Mechanism Of Protein Interactions Research Articles

Abstract A075: Establishing the interaction mechanism of oncoprotein, Mucin1, and extracellular vesicle marker protein, Alix, in pancreatic cancer

Abstract Pancreatic ductal adenocarcinoma (PDAC) remains an aggressive disease with devastating mortality rates largely due to a poor understanding of its progression mechanism. Small extracellular vesicles (sEVs) are used by cancer cells to aid in their progression, and tumor-derived EVs (TEVs) show a distinct protein cargo composition potentially contributing to this rapid progression and metastasis of PDAC. To investigate this phenomenon, we isolated sEVs from conditioned media of pancreatic cancer cell lines using ultracentrifugation and characterized them by transmission electron microscopy (TEM), nanoparticle tracking analysis, and immunoblotting. These sEVs were then used in several studies to investigate critical TEV cargo sorting machinery. For instance, PDAC-derived sEVs have selective enrichment of the oncogenic transmembrane protein Mucin1 (MUC1). Preliminary MUC1KO studies from our lab revealed that MUC1 potentially regulates sEV formation, where we saw a clear impact on sEV cargo in the absence of MUC1. Additional studies found that the cytoplasmic adaptor protein ALG-2-Interacting Protein X (Alix), a protein known to play a critical role during TEV formation, regulates MUC1’s presence in sEVs. From this discovery, we then identified a novel MUC1-Alix interaction, which was confirmed using several techniques, including co-immunoprecipitation (CoIP). To define the Alix-interacting domain of MUC1, we utilized in silico modeling and localized surface plasmon resonance (LSPR) of MUC1.CT and Alix to quantify the interaction. This revealed the cytoplasmic tail of MUC1 (MUC1.CT) as the Alix-interacting domain. Moving forward, our central hypothesis for this study is that this MUC1.CT-Alix interaction utilizes a conserved binding motif that targets Alix to the endosomal membrane and contributes to the formation of MUC1+ sEVs. While a distinct sEV biogenesis pathway employed by cancer cells has not yet been defined, our studies will provide insight into the potential sEV sorting mechanism of MUC1 and other cancer biomarkers and advance the understanding of PDAC progression. Citation Format: Kristine V Hoagstrom, Ying Huang, Gloria E Borgstahl, Michael A Hollingsworth. Establishing the interaction mechanism of oncoprotein, Mucin1, and extracellular vesicle marker protein, Alix, in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A075.

Revealing binding mechanism of β-casein to chrysin, apigenin, and luteolin and locating its binding pockets by molecular docking and molecular dynamics

Revealing the interaction mechanism of proteins with bioactive molecules and the location of their binding pockets is crucial for predicting the structure-function relationship of proteins in drug discovery and design. Despite some published papers on the interaction of β-casein with small bioactive molecules, the ambiguity of the location and constituent amino acids of β-casein binding pockets prompted us to identify them by in silico simulation of its interaction with three polyphenols, chrysin, apigenin, and luteolin. Molecular docking revealed that the primary β-casein binding pocket for chrysin consists of five nonpolar amino acids (Leu73, Phe77, Pro80, Ile89, and Pro196), three polar neutral amino acids (Ser137, Gln138, and Gln197), and two polar charged amino acids (Glu136, and Arg198). For β-casein/apigenin and β-casein/luteolin complexes, Asn83 also contributes to forming the pocket. Molecular dynamics provided more details, such as the relative contribution of determinative amino acids and the role of various forces. For example, we found that Glu210, Glu132, and Glu35 are the most destructive residues in the binding of chrysin, apigenin, and luteolin to β-casein, respectively. Also, we observed that hydrophobic forces mainly stabilize β-casein/chrysin and β-casein/apigenin, and polar solvation (including hydrogen bonds) stabilizes β-casein/luteolin, all by spontaneous processes.

