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DNA polymerase λ (Polλ) belongs to the same structural X-family as DNA polymerase β, the main polymerase of base excision repair. The role of Polλ in this process remains not fully understood. A significant difference between the two DNA polymerases is the presence of an extended non-catalytic N-terminal region in the Polλ structure. The influence of this region on the interaction of Polλ with DNA and multifunctional proteins, poly(ADP-ribose)polymerase 1 (PARP1) and replication protein A (RPA), was studied in detail for the first time. The data obtained suggest that non-catalytic Polλ domains play a suppressor role both in relation to the polymerase activity of the enzyme and in interaction with DNA and PARP1. [ABSTRACT FROM AUTHOR]

Glucose oxidase (GOD) is an oxidoreductase that catalyzes the aerobic oxidation of glucose into hydrogen peroxide (H2O2) and gluconic acid, which has been widely used in industrial raw materials production, biosensors and cancer treatment. However, natural GOD bears intrinsic disadvantages, such as poor stability and a complex purification process, which undoubtedly restricts its biomedical applications. Fortunately, several artificial nanomaterials have been recently discovered with a GOD-like activity and their catalytic efficiency toward glucose oxidation can be finely optimized for diverse biomedical applications in biosensing and disease treatments. In view of the notable progress of GOD-mimicking nanozymes, this review systematically summarizes the representative GOD-mimicking nanomaterials for the first time and depicts their proposed catalytic mechanisms. We then introduce the efficient modulation strategy to improve the catalytic activity of existing GOD-mimicking nanomaterials. Finally, the potential biomedical applications in glucose detection, DNA bioanalysis and cancer treatment are highlighted. We believe that the development of nanomaterials with a GOD-like activity will expand the application range of GOD-based systems and lead to new opportunities of GOD-mimicking nanomaterials for various biomedical applications. [ABSTRACT FROM AUTHOR]

Nanozymes have been viewed a kind of emerging nanomaterials with enzyme-mimicking catalytic activity, which have the advantage of low cost and good robustness. However, the complex nano-effect and surface interface effect of nanozymes hinder the in-depth understanding of their enzyme-like catalytic activities and the development of highly active nanozymes to some extent. To date, metal-organic frameworks (MOFs)-based nanozymes have been widely exploited due to the unique structural characteristics and customizability, which can mimic the active center and hydrophobic domain of natural enzymes, providing great opportunities in rationally developing MOFs with enhanced catalytic activity. Herein, we systematically summarize the activity regulatory strategies of MOFs-based nanozymes and their applications in biosensing. Firstly, the engineering design strategies containing modulation of metal node, ligand, defect, morphology, and topology are introduced. Then, the distinctive applications of MOFs-based nanozymes in biosensing are also discussed. At the end, the recent challenges and progressive directions are tentatively proposed. [Display omitted] • Engineering MOFs-based nanozymes for enhanced biosensing. • The de novo design of MOFs-based nanozymes. • Activity regulatory strategies of MOFs-based nanozymes. • The current challenges and future prospects of MOFs-based nanozymes. [ABSTRACT FROM AUTHOR]

Nanozymes are nanomaterials that exhibited high enzymatic activities and considered as a better alternative to natural enzymes. These nanoparticles are characterized by unique properties such as high catalytic activity with high stability, easy and low cost preparation. The multi-functional feature of nanozymes enables them to be applied in a wide range of applications such as biosensing, immunoassays, diseases diagnosis and therapeutics as well environmental management. In this context, this review provides a comprehensive overview about these nanoparticles, especially their types, preparation, characterization and enzymatic activities. In addition, some of their potential applications in the biocontrol of multi-drug resistant bacteria, medical field as well as environmental pollutants detection and removal have been highlighted. Nanozymes with both unique physicochemical properties of nanoparticles and enzyme-mimicking catalytic properties will attract a broad interest of scientists and offer promising strategies for diagnosis and treatment of many diseases and handling current environmental problems. [ABSTRACT FROM AUTHOR]

• Bionic modulation of catalytic activity of MOF nanozymes via a facile approach. • Increasing the amount of histidine modification to enhance the catalytic activity. • The established structure-activity of MOF nanozyme can direct practical sensing. • Pesticide detection by the sensor arrays is highly discriminatory and quantitative. Biosensors provide simple, rapid and sensitive detection of a wide range of analytes. Recently, they have been widely used for the rapid detection of pesticides, which makes up for the shortcomings of traditional detection methods. However, the catalytic activity of some nanozymes is not satisfactory in practical applications, limiting the performance of biosensors. Further development of highly active and stable nanozymes is conducive to improving the sensitivity of the sensors and expanding their application in practical detection. Herein we simulated the amino acid microenvironment of natural enzymes and synthesized His-MIL-101(Fe)-X with different histidine (His) modification amounts (X = 0, 25%, 50%, 75%) by regulating the ratio of histidine and terephthalic acid ligands using a one-step solvothermal method. With increasing histidine doping, the peroxidase-like activity of His-MIL-101(Fe)-X was gradually enhanced, and the sensing performance of the sensor arrays constructed by combining His-MIL-101(Fe)-X with three peroxidase substrates was also gradually improved, with a 25-fold increase in detection limit. The His-MIL-101(Fe)-75% sensor array was not only able to accurately discriminate five pesticides in the range of 2-100 μM, but also to quantitatively identify different concentrations of pesticides. Moreover, the His-MIL-101(Fe)-75% sensor array showed good anti-interference capability and was able to discriminate five pesticides at only 2 μM in soil, lake water, seawater, and apple samples, as well as quantitatively detecting diafenthiuron, which has great potential for practical application. [ABSTRACT FROM AUTHOR]

