The biochemically defined super relaxed state of myosin-A paradox.

The biochemical SRX (super-relaxed) state of myosin has been defined as a low ATPase activity state. This state can conserve energy when the myosin is not recruited for muscle contraction. The SRX state has been correlated with a structurally defined ordered (versus disordered) state of muscle thick filaments. The two states may be linked via a common interacting head motif (IHM) where the two heads of heavy meromyosin (HMM), or myosin, fold back onto each other and form additional contacts with S2 and the thick filament. Experimental observations of the SRX, IHM, and the ordered form of thick filaments, however, do not always agree, and result in a series of unresolved paradoxes. To address these paradoxes, we have reexamined the biochemical measurements of the SRX state for porcine cardiac HMM. In our hands, the commonly employed mantATP displacement assay was unable to quantify the population of the SRX state with all data fitting very well by a single exponential. We further show that mavacamten inhibits the basal ATPases of both porcine ventricle HMM and S1 (Ki, 0.32 and 1.76 µM respectively) while dATP activates HMM cooperatively without any evidence of an SRX state. A combination of our experimental observations and theories suggests that the displacement of mantATP in purified proteins is not a reliable assay to quantify the SRX population. This means that while the structurally defined IHM and ordered thick filaments clearly exist, great care must be employed when using the mantATP displacement assay.

A Reference Range for Plasma Levels of Inorganic Pyrophosphate in Children Using the ATP Sulfurylase Method.

PURPOSE: Generalized arterial calcification of infancy, pseudoxanthoma elasticum, autosomal recessive hypophosphatemic rickets type 2, and hypophosphatasia are rare inherited disorders associated with altered plasma levels of inorganic pyrophosphate (PPi). In this study, we aimed to establish a reference range for plasma PPi in the pediatric population, which would be essential to support its use as a biomarker in children with mineralization disorders. METHODS: Plasma samples were collected from 200 children aged 1 day to 18 years who underwent blood testing for medical conditions not affecting plasma PPi levels. PPi was measured in proband plasma utilizing a validated adenosine triphosphate (ATP) sulfurylase method. RESULTS: The analytical sensitivity of the ATP sulfurylase assay consisted of 0.15 to 10 µM PPi. Inter- and intra-assay coefficients of variability on identical samples were below 10%. The standard range of PPi in the blood plasma of children and adolescents aged 0 to 18 years was calculated as 2.36 to 4.44 µM, with a median of 3.17 µM, with no difference between male and female probands. PPi plasma levels did not differ significantly in different pediatric age groups. MAIN CONCLUSIONS: Our results yielded no noteworthy discrepancy to the reported standard range of plasma PPi in adults (2-5 µM). We propose the described ATP sulfurylase method as a diagnostic tool to measure PPi levels in plasma as a biomarker in the pediatric population.

Understanding LRRK2 kinase activity in preclinical models and human subjects through quantitative analysis of LRRK2 and pT73 Rab10.

Variants in the leucine-rich repeat kinase 2 (LRRK2) gene are associated with increased risk for familial and sporadic Parkinson's disease (PD). Pathogenic variants in LRRK2, including the common variant G2019S, result in increased LRRK2 kinase activity, supporting the therapeutic potential of LRRK2 kinase inhibitors for PD. To better understand the role of LRRK2 in disease and to support the clinical development of LRRK2 inhibitors, quantitative and high-throughput assays to measure LRRK2 levels and activity are needed. We developed and applied such assays to measure the levels of LRRK2 as well as the phosphorylation of LRRK2 itself or one of its substrates, Rab10 (pT73 Rab10). We observed increased LRRK2 activity in various cellular models of disease, including iPSC-derived microglia, as well as in human subjects carrying the disease-linked variant LRRK2 G2019S. Capitalizing on the high-throughput and sensitive nature of these assays, we detected a significant reduction in LRRK2 activity in subjects carrying missense variants in LRRK2 associated with reduced disease risk. Finally, we optimized these assays to enable analysis of LRRK2 activity following inhibition in human peripheral blood mononuclear cells (PBMCs) and whole blood, demonstrating their potential utility as biomarkers to assess changes in LRRK2 expression and activity in the clinic.