Postharvest ripening of newly harvested corn: Weakened interactions between starch and protein

The effects of postharvest ripening of corn on the mechanisms of starch and protein interactions were investigated using molecular dynamics and several chemical substances. Sodium dodecyl sulfate (SDS) treatment all significantly affected the starch content, molecular weight of proteins, relative crystallinity, pasting characteristics and dynamic viscoelasticity in samples before and after postharvest ripening. In the corn that had not undergone postharvest ripening, there were also significant electrostatic interactions and hydrogen bonds between starch and protein. In addition, molecular dynamics had demonstrated that the forces between starch and protein in corn were mainly hydrophobic interactions, electrostatic interaction, and hydrogen bonds. Compared with zein, corn glutelin was more tightly bound to starch. The binding energy of starch to both proteins was reduced in after postharvest-ripened corn. This study laid a rationale for investigating the change mechanism of corn postharvest ripening quality and improving processing property and edible quality of corn.

Integrated Multi-Spectroscopy and Molecular Dynamics Simulations to Explore the Interaction Mechanism of Phenolic Compounds and Sea Bass Myofibrillar Protein

Integrated Multi-Spectroscopy and Molecular Dynamics Simulations to Explore the Interaction Mechanism of Phenolic Compounds and Sea Bass Myofibrillar Protein

Mechanism of ultrasound-induced soybean/egg white composite gelation: Gel properties, morphological structure and co-aggregation kinetics

This study aims to develop ultrasound-assisted acid-induced egg white protein (EWP)-soy protein isolate (SPI) composite gels and to investigate the mechanistic relationship between the co-aggregation behavior of composite proteins and gel properties through aggregation kinetics monitored continuously by turbidity. The results showed that the inclusion of EWP caused the attenuation of gel properties and maximum aggregation (Amax) because EWP could aggregate with SPI at a higher rate (Kapp), which impeded the interaction between SPI and the formation of a continuous gelling network. In the EWP-dominated system, SPI with higher molecular weights also increased the fractal dimension of gels. Ultrasound improved properties of composite gels, especially the SPI-dominated system. After ultrasound treatment, the small, uniform size of co-aggregates and the decrease in potential led to an increase in the aggregation rate and formation of dense particles, consistent with an increase in gelation rate and texture properties. Excessively fast aggregation generated coarse chains and more pores. Still, the exposure of free sulfhydryl groups assisted the gel structure units to form a compact network through disulfide bonding. On the whole, the study could provide theoretical support for a deeper understanding on the interaction mechanism and gelation of composite proteins.

Calcium carbonate polymorph selection in fish otoliths: A key role of phosphorylation of Starmaker-like protein

Fish otoliths are calcium carbonate biominerals found in the inner ear commonly used for tracking fish biochronologies and as a model system for biomineralization. The process of fish otolith formation is biologically controlled by numerous biomacromolecules which not only affect crystal size, shape, mechanical properties, but also selection of calcium carbonate polymorph (e.g., aragonite, vaterite). The proteinaceous control over calcium carbonate polymorph selection occurs in many other species (e.g., corals, mollusks, echinoderms) but the exact mechanism of protein interactions with calcium and carbonate ions – constituents of CaCO3 – are not fully elucidated. Herein, we focus on a native Starmaker-like protein isolated from vaterite asteriscus otoliths from Cyprinus carpio. The proteomic studies show the presence of the phosphorylated protein in vaterite otoliths. In a series of in vitro mineralization experiments with Starmaker-like, we show that native phosphorylation is a crucial determinant for the selection of a crystal's polymorphic form. This is the first report showing that the switch in calcium carbonate phase depends on the phosphorylation pattern of a single isolated protein. Statement of SignificanceCalcium carbonate has numerous applications in industry and medicine. However, we still do not understand the mechanism of biologically driven polymorph selection which results in specific biomineral properties. Previous work on calcium carbonate biominerals showed that either several macromolecular factors or high magnesium concentration (non-physiological) are required for proper polymorph selection (e.g., in mollusk shells, corals and otoliths). In this work, we showed for the first time that protein phosphorylation is a crucial factor for controlling the calcium carbonate crystal phase. This is important because a single protein from the otolith organic matrix could switch between polymorphs depending on the phosphorylation level. It seems that protein post-translational modifications (native, not artificial) are more important for biomolecular control of crystal growth than previously considered.