Patients with chronic fatigue receive advice to improve symptom management and well-being. This advice is based on ideas of self-management and is conveyed during clinical assessment as "activity regulation." Based on ethnographic fieldwork in a hospital clinic in Norway, we show how these patients attempt to demonstrate their competences and everyday concerns, and how the ideology of self-management frames the hope for recovery and crafts a subject with the ability to improve. Patients, however, linger between everyday social predicaments and ideals of healthy living, and are caught up in cultural models of care that deflect everyday concerns and agency. [ABSTRACT FROM AUTHOR]

Glutamate dehydrogenase (GDH) is an important enzyme in ammonium metabolism, the activity of which is regulated by multiple factors. In this study, we investigate the effects of ammonium and potassium on the activity of maize GDH. Our results show that both ammonium and potassium play multiple roles in regulating the activity of maize GDH, with the specific roles depending on the concentration of potassium. Together with the structural information of GDH, we propose models for the substrate inhibition of ammonium, and the elimination of substrate inhibition by potassium. These models are supported by the analysis of statistic thermodynamics. We also analyze the binding sites of ammonium and potassium on maize GDH, and the conformational changes of maize GDH. The findings provide insight into the regulation of maize GDH activity by ammonium and potassium and reveal the importance of the dose and ratio of nitrogen and potassium in crop cultivation. [ABSTRACT FROM AUTHOR]

DesK is a Bacillus thermosensor kinase that is inactive at high temperatures but turns activated when the temperature drops below 25 °C. Surprisingly, the catalytic domain (DesKC) lacking the transmembrane region is more active at higher temperature, showing an inverted regulation regarding DesK. How does the transmembrane region control the catalytic domain, repressing activity at high temperatures, but allowing activation at lower temperatures? By designing a set of temperature minimized sensors that share the same catalytic cytoplasmic domain but differ in number and position of hydrogen-bond (H-bond) forming residues along the transmembrane helix, we are able to tune, invert or disconnect activity from the input signal. By favoring differential H-bond networks, the activation peak could be moved towards lower or higher temperatures. This principle may be involved in regulation of other sensors as environmental physicochemical changes or mutations that modify the transmembrane H-bond pattern can tilt the equilibrium favoring alternative conformations. [ABSTRACT FROM AUTHOR]

Nucleotide excision repair (NER) is one of the major DNA repair pathways aimed at maintaining genome stability. Correction of DNA damage by the NER system is a multistage process that proceeds with the formation of multiple DNA-protein and protein-protein intermediate complexes and requires precise coordination and regulation. NER proteins undergo post-translational modifications, such as ubiquitination, sumoylation, phosphorylation, acetylation, and poly(ADP-ribosyl)ation. These modifications affect the interaction of NER factors with DNA and other proteins and thus regulate either their recruitment into the complexes or dissociation from these complexes at certain stages of DNA repair, as well as modulate the functional activity of NER proteins and control the process of DNA repair in general. Here, we review the data on the post-translational modifications of NER factors and their effects on DNA repair. Protein poly(ADP-ribosyl)ation catalyzed by poly(ADP-ribose) polymerase 1 and its impact on NER are discussed in detail, since such analysis has not been done before. [ABSTRACT FROM AUTHOR]

Fungal lipases are efficient and environment‐friendly biocatalysts for many industrially relevant processes. One of the most widely applied lipases in the manufacturing industry is Candida antarctica lipase B (CALB). Here, we report the biochemical and structural characterization of a novel CALB‐like lipase from an important human pathogen—Aspergillus fumigatus (AFLB), which has high sn‐1,3‐specificity toward triolein. AFLB crystal structure displays a CALB‐like catalytic domain and hosts a unique tightly closed 'lid' domain that contains a disulfide bridge, as well as an extra N‐terminal subdomain composed of residues 1–128 (including the helix α1–α5 located above the active site). To gain insight into the function of this novel lid and N‐terminal subdomain, we constructed and characterized a series of mutants in these two domains. Deleting the protruding bulk lid's residues, replacing the bulk and tight lid with a small and loose lid from CALB, or breaking the disulfide bridge increased the affinity of CALB for glyceride substrates and improved its catalytic activity, along with the loss of enzyme fold stability and thermostability. N‐terminal truncation mutants revealed that the N‐terminal peptide (residues 1–59) is a strong inhibitor of AFLB binding to lipid films. This peptide thus limits AFLB's penetration power and specific activity, revealing a unique enzyme activity regulatory mechanism. Our findings on the functional and structural properties of AFLB provide a better understanding of the functions of the CALB‐like lipases and pave the way for its future protein engineering. Database: Structural data are available in the Protein Data Bank under the accession numbers 6IDY. [ABSTRACT FROM AUTHOR]

Multi‐step biocatalytic reactions have gained increasing importance in recent years because the combination of different enzymes enables the synthesis of a broad variety of industrially relevant products. However, the more enzymes combined, the more crucial it is to avoid cross‐reactivity in these cascade reactions and thus achieve high product yields and high purities. The selective control of enzyme activity, i.e. remote on‐/off‐switching of enzymes, might be a suitable tool to avoid the formation of unwanted by‐products in multi‐enzyme reactions. This review compiles a range of methods that are known to modulate enzyme activity in a stimulus‐responsive manner. It focuses predominantly on in vitro systems and is subdivided into reversible and irreversible enzyme activity control. Furthermore, a discussion section provides indications as to which factors should be considered when designing and choosing activity control systems for biocatalysis. Finally, an outlook is given regarding the future prospects of the field. [ABSTRACT FROM AUTHOR]

