Corpus ID: 235436195

Stochastic fluctuations in protein interaction networks are nearly Poissonian

@inproceedings{Albert2021StochasticFI,
  title={Stochastic fluctuations in protein interaction networks are nearly Poissonian},
  author={J. Albert},
  year={2021}
}
Gene regulatory networks are comprised of biochemical reactions, which are inherently stochastic. Each reaction channel contributes to this stochasticity in different measure. In this paper we study the stochastic dynamics of protein interaction networks (PIN) that are made up of monomers and dimers. The network is defined by the dimers, which are formed by hybridizing two monomers. The size of a PIN was defined as the number of monomers that interacts with at least one other monomer (including… Expand

Figures from this paper

References

SHOWING 1-10 OF 15 REFERENCES
Deciphering noise amplification and reduction in open chemical reaction networks
TLDR
Using the Itō stochastic differential equation formalism, analytic and numerical analyses of model systems containing different molecular species in contact with the environment and interacting with each other through mass-action kinetics are performed. Expand
A stochastic model of gene expression with polymerase recruitment and pause release
TLDR
An alternative model that is consistent with the data and which explicitly describes RNA polymerase recruitment and polymerase pause release, two steps necessary for mRNA production is studied, yielding an exact solution for the mRNA distribution in steady-state conditions, an approximate time-dependent solution and showing the model can explain gene dosage compensation. Expand
Transcriptional Bursting Diversifies the Behaviour of a Toggle Switch: Hybrid Simulation of Stochastic Gene Expression
TLDR
The distribution of burst times is determined and used as a basis for the development of exact simulation algorithms for gene expression dynamics and reveals a number of qualitatively distinct scenarios with implications for the modelling of cell-fate selection. Expand
Regulation of noise in the expression of a single gene
TLDR
The results provide the first direct experimental evidence of the biochemical origin of phenotypesic noise, demonstrating that the level of phenotypic variation in an isogenic population can be regulated by genetic parameters. Expand
Stochastic noise reduction upon complexification: positively correlated birth-death type systems.
TLDR
This work investigated the difference between a single system containing molecules that are produced and degraded, and the same system - with the same average number of molecules - connected to a buffer, and found that the sum of the noise levels in the two systems generally decreases upon interconnection if the molecules they contain are positively correlated. Expand
Transcriptional bursting is intrinsically caused by interplay between RNA polymerases on DNA
TLDR
An in vitro single-molecule measurement system is designed and the results indicate that transcriptional bursting is caused by interplay between RNA polymerases on DNA. Expand
Bursting noise in gene expression dynamics: linking microscopic and mesoscopic models
  • Y. Lin, T. Galla
  • Biology, Physics
  • Journal of The Royal Society Interface
  • 2016
TLDR
This work provides a systematic embedding of the PDMP model into the landscape of existing approaches, and presents analytical methods to calculate its stationary distribution and switching frequencies. Expand
Linking stochastic dynamics to population distribution: an analytical framework of gene expression.
TLDR
This model allows for the extraction of kinetic parameters of gene expression from steady-state distributions of protein concentration in a cell population, which are available from single cell data obtained by flow cytometry or fluorescence microscopy. Expand
Mixture distributions in a stochastic gene expression model with delayed feedback: a WKB approximation approach
TLDR
A mathematical model with bursty production of protein, a one-step production delay, and feedback in the frequency of bursts is considered, focusing on examining the steady-state behaviour of the model in the slow-activation (i.e. large-delay) regime. Expand
Beyond initiation-limited translational bursting: the effects of burst size distributions on the stability of gene expression.
TLDR
A new analytical approach is presented that can evaluate biological consequences of the protein burst size with a general distribution and enable deeper insights into the control of cell fate decision-making, the evolution of cryptic genetic variations, and fine-tuning of gene circuits. Expand
...
1
2
...