STRING-ing together protein complexes: Corpus and methods for extracting physical protein interactions from the biomedical literature.

MOTIVATION: Understanding biological processes relies heavily on curated knowledge of physical interactions between proteins. Yet, a notable gap remains between the information stored in databases of curated knowledge and the plethora of interactions documented in the scientific literature. RESULTS: To bridge this gap, we introduce ComplexTome, a manually annotated corpus designed to facilitate the development of text-mining methods for the extraction of complex formation relationships among biomedical entities targeting the downstream semantics of the physical interaction sub-network of the STRING database. This corpus comprises 1,287 documents with ∼3,500 relationships. We train a novel relation extraction model on this corpus and find that it can highly reliably identify physical protein interactions (F1-score = 82.8%). We additionally enhance the model's capabilities through unsupervised trigger word detection and apply it to extract relations and trigger words for these relations from all open publications in the domain literature. This information has been fully integrated into the latest version of the STRING database. AVAILABILITY AND IMPLEMENTATION: We provide the corpus, code, and all results produced by the large-scale runs of our systems biomedical on literature via Zenodo https://doi.org/10.5281/zenodo.8139716, Github https://github.com/farmeh/ComplexTome_extraction, and the latest version of STRING database https://string-db.org/. SUPPLEMENTARY INFORMATION: Supplementary information are available at Bioinformatics online.

L-cysteine mediated rapid separation of Hg2+ and MeHg+ by anion-exchange HPLC.

Owing to the on-going emission of Hg into the global environment, new insight into their bioinorganic chemistry in mammals is urgently required to better understand their adverse health effects and analytical methods to quantify Hg2+ and MeHg+ in environmental samples are needed. Analytical separations can help to address both of these needs. While Hg2+ and MeHg+ have been most frequently separated by cation and reversed-phase (RP) HPLC, we here report on using anion-exchange (AEX) HPLC in conjunction with a flame atomic absorption spectrometer (FAAS) to observe the retention behavior of these mercury species in the pH range 5.0-8.0 using mobile phases comprised of 10 mM l-cysteine (Cys) in 100 mM phosphate buffer. The results obtained for pH 5.0 served as a starting point to develop a rapid HPLC separation for these mercurials. The addition of 5-20 % methanol (MeOH) to this mobile phase revealed that MeOH did not appreciably change the retention of Hg2+, but significantly reduced the retention of MeHg+. A 15 % MeOH-containing mobile phase offered the best compromise between achieving a rapid baseline separation in <400 s at affordable costs. To assess the suitability and robustness of the developed AEX-HPLC separation method for the analysis of environmental samples an inductively coupled plasma atomic emission spectrometer (ICP-AES) was employed as the mercury-specific detector. The developed AEX-HPLC-ICP-AES method allowed to achieve detection limits of 1.5 ppm for Hg2+ and 2.9 ppm for MeHg+ and was successfully applied to analyze wastewater that had been spiked with Hg2+ and MeHg+.

Mononuclear high-spin iron(III) phthalocyanines.

2,9(or 10),16(or 17), 23(or 24)-Tetradecyloxycarbonylphthalocyaninatoiron, FeTDPc, and 2,3,9,10,16,17,23,24-octadecyloxycarbonylphthalocyaninatoiron, FeODPc, were synthesized and characterized. These compounds seem to be in trivalent iron high-spin state in solvents such as chloroform, dichloromethane, benzene, and chlorobenzene, although their counter anion could not be detected by elemental analyses. They react with strong bases such as pyridine and imidazoles to form their mono- and subsequently their di-base complexes with formation constant of >106 and < 200 dm3 mol-1, respectively, in dichloromethane at 20 °C. The resultant mono-adducts appear to be trivalent iron low-spin while the di-base adducts are bivalent iron low-spin state complexes. The addition of ca. 10-30 equivalent of tetrabutylammonium-chloride or -bromide (electrolyte) to the solution containing FeTDPc or FeODPc, causes their spin-state change from iron(III) high to low-spin state. In a solid power state, however, both FeTDPc and FeODPc exist as a mixture of high-spin iron(III)- and intermediate-spin iron(II) species. Strangely, when these compounds are dissolved in polystyrene, i.e. each molecules are isolated from each other, the signals originated from the iron(II) component disappear.