Abstract As alkaline phosphatase (ALP) plays crucial roles in disease warning and dephosphorylation-related cellular regulation, it is widely recognized as an important biomarker for clinical diagnosis. In this work, we proposed a facile colorimetric assay based on phosphate anion-quenched oxidase-mimicking activity of Ce(Ⅳ) ions for sensitive and selective detection of ALP activity. Free Ce(Ⅳ) ions exhibited a strong oxidase-like capability (providing a 40-fold catalytic turnover number compared with CeO 2) to catalyze the oxidation of colorless 3,3′,5,5′-tetramethylbenzidine (TMB) into its blue product TMBox mediated by dissolved O 2 at neutral pH, thus triggering a remarkable color reaction visually. When PO 4 3− was added, its strong affinity to Ce(Ⅳ) ions rapidly precipitated the free Ce(Ⅳ) ions, resulting in the quenching of their enzymatic ability. Given that ALP catalyzed the hydrolysis of adenosine triphosphate to produce PO 4 3−, determination of ALP activity could be achieved using the colorimetric assay with no need of complicated instrumentation and protocol. As demonstrated, our assay offered a highly sensitive readout for ALP activity in two linear scopes of 0–50 U L−1 and 50–250 U L−1, providing a detection limit down to 2.3 U L−1. Besides, it could provide specific response toward ALP against other enzymes and biological species. Furthermore, the developed assay was successfully applied to evaluate ALP activity in human plasma accurately and reliably, indicating its great promise as a powerful and convenient tool for monitoring of ALP activity in clinical practice. Graphical abstract Image 1 Highlights • Free Ce(Ⅳ) ions act as a potential oxidase mimic. • The homogeneous nature makes Ce(Ⅳ) ions have high oxidase-like activity. • PO 4 3− can quench the catalytic activity of Ce(Ⅳ) ions by forming precipitates. • A colorimetric assay of ALP activity is developed based on the above principle. [ABSTRACT FROM AUTHOR]

In this work, we proposed a new and facile strategy for the high-performance colorimetric detection of Ag + based on the tunable peroxidase-like activity of Pd nanoparticles (NPs) mediated by histidine (His). Bare Pd NPs possess intrinsic catalytic ability to trigger the oxidation of colorless 3,3′,5,5′-tetramethylbenzidine (TMB) to blue TMBox in the presence of H 2 O 2 . After being decorated by His, the formed His-Pd nanozyme exhibits significantly improved mimetic activity due to its favorable physicochemical characteristics including smaller size, interactions between Pd and His, and better hydrophilicity, and such that an enhanced TMB color reaction is observed. When Ag + exists, it is able to despoil the His modifier from the His-Pd surface via the specific interaction between Ag + and His, resulting in the bald Pd again with weak activity. With this principle, highly sensitive determination of Ag + in a linear scope of 30–300 nM was achieved with a limit of detection down to 4.7 nM. In addition, the colorimetric sensor based on the tunable enzymatic activity of nanosized Pd adjusted by His could provide excellent selectivity for Ag + sensing against common interferents. Reliability of the strategy for practical detection of Ag + was also demonstrated. [ABSTRACT FROM AUTHOR]

Abstract It has been postulated that gaining control over activity in the dorsolateral prefrontal cortex (DLPFC), a key region of the working memory brain network, may be beneficial for cognitive performance and treatment of certain psychiatric disorders. Several studies have reported that, with neurofeedback training, subjects can learn to increase DLPFC activity. However, improvement of dynamic control in terms of switching between low and high activity in DLPFC brain states may potentially constitute more effective self-regulation. Here, we report on feasibility of obtaining dynamic control over DLPFC, meaning the ability to both in- and decrease activity at will, within a single functional MRI scan session. Two groups of healthy volunteers (N = 24) were asked to increase and decrease activity in the left DLPFC as often as possible during fMRI scans (at 7 Tesla), while receiving real-time visual feedback. The experimental group practiced with real-time feedback, whereas the control group received sham feedback. The experimental group significantly increased the speed of intentionally alternating DLPFC activity, while performance of the control group did not change. Analysis of the characteristics of the BOLD signal during successful trials revealed that training with neurofeedback predominantly reduced the time for the DLPFC to return to baseline after activation. These results provide a preliminary indication that people may be able to learn to dynamically down-regulate the level of physiological activity in the DLPFC, and may have implications for psychiatric disorders where DLPFC plays a role. [ABSTRACT FROM AUTHOR]

Ubiquitination, the covalent attachment of ubiquitin to proteins, by E3 ligases of the HECT (homologous to E6AP C terminus) family is critical in controlling diverse physiological pathways. Stringent control of HECT E3 ligase activity and substrate specificity is essential for cellular health, whereas deregulation of HECT E3s plays a prominent role in disease. The cell employs a wide variety of regulatory mechanisms to control HECT E3 activity and substrate specificity. Here, we summarize the current understanding of these regulatory mechanisms that control HECT E3 function. Substrate specificity is generally determined by interactions of adaptor proteins with domains in the N-terminal extensions of HECT E3 ligases. These N-terminal domains have also been found to interact with the HECT domain, resulting in the formation of inhibitory conformations. In addition, catalytic activity of the HECT domain is commonly regulated at the level of E2 recruitment and through HECT E3 oligomerization. The previously mentioned regulatory mechanisms can be controlled through protein-protein interactions, post-translational modifications, the binding of calcium ions, and more. Functional activity is determined not only by substrate recruitment and catalytic activity, but also by the type of ubiquitin polymers catalyzed to the substrate. While this is often determined by the specific HECT member, recent studies demonstrate that HECT E3s can be modulated to alter the type of ubiquitin polymers they catalyze. Insight into these diverse regulatory mechanisms that control HECT E3 activity may open up new avenues for therapeutic strategies aimed at inhibition or enhancement of HECT E3 function in disease-related pathways. [ABSTRACT FROM AUTHOR]

