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1.
BackgroundTagging a luminescent quantum dot (QD) with a biological like enzyme (Enz) creates value-added entities like quantum dot–enzyme bioconjugates (QDEnzBio) that find utility as sensors to detect glucose or beacons to track enzymes in vivo. For such applications, it is imperative that the enzyme remains catalytically active while the quantum dot is luminescent in the bioconjugate. A critical feature that dictates this is the quantum dot–enzyme linkage chemistry. Previously such linkages have put constraints on polypeptide chain dynamics or hindered substrate diffusion to active site, seriously undermining enzyme catalytic activity. In this work we address this issue using avidin–biotin linkage chemistry together with a flexible spacer to conjugate enzyme to quantum dot.MethodsThe catalytic activity of three biotinylated hydrolytic enzymes, namely, hen egg white lysozyme (HEWL), alkaline phosphatase (ALP) and acetylcholinesterase (AChE) was investigated post-conjugation to streptavidin linked quantum dot for multiple substrate concentrations and varying degrees of biotinylation.ResultsWe demonstrate that all enzymes retain full catalytic activity in the quantum dot–enzyme bioconjugates in comparison to biotinylated enzyme alone. However, unlike alkaline phosphatase and acetylcholinesterase, the catalytic activity of hen egg white lysozyme was observed to be increasingly susceptible to ionic strength of medium with rising level of biotinylation. This susceptibility was attributed to arise from depletion of positive charge from lysine amino groups after biotinylation.ConclusionsWe reasoned that avidin–biotin linkage in the presence of a flexible seven atom spacer between biotin and enzyme poses no constraints to enzyme structure/dynamics enabling retention of full enzyme activity.General significanceOverall our results demonstrate for the first time that streptavidin–biotin chemistry can yield quantum dot enzyme bioconjugates that retain full catalytic activity as native enzyme.  相似文献   

2.
Abstract

Lippia nodiflora L. is extensively used in traditional medicine for several medicinal purposes, including their use in inflammatory disorders. In this study, the folk use of L. nodiflora was validated using the isolated natural compound, 5-hydroxy-3,4,7-trimethoxyflavone (HTMF) by in vitro, fluorescence spectroscopic and molecular modeling studies with lipoxygenase (LOX), because LOX plays an essential role in inflammatory responses. In this perspective, the methanol extract and HTMF are shown to demonstrate prominent inhibitory activity against soybean lipoxygenase, with an IC50 value of 21.12 and 23.97?µg/ml, respectively. The data obtained from the spectroscopic method revealed that the quenching of intrinsic fluorescence of LOX is produced as a result of the complex formation of LOX–HTMF. The binding mode analysis of HTMF within the LOX enzyme suggested that hydrogen bond formation, hydrophobic interaction and π–π stacking could account for the binding of HTMF. Molecular dynamics results indicated the interaction of HTMF with LOX and the stability of ligand–enzyme complex was maintained throughout the simulation. The computational results are reliable with experimental facts and provided a good representation for understanding the binding mode of HTMF inside the active site of lipoxygenase enzyme.  相似文献   

3.
Tyrosinase is known for an enzyme that plays a key role in producing the initial precursor of melanin biosynthesis. Inhibition of the catalytic reaction of this enzyme led to some advantage such as skin-whitening and anti-insect agents. To find a natural compound with inhibitory activity towards tyrosinase, the five flavonoids of kushenol A (1), 8-prenylkaempferol (2), kushenol C (3), formononetin (4) and 8-prenylnaringenin (5) were isolated by column chromatography from a 95% methanol extract of Sophora flavescens. The ability of these flavonoids to block the conversion of L-tyrosine to L-DOPA by tyrosinase was tested in vitro. Compounds 1 and 2 exhibited potent inhibitory activity, with IC50 values less than 10?µM. Furthermore, enzyme kinetics and molecular docking analysis revealed the formation of a binary encounter complex between compounds 1–4 and the enzyme. Also, all of the isolated compounds (1–5) were confirmed to possess antioxidant activity.  相似文献   