Application of a six sigma model to the evaluation of the analytical performance of serum enzyme assays and the design of a quality control strategy for these assays: A multicentre study.

BACKGROUND: Six medical testing laboratories at six different sites in China participated in this study. We applied a six sigma model for (a) the evaluation of the analytical performance of serum enzyme assays at each of the laboratories, (b) the design of individualized quality control programs and (c) the development of improvement measures for each of the assays, as appropriate. METHODS: Internal quality control (IQC) and external quality assessment (EQA) data for selected serum enzyme assays were collected from each of the laboratories. Sigma values for these assays were calculated using coefficients of variation, bias, and total allowable error (TEa). Normalized sigma method decision charts were generated using these parameters. IQC design and improvement measures were defined using the Westgard sigma rules. The quality goal index (QGI) was used to assist with identification of deficiencies (bias problems, precision problems, or their combination) affecting the analytical performance of assays with sigma values <6. RESULTS: Sigma values for the selected serum enzyme assays were significantly different at different levels of enzyme activity. Differences in assay quality in different laboratories were also seen, despite the use of identical testing instruments and reagents. Based on the six sigma data, individualized quality control programs were outlined for each assay with sigma <6 at each laboratory. CONCLUSIONS: In multi-location laboratory systems, a six sigma model can evaluate the quality of the assays being performed, allowing management to design individualized IQC programs and strategies for continuous improvement as appropriate for each laboratory. This will improve patient care, especially for patients transferred between sites within multi-hospital systems.

Commutability Assessment of Candidate External Quality Assessment Materials for Aminotransferase Activity Measurements Based on Different Approaches in China.

BACKGROUND: Using commutable external quality assessment (EQA) materials is important for monitoring successful harmonization efforts. We assessed the commutability of four human serum pool (HSP) preparations to identify candidate EQA materials for alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activity measurement. METHODS: One set each of 85 clinical samples (CSs) was collected for ALT and AST activity measurement. The 15 candidate EQA materials included four types of HSP preparations (A to D): materials A, C, and D contained human original recombinant (HOR) aminotransferases; materials B was mixed leftover samples. The CSs and 15 candidate EQA materials were analyzed using seven routine assays, and the ln-transformed results were analyzed in 21 assay pairs. Commutability was assessed using Deming regression, with a 95% prediction interval (CLSI approach) and the difference in bias with an error component model (International Federation of Clinical Chemistry and Laboratory Medicine [IFCC] approach). RESULTS: For ALT, all materials were commutable for 14-21 assay pairs according to the CLSI and IFCC approaches. For AST, B01-03 showed commutability for 14-21 assay pairs, and C01-03 and D01-03 showed commutability for no less than 10 assay pairs according to the two approaches. A01-06 were commutable for 9-16 assay pairs according to the CLSI approach, but for 6-9 assay pairs according to the IFCC approach. CONCLUSIONS: Mixed leftover samples showed desirable commutability characteristics as candidate EQA materials for routine aminotransferase activity measurements. Human serum bases supplemented with HOR were commutable for most routine ALT activity measurements.

interferENZY: A Web-Based Tool for Enzymatic Assay Validation and Standardized Kinetic Analysis.

Enzymatic assays are widely employed to characterize important allosteric and enzyme modulation effects. The high sensitivity of these assays can represent a serious problem if the occurrence of experimental errors surreptitiously affects the reliability of enzyme kinetics results. We have addressed this problem and found that hidden assay interferences can be unveiled by the graphical representation of progress curves in modified reaction coordinates. To render this analysis accessible to users across all levels of expertise, we have developed a webserver, interferENZY, that allows (i) an unprecedented tight quality control of experimental data, (ii) the automated identification of small and major assay interferences, and (iii) the estimation of bias-free kinetic parameters. By eliminating the subjectivity factor in kinetic data reporting, interferENZY will contribute to solving the "reproducibility crisis" that currently challenges experimental molecular biology. The interferENZY webserver is freely available (no login required) at https://interferenzy.i3s.up.pt.