Impact of protein and small molecule interactions on kinase conformations.

Protein kinases act as central molecular switches in the control of cellular functions. Alterations in the regulation and function of protein kinases may provoke diseases including cancer. In this study we investigate the conformational states of such disease-associated kinases using the high sensitivity of the kinase conformation (KinCon) reporter system. We first track BRAF kinase activity conformational changes upon melanoma drug binding. Second, we also use the KinCon reporter technology to examine the impact of regulatory protein interactions on LKB1 kinase tumor suppressor functions. Third, we explore the conformational dynamics of RIP kinases in response to TNF pathway activation and small molecule interactions. Finally, we show that CDK4/6 interactions with regulatory proteins alter conformations which remain unaffected in the presence of clinically applied inhibitors. Apart from its predictive value, the KinCon technology helps to identify cellular factors that impact drug efficacies. The understanding of the structural dynamics of full-length protein kinases when interacting with small molecule inhibitors or regulatory proteins is crucial for designing more effective therapeutic strategies.

Refinement of Docked Protein-Protein Complexes Using Repulsive Scaling Replica Exchange Simulations.

Accurate prediction and evaluation of protein-protein complex structures is of major importance to understand the cellular interactome. Predicted complex structures based on deep learning approaches or traditional docking methods require often structural refinement and rescoring for realistic evaluation. Standard molecular dynamics (MD) simulations are time-consuming and often do not structurally improve docking solutions. Better refinement can be achieved with our recently developed replica-exchange-based scheme employing different levels of repulsive biasing between proteins in each replica simulation (RS-REMD). The bias acts specifically on the intermolecular interactions based on an increase in effective pairwise van der Waals radii without changing interactions within each protein or with the solvent. It allows for an improvement of the predicted protein-protein complex structure and simultaneous realistic free energy scoring of protein-protein complexes. The setup of RS-REMD simulations is described in detail including the application on two examples (all necessary scripts and input files can be obtained from https://gitlab.com/TillCyrill/mmib ).

Inhibitory effect of organogermanium compound 3-(trihydroxygermyl)propanoic acid on fructose-induced glycation of amino compounds.

3-(Trihydroxygermyl)propanoic acid (THGP), a hydrolysate of poly-trans-[(2-carboxyethyl)germasesquioxane] (Ge-132, also known as repagermanium), can inhibit glycation between glucose/ribose and amino compounds. In addition, THGP may inhibit glycation by inhibiting reactions that occur after Amadori rearrangement and inducing the reversible solubilization of AGEs. In this study, we first investigated the effects and mechanisms on the glycation of fructose and amino compounds by THGP, as a greater reactivity was obtained with fructose than with glucose. Unlike other anti-glycation materials, THGP can form a complex with fructose, the initial compound of glycation. THGP also inhibited the production of AGEs and suppressed the reduction of fructose in a reaction between fructose and arginine. These results indicate that THGP forms a complex with cyclic fructose possessing a cis-diol structure at a reducing end, and that it suppresses the ring-opening of fructose and the progress of the initial glycation reaction. We next tried to evaluate the suppressive effect of glucosyl hesperidin (GHes) and THGP on the reaction of glycation between fructose and collagen. Both compounds effectively reduced the production of AGEs individually, and the combination of them led to a synergistic suppression. Therefore, through combination with other antiglycation materials, THGP may cooperatively exhibit glycation-inhibitory effects and be able to suppress the AGE production.

Characterization of a novel format scFv×VHH single-chain biparatopic antibody against metal binding protein MtsA.