FOX family is a highly conserved transcription factor in structure, its function and molecular mechanism has gradually become a hot topic in the field of immunology, genetics, medicine and oncology. FOX transcription factor family has 19 subfamilies. FOXOs are important members of the FOX family, which contain FOXO1, FOXO3a, FOXO4 and FOXO6. These transcription factors respectively express in different tissues and organs. FOXOs are closely related with cell development and metabolism, participating in many cellular physiological processes such as oxidative stress, DNA repair, cell cycle regulation, cell apoptosis and autophagy. FOXOs also play a key role in the development of cancer, osteoporosis, cardiovascular disease, nerve tissue degradation and many other age-related diseases. The study of their function and molecular regulation mechanism can provide new ideas for the prevention and treatment of age-related diseases. In this review, we will discuss the recent advances in the researches of transcription factors FOXOs and their activity regulation, cell oxidative stress, cell cycle and apoptosis. [ABSTRACT FROM AUTHOR]

• Bifunctional catalyst was fabricated by compositing N-doped carbon with FeCo species. • Biomass potato was utilized as sustainable material. • OER performance was positively regulated by Co(OH) 2. • The catalyst exhibits satisfactory activity to ORR and OER. An N-doped carbon-based bifunctional catalyst (Po-FeCo-N-C) is prepared. Biomass potato is utilized a sustainable material and the OER performance of the catalyst is positively regulated. Potato is carbonized to N-doped carbon nanoparticles with the facilitation of carbon black to anchor more nitrogen, generating pyridinic N and graphitic N dominated ORR active sites. The Po-FeCo-N-C with 3:1 of Fe/Co ratio exhibits 0.830 V of ORR half wave potential and 5.19 mA cm−2 of current density in 0.1 M KOH. Meanwhile, 85 mV of improvement on OER potential is achieved with regulation of Co(OH) 2 , demonstrating the remarkably bifunctional catalytic activity. The rechargeable zinc-air battery of Po-FeCo-N-C outputs higher open circuit voltage, and delivers higher specific capacities, larger power densities and excellent cyclic durability. This work provides a feasible method for the preparation of nonprecious metal-based bifunctional catalyst to ORR and OER from sustainable biomass material with low cost and wide resources. [ABSTRACT FROM AUTHOR]

Casein kinase CK2 is a highly conserved serine/threonine protein kinase and exists in all eukaryotes. It has been demonstrated to be widely involved in the biological processes of plants. The CK2 holoenzyme is a heterotetramer consisting of two catalytic subunits (α and/or α′) and two regulatory subunits (β). CK2 in plants is generally encoded by multiple genes, with monomeric and oligomeric forms present in the tissue. Various subunit genes of CK2 have been cloned and characterized from Arabidopsis thaliana , tobacco, maize, wheat, tomato, and other plants. This paper reviews the structural features of CK2, provides a clear classification of its physiological functions and mechanisms of action, and elaborates on the regulation of CK2 activity to provide a knowledge base for subsequent studies of CK2 in plants. [ABSTRACT FROM AUTHOR]

Phage-encoded cell wall peptidoglycan hydrolyzing enzymes, called endolysins, are essential for efficient release of virions from bacteria, and show species-specific killing of the host. We have demonstrated previously that the interaction between N-terminal catalytic and C-terminal cell wall binding domains of mycobacteriophage D29 endolysin makes the enzyme inactive in Escherichia coli . Here, we demonstrate that such interaction occurs intramolecularly and is facilitated by a charged linker that connects the two domains. We also show that linker composition is crucial for the inactivation of PG hydrolase in E. coli . Such knowledge will immensely help in bioengineering of endolysins with narrow or broad spectrum antimicrobial activity. [ABSTRACT FROM AUTHOR]

To identify and isolate genes related to abiotic stress (salinity and drought) tolerance in grapevine, a candidate gene approach led to the isolation from Cabernet Sauvignon cultivar of a full-length cDNA of dehydrin gene. he latter, named VvDhn, which is highly and mainly induced in late embryogenesis in seeds, encodes for a protein of 124 amino acids with a predicted molecular mass of 13.3 kDa. Details of the physicochemical parameters and structural properties (molecular mass, secondary structure, conserved domains and motives, and putative posttranslational modification sites) of the encoded protein have also been elucidated. he expression study of VvDhn was carried out within plant organs and tissues as well as under drought and salt stresses. VvDhn was not detected in vegetative tissue, whereas it was only expressed during seed development (during late embryogenesis) at extremely high levels and was induced by salt and drought stresses as well as ABA application. Moreover, salt stress induced VvDhn expression in the tolerant variety (Razegui) but not the sensitive variety (Syrah), which did not display expression variation during stress; VvDhn expression level and salt-stress response depend on regulatory mechanisms that are efficient only in the tolerant variety. On the other hand, under drought stress VvDhn was induced in both tolerant and sensitive varieties, with higher levels in the tolerant variety. In addition, stress signal molecules such as ABA (applied alone or in combination with saccharose) induced VvDhn expression, even at low levels. Minimal knowledge about the role and functionality of this gene is necessary and constitutes a prerequisite for including VvDhn in grapevine abiotic stress tolerance improvement programs. [ABSTRACT FROM AUTHOR]