Mechanism of Interaction between hsa_circ_0002854 and MAPK1 Protein in PM2.5-Induced Apoptosis of Human Bronchial Epithelial Cells.

Fine particulate matter (PM2.5) pollution increases the risk of respiratory diseases and death, and apoptosis is an important factor in the occurrence of respiratory diseases caused by PM2.5 exposure. In addition, circular RNAs (circRNAs) can interact with proteins and widely participate in physiological and pathological processes in the body. The aim of this study was to investigate the mechanism of circRNA and protein interaction on PM2.5-induced apoptosis of human bronchial epithelial cells (16HBE) in vitro. In this study, we exposed human bronchial epithelial cells to a PM2.5 suspension with different concentration gradients for 24 h. The results showed that apoptosis of 16HBE cells after PM2.5 treatment was accompanied by cell proliferation. After exposure of PM2.5 to 16HBE cells, circRNAs related to apoptosis were abnormally expressed. We further found that the expression of hsa_circ_0002854 increased with the increase in exposure concentration. Functional analysis showed that knocking down the expression of hsa_circ_0002854 could inhibit apoptosis induced by PM2.5 exposure. We then found that hsa_circ_0002854 could interact with MAPK1 protein and inhibit MAPK1 phosphorylation, thus promoting apoptosis. Our results suggest that hsa_circ_0002854 can promote 16HBE apoptosis due to PM2.5 exposure, which may provide a gene therapy target and scientific basis for PM2.5-induced respiratory diseases.

Anti-Viral Activity of Bioactive Molecules of Silymarin against COVID-19 via In Silico Studies.

The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection drove the global coronavirus disease 2019 (COVID-19) pandemic, causing a huge loss of human life and a negative impact on economic development. It is an urgent necessity to explore potential drugs against viruses, such as SARS-CoV-2. Silymarin, a mixture of herb-derived polyphenolic flavonoids extracted from the milk thistle, possesses potent antioxidative, anti-apoptotic, and anti-inflammatory properties. Accumulating research studies have demonstrated the killing activity of silymarin against viruses, such as dengue virus, chikungunya virus, and hepatitis C virus. However, the anti-COVID-19 mechanisms of silymarin remain unclear. In this study, multiple disciplinary approaches and methodologies were applied to evaluate the potential mechanisms of silymarin as an anti-viral agent against SARS-CoV-2 infection. In silico approaches such as molecular docking, network pharmacology, and bioinformatic methods were incorporated to assess the ligand-protein binding properties and analyze the protein-protein interaction network. The DAVID database was used to analyze gene functions, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment. TCMSP and GeneCards were used to identify drug target genes and COVID-19-related genes. Our results revealed that silymarin compounds, such as silybin A/B and silymonin, displayed triplicate functions against SARS-CoV-2 infection, including directly binding with human angiotensin-converting enzyme 2 (ACE2) to inhibit SARS-CoV-2 entry into the host cells, directly binding with viral proteins RdRp and helicase to inhibit viral replication and proliferation, and regulating host immune response to indirectly inhibit viral infection. Specifically, the targets of silymarin molecules in immune regulation were screened out, such as proinflammatory cytokines TNF and IL-6 and cell growth factors VEGFA and EGF. In addition, the molecular mechanism of drug-target protein interaction was investigated, including the binding pockets of drug molecules in human ACE2 and viral proteins, the formation of hydrogen bonds, hydrophobic interactions, and other drug-protein ligand interactions. Finally, the drug-likeness results of candidate molecules passed the criteria for drug screening. Overall, this study demonstrates the molecular mechanism of silymarin molecules against SARS-CoV-2 infection.

