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In this work, we report an unexplored heterostructured catalyst consisting of Ni–Co-phosphate/sulphide phases (NCPSP) on carbon fibre paper through a single-step gas–solid reaction route for hydrogen evolution reaction (HER) in an acidic medium. The heterostructured electrode film of NCPSP depicted considerably enhanced electrochemical HER performance compared to the heterostructured controlled catalyst films consisting of Ni–Co-phosphide phases (NCPP), Ni–Co-sulphide phases (NCSP), and Ni–Co-phosphate/phosphide phases (NCPPP). Electrochemical and structural characterization reveals that superior catalytic credentials of NCPSP can be attributed to kinetically favourable H binding on the sulphur sites of transition metal (TM) sulphides and their beneficial heterostructure with TM phosphate component. Specifically, the minimum overpotential of 53 mV and 97 mV is observed for cathodic HER current of 10 mA cm−2 and 100 mA cm−2, respectively. The low Tafel slope of 43 mV dec−1 reveals the favourable Volmer–Heyrovsky mechanism. Also, superior kinetics was revealed by the low charge transfer resistance of 28 Ω. The catalytic credentials of NCPSP are also well in alignment with the highest values reported for the best state of art catalysts. [ABSTRACT FROM AUTHOR]

In this article, for the first time, we have reported a novel CHEF-PET fluorescence sensor L based on calix[4]arene containing four pyrene groups as binding sites, which is highly selective and sensitive towards Zn2+, Hg2+ and I−. This fluorescence probe was synthesized and characterized using the emission study, UV-vis titration, 1H NMR spectroscopy and ESI-MS investigation. The linear concentration range at pH 7 of L for Zn2+, Hg2+ and I− is 0–135 nM, 0–140 nM and 0–120 nM, respectively, with the detection limit of 6.43 nM for Zn2+, 2.94 nM for Hg2+ and 20.93 nM for I−. The binding ability was determined through Benesi–Hildebrand equation, which was found to be 7.535 × 108 M−1 for Zn2+, 9.001 × 108 M−1 for Hg2+ and 8.139 × 108 M−1 for I−. Further, we reported an easy-to-use, low-cost and disposable paper-based sensing device for the rapid chemical screening of Zn2+, Hg2+ and I−. The device comprises luminescent sensing probes embedded into a cellulose matrix, where the resonance energy transfer phenomenon seems to be the sensing mechanism. It opens up new opportunities for simple and fast screening in remote settings, where sophisticated instrumentation is not always available. The MOPAC-2016 software package was used to optimize the L using the well-established PM7 method and calculate the HOMO–LUMO energy band gap for structure L and L with Zn2+, Hg2+ and I− ion-based structures. The molecular docking study was carried out using HEX software. [ABSTRACT FROM AUTHOR]

Further studies have been performed to define the kinetic characteristics of nuclear triiodothyronine (T(3)) binding sites in rat liver (J. Clin. Endocrinol. Metab. 1972. 35: 330). Sequential determination of labeled T(3) associated with nuclei and cytoplasm over a 4-h period allowed analysis of the relationship of T(3) in nuclear and cytoplasmic compartments. A rapid interchange of hormone between nuclei and cytoplasm was demonstrated, and in vitro incubation experiments with nuclei yielded no evidence favoring metabolic transformation of T(3) by the nuclei. In vivo displacement experiments were performed by subcellular fractionation of liver (1/2) h after injection of [(125)I]T(3) with increasing quantities of unlabeled T(3). The nuclear binding capacity for T(3) could be defined (0.52 ng/mg DNA). Analysis of these experiments also allowed an estimation of the association constant of nuclear sites for T(3) (4.7 x 10(11)M(-1)). The affinity of these sites for T(3) was estimated to be 20-40 fold greater than for thyroxine (T(4)). Chromatographic analysis of the nuclear radioactivity after injection of labeled T(4) indicated that the binding of T(4) by the nucleus could not be attributed to in vivo conversion of T(4) to T(3) but reflected intrinsic cross-reactivity of the two iodothyronines at the nuclear binding sites.