Biparatopic antibodies (bpAbs) are engineered antibodies that bind to multiple different epitopes within the same antigens. bpAbs comprise diverse formats, including fragment-based formats, and choosing the appropriate molecular format for a desired function against a target molecule is a challenging task. Moreover, optimizing the design of constructs requires selecting appropriate antibody modalities and adjusting linker length for individual bpAbs. Therefore, it is crucial to understand the characteristics of bpAbs at the molecular level. In this study, we first obtained single-chain variable fragments and camelid heavy-chain variable domains targeting distinct epitopes of the metal binding protein MtsA and then developed a novel format single-chain bpAb connecting these fragment antibodies with various linkers. The physicochemical properties, binding activities, complex formation states with antigen, and functions of the bpAb were analyzed using multiple approaches. Notably, we found that the assembly state of the complexes was controlled by a linker and that longer linkers tended to form more compact complexes. These observations provide detailed molecular information that should be considered in the design of bpAbs.

Formation and Application of Starch-Polyphenol Complexes: Influencing Factors and Rapid Screening Based on Chemometrics.

Understanding the nuanced interplay between plant polyphenols and starch could have significant implications. For example, it could lead to the development of tailor-made starches for specific applications, from bakinag and brewing to pharmaceuticals and bioplastics. In addition, this knowledge could contribute to the formulation of functional foods with lower glycemic indexes or improved nutrient delivery. Variations in the complexes can be attributed to differences in molecular weight, structure, and even the content of the polyphenols. In addition, the unique structural characteristics of starches, such as amylose/amylopectin ratio and crystalline density, also contribute to the observed effects. Processing conditions and methods will always alter the formation of complexes. As the type of starch/polyphenol can have a significant impact on the formation of the complex, the selection of suitable botanical sources of starch/polyphenols has become a focus. Spectroscopy coupled with chemometrics is a convenient and accurate method for rapidly identifying starches/polyphenols and screening for the desired botanical source. Understanding these relationships is crucial for optimizing starch-based systems in various applications, from food technology to pharmaceutical formulations.

The role of C18 fatty acids in improving the digestion and retrogradation properties of highland barley starch.

In this study, five C18 fatty acids (FA) with different numbers of double bonds and configurations including stearic acid (SA), oleic acid (OA), elaidic acid (EA), linoleic acid (LA), and α-linolenic acid (ALA), were selected to prepare highland barely starch (HBS)-FA complexes to modulate digestibility and elaborate the underlying mechanism. The results showed that HBS-SA had the highest complex index (34.18 %), relative crystallinity (17.62 %) and single helix content (25.78 %). Furthermore, the HBS-C18 FA complexes were formed by EA (C18 FA with monounsaturated bonds) that had the highest R1047/1022 (1.0509) and lowest full width at half-maximum (FWHM, 20.85), suggesting good short-range ordered structure. Moreover, all C18 FAs could form two kinds of V-type complexes with HBS, which can be confirmed by the results of CLSM and DSC measurements, and all of them showed significantly lower digestibility. HBS-EA possessed the highest resistant starch content (20.17 %), while HBS-SA had the highest slowly digestible starch content (26.61 %). In addition, the inhibition of HBS retrogradation by fatty acid addition was further proven, where HBS-SA gel firmness (37.80 g) and aging enthalpy value were the lowest, indicating the most effective. Overall, compounding with fatty acids, especially SA, could be used as a novel way to make functional foods based on HBS.

The Chemistry of Chelation for Built Heritage Cleaning: The Removal of Copper and Iron Stains.

Chelators are widely used in conservation treatments to remove metal stains from marble, travertine, and limestone surfaces. In the current review the chemical aspects underlying the use of chelators for the removal of copper and iron stains from built heritage are described and clear criteria for the selection of the most efficient stain removal treatment are given. The main chelator structural features are outlined and the operating conditions for effective metal stain removal (pH, time of application, etc.) discussed, with a particular emphasis on the ability to form stable metal complexes, the high selectivity towards the metal that should be removed, and the high sustainability for the environment. Dense matrices often host chelators for higher effectiveness, and further research is required to clarify their role in the cleaning process. Then, relevant case studies of copper and iron stain removal are discussed. On these bases, the most effective chelators for copper and stain removal are indicated, providing chemists and conservation scientists with scientific support for conservation operations on stone works of art and opening the way to the synthesis of new chelators.