4.
PurposeTo review the methodologies used to assess muscle co-contraction (MCo) with surface electromyography (sEMG) during gait in people with neurological impairment.MethodsThe Scopus (1995–2013), Web of Science (1970–2013), PubMed (1948-2013) and B-on (1999–2013) databases were searched. Articles were included when sEMG was used to assess MCo during gait in people with impairment due to central nervous system disorders (CNS).ResultsNineteen articles met the inclusion criteria and most studied people with cerebral palsy and stroke. No consensus was identified for gait assessment protocols (surfaces, speed, distance), sEMG acquisition (electrodes position), analysis of sEMG data (filters, normalisation techniques) and quantification of MCo (agonist-antagonist linear envelopes overlapping or agonist-antagonist overlapping periods of muscles activity, onset delimited).ConclusionGiven the wide range of methodologies employed, it is not possible to recommend the most appropriate for assessing MCo. Researchers should adopt recognized standards in future work. This is needed before consensus about the role that MCo plays in gait impairment in neurological diseases and its potential as a target for gait rehabilitation can be determined.  相似文献   

5.
Abstract

The results of 1-nanosecond molecular dynamics simulations of the enzyme ribonuclease T1 and its 2′GMP complex in water are presented. A classification of the angular reorientations of the backbone amide groups is achieved via a transformation of NH-vector trajectories into several coordinate frames, thus unravelling contributions of NH-bond librations and backbone dihedral angle fluctuations.

The former turned out to be similar for all amides, as characterized by correlation times of librational motions in a subpicosecond scale, angular amplitudes of about 10–12° for out-of-peptide-plane displacements of the NH-bond and 3–5° for the in-plane displacements, whereas the contributions of much slower backbone dihedral angle fluctuations strongly depend on the secondary structure. Correlation functions relevant for NMR were obtained and analyzed utilizing the ‘model-free’ approach (Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546–4559,4559-4570; Clore et al., (1990) J. Am. Chem. Soc. 112, 4989–4991). The dependence of the amplitude of local motion on the residue location in the backbone is in good agreement with the results of NMR relaxation measurements and X-ray data. The protein dynamics is characterized by a highly restricted local motion of those parts of the backbone with defined secondary structure as well as by a high flexibility in loop regions. The comparison of results derived from different periods of the trajectory (of 50 ps and 1 ns duration, 1000 points sampled) reveals a dependence of the observed dynamic picture on the characteristic time scale of the experimental method used. Comparison of the MD data for the free and liganded enzyme clearly indicates a restriction of the mobility within certain regions of the backbone upon inhibitor binding.  相似文献   

6.
Abstract

In this study, the different mole ratios of glucose oxidase/chitosan/dextran–aldehyde and glucose oxidase/chitosan/dextran–sulfate complexes were synthesized. The modification of glucose oxidase by non-covalent complexation with dextran and chitosan in different molar ratios was studied in order to increase the enzyme activity. The enzyme/polymer complexes obtained were investigated by UV spectrophotometer and dynamic light scattering. Activity determination of synthesized complexes and free enzyme were performed at a temperature range. The best results were obtained by Cchitosan/Cdextran–aldehyde = 10/1 ratio and Cchitosan/Cdextran–sulfate = 1/5 ratio that were used in thermal stability, shelf life, salt stress, and ethanol effect experiments. The results demonstrated that both complexes were thermally stable at 60?°C and had superior storage stability compared to the free glucose oxidase. Complexes showed higher enzymatic activity than free enzyme in the organic solvent environment using 10% ethanol. The complexes were resistant to salt stress containing 0.1?M NaCl or CaCl2. The particle size distribution results of the triple complex evaluated the complexation of the chitosan, dextran derivative, and glucose oxidase. The average size of the triple complex in diameter was found to be 325.8?±?9.3?nm. Overall findings suggest that the complexes of glucose oxidase, chitosan, and dextran showed significant enhancement in the enzyme activity.  相似文献   

