Enzyme Kinetics Analysis (EKA): an online tool for analysing enzyme initial rate data and teaching enzyme kinetics

Type of content
Journal Article
Thesis discipline
Degree name
Publisher
Wiley
Journal Title
Journal ISSN
Volume Title
Language
en
Date
2024
Authors
Mak D
Dunn S
Coombes D
Carere C
Allison JR
Nock, Volker
Hudson A
Dobson R
Abstract

Enzymes are nature's catalysts, mediating chemical processes in living systems. The study of enzyme function and mechanism includes defining the maximum catalytic rate and affinity for substrate/s (among other factors), referred to as enzyme kinetics. Enzyme kinetics is a staple of biochemistry curricula and other disciplines, from molecular and cellular biology to pharmacology. However, because enzyme kinetics involves concepts rarely employed in other areas of biology, it can be challenging for students and researchers. Traditional graphical analysis was replaced by computational analysis, requiring another skill not core to many life sciences curricula. Computational analysis can be time‐consuming and difficult in free software (e.g., R) or require costly software (e.g., GraphPad Prism). We present Enzyme Kinetics Analysis (EKA), a web‐tool to augment teaching and learning and streamline EKA. EKA is an interactive and free tool for analyzing enzyme kinetic data and improving student learning through simulation, built using R and RStudio's ShinyApps. EKA provides kinetic models (Michaelis–Menten, Hill, simple reversible inhibition models, ternary‐complex, and ping‐pong) for users to fit experimental data, providing graphical results and statistics. Additionally, EKA enables users to input parameters and create data and graphs, to visualize changes to parameters (e.g., or number of measurements). This function is designed for students learning kinetics but also for researchers to design experiments. EKA provides a simple, interactive interface for teachers, students, and researchers to explore enzyme kinetics. It gives researchers the ability to design experiments and analyze data without specific software requirements.

Description
Citation
Mak D, Dunn S, Coombes D, Carere C, Allison JR, Nock V, Hudson A, Dobson R (2024). Enzyme Kinetics Analysis (EKA): an online tool for analysing enzyme initial rate data and teaching enzyme kinetics. Biochemistry and Molecular Biology Education. 1-11.
Keywords
computational modeling, enzyme kinetics, online analysis, R, teaching
Ngā upoko tukutuku/Māori subject headings
ANZSRC fields of research
31 - Biological sciences::3101 - Biochemistry and cell biology::310106 - Enzymes
31 - Biological sciences::3101 - Biochemistry and cell biology::310199 - Biochemistry and cell biology not elsewhere classified
39 - Education::3901 - Curriculum and pedagogy::390113 - Science, technology and engineering curriculum and pedagogy
39 - Education::3904 - Specialist studies in education::390405 - Educational technology and computing
31 - Biological sciences::3102 - Bioinformatics and computational biology::310299 - Bioinformatics and computational biology not elsewhere classified
Rights
All rights reserved unless otherwise stated