Conductometric investigation of nano MnSO4 association parameters and complex formation with glycylglycine in aqueous and methanol-water mixtures: Thermodynamic parameters and potential applications.

This study aimed to investigate the ion pair association values and association parameters of nano MnSO4 in water and methanol-water mixtures (20 % and 40 % methanol by mass percentage) at varying temperatures (298.15, 303.15, 308.15, and 313.15 K) using the conductometric technique. Additionally, the parameters for complex formation between nano MnSO4 and glycylglycine as a ligand were determined. The focus was on elucidating the thermodynamic formation parameters for the nano Mn2+-glycylglycine interaction, with particular emphasis on comparing the 1: 1 and 1: 2 (M: L) complexes to understand the complexation behavior more comprehensively. The results indicated that the complexation process was spontaneous, as evidenced by negative ΔGf (formation free energy change) values, which increased with temperature, highlighting the enhanced spontaneity of the process. The findings provide valuable insights into designing new materials and procedures by enhancing our understanding of the complexation behavior of nano MnSO4 with ligands like glycylglycine, thus contributing to advancements in various applications such as chemical synthesis, medicines, and environmental remediation. By elucidating the thermodynamic aspects of these interactions, the study aimed to provide valuable information that could be utilized in practical applications and further research endeavors.

Chemical characterization of heavy actinides and light transactinides - Experimental achievements at JAEA.

The chemical characterization of the heaviest elements at the farthest reach of the periodic table (PT) and the classification of these elements in the PT are undoubtedly crucial and challenging subjects in chemical and physical sciences. The elucidation of the influence of relativistic effects on their outermost electronic configuration is also a critical and fascinating aspect. However, the heaviest elements with atomic numbers Z ≳ 100 must be produced at accelerators using nuclear reactions of heavy ions and target materials. Therefore, production rates for these elements are low, and their half-lives are as short as a few seconds to a few minutes; they are usually available in a quantity of only a few atoms at a time. Here, we review some highlighted studies on heavy actinide and light transactinide chemical characterization performed at the Japan Atomic Energy Agency tandem accelerator facility. We discuss briefly the prospects for future studies of the heaviest elements.

Wheat Protein Hydrolysates Improving the Stability of Purple Sweet Potato Anthocyanins under Neutral pH after Commercial Sterilization at 121 °C.

Anthocyanins are prone to degradation and color fading after sterilization. This work examined the potential of wheat protein hydrolysates (WPHs, 40 g/L) in improving the stability of purple sweet potato anthocyanins (PSPAs) under a pH of 6.8 after sterilization at 121 °C followed by storage. Results showed that WPHs increased the thermal degradation half-life of PSPAs 1.65 times after sterilization. Compared to PSPAs alone, after being stored at 37 °C and 45 °C for 7 days, the retention concentration of PSPAs with WPHs was 5.4 and 32.2 times higher, and the color change of PSPAs with WPHs decreased from 6.19 and 10.46 to 0.29 and 0.77, respectively. AFM data, fluorescence and UV spectrograms indicated the formation of complexes between PSPAs and WPHs by hydrophobic attraction confirmed by zeta-potential data. PSPAs with WPHs had stable particle size and zeta potential, which may also significantly increase the concentrations after digestion and antioxidant power of PSPAs. This work indicated that the assembled PSPAs composite structure by WPHs significantly reduced the degradation of PSPAs at a pH of 6.8 after sterilization at 121 °C followed by long-term storage.

Quantitative analysis of MBW complex formation in the context of trichome patterning.

Trichome patterning in Arabidopsis is regulated by R2R3MYB, bHLH and WDR (MBW) genes. These are considered to form a trimeric MBW protein complex that promotes trichome formation. The MBW proteins are engaged in a regulatory network to select trichome cells among epidermal cells through R3MYB proteins that can move between cells and repress the MBW complex by competitive binding with the R2R3MYB to the bHLHL protein. We use quantitative pull-down assays to determine the relative dissociation constants for the protein-protein interactions of the involved genes. We find similar binding strength between the trichome promoting genes and weaker binding of the R3MYB inhibitors. We used the dissociation constants to calculate the relative percentage of all possible complex combinations and found surprisingly low fractions of those complexes that are typically considered to be relevant for the regulation events. Finally, we predict an increased robustness in patterning as a consequence of higher ordered complexes mediated by GL3 dimerization.