Protein interactions with osseointegrable titanium implants

This review aims to present the mechanisms of protein interactions with titanium dental implant surfaces. Methods: the analyses were based on searches of scientific articles available in English and Portuguese in PubMed (MEDLINE), Bireme (LILACS), Scielo, Web of Science and Google Scholar. Results: titanium dental implant treatments success rates (95-98%) are mainly due to the biocompatibility of titanium oxide on the implant surface, surgical techniques adopted, good implants manufacturing processes and biomechanical knowledge of the systems. Studies in past decades has empirically developed implant surfaces with significant changes in morphologies, roughness, wettability, surface energy, chemical composition, and chemical groups density or deposited molecules. These changes promoted better protein adsorption, osteoblast adhesion, and changes in the mechanisms involved in osseointegration. Thus, the time to put the implant in function has been reduced and the success rates have increased. In the osseointegration process, at the nanoscale, there is no contact between the bone and the implant surface, but there is the formation of a protein anchorage between the periosteum and the implant with an interface formed by proteins. In all the reactions between the body and the implant surface, the activities of fibronectin and integrin are essential, since they are responsible for transmitting information to the cell for its differentiation, adhesion and mobility. Conclusion: thus, the analyses of protein-implant interactions are indispensable for a better understanding of the performance of osseointegrated dental implants.

Heat treatment effect on whey protein–epigallocatechin gallate interaction: A fluorescence spectroscopic analysis

This study aimed to examine the interaction mechanism of polyphenol protein in a heat-treated aqueous solution system using epigallocatechin gallate (EGCG) and whey protein (WP) as raw materials. Further, we hypothesized the binding characteristics of these two compounds. The results were as follows: The quenching mechanism between WP and EGCG was characterized as static quenching. As the temperature increased, the binding constant and the binding force between EGCG and WP both increased. The number of binding sites (denoted as n) between WP and EGCG was approximately 1. Hence, WP provided a single site to bind to EGCG to form a complex. The main binding modes between WP and EGCG were hydrophobic and electrostatic interactions, and they were spontaneously combined into complexes (ΔG < 0). This study provided a basis for the interaction between WP and EGCG under different heating conditions and their combination mode.

Interaction mechanism of pea proteins with selected pyrazine flavors: Differences in alkyl numbers and flavor concentration

The mechanism of pea protein (PPI) adsorbing flavor components of cooked beef (pyrazine flavor compounds with different concentrations and different numbers of alkyl groups) was researched by spectroscopic and molecular docking approaches. The binding ability results showed that the concentration of pyrazines and the number of alkyl groups in pyrazine strongly influenced the adsorbing ability of PPI. The binding ability of PPI to the pyrazines decreased in the order 2,3,5-trimethyl-pyrazine (TRP) > 2,5-dimethyl pyrazine (DP) > 2-methylpyrazine (MP). The increase in the concentration of pyrazine flavor compounds promoted the enhancement of the adsorption capacity of PPI. Fluorescence and time-resolved fluorescence analysis showed that different molecular structures caused by the amount of alkyl groups on a pyrazine ring showed different quenching types: MP and DP were mainly subjected to static quenching, and TRP with more alkyl groups was mainly subjected to dynamic quenching. During the adsorption of pyrazine flavor compounds, the structure on the peptide bond of pea protein is destroyed. The conformation of pea protein expanded gradually, and the protein changed from ordered structure to disordered structure with lower ΔH. The interactions between pyrazine and pea protein were spontaneous from thermodynamic analysis. Combined with the results of molecular docking, hydrophobic interactions were dominant in the noncovalent interactions between MP and pea protein, whereas hydrogen bonding was dominant between DP/TRP and pea protein. TRP with more alkyl groups could generate new interactions with PPI (π-π stacking interaction) to improve the adsorption capacity of PPI. Pyrazine with more alkyl groups showed a stronger binding force with pea protein to improve the ability of pea protein to adsorb pyrazine flavor compounds, and they displayed different fluorescence quenching mechanisms. This study could provide a theoretical basis for flavor selection and control in the production of pea protein-based meat analogs and thus improve the overall flavor of plant protein-based meat analog products.

Revealing the SARS-CoV-2 Spike Protein and Specific Antibody Immune Complex Formation Mechanism for Precise Evaluation of Antibody Affinity.

