruction of a 100-kDa protein complex (ACE2-RBD), which shows strong preferential orientation using traditional specimen preparation protocol. Additionally, we demonstrate that GSAMs enables the successful determinations of small proteins (<100 kDa) at near-atomic resolution. This study expands the understanding of SAMs and provides a key to better control the interaction of protein with air-water interface.