Coevolution of compositional protocells and their environment

The coevolution of environment and living organisms is well known in nature. Here, it is suggested that similar processes can take place before the onset of life, where protocellular entities, rather than full-fledged living systems, coevolve along with their surroundings. Specifically, it is suggested that the chemical composition of the environment may have governed the chemical repertoire generated within molecular assemblies, compositional protocells, while compounds generated within these protocells altered the chemical composition of the environment. We present an extension of the graded autocatalysis replication domain (GARD) model--the environment exchange polymer GARD (EE-GARD) model. In the new model, molecules, which are formed in a protocellular assembly, may be exported to the environment that surrounds the protocell. Computer simulations of the model using an infinite-sized environment showed that EE-GARD assemblies may assume several distinct quasi-stationary compositions (composomes), similar to the observations in previous variants of the GARD model. A statistical analysis suggested that the repertoire of composomes manifested by the assemblies is independent of time. In simulations with a finite environment, this was not the case. Composomes, which were frequent in the early stages of the simulation disappeared, while others emerged. The change in the frequencies of composomes was found to be correlated with changes induced on the environment by the assembly. The EE-GARD model is the first GARD model to portray a possible time evolution of the composomes repertoire.     

Physics underlying the formation of protocells

The emergence of the first cellular organization on the primitive earth could be associated with pronounced heterotrophic activity embodied in heat engines actualized in local material aggregates. Heterotrophic activity intrinsically rests upon the capacity of local detection upholding the conservation of energy on the global scale.     

The emergence of ribozymes synthesizing membrane components in RNA-based protocells

A significant problem of the origin of life is the emergence of cellular self-replication. In the context of the “RNA world”, a crucial concern is how the RNA-based protocells could achieve the ability to produce their own membrane. Here we show, with the aid of a computer simulation, that for these protocells, there would be “immediately” a selection pressure for the emergence of a ribozyme synthesizing membrane components. The ribozyme would promote the enlargement of cellular space and favor the incoming (by permeation) of RNA's precursors, thus benefit the replication of inner RNA, including itself. Via growth and division, protocells containing the ribozyme would achieve superiority and spread in the system, and meanwhile the ribozyme would spread in the system. The present work is inspiring because it suggests that the transition from molecular self-replication to cellular self-replication might have occurred naturally (and necessarily) in the origin of life, leading to the emergence of Darwinian evolution at the cellular level.     

Social and ethical checkpoints for bottom-up synthetic biology, or protocells

An alternative to creating novel organisms through the traditional “top-down” approach to synthetic biology involves creating them from the “bottom up” by assembling them from non-living components; the products of this approach are called “protocells.” In this paper we describe how bottom-up and top-down synthetic biology differ, review the current state of protocell research and development, and examine the unique ethical, social, and regulatory issues raised by bottom-up synthetic biology. Protocells have not yet been developed, but many expect this to happen within the next five to ten years. Accordingly, we identify six key checkpoints in protocell development at which particular attention should be given to specific ethical, social and regulatory issues concerning bottom-up synthetic biology, and make ten recommendations for responsible protocell science that are tied to the achievement of these checkpoints.     

Synthetic protocells interact with viral nanomachinery and inactivate pathogenic human virus

We present a new antiviral strategy and research tool that could be applied to a wide range of enveloped viruses that infect human beings via membrane fusion. We test this strategy on two emerging zoonotic henipaviruses that cause fatal encephalitis in humans, Nipah (NiV) and Hendra (HeV) viruses. In the new approach, artificial cell-like particles (protocells) presenting membrane receptors in a biomimetic manner were developed and found to attract and inactivate henipavirus envelope glycoprotein pseudovirus particles, preventing infection. The protocells do not accumulate virus during the inactivation process. The use of protocells that interact with, but do not accumulate, viruses may provide significant advantages over current antiviral drugs, and this general approach may have wide potential for antiviral development.     