Terminal regions of UAP56 and URH49 are required for their distinct complex formation functioning to an essential role in mRNA processing and export.

UAP56 and URH49 are closely related RNA helicases that function in selective mRNA processing and export pathways to fine-tune gene expression through distinct complex formations. The complex formation of UAP56 and URH49 is believed to play a crucial role in regulating target mRNAs. However, the mechanisms underlying this complex formation have not been fully elucidated. Here we identified the regions essential for the complex formation of both helicases. The terminal regions of UAP56 and the C-terminal region of URH49 were indispensable for their respective complex formation. Further analysis revealed that a specific amino acid at the C-terminus of UAP56 is critical for its complex formation. Alanine substitution of this amino acid impairs its complex formation and subsequently affected its mRNA processing and export activity. Our study provides a deeper understanding of the basis for the complex formation between UAP56 and URH49.

Analyzing (3-Aminopropyl)triethoxysilane-Functionalized Porous Silica for Aqueous Uranium Removal: A Study on the Adsorption Behavior.

This study synthesized (3-aminopropyl)triethoxysilane-functionalized porous silica (AP@MPS) to adsorb aqueous uranium (U(VI)). To comprehensively analyze the surface properties of the AP@MPS materials, a combination of SEM, BET, XPS, NMR, and zeta potential tests were conducted. The adsorption experiments for U(VI) revealed the rapid and efficient adsorption capacity of AP@MPS, with the solution condition of a constant solution pH = 6.5, an initial U(VI) concentration of 600 mg × L-1, a maximum U(VI) capacity of AP@MPS reaching 381.44 mg-U per gram of adsorbent, and a removal rate = 63.6%. Among the four types of AP@MPS with different average pore sizes tested, the one with an average pore size of 2.7 nm exhibited the highest U(VI) capacity, particularly at a pH of 6.5. The adsorption data exhibited a strong fit with the Langmuir model, and the calculated adsorption energy aligned closely with the findings from the Potential of Mean Force (PMF) analysis. The outcomes obtained using the Surface Complex Formation Model (SCFM) highlight the dominance of the coulombic force ΔG0coul as the principal component of the adsorption energy (ΔG0ads). This work garnered insights into the adsorption mechanism by meticulously examining the ΔG0ads across a pH ranging from 4 to 8. In essence, this study's findings furnish crucial insights for the future design of analogous adsorbents, thereby advancing the realm of uranium(VI) removal methodologies.

Measuring Protein-Protein Interactions and Quantifying Their Dissociation Constants with Mass Photometry.

Protein-protein interactions underlie most biological processes, and determining the affinity and abundance of binding partners for each interaction is often a challenging task because these interactions often involve multiple ligands and binding sites. Standard methods for determining the affinity of protein interactions often require a large amount of starting material in addition to potentially disruptive labeling or immobilization of the binding partners. Mass photometry is a bioanalytical technique that measures the mass of single biomolecules in solution, quickly and with minimal sample requirements. This article describes how mass photometry can be used to determine the mass distribution of binding partners, the complexes they form, the relative abundance of each species, and, accordingly, the dissociation constant (KD ) of their interactions. © 2024 Refeyn Ltd. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Using mass photometry to measure protein-protein binding and quantify the KD of this interaction.

In vitro and in vivo evaluation of iRoot BP Plus as a coronal sealing material for regenerative endodontic procedures.