7.
White-rot fungi of the Phylum Basidiomycota are quite promising in ligninolytic enzyme production and the optimization of their synthesis is of particular significance. The aim of this study was to investigate the effect of enhanced concentration of copper (Cu) ions (25–1000 μg/ml) on the activity of the ligninolytic enzyme complex (laccase, Lac; lignin peroxidase, LiP; Mn-peroxidase, MnP) in Trametes trogii 46, as well as the changes in the antioxidant cell response. All concentrations tested reduced significantly in growth and glucose consumption. Cu ions affected the ligninolytic enzyme activity in a dose dependent manner. Concentrations in the range of 25–100 μg/ml strongly stimulated Lac production (a 5–6-fold increase compared to the control). LiP activity was also induced by Cu, with the peak value being recorded following exposure to 50 μg/ml metal ions. In contrast, the addition of Cu ions had a positive effect on MnP activity at a concentration higher than 100 μg/ml. The maximum enzyme level was achieved at 1000 μg/ml. The results obtained on superoxide dismutase and catalase activities indicated that exposure of T. trogii 46 mycelia to Cu ions promoted oxidative stress. Both enzyme activities were co-ordinately produced with Lac and LiP but not co-ordinately with MnP.  相似文献   

8.
BackgroundThe ubiquitin system is a modification process with many different cellular functions including immune signaling and antiviral functions. E3 ubiquitin ligases are enzymes that recruit an E2 ubiquitin-conjugating enzyme bound to ubiquitin in order to catalyze the transfer of ubiquitin from the E2 to a protein substrate. The RING E3s, the most abundant type of ubiquitin ligases, are characterized by a zinc (II)-binding domain called RING (Really Interesting New Gene). Viral replication requires modifying and hijacking key cellular pathways within host cells such as cellular ubiquitination. There are well-established examples where a viral proteins bind to RING E3s, redirecting them to degrade otherwise long-lived host proteins or inhibiting E3’s ubiquitination activity. Recently, three binary interactions between SARS-CoV-2 proteins and innate human immune signaling Ε3 RING ligases: NSP15-RNF41, ORF3a-TRIM59 and NSP9-MIB1 have been experimentally established.MethodsIn this work, we have investigated the mode of the previous experimentally supported NSP15-RNF41, ORF3a,-TRIM59 and NSP9-MIB1 binary interactions by in silico methodologies intending to provide structural insights of E3-virus interplay that can help identify potential inhibitors that could block SARS-CoV-2 infection of immune cells.ConclusionIn silico methodologies have shown that the above human E3 ligases interact with viral partners through their Zn(II) binding domains. This RING mediated formation of stable SARS-CoV-2-E3 complexes indicates a critical structural role of RING domains in immune system disruption by SARS-CoV-2-infection.Data AvailabilityThe data used to support the findings of this research are included within the article and are labeled with references.  相似文献   

9.
BackgroundAlthough considered an unusual etiological agent, Cyberlindnera (Candida) fabianii has been related to septicemia in several reports in recent years. Its doubtful or uncertain identification when using tests such as CHROMagar Candida, API® Candida, API® ID32C or VITEK® MS, leads to an underestimation of the cases produced by this yeast.AimsTo report the first isolation of C. fabianii in Chile and its identification.MethodsThe sequencing of the internal transcribed spacer region (ITS) was performed. Antifungal susceptibility profiles were obtained by means of the broth microdilution technique.ResultsThe identification was only reached by sequencing the ITS regions, which shows the limited usefulness of the conventional techniques in the identification of some yeast species. A dendrogram shows the phylogenetic relationship of the isolated strain with some other yeast species.ConclusionIn the identification of fastidious microorganisms or microorganisms whose identification is not completely reliable when using classical or even advanced methodologies, such as mass spectrometry, sequencing techniques are essential.  相似文献   

10.
ABSTRACT

Background: Plant communities are usually characterised by species composition and abundance, but also underlie a multitude of complex interactions that we have only recently started unveiling. Yet, we are still far from understanding ecological and evolutionary processes shaping the network-level organisation of plant diversity, and to what extent these processes are specific to certain spatial scales or environments.

Aims: Understanding the systemic mechanisms of plant–plant network assembly and their consequences for diversity patterns.

Methods: We review recent methods and results of plant–plant networks.

