Streptococcus gordonii soluble inorganic pyrophosphatase: An important role for the interdomain region in enzyme activity

Ultrasensitive NIR fluorometric assay for inorganic pyrophosphatase detection via Cu2+-PPi interaction using bimetallic Au-Ag nanoclusters

BACKGROUND

Inorganic pyrophosphatase (PPase) is key enzyme playing a key role in biochemical transformations such as biosynthesis of DNA and RNA, bone formation, metabolic pathways associated with lipid, carbohydrate and phosphorous. It has been reported that lung adenocarcinomas, colorectal cancer, and hyperthyroidism disorders can result from abnormal level of PPase. Therefore, it is of notable significance to develop simple and effective real time assay for PPase enzyme activity monitoring for screening of many metabolic pathways as well as for early disease diagnosis.

RESULT

The fluorometric detection of PPase enzyme in near infrared region-1 (NIR-1) has been carried out using bimetallic nanoclusters (LA@AuAg NCs). The developed sensing strategy was based on quenching of fluorescence intensity of LA@AuAg NCs upon interaction with copper (Cu2+) ions. The off state of LA@AuAg_Cu2+ ensemble was turned on upon addition of pyrophosphate anion (PPi) due to strong binding interaction between PPi and Cu2+. The catalytic conversion of PPi into phosphate anion (Pi) in the presence of PPase led to liberation of Cu2+ ions, and again quenched off state was retrieved due to interaction of free Cu2+ with LA@AuAg NCs. The ultrasensitive detection of PPase was observed in the linear range of 0.06-250 mU/mL with LOD as 0.0025 mU/mL. The designed scheme showed good selectivity towards PPase enzyme in comparison to other bio-substrates, along with good percentage recovery for PPase detection in real human serum samples.

SIGNIFICANCE

The developed NIR based assay is ultrasensitive, highly selective and robust for PPase enzyme and can be safely employed for other enzymes detection. This highly sensitive nature of biosensor was result of involvement of fluorescence-based technique and synergistic effect of dual metal in NIR based bimetallic NCs. Moreover, owing to the emission in NIR domain, in future, these nanoclusters can be safely employed for many biomedical applications for In vivo studies.

The iTRAQ-based quantitative proteomics reveals metabolic changes in Scylla paramamosain under different light intensities during indoor overwintering

Light intensity is one of the ecological factors that appreciably affects the metabolism of Scylla paramamosain during overwintering. This study adopted the isobaric tag for relative and absolute quantitation (iTRAQ) method to investigate metabolic changes of S. paramamosain under three illumination levels (0, 1.43 and 40.31 μmol m^-2·s^-1) for four months during indoor overwintering. The iTRAQ identified 3282 proteins, among which 267 exhibited significant differential expression (122 upregulated and 145 downregulated) in the low light group, and 299 with significant differential expression (252 upregulated and 47 downregulated) in the high light group. Analysis of these results showed that there were different metabolic regulatory patterns under different light intensities. Low light is more conducive to the survival of S. paramamosain, which needs to produce and consume relatively less energy to sustain physiological activities. Thus, the essential proteins associated with physiological activities were significantly upregulated, while those related to energy production were significantly downregulated. In contrast, high light exerts a certain stress on the survival of S. paramamosain and required more energy to cope with this stress, which forced a significant upregulation of proteins related to stress response and energy production. The findings of this study highlighted the metabolic regulatory mechanisms of S. paramamosain under different light intensities.

Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments

Recent experiments have suggested that the energy released by a chemical reaction can propel its enzyme catalyst (for example, alkaline phosphatase). However, this topic remains controversial, partially due to the indirect and ensemble nature of existing measurements. Here, we used recently developed single-molecule approaches to monitor directly the motions of individual proteins in aqueous solution and find that single alkaline phosphatase enzymes do not diffuse faster under catalysis. Instead, we demonstrate that interactions between the fluorescent dye and the enzyme’s substrate can produce the signature of apparent diffusion enhancement in fluorescence correlation spectroscopy, the standard ensemble assay currently used to study enzyme diffusion and indicate that single-molecule approaches provide a more robust means to investigate diffusion at the nanoscale.