OBJECTIVES: To investigate in vitro effects of a nanoparticle bioceramic material, iRoot BP Plus, on stem cells from apical papilla (SCAP) and in vivo capacity to induce pulp-dentin complex formation. MATERIALS AND METHODS: The sealing ability of iRoot BP Plus was measured via scanning electron microscopy (SEM). SCAP were isolated and treated in vitro by iRoot BP Plus conditioned medium, with mineral trioxide aggregate (MTA) conditioned medium and regular medium used as controls, respectively. Cell proliferation was assessed by BrdU labeling and MTT assay and cell migration was evaluated with wound healing and transwell assays. Osteo/odontogenic potential was evaluated by Alizarin red S staining and qPCR. Pulp-dentin complex formation in vivo was assessed by a tooth slice subcutaneous implantation model. RESULTS: iRoot BP Plus was more tightly bonded with the dentin. There was no difference in SCAP proliferation between iRoot BP Plus and control groups (P > 0.05). iRoot BP Plus had a greater capacity to elevated cell migration (P < 0.05) and osteo/odontogenic marker expression and mineralization nodule formation of SCAP compared with MTA groups (P < 0.05). Furthermore, the new continuous dentine layer and pulp-like tissue was observed in the iRoot BP Plus group in vivo. CONCLUSIONS: iRoot BP Plus showed excellent sealing ability, promoted the migration and osteo/odontogenesis of SCAP and induced pulp-dentin complex formation without affecting the cell proliferation, which indicated iRoot BP Plus was a promising coronal sealing material in REPs. CLINICAL RELEVANCE: The coronal sealing materials play crucial roles for the outcomes of REPs. This study showed that iRoot BP Plus has good coronal sealing and promote pulp-dentin complex formation compared with MTA, providing experimental evidences for the clinical application of iRoot BP Plus as a promising coronal seal material in REPs.

Cu-nanoparticles@ graphene nanocomposite: A robust and efficient nanocomposite for micro-solid phase extraction of trace aflatoxins in different foodstuffs.

Cu-nanoparticles-immobilized graphene (Cu@G) nanocomposite was fabricated in this study by reducing Cu(II) ions in the presence of graphene oxide using a simple chemical reduction step. Cu@G nanocomposite was applied as a sorbent for the SPE of four aflatoxins (AFs). A reusable syringe was filled with the fabricated nanocomposite and used as a sorbent for the micro-solid phase extraction of four AFs (AFB1, AFB2, AFG1, AFG2). The impact of different analytical factors was fully investigated and optimized. Excellent recoveries, ranging from 92.0 to 108.5 %, were detected when evaluating target AFs in samples of rice, maize, and pistachio. The LOD, LOQ, and linear ranges were attained under optimal circumstances in the ranges of 0.0062 µg kg-1, 0.0192 µg kg-1, and 0.0-20 µg kg-1, respectively. The discovered approach provided the dual benefits of a high enrichment capability of Cu-nanoparticles via AFs complexation and a huge porosity of graphene sheets.

Influence of myoglobin on the antibacterial activity of carvacrol and the binding mechanism between the two compounds.

BACKGROUND: Myoglobin (MB), a pigmentation protein, can adversely affect the antibacterial activity of carvacrol (CAR) and weaken its bacteriostasis effect. This study aimed to clarify the influence of MB on the antibacterial activity of CAR and ascertain the mechanism involved in the observed influence, especially the interaction between the two compounds. RESULTS: Microbiological analysis indicated that the presence of MB significantly suppressed the antibacterial activity of CAR against Listeria monocytogenes. Ultraviolet-visible spectrometry and fluorescence spectroscopic analysis confirmed the interaction between CAR and MB. The stoichiometric number was determined as ~0.7 via double logarithmic Stern-Volmer equation analysis, while thermodynamic analysis showed that the conjugation of the two compounds occurred as an exothermal reaction (ΔH° = -32.3 ± 11.4 kJ mol-1 and ΔS° = -75 J mol-1 K-1 ). Circular dichroism, Fourier transform infrared spectroscopy and nuclear magnetic resonance spectroscopy showed hydrogen bonding in the carvacrol-myoglobin complex (CAR-MB). Molecular docking analysis confirmed that amino acid residues, including GLY80 and HIS82, were most likely to form hydrogen bonds with CAR, while hydrogen bonds represented the main driving force for CAR-MB formation. CONCLUSION: CAR antibacterial activity was significantly inhibited by the presence of MB in the environment due to the notable reduction in the effective concentration of CAR caused by CAR-MB formation. © 2023 Society of Chemical Industry.