The importance of kinetic modeling for understanding the control and regulation of complex metabolic networks is increasingly being recognized. Kinetic models encapsulate the available kinetic information of all the enzymes in a pathway, and then calculate the complex behavior that emerges from the interactions between these network components. Kinetic models are particularly useful because they can simulate untested scenarios and thus explore pathway behavior beyond the realm of what is experimentally available or currently feasible. Models can also suggest new experiments in a directed approach.This chapter provides a brief introduction to kinetic modeling and its application to plant metabolic pathways. A two-pronged strategy is followed: first, a method is presented for further analysis of existing published models, with references to the relevant databases housing such models and instructions on how to load the models into simulation software. Next, the requirements for and processes of constructing and validating a kinetic model from scratch are outlined. To conclude, potential applications of models are summarized.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-62703-661-0_16 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Unlabelled: Eastern equine encephalitis virus (EEEV) is an arthropod-borne, positive-sense RNA alphavirus posing a substantial threat to public health. Unlike similar viruses such as SARS-CoV-2, EEEV replicates efficiently in neurons, producing progeny viral particles as soon as 3-4 hours post-infection. EEEV infection, which can cause severe encephalitis with a human mortality rate surpassing 30%, has no licensed, targeted therapies, leaving patients to rely on supportive care.
View Article and Find Full Text PDFTraumatic brain injury (TBI) is a leading cause of mortality and disability worldwide and can lead to secondary sequelae such as increased seizure susceptibility. Emerging work suggests that the thalamus, the relay center of the brain that undergoes secondary damage after cortical TBI, is involved with heightened seizure risks after TBI. TBI also induces the recruitment of peripheral immune cells, including T cells, to the site(s) of injury, but it is unclear how these cells impact neurological sequelae post-TBI.
View Article and Find Full Text PDFObesity is a global health crisis, with its prevalence particularly severe in the United States, where over 42% of adults are classified as obese. Obesity is driven by complex molecular and tissue-level mechanisms that remain poorly understood. Among these, angiogenesis-primarily mediated by vascular endothelial growth factor (VEGF-A)-is critical for adipose tissue expansion but presents unique challenges for therapeutic targeting due to its intricate regulation.
View Article and Find Full Text PDFDissecting Methionine Oxidation by Hydrogen Peroxide in Proteins: Thermodynamics, Kinetics, and Susceptibility Descriptors.
J Chem Inf Model
January 2025
Department of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy.
The oxidation of Met residues in proteins is a complex process, where protein-specific structural and dynamical features play a relevant role in determining the reaction kinetics. Aiming to a full-side perspective, we report here a comprehensive characterization of Met oxidation kinetics by hydrogen peroxide in a leptin protein case study. To do that, we estimated the reaction-free energy profile of the Met oxidation via a QM/MM approach, while the kinetics of the formation of the reactive species were calculated using classical molecular dynamics (MD) simulations.
View Article and Find Full Text PDFThe Effect of Accessibility of Insoluble Substrate on the Overall Kinetics of Enzymatic Degradation.
Biotechnol Bioeng
January 2025
Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Graz, Austria.
The enzymatic reaction kinetics on cellulose and other solid substrates is limited by the access of the enzyme to the reactive substrate sites. We introduce a general model in which the reaction rate is determined by the active surface area, and the resulting kinetics consequently reflects the evolving relationship between the exposed substrate surface and the remaining substrate volume. Two factors influencing the overall surface-to-volume ratio are considered: the shape of the substrate particles, characterized by a single numerical parameter related to its dimensionality, and the distribution of the particle sizes.
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!