Misuse of the Michaelis–Menten rate law for protein interaction networks and its remedy
For over a century, the Michaelis–Menten (MM) rate law has been used to describe the rates
of enzyme-catalyzed reactions and gene expression. Despite the ubiquity of the MM rate …
of enzyme-catalyzed reactions and gene expression. Despite the ubiquity of the MM rate …
The concept of coupling in the mammalian circadian clock network
V Pilorz, M Astiz, KO Heinen, O Rawashdeh… - Journal of molecular …, 2020 - Elsevier
The circadian clock network regulates daily rhythms in mammalian physiology and behavior
to optimally adapt the organism to the 24-h day/night cycle. A central pacemaker, the …
to optimally adapt the organism to the 24-h day/night cycle. A central pacemaker, the …
The choroid plexus is an important circadian clock component
Mammalian circadian clocks have a hierarchical organization, governed by the
suprachiasmatic nucleus (SCN) in the hypothalamus. The brain itself contains multiple loci …
suprachiasmatic nucleus (SCN) in the hypothalamus. The brain itself contains multiple loci …
Long-range temporal coordination of gene expression in synthetic microbial consortia
Synthetic microbial consortia have an advantage over isogenic synthetic microbes because
they can apportion biochemical and regulatory tasks among the strains. However, it is …
they can apportion biochemical and regulatory tasks among the strains. However, it is …
Protein sequestration versus Hill‐type repression in circadian clock models
JK Kim - IET systems biology, 2016 - Wiley Online Library
Circadian (∼ 24 h) clocks are self‐sustained endogenous oscillators with which organisms
keep track of daily and seasonal time. Circadian clocks frequently rely on interlocked …
keep track of daily and seasonal time. Circadian clocks frequently rely on interlocked …
Spatially coordinated collective phosphorylation filters spatiotemporal noises for precise circadian timekeeping
The circadian (∼ 24h) clock is based on a negative-feedback loop centered around the
PERIOD protein (PER), translated in the cytoplasm and then enters the nucleus to repress its …
PERIOD protein (PER), translated in the cytoplasm and then enters the nucleus to repress its …
Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations
Transcriptional repression can occur via various mechanisms, such as blocking,
sequestration and displacement. For instance, the repressors can hold the activators to …
sequestration and displacement. For instance, the repressors can hold the activators to …
The validity of quasi-steady-state approximations in discrete stochastic simulations
In biochemical networks, reactions often occur on disparate timescales and can be
characterized as either fast or slow. The quasi-steady-state approximation (QSSA) utilizes …
characterized as either fast or slow. The quasi-steady-state approximation (QSSA) utilizes …
Stability of wake-sleep cycles requires robust degradation of the PERIOD protein
Robustness in biology is the stability of phenotype under diverse genetic and/or
environmental perturbations. The circadian clock has remarkable stability of period and …
environmental perturbations. The circadian clock has remarkable stability of period and …
Wake-sleep cycles are severely disrupted by diseases affecting cytoplasmic homeostasis
The circadian clock is based on a transcriptional feedback loop with an essential time delay
before feedback inhibition. Previous work has shown that PERIOD (PER) proteins generate …
before feedback inhibition. Previous work has shown that PERIOD (PER) proteins generate …