The profound understanding and detailed evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (SCoV2-S) protein and specific antibody interaction mechanism is of high importance in the development of immunosensors for COVID-19. In the present work, we studied a model system of immobilized SCoV2-S protein and specific monoclonal antibodies by molecular dynamics of immune complex formation in real time. We simultaneously applied spectroscopic ellipsometry and quartz crystal microbalance with dissipation to reveal the features and steps of the immune complex formation. We showed direct experimental evidence based on acoustic and optical measurements that the immune complex between covalently immobilized SCoV2-S and specific monoclonal antibodies is formed in two stages. Based on these findings it was demonstrated that applying a two-step binding mathematical model for kinetics analysis leads to a more precise determination of interaction rate constants than that determined by the 1:1 Langmuir binding model. Our investigation showed that the equilibrium dissociation constants (KD) determined by a two-step binding model and the 1:1 Langmuir model could differ significantly. The reported findings can facilitate a deeper understanding of antigen-antibody immune complex formation steps and can open a new way for the evaluation of antibody affinity towards corresponding antigens.

Advances in post-translational modifications of proteins and cancer immunotherapy.

Protein post-translational modification (PTM) is a regulatory mechanism for protein activity modulation, localization, expression, and interactions with other cellular molecules. It involves the addition or removal of specific chemical groups on the amino acid residues of proteins. Its common forms include phosphorylation, ubiquitylation, methylation, and acetylation. Emerging research has highlighted lactylation, succinylation, and glycosylation. PTMs are involved in vital biological processes. The occurrence and development of diseases depends on protein abundance and is regulated by various PTMs. In addition, advancements in tumor immunotherapy have revealed that protein PTM is also involved in the proliferation, activation, and metabolic reprogramming of immune cells in tumor microenvironment. These PTMs play an important role in tumor immunotherapy. In this review, we comprehensively summarize the role of several types of PTMs in tumor immunotherapy. This review could provide new insights and future research directions for tumor immunotherapy.

EPEN-01. ZFTA-RELA FUSION PROGRAMS CONVERGE ON YAP PATHWAY ACTIVATION IN EPENDYMOMA

Abstract Approximately two thirds of supratentorial ependymoma are driven by the ZFTA-RELA gene fusion. ZFTA is a recently described gene with a role in DNA binding and transcriptional regulation, while RELA (p65) is a known principal mediator of the canonical NFkB pathway, a pathway activated many human malignancies. The underlying mechanism of NFkB pathway protein interaction with the ZFTA-RELA fusion to drive tumorgenesis has not yet been described. In this study, we utilized our autochthonous mouse tumor model using in utero electroporation (IUE) of the embryonic mouse brain to explore these questions. Using rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) targeting HA-tagged ZFTA-RELA fusion in our IUE model, we demonstrate that both canonical and non-canonical NFkB proteins interact with ZFTA-RELA protein in ZFTA-RELA fusion ependymoma. Focusing on select key NFkB proteins, we performed chromatin immunoprecipitation sequencing (ChIP-Seq) targeting p50/NFkB1, a protein that partners with RELA/p65 in the canonical NFkB pathway, revealing that p50/NFkB1 regulatory programs define active genes that are both distinct from and shared with the ZFTA-RELA fusion protein. Functionally, we performed CRISPR-CAS9 knock out (KO) of p50/NFkB1 and identified no phenotypic effect, as KO lines demonstrated no growth impairment. Furthermore, NFkB targeting drugs did not impair tumor growth. Given these findings, suggesting redundant transcriptional programing, we identified that ZFTA and RELA intersect with TEAD transcription factor programs to activate YAP signaling and that p50 localizes to YAP-TEAD pathway members. Targeting TEAD 1 and 4 with ChIP-Seq, we found that TEAD 1 and 4 co-regulate p50/NFkB1 and ZFTA-RELA target genes. Finally, we demonstrate YAP pathway activation across all supratentorial ependymoma, including ZFTA-RELA ependymoma. Our pathway analysis consistently converged on YAP/TEAD pathways, suggesting collaboration of ZFTA-RELA fusion with YAP/TEAD in transcriptional regulation for these tumors. Targeting YAP/TEAD may therefore represent a promising therapeutic strategy for ZFTA-RELA fusion ependymoma.

Effect of maleylation and denaturation of human serum albumin on its interaction with scavenger receptors.