Improvement of Ficin-Based Inhibitive Enzyme Assay for Toxic Metals Using Response Surface Methodology and Its Application for Near Real-Time Monitoring of Mercury in Marine Waters.

Potentially toxic metals pollution in the Straits of Malacca warrants the development of rapid, simple and sensitive assays. Enzyme-based assays are excellent preliminary screening tools with near real-time potential. The heavy-metal assay based on the protease ficin was optimized for mercury detection using response surface methodology. The inhibitive assay is based on ficin action on the substrate casein and residual casein is determined using the Coomassie dye-binding assay. Toxic metals strongly inhibit this hydrolysis. A central composite design (CCD) was utilized to optimize the detection of toxic metals. The results show a marked improvement for the concentration causing 50% inhibition (IC50) for mercury, silver and copper. Compared to one-factor-at-a-time (OFAT) optimization, RSM gave an improvement of IC50 (mg/L) from 0.060 (95% CI, 0.030-0.080) to 0.017 (95% CI, 0.016-0.019), from 0.098 (95% CI, 0.077-0.127) to 0.028 (95% CI, 0.022-0.037) and from 0.040 (95% CI, 0.035-0.045) to 0.023 (95% CI, 0.020-0.027), for mercury, silver and copper, respectively. A near-real time monitoring of mercury concentration in the Straits of Malacca at one location in Port Klang was carried out over a 4 h interval for a total of 24 h and validated by instrumental analysis, with the result revealing an absence of mercury pollution in the sampling site.

Three-dimensional donor-acceptor-type photoactive material/conducting polyaniline hydrogel complex for sensitive photocathodic enzymatic bioanalysis.

Herein, an innovative photocathodic enzymatic biosensor is proposed with poly {4,8-bis[5-(2-ethylhexyl)thiophen-2-yl]-benzo[1,2-b:4,5-b']dithiophene-2,6-diyl-alt-3-fluoro-2-[(2-ethylhexyl)carbonyl]thieno[3,4-b]thiophene-4,6-diyl} (PTB7-Th) as donor-acceptor-type photoactive material and three-dimensional (3D) polyaniline hydrogels (PAniHs) as both electron transfer layer and biomolecule carrier. Based on the enhancement effect of PAniHs on the charge separation and electron transfer of PTB7-Th and the competitive consumption of dissolved oxygen (O2) between the xanthine oxidase (XOD)-guanine catalytic reaction and O2-sensitive PTB7-Th/PAniHs, the proposed photocathodic enzymatic biosensor has been demonstrated to detect guanine with the advantages of low limit of detection (0.02 µM), wide linear range (from 0.1 to 80 µM), simple and convenient preparation process, satisfactory stability, and photochemical signal amplification independent of any exogenous electron donor/acceptor or sensitizer. Remarkably, the proposed photocathodic enzymatic biosensor can not only be extended to other aerobic enzymatic bioanalyses, but also pave a horizon for the application of environmentally friendly conductive hydrogel materials in photoelectrochemical bioanalysis.

Membrane Protein Solubilization and Quality Control: An Example of a Primary Active Transporter.

When purifying a membrane protein, finding a detergent for solubilization is one of the first steps to master. Ideally, only little time is invested to identify the best-suited detergent, which on the one hand would solubilize large amounts of the target protein but on the other hand would sustain the protein's activity. Here we describe the solubilization screen and subsequent activity assay we have optimized for the bacterial P-type ATPase KdpFABC. In just 2 days, more than 70 detergents were tested for their solubilization potential. Afterwards, a smaller selection of the successful detergents was assayed for their ability to retain the activity of the membrane protein complex.

A simple and reliable method for determination of optimum pH in coupled enzyme assays.