Results: We synthetize how plant–plant networks can help us to: (a) assess how competition and facilitation may balance each other through the network; (b) analyse the role of plant–plant interactions beyond pairwise competition in structuring plant communities, and (c) forecast the ecological implications of complex species dependencies. We discuss pros and cons, assumptions and limitations of different approaches used for inferring plant–plant networks.

Conclusions: We propose novel opportunities for advancing plant ecology by using ecological networks that encompass different ecological levels and spatio-temporal scales, and incorporate more biological information. Embracing networks of interactions among plants can shed new light on mechanisms driving evolution and ecosystem functioning, helping us to mitigate diversity loss.  相似文献   

11.
Abstract

Thermodynamic parameters of the three hybrid (1–3,1–4)-β-glucanases H(A12-M), H(A12-M)ΔY13, and H(A16-M) composed of short N-terminal regions derived from the Bacillus amyloliquefaciens enzyme and a C-terminal region of the homologous Bacillus macerans enzyme were determined in 2mM sodium cacodylate pH 6.0,1.5 M guanidine hydrochloride, containing 1 mM CaCl2 or 1 mM EDTA Melting of H(A12-M)ΔY13 and H(A16-M) in the presence of calcium ions is characterized by two subtransitions; only one transition is observed in the case of H(A12-M). In calcium-free buffer each of the three hybrid enzymes melts in one two-state transition. Transition temperatures T m and molar enthalpy changes ΔH are reduced in the absence of calcium ions but the reduction is much more pronounced for H(A12-M)ΔY13 and H(A16-M) than for the less thermostable enzyme H(A12-M).  相似文献   

12.
Abstract

Previous equilibrium binding experiments (S.A. Winkle and T.R. Krugh, Nucleic Acids Res. 9, 3175–3186 (1981)) suggested that the carcinogen N-hydroxy-N-acetyl-2-aminofluorene might exhibit preferential binding to a small number of sites on phiXl 74 DNA To examine whether the covalently binding analogue N-acetoxy-N-acetyl-2-aminofluorene (acetoxyAAF) also possesses high affinity sites, the plasmid pBR322 was reacted with 3H labeled acetoxyAAF to give one to sixteen adducts per DNA molecule. Thus only higher affinity sites would be affected. The DNA was subsequently cleaved with either Alu I, Hae III, Hha I, Hinf I or Hpa II restriction endonuclease and the restriction fragments isolated by gel electrophoresis. Examination of the distribution of 3H acetoxyAAF among the fragments was not random but, rather, with each enzyme, the acetoxyAAF was found predominantly in a few fragments. The locations of the bands containing the acetoxyAAF for each enzyme overlap - suggesting that there are regions on pBR 322 which contain high affinity sites for acetoxyAAF binding.  相似文献   

13.
The subunit locations of the component enzymes of the pig heart trifunctional mitochondrial β-oxidation complex are suggested by analyzing the primary structure of the large subunit of this membrane-bound multienzyme complex [Yang S.-Y.et al. (1994) Biochem. biophys. Res. Commun. 198, 431–437] with those of the subunits of the E. coli fatty acid oxidation complex and the corresponding mitochondrial matrix β-oxidation enzymes. Long-chain enoyl-CoA hydratase and long-chain 3-hydroxyacyl-CoA dehydrogenase are located in the amino-terminal and the central regions of the 79 kDa polypeptide, respectively, whereas the long-chain 3-ketoacyl-CoA thiolase is associated with the 46 kDa subunit of this complex. The pig heart mitochondrial bifunctional β-oxidation enzyme is more homologous to the large subunit of the prokaryotic fatty acid oxidation complex than to the peroxisomal trifunctional β-oxidation enzyme. The evolutionary trees of 3-hydroxyacyl-CoA dehydrogenases and enoyl-CoA hydratases suggest that the mitochondrial inner membrane-bound bifunctional β-oxidation enzyme and the corresponding matrix monofunctional β-oxidation enzymes are more remotely related to each other than to their corresponding prokaryotic enzymes, and that the genes of E. coli multifunctional fatty acid oxidation protein and pig heart mitochondrial bifunctional β-oxidation enzyme diverged after the appearance of eukaryotic cells.  相似文献   