Synthetic Turing protocells: vesicle self-reproduction through symmetry-breaking instabilities

The reproduction of a living cell requires a repeatable set of chemical events to be properly coordinated. Such events define a replication cycle, coupling the growth and shape change of the cell membrane with internal metabolic reactions. Although the logic of such process is determined by potentially simple physico-chemical laws, modelling of a full, self-maintained cell cycle is not trivial. Here we present a novel approach to the problem that makes use of so-called symmetry breaking instabilities as the engine of cell growth and division. It is shown that the process occurs as a consequence of the breaking of spatial symmetry and provides a reliable mechanism of vesicle growth and reproduction. Our model opens the possibility of a synthetic protocell lacking information but displaying self-reproduction under a very simple set of chemical reactions.     

Templeting and self-assembly

Templeting and self-assembly represent the two extremes of the spectrum of determinate pattern-assembly processes. A templeted pattern can be defined as one that requires a prepattern or templet explicitly specifying the final topology of the pattern. Conversely, a self-assembling pattern can be defined as one for which the inherent constraints of the precursor elements alone are sufficient to specify the final pattern. Both concepts can be directly expressed in matrix notation, and a simple matrix measure, the templeting index, characterizes the relative amount of templeting or of self-assembly in any particular system. With this language, a fundamental principle of pattern-assembly becomes evident: in the determinate realm, some patterns can only be assembled using the same-sized templets--templets that are at least as large as the final pattern.     

A model for the origin of stable protocells in a primitive alkaline ocean

When a mixture of the eighteen proteinous amino acids are suitably heated in the dry state with seawater salts, a copolyamino acid results. One fraction of this polymer is found, through isoelectric focusing, to consist of a mixture of acidic and basic proteinoids, each of sharply limited heterogeneity. When one fraction of the seawater proteinoid is dissolved in hot water, and the solution is cooled, proteinoid microspheres result. These have properties in common with simpler types, but are also stable at pH values to 9, in common with microspheres prepared by mixing acidic and basic proteinoids. These processes thus constitute a simple model for the origin of a protocell stable in a primitive alkaline ocean.     

Thermodynamics of phospholipid self-assembly

Negatively charged phospholipids are an important component of biological membranes. The thermodynamic parameters governing self-assembly of anionic phospholipids are deduced here from isothermal titration calorimetry. Heats of demicellization were determined for dioctanoyl phosphatidylglycerol (PG) and phosphatidylserine (PS) at different ionic strengths, and for dioctanoyl phosphatidic acid at different pH values. The large heat capacity (ΔC^o_P ∼ −400 J.mol⁻¹ K⁻¹ for PG and PS), and zero enthalpy at a characteristic temperature near the physiological range (T^∗ ∼ 300 K for PG and PS), demonstrate that the driving force for self-assembly is the hydrophobic effect. The pH and ionic-strength dependences indicate that the principal electrostatic contribution to self-assembly comes from the entropy associated with the electrostatic double layer, in agreement with theoretical predictions. These measurements help define the thermodynamic effects of anionic lipids on biomembrane stability.     

Concentration-based self-assembly of phycocyanin

Cyanobacteria light-harvesting complexes can change their structure to cope with fluctuating environmental conditions. Studying in vivo structural changes is difficult owing to complexities imposed by the cellular environment. Mimicking this system in vitro is challenging, as well. The in vivo system is highly concentrated, and handling similar in vitro concentrated samples optically is difficult because of high absorption. In this research, we mapped the cyanobacteria antennas self-assembly pathways using highly concentrated solutions of phycocyanin (PC) that mimic the in vivo condition. PC was isolated from the thermophilic cyanobacterium Thermosynechococcus vulcanus and measured by several methods. PC has three oligomeric states: hexamer, trimer, and monomer. We showed that the oligomeric state was changed upon increase of PC solution concentration. This oligomerization mechanism may enable photosynthetic organisms to adapt their light-harvesting system to a wide range of environmental conditions.     

Inhibitor of fibrin self-assembly

The thermostable inhibitor with a molecular mass 1750 +/- 100 was found in human, bovine and albino rat blood sera. A ninhydrin-positive product containing no carbohydrates, lipids, nucleic acids was obtained while purifying the inhibitor by combining column ion-exchange chromatography and partition thin layer chromatography. An analogous inhibitor is extracted from the tissue of liver, kidneys, lungs, spleen, duodenum, heart, m. striatum, brain, aorta, where its content is higher than in the blood serum. The inhibitor differs from the already known ones in molecular mass, resistance to heating and dialysis. An assumption is advanced on its participation in maintaining the liquid blood state under conditions providing a possibility of accelerated thrombinogenesis and thrombin fibrinogen interaction.     