Determination of the optimum pH in a coupled enzyme assay poses significant challenges because altering the pH of the reaction mixture can affect the performance of both enzymes. Here, we demonstrate a simple and reliable method to determine the pH optimum for pyruvate kinase using the pyruvate kinase/lactate dehydrogenase coupled enzyme assay. This simple and reliable method can be broadly adapted to determine the pH optimum for various enzymes that are assayed using a coupled enzyme assay.

In Vitro Assays for Measuring Protein Histidine Phosphatase Activity.

In order to obtain a detailed kinetic characterization, identify inhibitors, and elucidate the biological roles of an enzyme, it is advantageous to have a facile, sensitive enzyme assay protocol. Here we present a brief overview of the techniques available to monitor histidine phosphatase activity and provide protocols for measuring the activity and inhibition of PHPT1 in vitro using the fluorescent probe 6,8-difluoro-4-methylumbelliferyl phosphate (DiFMUP). This assay uses small quantities of commercially available materials, making its use feasible for most laboratories.

A Simple In Vitro Assay to Measure the Activity of Geranylgeranyl Diphosphate Synthase and Other Short-Chain Prenyltransferases.

Most carotenoids are C40 metabolites produced from C20 geranylgeranyl diphosphate (GGPP). The enzymes that produce this precursor, GGPP synthases (GGPPS), are members of the short-chain prenyltransferase (SC-PT) family. SC-PTs are enzymes that catalyze the sequential head-to-tail addition of one or more C5 molecules of isopentenyl diphosphate (IPP) to dimethylallyl diphosphate (DMAPP) with the concomitant release of pyrophosphate (PPi). SC-PTs produce linear isoprenyl diphosphates of up to C20 (GGPP) that serve as precursors for many groups of isoprenoids with a wide range of essential biological functions in Eucarya, Bacteria, and Archaea. Enzymatic analysis of SC-PT activity normally requires complex, laborious and expensive methods such as radioactivity-based assays or liquid chromatography-mass spectrometry (LC-MS). Here we describe a fast and inexpensive spectrophotometric protocol for determining the kinetic parameters of SC-PTs in purified enzyme preparations, using an adapted assay for PPi quantification. We developed the method using the Arabidopsis thaliana GGPPS11 enzyme, which produces geranylgeranyl diphosphate for the synthesis of carotenoids in the chloroplast.

Investigations beyond standard operating procedure on internal standard response.

Internal standard response is routinely monitored in regulated studies to accept or reject individual samples with outlier results due to potential sample processing or instrumentation errors, and processes are typically governed by standard operating procedures. However, acceptance or rejection of individual samples is not always sufficient. Internal standard response trends and substantial systemic differences between spiked and incurred samples using a method with an otherwise stable internal standard response should be investigated. Investigations may range from informal evaluations to detailed studies with formal investigation reports. Atypical internal standard response can be an indicator of systemic problems with a bioanalytical method and modification to allow for a relatively stable internal standard response across an analytical run may be essential.

Use of lentiviral pseudotypes as an alternative to reassortant or Triton X-100-treated wild-type Influenza viruses in the neuraminidase inhibition enzyme-linked lectin assay.