14.
BackgroundIn this study, chromium (III) complex was synthesized from genistein (GEN) which had good hypoglycemic activity and inorganic chromium (III) element, and its hypoglycemic activity and sub-acute toxicity were studied.MethodsThe genistein-chromium (III) complex was synthesized by chelating chromium with genistein in ethanol and its structure was determined by LC–MS, atomic absorption spectroscopy, UV–vis spectroscopy, infrared spectroscopy, elemental and thermodynamic analysis. The anti-diabetic activity of the complex was assessed in db/db mice and C57 mice by daily oral gavage for 4 weeks. The sub-acute toxicity test was carried out on KM mice with this complex.ResultsThe molecular structure of this complex was inferred as a complex [CrGEN3] formed by three ligands and one chromium element. The complex could significantly improve the body weight of db/db mice, fasting blood glucose, random blood glucose, organ index, glycogen levels and the performance of OGTT (Oral Glucose Tolerance Test) and ITT (Insulin Tolerance Test) in db/db mice (p < 0.05). The morphology of liver, kidney, pancreas and skeletal muscle also had obviously improvement and repairment. Effects on serum indices and antioxidant enzymes activities of db/db mice showed that the serum profiles and antioxidant ability of complex group had significant improvement compared with the diabetic control group (p < 0.05 or p < 0.01), and some indices even returned to normal levels. In addition, this complex did not produce any hazardous symptoms or deaths in sub-acute toxicity test. High dose of [CrGEN3] had no significant influence on serum indices and antioxidant capacity in normal mice, and the organ tissues maintained organized and integrity in the sub-acute toxicity study.ConclusionThe study of the genistein-chromium (III) complex showed that the complex had good hypoglycemic activity in vivo, and did not have the potential toxicity. These results would provide an important reference for the development of functional hypoglycemic foods or pharmaceuticals.  相似文献   

15.
SummaryLipoprotein lipase (LPL) is a major lipolytic enzyme in the intravascular metabolism of postprandial triglyceride-rich lipoproteins. This enzyme is synthesized and secreted by tissues and transported to the capillary endothelial surface. Decreased activity of this enzyme is suggested to be involved in arterial sequestration of lipoproteins and thus in the progression of atherosclerosis. Titanium salts are widely used in industry, medicine, and pharmacy for tablet coating, pharmaceuticals and cosmetic products. In this study the effect of titanium on post-heparin LPL activity is reported in vivo and in vitro.MethodsGroups of Male Wistar rats were administered (i.p) with an acute dose of 2.5 mg/kg titanium chloride for 10 days and a chronic dose of 0.75 mg/kg for 30 and/or 60 days. Blood samples were then collected for LPL assay. For in vitro study, plasma aliquots were incubated in the presence of up to 50 mM titanium and the enzyme activity was measured.ResultsAnimals exposed to acute dose of titanium showed about 20% reduction in LPL activity, whereas 31% and 36% reductions were observed in animals chronically exposed for 30 and/or 60 days, respectively. Titanium in vitro also led to enzyme inhibition, so that a decrease of 28–53% was seen in the presence of 0.1–50 mM titanium. This inhibition by titanium was potentiated when citrate and/or bicarbonate was present.ConclusionAlthough the mechanism of titanium effect on LPL activity in vivo and in vitro demands more investigations, the inhibitory effect of titanium ion in vivo should be considered seriously in subjects exposed to this metal ion. Changes in LPL activity may affect whole body lipid metabolism, a condition favorable for development and progression of atherosclerosis.  相似文献   

