Matrix effect in oleate micelles-vesicles transformation

ISSN:0169-6149ISSN:1573-087

Self-replicating Reverse Micelles

Conditions are described, under which the hydrolysis of octyl octanoate (O-OA) takes place at the interface of reverse micelles fanned by sodium octanoate (OA) in isooctane. Since the micelle-mediated hydrolysis affords fresh OA, which spontaneously assemble into new micelles, the reaction can be seen as a self-replicating process. The kinetics and the spectroscopy of this self-replication process are presented

Research on the Origin of Life: Membrane-Assisted Polycondensations of Amino Acids and Peptides

The question as to whether and to what extent the phospholipid membrane of liposomes can assist in the polymerization of amino acids and peptides has been investigated. It has been found that the membrane can select hydrophobic amino acids and peptides, thus operating as a selection tool in the polymerization reaction and thus permitting the formation of oligopeptides not possible in water – in the absence of liposomes – as a result of the too low solubility

Quasi-cellular systems: Stochastic simulation analysis at nanoscale range

Background: The wet-lab synthesis of the simplest forms of life (minimal cells) is a challenging aspect in modern synthetic biology. Quasi-cellular systems able to produce proteins directly from DNA can be obtained by encapsulating the cell-free transcription/translation system PURESYSTEM™(PS) in liposomes. It is possible to detect the intra-vesicle protein production using DNA encoding for GFP and monitoring the fluorescence emission over time. The entrapment of solutes in small-volume liposomes is a fundamental open problem. Stochastic simulation is a valuable tool in the study of biochemical reaction at nanoscale range. QDC (Quick Direct-Method Controlled), a stochastic simulation software based on the well-known Gillespie's SSA algorithm, was used. A suitable model formally describing the PS reactions network was developed, to predict, from inner species concentrations (very difficult to measure in small-volumes), the resulting fluorescence signal (experimentally observable).Results: Thanks to suitable features specific of QDC, we successfully formalized the dynamical coupling between the transcription and translation processes that occurs in the real PS, thus bypassing the concurrent-only environment of Gillespie's algorithm. Simulations were firstly performed for large liposomes (2.67μm of diameter) entrapping the PS to synthetize GFP. By varying the initial concentrations of the three main classes of molecules involved in the PS (DNA, enzymes, consumables), we were able to stochastically simulate the time-course of GFP-production. The sigmoid fit of the GFP-production curves allowed us to extract three quantitative parameters which are significantly dependent on the various initial states. Then we extended this study for small-volume liposomes (575 nm of diameter), where it is more complex to infer the intra-vesicle composition, due to the expected anomalous entrapment phenomena. We identified almost two extreme states that are forecasted to give rise to significantly different experimental observables.Conclusions: The present work is the first one describing in the detail the stochastic behavior of the PS. Thanks to our results, an experimental approach is now possible, aimed at recording the GFP production kinetics in very small micro-emulsion droplets or liposomes, and inferring, by using the simulation as a reverse-engineering procedure, the internal solutes distribution, and shed light on the still unknown forces driving the entrapment phenomenon. © 2013 Calviello et al.; licensee BioMed Central Ltd

Ser-His catalyses the formation of peptides and PNAs

AbstractThe dipeptide seryl-histidine (Ser-His) catalyses the condensation of esters of amino acids, peptide fragments, and peptide nucleic acid (PNA) building blocks, bringing to the formation of peptide bonds. Di-, tri- or tetra-peptides can be formed with yields that vary from 0.5% to 60% depending on the nature of the substrate and on the conditions. Other simpler peptides as Gly-Gly, or Gly-Gly-Gly are also effective, although less efficiently. We discuss the results from the viewpoint of primitive chemistry and the origin of long macromolecules by stepwise fragment condensations

Massive non-natural proteins structure prediction using grid technologies

Background The number of natural proteins represents a small fraction of all the possible protein sequences and there is an enormous number of pr oteins never sampled by nature, the so called "never born proteins" (NBPs). A fundamental question in this regard is if the ensemble of natural proteins possesses peculiar chemical and physical properties or if it is just the product of contingency coupled to functional selection. A key feature of natural proteins is thei r ability to form a well defined three-dimensional structure. T hus, the structural study of NBPs can help to understand if natural protein sequences were selecte d for their peculiar properties or if they are just one of the possible stable and functional ensembles. Methods The structural characterization of a huge number of random proteins cannot be approached experimentally, thus the problem has been tackled using a computational approach. A large random protein sequences library (2 × 10 ^4 sequences) was generated, discarding amino acid sequences with significant simi larity to natural proteins, and the corresponding structures were predicted using Rosetta. Given th e highly computational demanding problem, Rosetta was ported in grid and a user friendly job submission environment was developed within the GENIUS Grid Portal. Protein structures generated were analysed in terms of net charge, secondary structure content, surface/volume ratio, hydrophobic core composition, etc. Results The vast majority of NBPs, according to the Rosetta mode l, are characterized by a compact three-dimensional structure with a high secondary structure content. Structure compactness and surface polarity are comparable to those of natural proteins, suggesting similar stability and solubility. Deviations are observed in α helix- β strands relative content and inydrophobic core composition, as NBPs appear to be richer in helical structure and aromatic amino acids with respect to natural proteins. Conclusion The results obtained suggest that the abil ity to form a compact, ordered and water-soluble structure is an intrinsic property of polypeptides. The tendency of random sequences to adopt α helical folds indicate that all-α proteins may have emerged ea rly in pre-biotic evolution. Further, the lower percentage of aromatic residu es observed in natural proteins has important evolutionary implications as far as tolerance to mutati ons is concerned