N-Acetyl-β-d-glucosaminidase (NAGase) is proved to be correlated with reproduction of male animals. In this study, enzymatic characterizations of NAGase from spermary of Nile tilapia (Oreochromis niloticus) were investigated in order to further study its reproductive function in fish. Tilapia NAGase was purified to be PAGE homogeneous by the following techniques: (NH4)2SO4 fractionation (40–55%), DEAE-cellulose (DE-32) ion exchange chromatography, Sephadex G-200 gel filtration and DEAE-Sephadex (A-50). The specific activity of the purified enzyme was 4100 U/mg. The enzyme molecular weight was estimated as 118.0 kD. Kinetic studies showed that the hydrolysis of p-nitrophenyl-N-acetyl-β-d-glucosaminide (pNP-NAG) by the enzyme followed Michaelis–Menten kinetics. The Michaelis–Menten constant (K m) and maximum velocity (V m) were determined to be 0.67 mM and 23.26 μM/min, respectively. The optimum pH and optimum temperature of the enzyme for hydrolysis of pNP-NAG was to be at pH 5.7 and 55°C, respectively. The enzyme was stable in a pH range from 3.3 to 8.1 at 37°C, and inactive at temperature above 45°C. The enzyme activity was regulated by the following ions in decreasing order: Hg2+ > Zn2+ > Cu2+ > Pb2+ > Mn2+. The IC 50 of Cu2+, Zn2+ and Hg2+ was 1.23, 0.28, and 0.0027 mM, respectively. However, the ions Li+, Na+, K+, Mg2+ and Ca2+ had almost no influence on enzyme activity. In conclusion, the enzymatic characterizations of NAGase from tilapia were special to the other animals, which were correlated with its living habit; besides, CuSO4 and ZnSO4 should used very carefully as insecticides in tilapia cultivation since they both had strong regulations on the enzyme. [ABSTRACT FROM AUTHOR]

Nek2A is an essential component of cell cycle progression. It regulates the reorganization of the microtubule network at the G2/M transition and controls the centriole-centriole linkage of the cells entering mitosis. The overexpression of Nek2A coding gene has been widely reported in several cancer-associated disorders. In order to design a potent inhibitor and to control its expression mechanism, it is important to understand the structural orientation and the underlying molecular mechanisms associated with its activity regulation. In this study we have summarized the important information that will help in understanding the functional and activity regulation of Nek2A splice variants, which will further facilitate in designing a potent inhibitor against the cancer associated cases. We have also presented previously reported studies on the domain specifications and inhibitor biosynthesis that provide an insight into its specific target residue regions for developing active and more potent inhibitors. [ABSTRACT FROM AUTHOR]

Nitrogen fixation is the vital biochemical process in which atmospheric molecular nitrogen is made available to the biosphere. The process is highly energetically costly and thus tightly regulated. The activity of the key enzyme, nitrogenase, is controlled by reversible mono- ADP-ribosylation of one of its components, the Fe protein. This protein provides the other component, the Mo Fe protein, with the electrons required for the reduction of molecular nitrogen. The Fe-protein is ADP-ribosylated and de- ADP-ribosylated by dinitrogenase reductase ADP-ribosyl transferase and dinitrogenase reductase activating glycohydrolase, respectively. Here we review the current biochemical and structural knowledge of this central regulatory reaction. [ABSTRACT FROM AUTHOR]

Antimicrobial agents have eradicated many infectious diseases and significantly improved our living environment. However, abuse of antimicrobial agents has accelerated the emergence of multidrug-resistant microorganisms, and there is an urgent need for novel antibiotics. Antimicrobial peptides (AMPs) have attracted attention as a novel class of antimicrobial agents because AMPs efficiently kill a wide range of species, including bacteria, fungi, and viruses, via a novel mechanism of action. In addition, they are effective against pathogens that are resistant to almost all conventional antibiotics. AMPs have promising properties; they directly disrupt the functions of cellular membranes and nucleic acids, and the rate of appearance of AMP-resistant strains is very low. However, as pharmaceuticals, AMPs exhibit unfavorable properties, such as instability, hemolytic activity, high cost of production, salt sensitivity, and a broad spectrum of activity. Therefore, it is vital to improve these properties to develop novel AMP treatments. Here, we have reviewed the basic biochemical properties of AMPs and the recent strategies used to modulate these properties of AMPs to enhance their safety. [ABSTRACT FROM AUTHOR]

Antibiotics have significantly improved our living environments. However, overuse of antibiotics has led to the emergence of multi-drug resistant microorganisms, and the subsequent constant demand for the exploration of novel antibiotics. To this end, antimicrobial peptides (AMPs) have attracted much attention as a novel class of antibiotics. AMPs have strong antimicrobial activity against a wide-range of species, including gram-positive and gram-negative bacteria, fungi, and viruses. In addition, they are also effective against pathogenic organisms that are resistant to conventional drugs. Despite their great potential, the hemolytic activity and a highly broad spectrum of activity of AMPs dictate the need for amendments to develop safe pharmaceuticals. The human body contains commensal microflora as an integral part of complex mucosal surfaces that offers protection against pathogenic organisms. Administration of antibiotics with broad spectra of activity disrupts the indigenous microflora and increases the risks of diarrhea and other fatal infections. Therefore, it is difficult, but vital, to develop treatments capable of rapidly eliminating pathogenic organisms while maintaining the commensal microbiota. As such, novel pharmaceuticals, safe designer AMPs have been heavily researched. In this article, we review recent attempts to spatially and temporally regulate AMPs to enhance the quality-of-life of patients. [ABSTRACT FROM AUTHOR]