The lysogenization of Pseudomonas aeruginosa strain BI with phage 2 resulted in the loss of the capacity to adsorb the same phage. The absence of phage 2 receptors on the surface of the lysogenized strain BI(2)(8) was confirmed by the failure of purified slime polysaccharide (SPB) or lipopolysaccharide (LPS) to inactivate phage 2. SPB and LPS from a phage 2-resistant strain also failed to inactivate phage 2 in contrast to the phage inactivation exhibited by the SPB and LPS obtained from the wild-type strain BI. Chemically, quantitative differences were apparent when the SPB and LPS of strains BI(2)(8) and BI/2S(2) were compared with those of the wild-type strain BI. The most striking difference noted was the absence of amino sugars in the SPB of strain BI/2S(2). The SPB of strain BI(2)(8) also contained a lower percentage of amino sugars compared with the SPB of the wild-type strain BI.

Bacteriophage-resistant strains of Staphylococcus aureus H were isolated after mutagenesis with N-methyl-N'-nitro-N-nitrosoguanidine. Cell walls isolated from about half of these resistant strains were incapable of inactivating phages and were shown to lack N-acetyl-d-glucosamine (GlcNAc) in their cell wall teichoic acid. Apart from the lack of GlcNAc, two of these mutant strains were deficient in cell wall phosphorus and ester-linked d-alanine. These two strains were also found to be resistant to both phage K and a host-range mutant isolated from the parent phage. These two phages could lyse the other phage-resistant mutants which lacked GlcNAc in their teichoic acid. Cell walls from the remaining phage-resistant mutant strains did inactivate phages and were found to have normal cell wall teichoic acid. Although GlcNAc in teichoic acid was required for phage inactivation, no difference in phage inactivation ability was detected with cell walls isolated from strains of S. aureus having exclusively alpha- or exclusively beta-linked GlcNAc in their cell wall teichoic acid.

Under restricted culture conditions, the growth and division of Saccharomyces cerevisiae was inhibited by the antimitotic drug Colcemid; in contrast, the related drug colchicine had no effect. The difference in the sensitivity of yeast to these two agents was not dependent on their ability to permeate the cell but rather reflected an inherent difference in the affinity of the two drugs for a cellular-binding site. The binding moiety was characterized by gel filtration as a macromolecule of approximately 110,000 mol wt with an affinity constant for Colcemid of 0.5 x 10(4) liters per mole; in addition, this macromolecule was retained by diethylaminoethyl (DEAE) ion exchangers. On the basis of these properties, the Colcemid-binding substance in S. cerevisiae cells was provisionally identified as microtubule subunits.

Pepsin reacts stoicheiometrically with the active-site-directed irreversible inhibitor N-diazoacetyl-l-phenylalanine methyl ester, with concomitant loss of all proteolytic and peptidolytic activity. The reagent esterifies a unique aspartic acid residue in pepsin, which is in the sequence:Ile-Val-Asp-Thr-Gly-Thr-Ser

This report demonstrates that the chick oviduct, a specific target organ for progesterone, contains both cytoplasmic and nuclear macromolecules which bind progestins. These binding molecules can be clearly distinguished from transcortin by centrifugation through sucrose gradients of low ionic strength and by agarose gel filtration. The cytoplasmic progesterone-binding molecules also bind 5-alpha-pregnane-3,20-dione, but have significantly lower affinity for cortisol, estrone, or aldosterone. They are absent from blood and nontarget organs such as lung and spleen. The tissue-specific binding components appear to be heat-labile proteins with an average dissociation constant for progesterone of about 8 x 10(-10) M at 2 degrees C. These results are consistent with the identification of the progesterone-binding molecules as the functional hormone receptors. In further support of this concept is the finding that treatment of the chicks with estrogen coordinately induces a 20-fold increase in the number of progesterone-binding molecules and enhances the capacity of progesterone to induce avidin synthesis.A progesterone-"receptor" complex can be detected in both the cytoplasm and nuclei of oviduct tissue after an injection of [(3)H]progesterone to estrogen-treated chicks. By contrast, incubation of oviduct tissue with [(3)H]progesterone in vitro at 2 degrees C for 5 min leads to labeling of the cytoplasmic "receptor" only. Transfer of the "receptor"-steroid complex into the nucleus then appears to occur upon subsequent incubation in vitro at 37 degrees C. This observation suggests that the transfer of bound progesterone across the nuclear membrane may be an energy-requiring enzymatic process.