16.
BackgroundOxygen exists in two gaseous and six solid allotropic modifications. An additional allotropic modification of oxygen, the cyclooctaoxygen, was predicted to exist in 1990.MethodsCyclooctaoxygen sodium was synthesized in vitro from atmospheric oxygen, or catalase effect-generated oxygen, under catalysis of cytosine nucleosides and either ninhydrin or eukaryotic low-molecular weight RNA. Thin-layer chromatographic mobility shift assays were applied on specific nucleic acids and the cyclooctaoxygen sodium complex.ResultsWe report the first synthesis and characterization of cyclooctaoxygen as its sodium crown complex, isolated in the form of three cytosine nucleoside hydrochloride complexes. The cationic cyclooctaoxygen sodium complex is shown to bind to nucleic acids (RNA and DNA), to associate with single-stranded DNA and spermine phosphate, and to be essentially non-toxic to cultured mammalian cells at 0.1–1.0 mM concentration.ConclusionsWe postulate that cyclooctaoxygen is formed in most eukaryotic cells in vivo from dihydrogen peroxide in a catalase reaction catalyzed by cytidine and RNA. A molecular biological model is deduced for a first epigenetic shell of eukaryotic in vivo DNA. This model incorporates an epigenetic explanation for the interactions of the essential micronutrient selenium (as selenite) with eukaryotic in vivo DNA.General significanceSince the sperminium phosphate/cyclooctaoxygen sodium complex is calculated to cover the active regions (2.6%) of bovine lymphocyte interphase genome, and 12.4% of murine enterocyte mitotic chromatin, we propose that the sperminium phosphate/cyclooctaoxygen sodium complex coverage of nucleic acids is essential to eukaryotic gene regulation and promoted proto-eukaryotic evolution.  相似文献   

17.
Abstract

Correlative techniques for estimating environmental requirements of species – variably termed ecological niche modeling or species distribution modeling – are becoming very popular tools for ecologists and biogeographers in understanding diverse aspects of biodiversity. These tools, however, are frequently applied in ways that do not fit well into knowledge frameworks in population ecology and biogeography, or into the realities of sampling biodiversity over real-world landscapes. We offer 10 “fixes” – adjustments to typical methodologies that will take into account population ecological and biogeographic frameworks to produce better models.  相似文献   

18.
《Journal of molecular biology》2019,431(11):2082-2094
Specificity engineering is challenging and particularly difficult for enzymes that have the catalytic machinery and specificity determinants in close proximity. Restriction endonucleases have been used as a paradigm for protein engineering, but successful cases are rare. Here, we present the results of a directed evolution approach to the engineering of a dimeric, blunt end cutting restriction enzyme NlaIV (GGN/NCC). Based on the remote similarity to EcoRV endonuclease, regions for random mutagenesis and in vitro evolution were chosen. The obtained variants cleaved target sites with an up to 100-fold kcat/KM preference for AT or TA (GGW/WCC) over GC or CG (GGS/SCC) in the central dinucleotide step, compared to the only ~ 17-fold preference of the wild-type enzyme. To understand the basis of the increased specificity, we determined the crystal structure of NlaIV. Despite the presence of DNA in the crystallization mix, the enzyme crystallized in the free form. We therefore constructed a computational model of the NlaIV–DNA complex. According to the model, the mutagenesis of the regions that were in the proximity of DNA did not lead to the desired specificity change, which was instead conveyed in an indirect manner by substitutions in the more distant regions.  相似文献   

19.
Abstract

Hyaluronidase (hyase) is a hyaluronic acid (HA) depolymerizing enzyme produced by many pathogenic bacteria as a virulence factor to establish and spread infections. Present studies established that a steroidal fraction (SF) isolated from leaves of Carissa carandas act as a strong hyase inhibitor. The kinetic parameters involved in the inhibition of hyase by purified SF were studied and compared with standard hyase inhibitor quercetin. The purified SF showed the highest inhibition with an IC50 of 5.19 mM in comparison with a standard inhibitor, quercetin (IC50 8.63 mM). The inhibition constant (Ki) of purified SF determined by Dixon plot was 8.32 mM, which was significantly lower than that of quercetin standard. The kinetic behavior of enzyme hyase revealed to be more complex than classical competitive and uncompetitive inhibition where inhibitor affects both Km and Vmax. The inhibitor (I) favored the binding to the enzyme–substrate (ES) complex where Km value appeared to decrease (Kmapp < Km). The inhibitor also leads to decrease in the apparent maximum velocity of the enzyme–substrate reaction (Vmaxapp < Vmax). These results signpost toward mixed nature of inhibition of enzyme hyase by purified SF. Anti-hyaluronidase activity by a bioactive metabolite from C. carandas has not been reported so far and has high therapeutic potential against spread of pathogen and its toxins in the host.  相似文献   

20.
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