Theoretical and experimental observations that catalysis enhances the diffusion of enzymes have generated exciting implications about nanoscale energy flow, molecular chemotaxis, and self-powered nanomachines. However, contradictory claims on the origin, magnitude, and consequence of this phenomenon continue to arise. To date, experimental observations of catalysis-enhanced enzyme diffusion have relied almost exclusively on fluorescence correlation spectroscopy (FCS), a technique that provides only indirect, ensemble-averaged measurements of diffusion behavior. Here, using an anti-Brownian electrokinetic (ABEL) trap and in-solution single-particle tracking, we show that catalysis does not increase the diffusion of alkaline phosphatase (ALP) at the single-molecule level, in sharp contrast to the ∼20% enhancement seen in parallel FCS experiments using p-nitrophenyl phosphate (pNPP) as substrate. Combining comprehensive FCS controls, ABEL trap, surface-based single-molecule fluorescence, and Monte Carlo simulations, we establish that pNPP-induced dye blinking at the ∼10-ms timescale is responsible for the apparent diffusion enhancement seen in FCS. Our observations urge a crucial revisit of various experimental findings and theoretical models––including those of our own––in the field, and indicate that in-solution single-particle tracking and ABEL trap are more reliable means to investigate diffusion phenomena at the nanoscale.

Cu(II)-Regulated On-Site Assembly of Highly Chemiluminescent Multifunctionalized Carbon Nanotubes for Inorganic Pyrophosphatase Activity Determination

A novel signal-on chemiluminescence (CL) assay for pyrophosphatase (PPase) activity determination was innovatively developed based on the Cu(II)-regulated on-site assembly of highly chemiluminescent Cu(II), N-(aminobutyl)-N-(ethylisoluminol) (ABEI), gold nanodot, and chitosan multifunctionalized carbon nanotubes (Cu(II)/ABEI-Au/cs-CNTs). First, ABEI-functionalized gold nanodots (ABEI-Au) were assembled on the surface of chitosan-modified carbon nanotubes (cs-CNTs) via the reduction of HAuCl₄ with ABEI in a cs-CNT suspension to form ABEI-Au/cs-CNTs. Then, it was found that the catalyst Cu(II) can be selectively, efficiently, and quickly adsorbed onto ABEI-Au/cs-CNTs via the high-affinity interactions between Cu(II) and cs-CNTs to form novel hybrid nanomaterials Cu(II)/ABEI-Au/cs-CNTs. The CL intensity of Cu(II)/ABEI-Au/cs-CNTs was enhanced by about 2 orders of magnitude compared with that of ABEI-Au/cs-CNTs. Furthermore, it was found that in the presence of pyrophosphate ions (PPi), PPi could coordinate with Cu(II) to form a stable PPi-Cu(II) complex and block the assembly of Cu(II)/ABEI-Au/cs-CNTs. After the addition of PPase, PPase could catalyze the hydrolysis of PPi into Pi and release Cu(II) from the PPi-Cu(II) complex. The released free Cu(II) could trigger the on-site assembly of highly chemiluminescent Cu(II)/ABEI-Au/cs-CNTs, resulting in an enhanced CL intensity. The enhanced CL intensity had a good linear relationship with the activity units of PPase ranging from 0.025 to 0.5 U, with a detection limit of 9 mU. The method was employed to monitor the PPase inhibitor efficiently. Cu(II)/ABEI-Au/cs-CNTs with excellent CL may also find more applications in the development of novel CL analytical methods.