The emergence of life. From chemical origins to synthetic biology

Preface page xi Acknowledgments xiii List of books on the origin of life xiv 1 Conceptual framework of research on the origin of life on Earth 1 Introduction 1 Determinism and contingency in the origin of life 4 Only one start or many? 10 The anthropic principle, SETI, and the creationists 12 Questions for the reader 16 2 Approaches to the definitions of life 17 Introduction 17 A historical framework 19 The visit of the Green Man 23 Main operational approaches to the origin of life 26 I. The prebiotic RNA world 27 II. The compartmentalistic approach 29 III. The prebiotic metabolism approach 31 Concluding remarks 36 Questions for the reader 37 3 Selection in prebiotic chemistry: why this . . . and not that? 38 Introduction 38 From Oparin to Miller and beyond 40 Other sources of organic molecules 46 Millers α-amino acids: why do they form? 50 Some notes on homochirality 52 Concluding remarks 56 Questions for the reader 58 4 The bottle neck: macromolecular sequences 59 Introduction 59 Proteins and nucleic acids are copolymers 60 The quest for macromolecular sequences 62 What about polynucleotides? 65 A grain of sand in the Sahara 68 The never-born proteins 70 A model for the aetiology of macromolecular sequences and a testable one 72 Homochirality in chains 76 Chain chirality and chain growth 78 Concluding remarks 82 Questions for the reader 84 5 Self-organization 85 Introduction 85 Self-organization of simpler molecular systems 87 Self-organization and autocatalysis 91 Polymerization 93 Self-organization and kinetic control 95 Self-organization and breaking of symmetry 97 Complex biological systems 100 Self-organization and finality 105 Out-of-equilibrium self-organization 106 Concluding remarks 109 Questions for the reader 111 6 The notion of emergence 112 Introduction 112 A few simple examples 114 Emergence and reductionism 116 Deducibility and predictability 117 Downward causation 119 Emergence and non-linearity 120 Life as an emergent property 123 Concluding remarks 125 Questions for the reader 128 7 Self-replication and self-reproduction 129 Introduction 129 Self-replication and non-linearity 129 Myths and realities of self-replication 132 Self-replicating, enzyme-free chemical systems 133 One more step towards complexity 141 Self-reproducing micelles and vesicles 143 Concluding remarks 153 Questions for the reader 154 8 Autopoiesis: the logic of cellular life 155 Introduction 155 Historical background 156 Basic autopoiesis 157 Criteria of autopoiesis 159 What autopoiesis does not include 160 Chemical autopoiesis 162 Autopoiesis and cognition 164 Cognition and enaction 167 Necessary and sufficient? 169 One glance further up: from autopoiesis to the cognitive domain 172 Social autopoiesis 175 Autopoiesis and the chemoton: a comparison of the views of Ganti with those of Maturana and Varela 177 Concluding remarks 179 Questions for the reader 181 9 Compartments 182 Introduction 182 Surfactant aggregates 182 Aqueous micelles 187 Compartmentation in reverse micelles 189 Cubic phases 1

Self-reproduction of micelles, reverse micelles and vesicles. Compartments disclose a general transformation pattern

The discovery of self-reproduction of micelles and vesicles about 15 years ago opened anew page in the field of the supramolecular chemistry of surfactant aggregation phenomena, both for the importance of dynamic aspects of complexity of these systems and for its biological meaning. In fact, the self-reproduction of vesicles has suggested that the growth and the population increase of structures resembling the cells may take place solely because of physical and chemical forces. An increasing number of reports demonstrate that reverse micelles, micelles, sub-micrometric as well as giant vesicles readily undergo self-reproduction, generating new particles from a suitable precursor.The process follows an autocatalytic pattern, namely, the progressive increase in particlenumber is a nonlinear time course.In this chapter, we will review the most significant studies on the self-reproduction ofdifferent compartments, by following a combined historical and classifying approach thatspans from the pioneering work on reverse micelles, to the case of normal (aqueous)micelles, to the studies on vesicles, giant vesicles, and water-in-oil emulsion droplets.Similarities and differences in reactive patterns are highlighted, indicating at the sametime the unanswered questions. Some of the theoretical models, which have beenproposed in the literature to interpret or model self-reproduction of micelles and vesicles,will be illustrated. We will also discuss whether and to what extent such processescomply with the theory of autopoiesis—from which they have been in fact generated,from the historical as well as strategic viewpoint.Finally, we will also shortly discuss the relevance of the self-reproduction of vesicles foremerging avenues of research, in particular for the field of minimal cells, meant as thecompartments having the minimal and sufficient complexity to be defined as living