Abstract: A novel biosensor (immuno-rotary biosensor) was developed by conjugating deoxynivalenol (DON) monoclonal antibodies with the “rotator” ε-subunit of F0F1–ATPase within chromatophores with an ε-subunit monoclonal antibody–biotin–avidin–biotin linker to capture DON residues. The conjugation conditions were then optimized. The capture of DON was based on the antibody–antigen reaction and it is indicated by the change in ATP synthetic activity of F0F1–ATPase, which is measured via chemiluminescence using the luciferin–luciferase system with a computerized microplate luminometer analyzer. 10−7 mg/ml of DON can be detected. The whole detection process requires only about 20min. This method has promising applications in the detection of small molecular compounds because of its rapidity, simplicity, and sensitivity. [Copyright &y& Elsevier]

Abstract: Drosophila melanogaster silver gene is the ortholog of the coding gene of mammalian carboxypeptidase D (CPD). The silver gene gives rise to eight different splicing variants of differing length that can contain up to three homologous repeats. Among the protein variants encoded, the short form 1B alias DmCPD1Bs (D . melanogaster CPD variant 1B short) is necessary and sufficient for viability of the fruit fly. It has one single repeat, it is active against standard peptide substrates, and it is localized to the secretory pathway. In this work, the enzyme was found as a monomer in solution and as a homodimer in the crystal structure, which features a protomer with an N-terminal 311-residue catalytic domain of α/β-hydrolase fold and a C-terminal 84-residue all-β transthyretin-like domain. Overall, DmCPD1Bs conforms to the structure of N/E-type funnelins/M14B metallopeptidases, but it has two unique structural elements potentially involved in regulation of its activity: (i) two contiguous surface cysteines that may become palmitoylated and target the enzyme to membranes, thus providing control through localization, and (ii) a surface hot spot targetable by peptidases that would provide a regulatory mechanism through proteolytic inactivation. Given that the fruit fly possesses orthologs of only two out of the five proteolytically competent N/E-type funnelins found in higher vertebrates, DmCPD1Bs may represent a functional analog of at least one of the missing mammalian CPs. [ABSTRACT FROM AUTHOR]

Escherichia coli phosphotransacetylase (Pta) catalyzes the reversible interconversion of acetyl-CoA and acetyl phosphate. Both compounds are critical in E. coli metabolism, and acetyl phosphate is also involved in the regulation of certain signal transduction pathways. Along with acetate kinase, Pta plays an important role in acetate production when E. coli grows on rich medium; alternatively, it is involved in acetate utilization at high acetate concentrations. E. coli Pta is composed of three different domains, but only the C-terminal one, called PTA_PTB, is specific for all Ptas. In the present work, the characterization of E. coli Pta and deletions from the N-terminal region were performed. E. coli Pta acetyl phosphate-forming and acetyl phosphate-consuming reactions display different maximum activities, and are differentially regulated by pyruvate and phosphoenolpyruvate. These compounds activate acetyl phosphate production, but inhibit acetyl-CoA production, thus playing a critical role in defining the rates of the two Pta reactions. The characterization of three truncated Ptas, which all display Pta activity, indicates that the substrate-binding site is located at the C-terminal PTA_PTB domain. However, the N-terminal P-loop NTPase domain is involved in expression of the maximal catalytic activity, stabilization of the hexameric native state, and Pta activity regulation by NADH, ATP, phosphoenolpyruvate, and pyruvate. The truncated protein Pta-F3 was able to complement the growth on acetate of an E. coli mutant defective in acetyl-CoA synthetase and Pta, indicating that, although not regulated by metabolites, the Pta C-terminal domain is active in vivo. [ABSTRACT FROM AUTHOR]

Abstract: FoF1-ATPase activity is regulated by external links on β subunits with different molecular weight. It is inhibited when anti-β subunit antibody, streptavidin and H9 antibody link on the β subunits successively, but is activated when virus was binded. Western blotting indicated that the employed anti-β antibody target was on the non-catalytic site of the β subunit. Furthermore, an ESR study of spin-labeled ATP (SL-ATP) showed that the affinity of ATP to the holoenzyme increases with increasing external links on the β subunits. This simple regulation method may have great potential in the design of rapid, free labeled, sensitive and selective biosensors. [Copyright &y& Elsevier]

Abstract: Thrombin aptamer was attempted to cage with Bhc (6-bromo-7-hydroxycoumarin-4-ylmethyl) group for controlling its specific affinity to target molecular through photolysis. By multiple-caging strategy, aptamer could be rendered biologically inert and partially restored with subsequently illumination. This provides a convenient method for photoregulating aptamer activity with exact spatiotemporal resolution. [Copyright &y& Elsevier]

