Dihydrofolate reductase from Escherichia coli (ecDHFR) serves as a model system for investigating the role of protein dynamics in enzyme catalysis. We discuss calculations predicting a network of dynamic motions that is coupled to the chemical step catalyzed by this enzyme. Kinetic studies testing these predictions are presented, and their potential use in better understanding the role of these...

Enzyme catalysis has been studied extensively, but the role of enzyme dynamics in the catalyzed chemical conversion is still an enigma. The enzyme dihydrofolate reductase (DHFR) is often used as a model system to assess a network of coupled motions across the protein that may affect the catalyzed chemical transformation. Molecular dynamics simulations, quantum mechanical/molecular mechanical st...

objective(s): enzyme immobilization via nanoparticles is perfectly compatible against the other chemical or biological approximate to improve enzyme functions and stability. in this study lactoperoxidase was immobilized onto silica-coated magnetite nanoparticles to improve enzyme properties in the presence of cadmium chloride as an inhibitor. materials and methods:  the process consists of the ...

The three dimensional structure of an enzyme is of fundamental importance to almost every function it performs. In this thesis, we aim to analyse the structures of many enzymes in order to gain insights into how they perform catalysis, and the role of structure in enzyme function. As well as improving our understanding of these important biological molecules, these insights will help in develop...

One of the primary mechanisms through which a cell exerts control over its metabolic state is by modulating expression levels of its enzyme-coding genes. However, the changes at the level of enzyme expression allow only indirect control over metabolite levels, for two main reasons. First, at the level of individual reactions, metabolite levels are non-linearly dependent on enzyme abundances as ...

The rapid development and applications of high throughput measurement techniques bring the biological sciences into a 'big data' era. The vast available data for enzyme and metabolite concentrations, fluxes, and kinetics under normal or perturbed conditions in biological networks provide unprecedented opportunities to understand the cell functions. On the other hand, it brings new challenges of...

A metabolic network models the relationship among three different groups of constituting elements: reactions, enzymes, and metabolites, from a given set of metabolic pathways integrally related via gene-regulatory mechanisms. Recent pathway/genome databases inevitably require development of a different methodology for including detail in the network-centric approach to answer concrete biologica...