To acquire extremely thermostable proteins of given functions is challenging for conventional protein engineering. Here we applied ABACUS, a statistical energy function we developed for de novo amino acid sequence design, to globally redesign a Ras-binding domain (RBD), and obtained an extremely thermostable RBD that unfolds reversibly at above 110°C, the redesigned RBD experimentally confirmed to have expected structure and Ras-binding interface. Directed evolution of the redesigned RBD improved its Ras-binding affinity to the native protein level without excessive loss of thermostability. The designed amino acid substitutions were mostly at the protein surface. For many substitutions, strong epistasis or significantly differentiated effects on thermostability in the native sequence context relative to the redesigned sequence context were observed, suggesting the globally redesigned sequence to be unreachable through combining beneficial mutations of the native sequence. Further analyses revealed that by replacing 38 of a total of 48 non-interfacial surface residues at once, ABACUS redesign was able to globally "invert" the protein's charge distribution pattern in an optimized way. Our study demonstrates that computational protein design provides powerful new tools to solve challenging protein engineering problems., (© 2021 Wiley Periodicals LLC.)

In recent decades, the effect of heavy metal pollution on the enzyme activity of plant rhizosphere soil has gained extensive attention. Through literature review, this paper systematically summarized the research status and recent progress on the response of rhizosphere soil enzyme activities to heavy metal pollution, and the main mechanisms were also discussed. Review on the mechanism of plant rhizosphere soil enzyme response to heavy metal pollution. [Extracted from the article]

Proteins that have a histidine triad in their active sites belong to the HIT-protein superfamily. They are ubiquitous, are involved in the metabolism of different nucleotides and catalyze their hydrolysis and/or phosphorolysis liberating either the corresponding 5′-NMP or 5′-NDP, respectively. We studied substrate specificity of nine recombinant HIT-proteins with adenosine 5′-phosphosulfate (1), adenosine 5′-phosphoramidate (2), adenosine 5′-phosphorothioate (3), adenosine 5′-phosphorofluoride (4), diadenosine 5′,5′′′-P1,P3-triphosphate (5), di(7-methylguanosine) 5′,5′′′-P1,P3-triphosphate (6) and adenosine 5′-hypophosphate (7). Preferences for the recognition of these compounds as substrates by individual proteins differed. All the proteins hydrolyzed (1) but the Arabidopsis thalianaHint1 did it very slowly. None of the proteins cleaved (7). Only A. thalianaHint1 and Escherichia coliHinT hydrolyzed (3). Three proteins known as dinucleoside triphosphatases, human and A. thalianaFhit-proteins and Trypanosoma bruceiHIT-45, cleaved (1), (2), (4), (5) and (6). Caenorhabditis elegansdecapping protein DcpS degraded (1), (5), (6) and poorly (4). A. thalianaaprataxin-like protein and Hint4 hydrolyzed only (1), (2) and (4), in that order of efficiency. Velocities of those reactions and some Kmvalues were determined. Applicability of this study to the metabolism of certain nucleotidyl-derivatives is discussed. [ABSTRACT FROM AUTHOR]

The aim of our study was to obtain new details on the role of phosphate residues in antigenomic hepatitis delta virus (HDV) ribozyme for the development of metal ion binding sites and their participation in the cleavage mechanism. In these studies, the wild-type ribozyme and four in vitroselected variants, R37, R20, R25 and R51, were used. The application of nucleotide phosphorothioates and the NAIM (nucleotide analog interference mapping) technique for the cis-acting ribozymes, wild-type, R25 and R51, revealed the importance of the J4/2 and P1.1 regions in the catalysis. Interestingly, in the wild-type ribozyme, the largest interference effects were observed close to catalytic C76 in the presence of Ca2+, while in the case of Mg2+were in the structurally important helix P1.1. The results obtained for R25 and R51 suggest different coordination of the divalent ions to the phosphate residues within the ribozyme catalytic core. Additionally, replacing the non-bridging oxygen atoms on sulfur in a phosphate group at the cleavage site in trans-acting ribozyme variants showed that interactions between pro-RPand pro-SPoxygen atoms, and catalytic metal ions, had moderate effects on the cleavage reaction. In the wild-type ribozyme, the ratio of SP/RPisomer cleavage rates decreased from 25 for Mg2+-induced cleavage to ca.4 when thiophilic Mn2+or Cd2+were added; thus a “rescue effect” was observed. Interestingly, the R37, R20, R25 and R51 ribozymes showed a reduced RP/SPratio of cleavage rates and much smaller “rescue effects”. This suggests that the binding of divalent metal ions in the vicinity of the phosphate group at the cleavage site is very sensitive to the overall ribozyme structure. [ABSTRACT FROM AUTHOR]