Abstract: Restriction endonuclease Bse634I is a homotetramer arranged as a dimer of two primary dimers. Bse634I displays its maximum catalytic efficiency upon binding of two copies of cognate DNA, one per each primary dimer. The catalytic activity of Bse634I on a single DNA copy is down-regulated due to the cross-talking interactions between the primary dimers. The mechanism of signal propagation between the individual active sites of Bse634I remains unclear. To identify communication pathways involved in the catalytic activity regulation of Bse634I tetramer we mutated a selected set of amino acid residues at the dimer–dimer interface and analysed the oligomeric state and catalytic properties of the mutant proteins. We demonstrate that alanine replacement of N262 and V263 residues located in the loop at the tetramerisation interface did not inhibit tetramer assembly but dramatically altered the catalytic properties of Bse634I despite of the distal location from the active site. Kinetic analysis using cognate hairpin oligonucleotide and one and two-site plasmids as substrates allowed us to identify two types of communication signals propagated through the dimer-dimer interface in the Bse634I tetramer: the inhibitory, or “stopper” and the activating, or “sync” signal. We suggest that the interplay between the two signals determines the catalytic and regulatory properties of the Bse634I and mutant proteins. [Copyright &y& Elsevier]

Protein phosphatase-1 (PP1) is a member of the eukaryotic serine/threonine phosphatase gene family. The β12-β13 loop is a prominent non-conserved region among the family, and extends from the surface and overhangs the active site. To investigate the function of the β12-β13 loop of PP1, we systematically examined all residues by site-directed deletion mutation. Deleting residues Y272, E275 or F276, caused enzyme activity to increase, while deleting residue C273, caused enzyme activity to decrease, when G274 was deleted no remarkable activity increase was observed, and almost all activity was lost when D277, N278 or A279 were deleted. These observations implied that each amino acid has a different effect on the activity of phosphatase, which may result from their different side chains and locations. The activity change of these PP1 mutants, from Y272 to A279, was comparable to that of calcineurin mutants, from Y311 to K318. By comparison, except for D277 (N316) and A279 (K318) of PP1 (calcineurin), each pair of equivalent mutants in the β12-β13 loop of PP1 and calcineurin have coincident activity change although they are non-conserved, which suggests that the β12-β13 loop of PP1 is not only involved in activity regulation but also involved in regulation similar to that of calcineurin. iubmb Life , 58: 487 – 492, 2006 [ABSTRACT FROM AUTHOR]

This paper describes the Electronic Schoolbag, a digital workspace developed at the University of Savoie (France) and analyses its usages. This online environment is dedicated to the educational world: it offers pupils, students, teachers, school staff, or parents, personal and group workspaces in which individual or collaborative activities can take place. The flexibility of this software, allowing synchronous or asynchronous activities, lies in the “participation model”. This model allows groups themselves to describe and organise their activities. The architecture that permits its implementation in the Electronic Schoolbag workspace is described. The study of the practices of the workspace is then presented. This requires different observation methods, according to the different procedures chosen: real practices provided by quantitative methods (analysis of the logs of the actions and questionnaires) and imagined practices provided by qualitative methods (semi-directive interviews). The results obtained from the university users allow us to assess the evolution of the usages for different periods and on different university sites. The observatory also lets us list the main uses of the Electronic Schoolbag for educative communication (collaborative vs. individual, informative vs. communicative). [ABSTRACT FROM AUTHOR]

The soil bacterium Corynebacterium glutamicum has to cope with frequent fluctuations of the external osmolarity and temperature. The consequences of hyperosmotic and chill stress seem to differ, either causing dehydration of the cytoplasm or leading to impairment of cellular functions due to low temperature. Nevertheless, a particular type of regulatory response, namely the accumulation of so-called compatible solutes, is induced under both conditions. Compatible solutes are known to stabilize the native conformation of enzymes, which may be affected by osmotic and chill stress. BetP is a high-affinity uptake carrier for the compatible solute glycine betaine in C. glutamicum. BetP includes, besides its catalytic function, the ability to sense hyperosmotic conditions and chill stress. As a consequence, the carrier is activated in dependence of the extent of these types of stress. The signal input related to these changes of the environmental conditions is based on at least two different mechanisms. In case of hyperosmotic stress, BetP responds to the internal potassium concentration as a measure for hypertonicity, whereas chill stress is detected by an independent signal, most probably changes of the physical state of the membrane. Copyright © 2005 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Abstract: Catalytic activity of a heme peptide (HP) modified-electrode for H2O2 reduction was controlled by use of poly(N-isopropylacrylamide) modified with an inhibitory moiety, imidazole group. The polymers inhibited the catalytic activity below their lower critical solution temperature (LCST) where the polymers were dissolved and did not inhibit the activity above the LCST where the polymers were precipitated. A polymer with a longer side chain connecting with the imidazole group was more inhibitory than a polymer with a shorter side chain at temperatures below the LCST. Formation constants of dissolved HP-imidazole complexes were evaluated by spectroscopic means, and it was found that the polymers were more inhibitory than the corresponding monomers. [Copyright &y& Elsevier]

In Corynebacterium glutamicum, four uptake systems for compatible solutes have been characterized so far. DHPE (ΔbetPΔputPΔproPΔectP), a derivative of the C. glutamicum type strain ATCC 13032 carrying deletions in the corresponding genes, still showed a low betaine uptake rate of 1.4 nmol/(min mg cdm). Genome analyses revealed the presence of a putative carrier, named low capacity osmoregulated permease (LcoP), which shows similarities to compatible solute transporters of the betaine/carnitine/choline transporter (BCCT)-family. Deletion of lcoP in DHPE resulted in betaine and ectoine uptake deficiency. LcoP, a betaine and ectoine permease is regulated at the expression and the activity level by the external osmolality. Addition of local anesthetics modulated the activity of BCCT-family members BetP, EctP, and LcoP in a different manner, indicating a different type of lipid–protein interaction. [Copyright &y& Elsevier]