The specific recognition of serum proteins by scavenger receptors is critical and fundamental in many biological processes. However, the underlying mechanism of scavenger receptor-serum protein interaction remains elusive. In this work, taking scavenger receptors class A1 (SR-A1) as an example, we systematically investigate its interaction with human serum albumin (HSA) at different states through a combination of molecular docking and all-atom molecular dynamics simulations. It is found that native HSA can moderately bind to collagen-like (CL) region or scavenger receptor cysteine-rich (SRCR) region, with both electrostatic (ELE) and van der Waals (VDW) interactions, playing important roles. After maleylation, the binding energy, particularly the ELE energy, between HSA and CL region is significantly enhanced, while the binding energy between HSA and SRCR region remains nearly unchanged. Additionally, we also observe that unfolding of the secondary structures in HSA leads to a larger contact surface area between denatured HSA and CL region, but has little impact on the HSA-SRCR region interaction. Therefore, similar to maleylated HSA, denatured HSA is also more likely to bind to the CL region of SR-A1.

Study on the Interaction Mechanism of Theaflavin with Whey Protein: Multi-Spectroscopy Analysis and Molecular Docking.

The interaction mechanism of whey proteins with theaflavin (TF1) in black tea was analyzed using multi-spectroscopy analysis and molecular docking simulations. The influence of TF1 on the structure of bovine serum albumin (BSA), β-lactoglobulin (β-Lg), and α-lactoalbumin (α-La) was examined in this work using the interaction of TF1 with these proteins. Fluorescence and ultraviolet-visible (UV-vis) absorption spectroscopy revealed that TF1 could interact with BSA, β-Lg and α-La through a static quenching mechanism. Furthermore, circular dichroism (CD) experiments revealed that TF1 altered the secondary structure of BSA, β-Lg and α-La. Molecular docking demonstrated that the interaction of TF1 with BSA/β-Lg/α-La was dominated by hydrogen bonding and hydrophobic interaction. The binding energies were -10.1 kcal mol-1, -8.4 kcal mol-1 and -10.4 kcal mol-1, respectively. The results provide a theoretical basis for investigating the mechanism of interaction between tea pigments and protein. Moreover, the findings offered technical support for the future development of functional foods that combine tea active ingredients with milk protein. Future research will focus on the effects of food processing methods and different food systems on the interaction between TF1 and whey protein, as well as the physicochemical stability, functional characteristics, and bioavailability of the complexes in vitro or in vivo.

Identification and mechanistic exploration of structural and conformational dynamics of NF-kB inhibitors: rationale insights from in silico and in vitro studies

Increased expression of target genes that code for proinflammatory chemical mediators results from a series of intracellular cascades triggered by activation of dysregulated NF-κB signaling pathway. Dysfunctional NF-kB signaling amplifies and perpetuates autoimmune responses in inflammatory diseases, including psoriasis. This study aimed to identify therapeutically relevant NF-kB inhibitors and elucidate the mechanistic aspects behind NF-kB inhibition. After virtual screening and molecular docking, five hit NF-kB inhibitors opted, and their therapeutic efficacy was examined using cell-based assays in TNF-α stimulated human keratinocyte cells. To investigate the conformational changes of target protein and inhibitor-protein interaction mechanisms, molecular dynamics (MD) simulations, binding free energy calculations together with principal component (PC) analysis, dynamics cross-correlation matrix analysis (DCCM), free energy landscape (FEL) analysis and quantum mechanical calculations were carried out. Among identified NF-kB inhibitors, myricetin and hesperidin significantly scavenged intracellular ROS and inhibited NF-kB activation. Analysis of the MD simulation trajectories of ligand–protein complexes revealed that myricetin and hesperidin formed energetically stabilized complexes with the target protein and were able to lock NF-kB in a closed conformation. Myricetin and hesperidin binding to the target protein significantly impacted conformational changes and internal dynamics of amino acid residues in protein domains. Tyr57, Glu60, Lys144 and Asp239 residues majorly contributed to locking the NF-kB in a closed conformation. The combinatorial approach employing in silico tools integrated with cell-based approaches substantiated the binding mechanism and NF-kB active site inhibition by the lead molecule myricetin, which can be explored as a viable antipsoriatic drug candidate associated with dysregulated NF-kB. Communicated by Ramaswamy H. Sarma