A novel cellulose microfibril swelling (Cms) gene of Bacillus sp. AY8 was successfully cloned and sequenced using a set of primers designed based on the conserved region of the gene from the genomic database. The molecular cloning of the Cms gene revealed that the gene consisted of 679 bp sequences encoding 225 amino acids. Further in silico analysis unveiled that the Cms gene contained the NlpC/P60 conserved region that exhibited a homology of 98% with the NlpC/P60 family proteins found in both the strains, Burkholderialata sp. and Burkholderia vietnamiensis. The recombinant Cms enzyme had a significant impact on the reduction of crystallinity indices (CrI) of various substrates including a 3%, a 3.97%, a 4.66%, and a substantial 14.07% for filter paper, defatted cotton fiber, avicel, and alpha cellulose, respectively. Additionally, notable changes in the spectral features were observed among the substrates treated with recombinant Cms enzymes compared to the untreated control. Specifically, there was a decrease in band intensities within the spectral regions of 3000–3450 cm−1, 2900 cm−1, 1429 cm−1, and 1371 cm−1 for the treated filter paper, cotton fiber, avicel, and alpha cellulose, respectively. Furthermore, the recombinant Cms enzyme exhibited a maximum cellulose swelling activity at a pH of 7.0 along with a temperature of 40 °C. The molecular docking data revealed that ligand molecules, such as cellobiose, dextrin, maltose 1-phosphate, and feruloyated xyloglucan, effectively bonded to the active site of the Cms enzyme. The molecular dynamics simulations of the Cms enzyme displayed stable interactions with cellobiose and dextrin molecules up to 100 ns. It is noteworthy to mention that the conserved region of the Cms enzyme did not match with those of the bioadditives like expansins and swollenin proteins. This study is the initial report of a bacterial cellulose microfibril swellase enzyme, which could potentially serve as an additive to enhance biofuel production by releasing fermentable sugars from cellulose. [ABSTRACT FROM AUTHOR]

Protein and nucleic acid binding site prediction is a critical computational task that benefits a wide range of biological processes. Previous studies have shown that feature selection holds particular significance for this prediction task, making the generation of more discriminative features a key area of interest for many researchers. Recent progress has shown the power of protein language models in handling protein sequences, in leveraging the strengths of attention networks, and in successful applications to tasks such as protein structure prediction. This naturally raises the question of the applicability of protein language models in predicting protein and nucleic acid binding sites. Various approaches have explored this potential. This paper first describes the development of protein language models. Then, a systematic review of the latest methods for predicting protein and nucleic acid binding sites is conducted by covering benchmark sets, feature generation methods, performance comparisons, and feature ablation studies. These comparisons demonstrate the importance of protein language models for the prediction task. Finally, the paper discusses the challenges of protein and nucleic acid binding site prediction and proposes possible research directions and future trends. The purpose of this survey is to furnish researchers with actionable suggestions for comprehending the methodologies used in predicting protein–nucleic acid binding sites, fostering the creation of protein-centric language models, and tackling real-world obstacles encountered in this field. [ABSTRACT FROM AUTHOR]

Schiefer and Winfree recently introduced the chemical reaction network-controlled tile assembly model (CRN-TAM), a variant of the abstract tile assembly model (aTAM). In the CRN-TAM, tile reactions are mediated via non-local chemical signals controlled by a chemical reaction network. This paper introduces ALCH, an imperative programming language for specifying CRN-TAM programs that can be compiled and simulated. ALCH includes standard language features such as Boolean variables, conditionals, loops, and CRN-TAM-specific constructs such as adding and removing tiles. ALCH also includes the branch and parallel structures which harness the nondeterministic and parallel nature of the CRN-TAM. ALCH also supports functional tileset specification. Using ALCH, we show that the discrete Sierpinski triangle and the discrete Sierpinski carpet can be strictly self-assembled in the CRN-TAM, which shows the CRN-TAM can self-assemble infinite shapes at scale 1 that the aTAM cannot. ALCH allows us to present these constructions at a high level, abstracting species and reactions into C-like code that is simpler to understand. We employ two new CRN-TAM techniques in our constructions. First, we use ALCH's nondeterministic branching feature to probe previously placed tiles of the assembly and detect the presence and absence of tiles. Second, we use scaffolding tiles to precisely control tile placement by occluding any undesired binding sites. This paper is an extension of our previous work, updated to include a Sierpinski carpet construction and the parallel command. [ABSTRACT FROM AUTHOR]