Multicomponent metal-ligand self-assembly

Self-assembly of pre-designed organic ligands with transition metal atoms is a powerful method for construction of novel supramolecular architectures. Particularly, various discrete 3-D hollow structures such as cages, cones, capsules and boxes have been obtained by multicomponent self-assembly of exo-multidentate ligands with cis-protected square planar metal complexes, [(L)M](NO(3))(2) (where L is ethylenediamine or 2,2'-bipyridine and M is Pd or Pt). Furthermore, these hollow structures act as molecular flasks to encapsulate guest molecules and regulate/promote specific reactions; for example, oligomerization of silanetriols and [2+2] intermolecular photodimerization of olefins.     

Structural aspects of biomolecular recognition and self-assembly

Proteins are capable of fulfilling two important features of any likely system of bioelectronics: the ability to recognise other molecules with exquisite specificity, and the ability to self-assemble, in vivo and in vitro, to generate an astonishing variety of three-dimensional structures. Much current work is aimed at the redesign of existing proteins, either as an end in itself or as a means of developing the knowledge-base necessary for the ab initio design of novel proteins. This type of study has been greatly facilitated by the discovery of the modular or domain structure of many proteins, leading to concepts of protein manipulation as a kind of molecular Lego.     

Dynamics of membrane nanotubulation and DNA self-assembly

A localized point-like force applied perpendicular to a vesicular membrane layer, using an optical tweezer, leads to membrane nanotubulation beyond a threshold force. Below the threshold, the force-extension curve shows an elastic response with a fine structure (serrations). Above the threshold the tubulation process exhibits a new reversible flow phase for the multilamellar membrane, which responds viscoelastically. Furthermore, with an oscillatory force applied during tubulation, broad but well-resolved resonances occur in the flow phase, presumably matching the time scales associated with the vesicle-nanotubule coupled system. These nanotubules, anchored to the optical tweezer also provide, for the first time, a direct probe of the real-time dynamics of DNA self-assembly on membranes. Our studies are a step in the direction of analyzing the dynamics of membrane self-assembly and artificial nanofluidic membrane networks.     

Layer-by-layer self-assembly of supramolecular and biomolecular films

In this paper, we give a short account on recent studies of layer-by-layer self-assembly of supramolecular and biomolecular films. Such films are built up from layers of macro-ions with opposing charge. A simple film can be obtained by alternating the adsorption of two components: a flexible, synthetic polycation chains and a supramolecular or biomolecular moiety. We focus on three examples, in which the second component consists either of a supramolecular metal-organic complex (MOC), a nucleic acid, or a biological membrane patch (purple membrane). While the flexible polvcation chains (as well as eventual annealing layers) ensure a uniform build-up of the chain, the second macromolecular component may be used to functionalize the films. The combination of layer-by-layer self-assembly and biotechnologically relevant macromolecules may lead to new devices or biomaterial applications. To this end, precise studies of the deposition process and the film structure are needed. Here, we focus on interface sensitive scattering techniques for the structural analysis.     

pH-induced self-assembly and capsules of sodium alginate

In this investigation, we used a kind of polyelectrolyte, sodium alginate, as a model biomacromolecule to investigate the aggregation behaviors in aqueous solution after partial protonation of carboxylate groups in the alginate molecules. It is demonstrated that the alginate assemblies with core-shell structure can be generated by the partial protonation of carboxylate groups in sodium alginate chains using the protons released gradually from the reaction of K(2)S(2)O(8) with water at 70 degrees C in aqueous solution. The partial cross-linked alginate assemblies are pH sensitive and can change to hollow structure in the medium with relatively high pH value. This approach avoids use of block or grafted copolymers as the precursors or any other template to prepare assemblies and capsules, and provides a functional surface for subsequent chemical reaction at the surface (e.g., for binding biomolecules and for surface grafting). Such unique assemblies are also expected to be useful in biomedical fields.