Effects of proteins on magnesium degradation - static vs. dynamic conditions

The interaction between organic molecules and biomaterial surfaces determines the fate of biomaterials during their service life, which is also the research hotspots in the field of biomaterials. To understand the mechanism of protein interaction with magnesium (Mg) degradation, alloying elements, immersion time, protein concentration and surface conditions have been previously considered for the effect of proteins on Mg degradation. However, fluid flow, as one of the critical factors, drew little attention in this case. In the present study, the effect of bovine serum albumin (BSA) and fetal bovine serum (FBS) on Mg degradation was compared under static and dynamic conditions. The results revealed that both BSA and FBS slightly decreased the degradation rate of Mg in Hanks’ balanced salt solution (HBSS) under static immersion due to the protein adsorption and the formation of a Ca/P-rich top layer on Mg surface, whereas under dynamic flow condition the degradation of Mg was significantly accelerated in the presence of BSA or FBS. The reasons seemed to stem from the weakened protein adsorption on Mg surface in this case and the dynamically enhanced interaction between proteins and ions/products in solutions, which largely weaken the combination of the top Ca/P-rich layer with the inner corrosion product layer. These results highlight the importance of testing conditions for Mg characterization in vitro and the synergistic effect between different parameters on Mg degradation.

Coevolutionary analysis of Forkhead box protein P3 and its physical binary interactors E3 ubiquitin-protein ligase CHIP, Zfp-90, and nuclear receptor ROR-α.

Forkhead box protein P3 (FOXP3) is known to orchestrate the development and maintenance of T regulatory cells, a cell population specialized in immune suppression and peripheral immune tolerance. FOXP3 activity is fine-tuned through its interaction with several protein-binding partners. By using IntAct database, we retrieved three physical binary interactors: E3 ubiquitin-protein ligase CHIP, Zfp-90, and nuclear receptor ROR-α. Coevolution clusters between FOXP3 and its interactors were identified with the use of iBIS2 algorithm, the iterative version of BIS/BIS2. Most of the coevolving pairs came from some species of monotremes and marsupials, as well as from a group of bats, thus suggesting that protein interactions of FOXP3 with its partners may be changed and/or modulated during mammalian speciation. Furthermore, our analysis would suggest the occurrence of a determinant role of FOXP3 in suppressing pregnancy alloreactions in placental mammals. Similarly, FOXP3, through its interaction with different protein interaction mechanisms, would explain the unique control of inflammatory response to infections in bats. By identifying several inter-protein clusters between the different protein pairs, our findings may provide a guide for new therapeutic approaches to modulate T regulatory suppression and/or enhance immune tolerance.

Comprehensive genome-wide identification and functional characterization of MAPK cascade gene families in Nelumbo

Mitogen-activated protein kinase (MAPK) cascade signaling pathway plays pivotal roles in various plant biological processes. However, systematic study of MAPK cascade gene families is yet to be conducted in lotus. Herein, 198 putative MAPK genes, including 152 MAP3Ks, 15 MKKs, and 31 MPKs genes were identified in Nelumbo. Segmental duplication was identified as the predominant factor driving MAPK cascade gene family expansion in lotus. MAPK cascade genes in N. nucifera and N. lutea shared high degree of sequence homologies, with 84, 9, and 19 homologous MAP3K, MKK, and MPK gene pairs being detected between the two species, respectively, with most genes predominantly undergoing purifying selection. Gene expression profiling indicated that NnMAPK cascade genes were extensively involved in plant development and submergence stress response. Co-expression analysis revealed potential interaction between transcription factors (TFs) and NnMAPK cascade genes in various biological processes. NnMKK showed predicted interactions with multiple NnMAP3K or NnMPK proteins, which suggested that functional diversity of MAPK cascade genes could be as a result of their complex protein interaction mechanisms. This first systematic analysis of MAPK cascade families in lotus provides deeper insights into their evolutionary dynamics and functional properties, which potentially could be crucial for lotus genetic improvement.