BACKGROUND: Formulation of neuraminidase (NA) within influenza vaccines is gaining importance in light of recent human studies. The enzyme-linked lectin assay (ELLA) is considered a reliable assay to evaluate human anti-NA antibodies. OBJECTIVES: To overcome interference by hemagglutinin (HA)-specific antibodies and detect neuraminidase inhibitory (NI) antibodies only, two different sources of antigen have been studied in ELLA: reassortant viruses with a mismatched avian origin-HA or Triton X-100 (Tx)-treated wild-type viruses. Pseudotypes or pseudovirus (PV), characterized by a lentivirus core bearing human influenza NA and avian influenza HA, were investigated as an alternative source of antigen and compared to HA-mismatched and Tx-treated viruses, since represent a safer product to be handled. METHODS: Two independent panels of sera were analyzed by ELLA to evaluate the anti-NA response against N1 (A/California/07/2009 (H1N1pdm)) and N2 (A/Hong Kong/4801/2014 (H3N2)). The NA inhibition (NI) antibody titers measured as either the 50% end point or 50% inhibitory concentration (IC50 ) were compared for every source of antigen. RESULTS: The ELLA assay performed well with all three sources of antigen. NI titers measured using each antigen type correlated well when reported either as end point titers or as the IC50 . CONCLUSIONS: This study suggests that HA-mismatched whole virus, Triton-treated wild-type virus or PV can be used to measure NI antibody titers of human sera, but further comparability/validation assays should be performed to assess statistical differences. The data support the use of PV as an attractive alternative source of antigen and justify further investigation to improve stability of this antigen source.

Screening for Tay-Sachs disease carriers by full-exon sequencing with novel variant interpretation outperforms enzyme testing in a pan-ethnic cohort.

BACKGROUND: Pathogenic variants in HEXA that impair ß-hexosaminidase A (Hex A) enzyme activity cause Tay-Sachs Disease (TSD), a severe autosomal-recessive neurodegenerative disorder. Hex A enzyme analysis demonstrates near-zero activity in patients affected with TSD and can also identify carriers, whose single functional copy of HEXA results in reduced enzyme activity relative to noncarriers. Although enzyme testing has been optimized and widely used for carrier screening in Ashkenazi Jewish (AJ) individuals, it has unproven sensitivity and specificity in a pan-ethnic population. The ability to detect HEXA variants via DNA analysis has evolved from limited targeting of a few ethnicity-specific variants to next-generation sequencing (NGS) of the entire coding region coupled with interpretation of any discovered novel variants. METHODS: We combined results of enzyme testing, retrospective computational analysis, and variant reclassification to estimate the respective clinical performance of TSD screening via enzyme analysis and NGS. We maximized NGS accuracy by reclassifying variants of uncertain significance and compared to the maximum performance of enzyme analysis estimated by calculating ethnicity-specific frequencies of variants known to yield false-positive or false-negative enzyme results (e.g., pseudodeficiency and B1 alleles). RESULTS: In both AJ and non-AJ populations, the estimated clinical sensitivity, specificity, and positive predictive value were higher by NGS than by enzyme testing. The differences were significant for all comparisons except for AJ clinical sensitivity, where NGS exceeded enzyme testing, but not significantly. CONCLUSIONS: Our results suggest that performance of an NGS-based TSD carrier screen that interrogates the entire coding region and employs novel variant interpretation exceeds that of Hex A enzyme testing, warranting a reconsideration of existing guidelines.

Estimating kinetic constants in the Michaelis-Menten model from one enzymatic assay using Approximate Bayesian Computation.

The Michaelis-Menten equation is one of the most extensively used models in biochemistry for studying enzyme kinetics. However, this model requires at least a couple (e.g., eight or more) of measurements at different substrate concentrations to determine kinetic parameters. Here, we report the discovery of a novel tool for calculating kinetic constants in the Michaelis-Menten equation from only a single enzymatic assay. As a consequence, our method leads to reduced costs and time, primarily by lowering the amount of enzymes, since their isolation, storage and usage can be challenging when conducting research.

Lower creatinine concentration values and lower inter-laboratory variation among Swedish hospital laboratories in 2014 compared to 1996: results from the Equalis external quality assessment program.

