Monte Carlo Simulations of Vesicles and Fluid Membranes Transformations

The appearance of compartmentalization is recognized as a key step in biogenesis. The study of the dynamical behaviour of amphiphilic close membranes at equilibrium or under some external stress (osmotic pressure or dehydration process) can be useful in order to better elucidate the role of vesicles in the origin of life and to get insight into the molecular and membrane properties that bring to a spontaneous vesicle division. A Monte Carlo approach to simulate the evolution of close membranes under an external stress will be presented. This approach is mainly based on the accepted surface energy model introduced by Helfrich (1973) and Seifert (1997a). Some preliminary results will be also illustrated and possible developments and limits of this method discusse

Matrix Effect in Oleate Micelles-Vesicles Transformation

It is accepted by many authors that the formation of closed molecular structures is a key step in the evolution of life. Oleate vesicles represent a good model system in this framework due to the fact that they self-assemble spontaneously and that fatty acids are considered as possible prebiotic structures. In this contribution, we will focus the attention on the transition from oleate micelles to oleic acid/oleate vesicles induced by a pH change. This transformation is strongly influenced by the presence of pre-formed vesicles. We called this phenomenon the matrix effect. The influence of pre-added POPC liposomes (POPC = 1-palmitoyl-2-oleoyl- {sn}-glycerol-3-phosphocholine) and oleic acido leate vesicles on the process rate and on the final size distribution will be discussed elucidating the main differences between these two system

Matrix effect in oleate micelles-vesicles transformation

ISSN:0169-6149ISSN:1573-087

recent theoretical approaches to minimal artificial cells

Minimal artificial cells (MACs) are self-assembled chemical systems able to mimic the behavior of living cells at a minimal level, i.e. to exhibit self-maintenance, self-reproduction and the capability of evolution. The bottom-up approach to the construction of MACs is mainly based on the encapsulation of chemical reacting systems inside lipid vesicles, i.e. chemical systems enclosed (compartmentalized) by a double-layered lipid membrane. Several researchers are currently interested in synthesizing such simple cellular models for biotechnological purposes or for investigating origin of life scenarios. Within this context, the properties of lipid vesicles (e.g., their stability, permeability, growth dynamics, potential to host reactions or undergo division processes…) play a central role, in combination with the dynamics of the encapsulated chemical or biochemical networks. Thus, from a theoretical standpoint, it is very important to develop kinetic equations in order to explore first—and specify later—the conditions that allow the robust implementation of these complex chemically reacting systems, as well as their controlled reproduction. Due to being compartmentalized in small volumes, the population of reacting molecules can be very low in terms of the number of molecules and therefore their behavior becomes highly affected by stochastic effects both in the time course of reactions and in occupancy distribution among the vesicle population. In this short review we report our mathematical approaches to model artificial cell systems in this complex scenario by giving a summary of three recent simulations studies on the topic of primitive cell (protocell) systems

The Rise of the Nested Multicompartment Model in Synthetic Cell Research

The Rise of the Nested Multicompartment Model in Synthetic Cell Researc

Measurement and Numerical Modeling of Cell-Free Protein Synthesis: Combinatorial Block-Variants of the PURE System

Protein synthesis is at the core of bottom-up construction of artificial cellular mimics. Intriguingly, several reports have revealed that when a transcription–translation (TX–TL) kit is encapsulated inside lipid vesicles (or water-in-oil droplets), high between-vesicles diversity is observed in terms of protein synthesis rate and yield. Stochastic solute partition can be a major determinant of these observations. In order to verify that the variation of TX–TL components concentration brings about a variation of produced protein rate and yield, here we directly measure the performances of the 'PURE system' TX–TL kit variants. We report and share the kinetic traces of the enhanced Green Fluorescent Protein (eGFP) synthesis in bulk aqueous phase, for 27 combinatorial block-variants. The eGFP production is a sensitive function of TX–TL components concentration in the explored concentration range. Providing direct evidence that protein synthesis yield and rate actually mirror the TX–TL composition, this study supports the above-mentioned hypothesis on stochastic solute partition, without excluding, however, the contribution of other factors (e.g., inactivation of components)

Enzymatic reactions in confined environments

Within each biological cell, surface- and volume-confined enzymes control a highly complex network of chemical reactions. These reactions are efficient, timely, and spatially defined. Efforts to transfer such appealing features to in vitro systems have led to several successful examples of chemical reactions catalysed by isolated and immobilized enzymes. In most cases, these enzymes are either bound or adsorbed to an insoluble support, physically trapped in a macromolecular network, or encapsulated within compartments. Advanced applications of enzymatic cascade reactions with immobilized enzymes include enzymatic fuel cells and enzymatic nanoreactors, both for in vitro and possible in vivo applications. In this Review, we discuss some of the general principles of enzymatic reactions confined on surfaces, at interfaces, and inside small volumes. We also highlight the similarities and differences between the in vivo and in vitro cases and attempt to critically evaluate some of the necessary future steps to improve our fundamental understanding of these systems

Effects of Fe(III) binding to the nucleotide-independent site of F1-ATPase: enzyme thermostability and response to activating anions

AbstractMitochondrial F1-ATPase was induced in different conformations by binding of specific ligands, such as nucleotides. Then, Fourier transform infrared spectroscopy (FT-IR) and kinetic analyses were run to evaluate the structural and functional effects of Fe(III) binding to the nucleotide-independent site. Binding of one equivalent of Fe(III) induced a localised stabilising effect on the F1-ATPase structure destabilised by a high concentration of NaCl, through rearrangements of the ionic network essential for the maintenance of enzyme tertiary and/or quaternary structure. Concomitantly, a lower response of ATPase activity to activating anions was observed. Both FT-IR and kinetic data were in accordance with the hypothesis of the Fe(III) site location near one of the catalytic sites, i.e. at the α/β subunit interface

Extrinsic stochastic factors (solute partition) in gene expression inside lipid vesicles and lipid-stabilized water-in-oil droplets: a review

Abstract The encapsulation of transcription–translation (TX–TL) machinery inside lipid vesicles and water-in-oil droplets leads to the construction of cytomimetic systems (often called 'synthetic cells') for synthetic biology and origins-of-life research. A number of recent reports have shown that protein synthesis inside these microcompartments is highly diverse in terms of rate and amount of synthesized protein. Here, we discuss the role of extrinsic stochastic effects (i.e. solute partition phenomena) as relevant factors contributing to this pattern. We evidence and discuss cases where between-compartment diversity seems to exceed the expected theoretical values. The need of accurate determination of solute content inside individual vesicles or droplets is emphasized, aiming at validating or rejecting the predictions calculated from the standard fluctuations theory. At the same time, we promote the integration of experiments and stochastic modeling to reveal the details of solute encapsulation and intra-compartment reactions