AI Article Synopsis
Article Abstract
Background: Continuous enzyme kinetic assays are often used in high-throughput applications, as they allow rapid acquisition of large amounts of kinetic data and increased confidence compared to discontinuous assays. However, data analysis is often rate-limiting in high-throughput enzyme assays, as manual inspection and selection of a linear range from individual kinetic traces is cumbersome and prone to user error and bias. Currently available software programs are specialized and designed for the analysis of complex enzymatic models. Despite the widespread use of initial rate determination for processing kinetic data sets, no simple and automated program existed for rapid analysis of initial rates from continuous enzyme kinetic traces.
Results: An Interactive Continuous Enzyme Kinetics Analysis Tool (ICEKAT) was developed for semi-automated calculation of initial rates from continuous enzyme kinetic traces with particular application to the evaluation of Michaelis-Menten and EC/IC kinetic parameters, as well as the results of high-throughput screening assays. ICEKAT allows users to interactively fit kinetic traces using convenient browser-based selection tools, ameliorating tedious steps involved in defining ranges to fit in general purpose programs like Microsoft Excel and Graphpad Prism, while still maintaining simplicity in determining initial rates. As a test case, we quickly analyzed over 500 continuous enzyme kinetic traces resulting from experimental data on the response of the protein lysine deacetylase SIRT1 to small-molecule activators.
Conclusions: ICEKAT allows simultaneous visualization of individual initial rate fits and the resulting Michaelis-Menten or EC/IC kinetic model fits, as well as hits from high-throughput screening assays. In addition to serving as a convenient program for practicing enzymologists, ICEKAT is also a useful teaching aid to visually demonstrate in real-time how incorrect initial rate fits can affect calculated Michaelis-Menten or EC/IC kinetic parameters. For the convenience of the research community, we have made ICEKAT freely available online at https://icekat.herokuapp.com/icekat.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222511 | PMC |
| http://dx.doi.org/10.1186/s12859-020-3513-y | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Background: Hepatic glycogen storage diseases (GSDs) are characterised by enzyme defects affecting liver glycogen metabolism, where carbohydrate supplementation to prevent overnight hypoglycaemia is common. Concerns around sleep quality in hepatic GSDs relate to emerging evidence that overnight dysglycaemia impacts sleep quality.
Methods: This prospective observational study reported sleep quality and duration in children with hepatic GSDs over 7 days utilising: actigraphy (Actiwatch 2 by Phillips Respironics), sleep diaries, proxy reported age-appropriate sleep and quality-of-life (QoL) questionnaires, in the context of nocturnal glycaemic profiles continuous glucose monitor (CGM, Dexcom G6) and nocturnal dietary management strategies.
Diethyl nitrosamine-induces neurobehavioral deficit, oxido-nitrosative stress in rats' brain: a neuroprotective role of diphenyl diselenide.
BMC Neurosci
December 2024
Department of Anatomy, Faculty of Basic Medical Sciences, University of Ibadan, Ibadan, Oyo State, Nigeria.
Diethylnitrosamine (DEN), a common dietary carcinogen, is associated with neurotoxicity in humans and animals. This study investigated the neuroprotective effects of diphenyl diselenide (DPDS) against DEN-induced neurotoxicity in male Albino Wistar rats (n = 40). Rats were randomly distributed into cohorts and treated as follows: vehicle control (corn oil 2 mL/kg; gavage), DPDS-only (5 mg/kg; gavage) and DEN-only (200 mg/kg; single dose i.
View Article and Find Full Text PDFElucidating the impact of mulching film on organic carbon mineralization from the perspective of aggregate level.
Sci Total Environ
December 2024
Key Laboratory of Low-carbon Green Agriculture in Northwestern China, Ministry of Agriculture and Rural Affairs, College of Natural Resources and Environment, Northwest A & F University, Yangling 712100, China. Electronic address:
Plastic films mulching, a management strategy designed to boost agricultural productivity, significantly impacts soil fertility and the turnover of soil organic carbon (SOC). Aggregates in the soil play a crucial role in this SOC cycling. Yet, the effect of mulching on the changes in organic carbon components and the mineralization at the aggregate scale is still not well understood.
View Article and Find Full Text PDFBioisosteric replacement of pyridoxal-5'-phosphate to pyridoxal-5'-tetrazole targeting Bacillus subtilis GabR.
Protein Sci
January 2025
Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA.
Antimicrobial resistance is a significant cause of mortality globally due to infections, a trend that is expected to continue to rise. As existing treatments fail and new drug discovery slows, the urgency to develop novel antimicrobial therapeutics grows stronger. One promising strategy involves targeting bacterial systems exclusive to pathogens, such as the transcription regulator protein GabR.
View Article and Find Full Text PDFInborn Errors of Immunity: New Insights.
Acta Med Acad
December 2024
University of Rijeka, Faculty of Medicine, Rijeka, Croatia.
This paper presents a comprehensive and updated overview of inborn errors of immunity (IEIs), focusing on the optimal treatment strategies. IEIs or primary immunodeficiencies (PIDs) are a heterogeneous group of approximately 500 disorders, classified into ten categories according to the affected component of the immune system. The clinical presentation varies, based on the type of the disorder and the patient's age.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!