Background Creatinine measurement for estimation of glomerular filtration rate (GFR) is a frequently used laboratory test. Differences in analytic creatinine methods have caused large inter-laboratory variation. International and national standardization efforts have been made in the last decade. Methods This study describes the results of the standardization efforts in Sweden by summarizing data for creatinine concentration in blood plasma in the Equalis quality assessment program during 1996-2014. Results Non-compensated Jaffe methods dominated in 1996-2001 (91 of 103 laboratories; 90%) and were then gradually replaced by either compensated Jaffe methods or enzymatic creatinine methods. In 2014 a majority of Swedish hospital laboratories (139 of 159; 87%) used enzymatic methods. The reported mean creatinine value by the Swedish laboratories was about 10 µmol/L higher than the isotope dilution mass spectrometry (IDMS) assured reference value in 2003, but consistent with the reference value from 2009 to 2014. The inter-laboratory CV was 7%-9% for creatinine values until 2007, and thereafter gradually decreased to about 4%-5% in 2014. Conclusions The introduction of enzymatic methods in Swedish laboratories has contributed to achieving a low inter-laboratory variation. Also, the reported values are lower for enzymatic methods compared to Jaffe methods, and the values obtained with enzymatic methods were consistent with IDMS certified values established at reference laboratories. Thus, many Swedish hospital laboratories reported 10 µmol/L lower, and more true, creatinine concentrations in 2012 than in 2003, which may cause bias in longitudinal studies.

INFOGEST static in vitro simulation of gastrointestinal food digestion.

Developing a mechanistic understanding of the impact of food structure and composition on human health has increasingly involved simulating digestion in the upper gastrointestinal tract. These simulations have used a wide range of different conditions that often have very little physiological relevance, and this impedes the meaningful comparison of results. The standardized protocol presented here is based on an international consensus developed by the COST INFOGEST network. The method is designed to be used with standard laboratory equipment and requires limited experience to encourage a wide range of researchers to adopt it. It is a static digestion method that uses constant ratios of meal to digestive fluids and a constant pH for each step of digestion. This makes the method simple to use but not suitable for simulating digestion kinetics. Using this method, food samples are subjected to sequential oral, gastric and intestinal digestion while parameters such as electrolytes, enzymes, bile, dilution, pH and time of digestion are based on available physiological data. This amended and improved digestion method (INFOGEST 2.0) avoids challenges associated with the original method, such as the inclusion of the oral phase and the use of gastric lipase. The method can be used to assess the endpoints resulting from digestion of foods by analyzing the digestion products (e.g., peptides/amino acids, fatty acids, simple sugars) and evaluating the release of micronutrients from the food matrix. The whole protocol can be completed in ~7 d, including ~5 d required for the determination of enzyme activities.

Measuring lipoprotein-associated phospholipase A2 activity in China: Protocol comparison and recalibration.

BACKGROUND: Lp-PLA2 is a novel inflammation marker in cardiovascular disease. While several manufactures have registered Lp-PLA2 activity reagents, few studies have investigated the consistency among these assays. In this study, we compared and recalibrated Lp-PLA2 activity assays. METHODS: Serum samples from 110 patients and 140 healthy individuals were collected for method comparison and reference interval validation, respectively. Fresh human serum pools (847 and 442 U/L) were used for recalibration. Lp-PLA2 activity was analyzed using all five assays with a Beckman AU 5800 analyzer. Passing-Bablok regression equations and Bland-Altman plots were used to estimate the relationship and bias among the results. A 2.5% confidence interval (CI) and 97.5% CI were used to establish a laboratory reference interval. RESULTS: Assay imprecision varied from 0.8%-2.9%, while the overall coincidence rates ranged from 75.5%-98.2%. Passing-Bablok regression shows excellent linear correlation between Evermed and Diasys (R2  = 0.999), while that between Diazyme and Evermed was poor (R2  = 0.846). The R2 and correlation coefficient r among assays were 0.846-0.999 and 0.8947-0.9993, respectively. The mean bias percentages ranged from -71.5%-1.6% and -2.0%-11.6% before and after recalibration. As Diazyme and Diasys were not comparable, the Diazyme assay was not recalibrated. The reference intervals determined for Diasys, Evermed, Hengxiao, and Zybio were 184-605, 208-704, 81-328, and 273-696 U/L, respectively. CONCLUSIONS: Our results indicate that recalibration increased assay agreement and also highlight the need for each laboratory to establish its own reference interval for Lp-PLA2 activity.