604 research outputs found
A model of protocell based on the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks
In this work we introduce some preliminary analyses on the role of a
semi-permeable membrane in the dynamics of a stochastic model of catalytic
reaction sets (CRSs) of molecules. The results of the simulations performed on
ensembles of randomly generated reaction schemes highlight remarkable
differences between this very simple protocell description model and the
classical case of the continuous stirred-tank reactor (CSTR). In particular, in
the CSTR case, distinct simulations with the same reaction scheme reach the
same dynamical equilibrium, whereas, in the protocell case, simulations with
identical reaction schemes can reach very different dynamical states, despite
starting from the same initial conditions.Comment: In Proceedings Wivace 2013, arXiv:1309.712
A stochastic model of catalytic reaction networks in protocells
Protocells are supposed to have played a key role in the self-organizing
processes leading to the emergence of life. Existing models either (i) describe
protocell architecture and dynamics, given the existence of sets of
collectively self-replicating molecules for granted, or (ii) describe the
emergence of the aforementioned sets from an ensemble of random molecules in a
simple experimental setting (e.g. a closed system or a steady-state flow
reactor) that does not properly describe a protocell. In this paper we present
a model that goes beyond these limitations by describing the dynamics of sets
of replicating molecules within a lipid vesicle. We adopt the simplest possible
protocell architecture, by considering a semi-permeable membrane that selects
the molecular types that are allowed to enter or exit the protocell and by
assuming that the reactions take place in the aqueous phase in the internal
compartment. As a first approximation, we ignore the protocell growth and
division dynamics. The behavior of catalytic reaction networks is then
simulated by means of a stochastic model that accounts for the creation and the
extinction of species and reactions. While this is not yet an exhaustive
protocell model, it already provides clues regarding some processes that are
relevant for understanding the conditions that can enable a population of
protocells to undergo evolution and selection.Comment: 20 pages, 5 figure
On RAF Sets and Autocatalytic Cycles in Random Reaction Networks
The emergence of autocatalytic sets of molecules seems to have played an
important role in the origin of life context. Although the possibility to
reproduce this emergence in laboratory has received considerable attention,
this is still far from being achieved. In order to unravel some key properties
enabling the emergence of structures potentially able to sustain their own
existence and growth, in this work we investigate the probability to observe
them in ensembles of random catalytic reaction networks characterized by
different structural properties. From the point of view of network topology, an
autocatalytic set have been defined either in term of strongly connected
components (SCCs) or as reflexively autocatalytic and food-generated sets
(RAFs). We observe that the average level of catalysis differently affects the
probability to observe a SCC or a RAF, highlighting the existence of a region
where the former can be observed, whereas the latter cannot. This parameter
also affects the composition of the RAF, which can be further characterized
into linear structures, autocatalysis or SCCs. Interestingly, we show that the
different network topology (uniform as opposed to power-law catalysis systems)
does not have a significantly divergent impact on SCCs and RAFs appearance,
whereas the proportion between cleavages and condensations seems instead to
play a role. A major factor that limits the probability of RAF appearance and
that may explain some of the difficulties encountered in laboratory seems to be
the presence of molecules which can accumulate without being substrate or
catalyst of any reaction.Comment: pp 113-12
The Stochastic Evolution of a Protocell: The Gillespie Algorithm in a Dynamically Varying Volume
We propose an improvement of the Gillespie
algorithm allowing us to study the time evolution of an ensemble of chemical
reactions occurring in a varying volume, whose growth is directly related to
the amount of some specific molecules, belonging to the reactions set.
This allows us to study the stochastic evolution of a protocell, whose volume
increases because of the production of container molecules. Several protocell
models are considered and compared with the deterministic models
Mechanism and substrate specificity of the flavin reductase ActVB from Streptomyces coelicolor.
International audienceActVB is the NADH:flavin oxidoreductase participating in the last step of actinorhodin synthesis in Streptomyces coelicolor. It is the prototype of a whole class of flavin reductases with both sequence and functional similarities. The mechanism of reduction of free flavins by ActVB has been studied. Although ActVB was isolated with FMN bound, we have demonstrated that it is not a flavoprotein. Instead, ActVB contains only one flavin binding site, suitable for the flavin reductase activity and with a high affinity for FMN. In addition, ActVB proceeds by an ordered sequential mechanism, where NADH is the first substrate. Whereas ActVB is highly specific for NADH, it is able to catalyze the reduction of a great variety of natural and synthetic flavins, but with K(m) values ranging from 1 microm (FMN) to 69 microm (lumiflavin). We show that both the ribitol-phosphate chain and the isoalloxazine ring contribute to the protein-flavin interaction. Such properties are unique and set the ActVB family apart from the well characterized Fre flavin reductase family
The flavin reductase ActVB from Streptomyces coelicolor: characterization of the electron transferase activity of the flavoprotein form.
International audienceThe flavin reductase ActVB is involved in the last step of actinorhodin biosynthesis in Streptomyces coelicolor. Although ActVB can be isolated with some FMN bound, this form was not involved in the flavin reductase activity. By studying the ferric reductase activity of ActVB, we show that its FMN-bound form exhibits a proper enzymatic activity of reduction of iron complexes by NADH. This shows that ActVB active site exhibits a dual property with regard to the FMN. It can use it as a substrate that goes in and off the active site or as a cofactor to provide an electron transferase activity to the polypeptide
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