Quantum Dot Doping-Induced Photoluminescence for Facile, Label-Free, and Sensitive Pyrophosphatase Activity Assay and Inhibitor Screening

Development of simple, convenient, and sensitive assay methods for pyrophosphatase (PPase) activity is of importance, for disease diagnosis and drug discovery. Herein, a simple, rapid, label-free, and sensitive fluorescence sensor for PPase activity assay is developed, using Cu²⁺ doping-induced quantum dot (QD) photoluminescence as a signal reporter. The Cu²⁺ doping of ZnSe QD can induce a dopant-dependent emission response, which will be inhibited after the premixing of Cu²⁺ with pyrophosphate (PPi), to form a Cu²⁺-PPi complex. Then, the hydrolysis of PPi into phosphate (Pi), specifically catalyzed by PPase, liberates the free Cu²⁺ to regain the QD doping for the fluorescence response, which is highly dependent on the PPase activity. The PPase can be sensitively and selectively assayed, with a detection limit of 0.1 mU/mL. The developed sensing strategy can be also employed for the PPase inhibitor screening. Thus, the current QD doping-based sensing strategy offers an efficient and promising avenue for Cu²⁺, PPi, or PPase-related target analysis, and might hold great potential for the further applications in the clinical disease diagnosis.

A novel fluorometric method for inorganic pyrophosphatase detection based on G-quadruplex-thioflavin T

In this paper, we propose a fluorometric approach for the highly sensitive detection of inorganic pyrophosphatase (PPase) based on G-quadruplex-thioflavin T (ThT). In the absence of PPase, Cu²⁺ can coordinate with pyrophosphate (PPi) to generate a Cu²⁺/PPi complex. Then the G-rich sequence folds into the G-quadruplex structure, which can combine with ThT to generate a remarkable fluorescent signal. In the presence of PPase, the coordinated compound can be destroyed by the PPase catalyzed hydrolysis of PPi into inorganic phosphate (Pi). The subsequent release of Cu²⁺ can compete with ThT to induce a tighter G-quadruplex structure, causing the release of ThT and a sharp fluorescence decrease. Based on this mechanism, a facile and quantitative strategy for PPase detection was developed. The fluorescence intensity of the system shows a linear relationship with the PPase activities in the range of 0.5-30 U/L with a detection limit as low as 0.48 U/L. The proposed strategy for fluorescence spectrometric PPase detection is convenient, cost effective, and sensitive. This can be utilized to evaluate the inhibition effect of NaF on PPase as well as diagnose PPase-related diseases.

Inorganic pyrophosphatases of Family II-two decades after their discovery

Inorganic pyrophosphatases (PPases) convert pyrophosphate (PP_i ) to phosphate and are present in all cell types. Soluble PPases belong to three nonhomologous families, of which Family II is found in approximately a quarter of prokaryotic organisms, often pathogenic ones. Each subunit of dimeric canonical Family II PPases is formed by two domains connected by a flexible linker, with the active site located between the domains. These enzymes require both magnesium and a transition metal ion (manganese or cobalt) for maximal activity and are the most active (k_cat ≈ 10⁴ s^-1 ) among all PPase types. Catalysis by Family II PPases requires four metal ions per substrate molecule, three of which form a unique trimetal center that coordinates the nucleophilic water and converts it to a reactive hydroxide ion. A quarter of Family II PPases contain an autoinhibitory regulatory insert formed by two cystathionine β-synthase (CBS) domains and one DRTGG domain. Adenine nucleotide binding either activates or inhibits the CBS domain-containing PPases, thereby tuning their activity and, hence, PP_i levels, in response to changes in cell energy status (ATP/ADP ratio).

