相关论文: Computational modeling of protein interactions and…
In a recent series of ground-breaking experiments, Nakajima et al. [Science 308, 414-415 (2005)] showed that the three cyanobacterial clock proteins KaiA, KaiB, and KaiC are sufficient in vitro to generate circadian phosphorylation of KaiC.…
When three cyanobacterial proteins, KaiA, KaiB, and KaiC, are incubated with ATP in vitro, the phosphorylation level of KaiC hexamers shows stable oscillation with approximately 24 h period. In order to understand this KaiABC clockwork, we…
The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a homohexamer, with each monomer consisting of two domains,…
By incubating the mixture of three cyanobacterial proteins, KaiA, KaiB, and KaiC, with ATP in vitro, Kondo and his colleagues reconstituted the robust circadian rhythm of the phosphorylation level of KaiC (Science, 308; 414-415 (2005)).…
Biological oscillators are very diverse but can be classified based on dynamical motifs such as the types of feedback loops present. The S. Elongatus circadian clock is a remarkable phosphorylation-based oscillator that can be reconstituted…
It is possible that there are post-translational circadian oscillators that continue functioning in the absence of negative feedback transcriptional repression in many cell types from diverse organisms. Apart from the KaiABC system from…
The simple circadian oscillator found in cyanobacteria can be reconstituted in vitro using three proteins-KaiA, KaiB and KaiC. The total phosphorylation level of KaiC oscillates with a circadian period. Recent experiments elucidated the…
Circadian rhythms in living organisms are temporal orders emerging from biochemical circuits driven out of equilibrium. Here, considering the KaiABC system, a minimal model in the synthetic biology, we study how the oscillation emerges from…
Biochemical circadian rhythm oscillations play an important role in many signalling mechanisms. In this work, we explore some of the biophysical mechanisms responsible for sustaining robust oscillations by constructing a minimal but…
Active biological molecules present a powerful, yet largely untapped, opportunity to impart autonomous regulation to materials. Because these systems can function robustly to regulate when and where chemical reactions occur, they have the…
Circadian clocks ubiquitous in life forms ranging bacteria to multi-cellular organisms, often exhibit intrinsic temperature compensation; the period of circadian oscillators is maintained constant over a range of physiological temperatures,…
The cyanobacterium Synechococcus elongatus uses both a protein phosphorylation cycle and a transcription-translation cycle to generate circadian rhythms that are highly robust against biochemical noise. We use stochastic simulations to…
Circadian clocks are the central timekeepers of life, allowing cells to anticipate changes between day and night. Experiments in recent years have revealed that circadian clocks can be highly stable, raising the question how reliably they…
The circadian clock is the molecular mechanism responsible for the adaptation to daily rhythms in living organisms. Oscillations and fluctuations in environmental conditions regulate the circadian clock through signaling pathways. We study…
Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian…
Protein sequestration motifs appear in many biological regulatory networks and introduce special properties into the network dynamics. Sequestration can be described as a mode of inactivation of a given protein by its binding to a second…
A model of coupled molecular oscillators is proposed to study nonequilibrium thermodynamics of synchronization. We find that synchronization of nonequilibrium oscillators costs energy even when the oscillator-oscillator coupling is…
Long and stable timescales are often observed in complex biochemical networks, such as in emergent oscillations. How these robust dynamics persist remains unclear, given the many stochastic reactions and shorter time scales demonstrated by…
Hour-glass clocks do not free-run; they keep time by riding an external rhythm. Motivated by the primordial KaiBC system in cyanobacteria, we study a driven, finite-state molecular clock that advances through a small number of biochemical…
The mammalian circadian system comprises a network of cell-autonomous oscillators, spanning from the central clock in the brain to peripheral clocks in other organs. These clocks are tightly coordinated to orchestrate rhythmic physiological…