title: Stochastic models of gene expression with delayed degradation.
abstract: In many biochemical reactions occurring in living cells, number of various molecules might be low which results in significant stochastic fluctuations. In addition, most reactions are not instantaneous, there exist natural time delays in the evolution of cell states. It is a challenge to develop a systematic and rigorous treatment of stochastic dynamics with time delays and to investigate combined effects of stochasticity and delays in concrete models.We propose a new methodology to deal with time delays in biological systems and apply it to simple models of gene expression with delayed degradation. We show that time delay of protein degradation does not cause oscillations as it was recently argued. It follows from our rigorous analysis that one should look for different mechanisms responsible for oscillations observed in biological experiments.We develop a systematic analytical treatment of stochastic models of time delays. Specifically we take into account that some reactions, for example degradation, are consuming, that is: once molecules start to degrade they cannot be part in other degradation processes.We introduce an auxiliary stochastic process and calculate analytically the variance and the autocorrelation function of the number of protein molecules in stationary states in basic models of delayed protein degradation.
authors.affiliation: Institute of Applied Mathematics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland. j.miekisz@mimuw.edu.pl
authors.forename: Jacek
authors.initials: J
authors.lastname: Miękisz
authors.forename: Jan
authors.initials: J
authors.lastname: Poleszczuk
authors.forename: Marek
authors.initials: M
authors.lastname: Bodnar
authors.forename: Urszula
authors.initials: U
authors.lastname: Foryś
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D005786:Gene Expression Regulation; D008957:Models, Genetic; D014176:Protein Biosynthesis / Q000235:genetics; D011506:Proteins / Q000235:genetics / Q000378:metabolism*; D059748:Proteolysis; D013269:Stochastic Processes
chemical_list: D011506:Proteins