Colorimetric Logic Gate for Pyrophosphate and Pyrophosphatase via Regulating the Catalytic Capability of Horseradish Peroxidase

By regulating the catalytic capability of horseradish peroxidase (HRP), an artful colorimetric assay platform for pyrophosphate (PPi) and pyrophosphatase (PPase) was unprecedentedly designed. In this work, Cu(I), generated by reducing Cu(II) in the presence of ascorbate, could inhibit HRP's catalytic capability of transforming colorless 3,3',5,5'-tetramethylbenzidine (TMB) into blue oxidized TMB (oxTMB). The robust coordination between PPi and Cu(II) is able to discourage the reduction of Cu(II) to Cu(I) effectively, thus restoring the original catalytic capability of HRP and regenerating blue-colored oxTMB. Upon PPase introduction, PPi would be hydrolyzed into orthophosphate, which could release Cu(II) free from the Cu(II)-PPi complex, and thus in turn allows the catalytic capability of HRP to be inhibited by Cu(I). HRP was activated or deactivated to different degrees depending on PPi or PPase levels, which could be indicated by using HRP-triggered catalytic system as a signal amplifier, thus paving a way for PPi and PPase sensing. Based on the colorimetric sensor for PPi and PPase, an "INH" logic gate was rationally constructed. With the merits of high sensitivity and selectivity, cost-effectiveness, and simplification, our proposed analytical system has also been verified to have potential to be utilized for enzyme inhibitor screening and diagnosis of PPase-related diseases.

Construction of a Turn Off-On-Off Fluorescent System Based on Competitive Coordination of Cu2+ between 6,7-Dihydroxycoumarin and Pyrophosphate Ion for Sensitive Assay of Pyrophosphatase Activity

The detection of pyrophosphatase (PPase) activity is of great significance in diagnosing diseases and understanding the function of PPase-related biological events. This study constructed a turn off-on-off fluorescent system for PPase activity assay based on PPase-regulated competitive coordination of Cu²⁺ between a water-soluble fluorescent probe 6,7-dihydroxycoumarin (DHC) and pyrophosphate (PPi). The probe DHC can coordinate with Cu²⁺ and consequently display on-off type fluorescence response. Furthermore, the in situ formed nonfluorescent Cu²⁺-DHC complex can act as an effective off-on type fluorescent probe for sensing PPi due to the higher coordination reactivity between Cu²⁺ and PPi than that between Cu²⁺ and DHC. The subsequent addition of PPase to the mixture containing Cu²⁺, DHC, and PPi leads to the fluorescence requenching of the system again (an off state) because PPase catalyzes the hydrolysis of PPi into orthophosphate in the reaction system. Under the optimum conditions, the decrease of the fluorescence intensity of DHC-Cu²⁺-PPi system was linear with the increase of the PPase activity in the range from 0.1 to 0.3 U. The detection limit was down to 0.028 U PPase (S/N = 3). Moreover, the as-established system was also applied to evaluate PPase inhibitor. This study offers a simple yet effective method for the detection of PPase activity.

A novel fluorescence assay for inorganic pyrophosphatase based on modulated aggregation of graphene quantum dots

A simple and highly sensitive fluorometric method has been developed for inorganic pyrophosphatase (PPase) activity detection based on the disaggregation and aggregation of graphene quantum dots (GQDs).

Visualization and quantification of neurochemicals with gold nanoparticles: opportunities and challenges

Gold nanoparticle (Au-NP)-based colorimetric assays offer new opportunitites for the visualization and quantification of neurochemicals involved in physiological and pathological processes due to their high sensitivity, designability, and low technical demands. In this Research News, we systematically review the advances on the development of Au-NP-based colorimetric methods for visualization and quantification of neurochemicals and their potential applications for effectively monitoring neurochemicals in the central nervous system. By integration of the favourable surface chemistry with the high extinction coefficient of Au-NPs, some new principles and methods could be developed for the quantification of neurochemicals involved in brain functions. New strategies to design the surface chemistry of Au-NPs, along with the key challenges yet to be addressed to achieve online visualization and quantification of neurochemicals in the central nervous system, are illustrated and discussed. The questions opened here should inspire future investigations and lead to discoveries that continue the development of the effective analytical protocols based on Au-NPs for neurochemical visualization and quantification.