The activity of outer membrane phospholipase A (OMPLA) is regulated by reversible dimerization. However, native OMPLA reconstituted in phospholipid vesicles was found to be present as a dimer but nevertheless inactive. To investigate the importance of dimerization for control of OMPLA activity, a covalent OMPLA dimer was constructed and its properties were compared to native OMPLA both in a micellar detergent and after reconstitution in a phospholipid bilayer. Unlike native OMPLA, activity of the covalent OMPLA dimer was independent of type and concentration of detergent in micellar systems. In such systems, the covalent OMPLA dimer invariantly displayed high calcium affinity. In contrast, high calcium concentrations were required to activate a covalent OMPLA dimer when present in intact vesicles. Solubilization of the vesicles increased the affinity for calcium, suggesting that in an intact bilayer the dimer interface is not properly formed. This was supported by the observation that OMPLA variants having an impaired dimeric interface also lacked high affinity calcium binding. A covalent linkage was not able to restore high affinity calcium binding in these variants, demonstrating that a proper dimer interface is essential for optimal catalysis. [ABSTRACT FROM AUTHOR]

NADPH oxidases (NOXs), mostly known as respiratory burst oxidase homologs (RBOHs), are the key producers of reactive oxygen species (ROS) in plants. A lot of literature has addressed ROS signaling in plant development regulation and stress responses as well as on the enzyme's structure, evolution, function, regulation and associated mechanisms, manifesting the role of NOXs/RBOHs as the vital performers and center hubs during plant growth and signaling. This review focuses on recent advances of NOXs/RBOHs on cell growth, hormone interaction, calcium signaling, abiotic stress responses, and immunity. Several primary particles, including Ca2+, CDPKs, BIK1, ROPs/RACs, CERK, FER, ANX, SnRK and SIK1-mediated regulatory mechanisms, are fully summarized to illustrate the signaling behavior of NOXs/RBOHs and their sophisticated and dexterous crosstalks. Diverse expression and activation regulation models endow NOXs/RBOHs powerful and versatile functions in plants to maintain innate immune homeostasis and development integrity. NOXs/RBOHs and their related regulatory items are the ideal targets for crop improvement in both yield and quality during agricultural practices. [ABSTRACT FROM AUTHOR]

Natural enzymes, such as biocatalysts, are widely used in biosensors, medicine and health, the environmental field, and other fields. However, it is easy for natural enzymes to lose catalytic activity due to their intrinsic shortcomings including a high purification cost, insufficient stability, and difficulties of recycling, which limit their practical applications. The unexpected discovery of the Fe3O4 nanozyme in 2007 has given rise to tremendous efforts for developing natural enzyme substitutes. Nanozymes, which are nanomaterials with enzyme-mimetic catalytic activity, can serve as ideal candidates for artificial mimic enzymes. Nanozymes possess superiorities due to their low cost, high stability, and easy preparation. Although great progress has been made in the development of nanozymes, the catalytic efficiency of existing nanozymes is relatively low compared with natural enzymes. It is still a challenging task to develop nanozymes with a precise regulation of catalytic activity. This review summarizes the classification and various strategies for modulating the activity as well as research progress in the different application fields of nanozymes. Typical examples of the recent research process of nanozymes will be presented and critically discussed. [ABSTRACT FROM AUTHOR]

Ribozymes are functional RNA molecules that can catalyze biochemical reactions. Since the discovery of the first catalytic RNA, various functional ribozymes (e.g. , self-cleaving ribozymes, splicing ribozymes, RNase P, etc.) have been uncovered, and their structures and mechanisms have been identified. Ribozymes have the advantage of possessing features of "RNA" molecules; hence, they are highly applicable for manipulating various biological systems. To fully employ ribozymes in a broad range of biological applications in synthetic biology, a variety of ribozymes have been developed and engineered. Here, we summarize the main features of ribozymes and the methods used for engineering their functions. We also describe the past and recent efforts towards exploiting ribozymes for effective and novel applications in synthetic biology. Based on studies on their significance in biological applications till date, ribozymes are expected to advance technologies in artificial biological systems. • Unique features of catalytic RNAs over protein enzymes. • Characteristics of ribozymes and their engineering strategies. • Interesting applications of ribozymes in the field of synthetic biology. • Current challenges of ribozyme-based biotechnology and future perspectives. [ABSTRACT FROM AUTHOR]

Hox proteins frequently select and regulate their specific target genes with the help of cofactors like Extradenticle (Exd) and Homothorax (Hth). For the Drosophila Hox protein Sex combs reduced (Scr), Exd has been shown to position a normally unstructured portion of Scr so that two basic amino acid side chains can insert into the minor groove of an Scr-specific DNA-binding site. Here we provide evidence that another Drosophila Hox protein, Deformed (Dfd), uses a very similar mechanism to achieve specificity in vivo, thus generalizing this mechanism. Furthermore, we show that subtle differences in the way Dfd and Scr recognize their specific binding sites, in conjunction with non-DNA-binding domains, influence whether the target gene is transcriptionally activated or repressed. These results suggest that the interaction between these DNA-binding proteins and the DNA-binding site determines the architecture of the Hox-cofactor-DNA ternary complex, which in turn determines whether the complex recruits coactivators or corepressors. [ABSTRACT FROM AUTHOR]