1,128 research outputs found

    Spontaneous chiral symmetry breaking in early molecular networks

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    Background: An important facet of early biological evolution is the selection of chiral enantiomers for molecules such as amino acids and sugars. The origin of this symmetry breaking is a long-standing question in molecular evolution. Previous models addressing this question include particular kinetic properties such as autocatalysis or negative cross catalysis. Results: We propose here a more general kinetic formalism for early enantioselection, based on our previously described Graded Autocatalysis Replication Domain (GARD) model for prebiotic evolution in molecular assemblies. This model is adapted here to the case of chiral molecules by applying symmetry constraints to mutual molecular recognition within the assembly. The ensuing dynamics shows spontaneous chiral symmetry breaking, with transitions towards stationary compositional states (composomes) enriched with one of the two enantiomers for some of the constituent molecule types. Furthermore, one or the other of the two antipodal compositional states of the assembly also shows time-dependent selection. Conclusion: It follows that chiral selection may be an emergent consequence of early catalytic molecular networks rather than a prerequisite for the initiation of primeval life processes. Elaborations of this model could help explain the prevalent chiral homogeneity in present-day living cells. Reviewers: This article was reviewed by Boris Rubinstein (nominated by Arcady Mushegian), Arcady Mushegian, Meir Lahav (nominated by Yitzhak Pilpel) and Sergei Maslov

    Association of Protein Helices and Assembly of Foldamers: Stories in Membrane and Aqueous Environments

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    Solvents play an important role in association and assembly of molecules. Here we studied solvent effects on proteins and organic chemicals in different contexts. First, X-ray crystal structures show that helix dimers in membrane- and water-soluble proteins have distinct behaviors in packing and sequence selection. Transmembrane dimers are stabilized by compact packing and hydrogen bonding between small residues. Meanwhile, water-soluble dimers utilize hydrophobic residues for packing irrespective of the size of the interface and tight dimers are rare. Secondly, we apply the results learned above to a complex system in which a designed protein binds to single-walled carbon-nanotube in aqueous environments. Previous designs of the hexameric helical bundles utilized leucine and alanine residues to make two distinct helix-helix interfaces. Our molecular dynamics simulations showed that the alanine-comprising interface is much more labile than the leucine-comprising one. This result can be interpreted by the scarcity of tight soluble helix dimers as mentioned above. Thus more stable modular helix-helix interfaces have to be employed to design peptides binding to carbon-nanotubes with higher affinities. Lastly, we describe a serendipitous discovery of the crystalline framework structure by an amphiphilic triarylamide foldamer. Foldamers are peptide-like polymers of non-natural monomers arranged in defined sequence and chain length that are able to adopt protein-like secondary and tertiary structures. In contrast with traditional metal-organic and organic frameworks, which exploit strong directional coordination and hydrogen bonding for assembly in organic solvents, the crystal herein is built up from a combination of noncovalent hydrophobic, hydrogen-bonded, and electrostatic interactions in aqueous solution. The structure is in honeycomb geometry with each cubicle as a truncated octahedron. A new supramolecular synthon, in which hydrogen bonding and π-π stacking are encompassed, was discovered in the crystal structure. Through NMR experiments we probed the oligomeric states of the foldamer in the early stages prior to crystallization. The hierarchic crystal structure was discussed in terms of supramolecular synthons in crystal engineering

    Pickering Emulsion and Derived Materials

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    Particle-stabilized emulsions, today often referred to as Pickering/Ramsden emulsions, are vital in many fields, including personal care products, foods, pharmaceuticals, and oil recovery. The exploitation of these Pickering emulsions for the manufacture of new functional materials has also recently become the subject of intense investigation. While much progress has been made over the past decade, Pickering emulsion still remains a rich topic since many aspects of their behavior have yet to be investigated. The present “Pickering Emulsion and Derived Materials” Special Issue aims to bring together research and review papers pertaining to the recent developments in the design, fabrication, and application of Pickering emulsions. The themes include, but are not limited to: 1. Interactions of colloidal particles confined at fluid interfaces 2. Pickering emulsion-based polymerization 3. Interfacial assembly and emulsion stabilization 4. Rheology of particle laden interfaces and Pickering emulsions 5. Functional materials templated from Pickering emulsion

    Surfactant Assemblies and their Various Possible Roles for the Origin(S) of Life

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    A large number of surfactants (surface active molecules) are chemically simple compounds that can be obtained by simple chemical reactions, in some cases even under presumably prebiotic conditions. Surfactant assemblies are self-organized polymolecular aggregates of surfactants, in the simplest case micelles, vesicles, hexagonal and cubic phases. It may be that these different types of surfactant assemblies have played various, so-far underestimated important roles in the processes that led to the formation of the first living systems. Although nucleic acids are key players in the formation of cells as we know them today (RNA world hypothesis), it is still unclear how RNA could have been formed under prebiotic conditions. Surfactants with their self-organizing properties may have assisted, controlled and compartimentalized some of the chemical reactions that eventually led to the formation of molecules like RNA. Therefore, surfactants were possibly very important in prebiotic times in the sense that they may have been involved in different physical and chemical processes that finally led to a transformation of non-living matter to the first cellular form(s) of life. This hypothesis is based on four main experimental observations: (i) Surfactant aggregation can lead to cell-like compartimentation (vesicles). (ii) Surfactant assemblies can provide local reaction conditions that are very different from the bulk medium, which may lead to a dramatic change in the rate of chemical reactions and to a change in reaction product distributions. (iii) The surface properties of surfactant assemblies that may be liquid- or solid-like, charged or neutral, and the elasticity and packing density of surfactant assemblies depend on the chemical structure of the surfactants, on the presence of other molecules, and on the overall environmental conditions (e. g. temperature). This wide range of surface characteristics of surfactant assemblies may allow a control of surface-bound chemical reactions not only by the charge or hydrophobicity of the surface but also by its "softness”. (iv) Chiral polymolecular assemblies (helices) may form from chiral surfactants. There are many examples that illustrate the different roles and potential roles of surfactant assemblies in different research areas outside of the field of the origin(s) of life, most importantly in investigations of contemporary living systems, in nanotechnology applications, and in the development of drug delivery systems. Concepts and ideas behind many of these applications may have relevance also in connection to the different unsolved problems in understanding the origin(s) of lif
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