Journal of systems chemistry最新文献

{"title":"Cyclic growth of hierarchical structures in the aluminum-silicate system.","authors":"Agnieszka Dyonizy,&nbsp;Vitaliy Kaminker,&nbsp;Joanna Wieckowska,&nbsp;Tomasz Krzywicki,&nbsp;Jim Pantaleone,&nbsp;Piotr Nowak,&nbsp;Jerzy Maselko","doi":"10.1186/s13322-015-0007-9","DOIUrl":"https://doi.org/10.1186/s13322-015-0007-9","url":null,"abstract":"<p><strong>Background: </strong>Biological structures grow spontaneously from a seed, using materials supplied by the environment. These structures are hierarchical, with the 'building blocks' on each level constructed from those on the lower level. To understand and model the processes that occur on many levels, and later construct them, is a difficult task. However interest in this subject is growing. It is now possible to study the spontaneous growth of hierarchical structures in simple, two component chemical systems.</p><p><strong>Results: </strong>Aluminum-silicate systems have been observed to grow into structures that are approximately conical. These structures are composed of multiple smaller cones with several hierarchical levels of complexity. On the highest level the system resembles a metropolis, with a horizontal resource distribution network connecting vertical, conical structures. The cones are made from many smaller cones that are connected together forming a whole with unusual behavior. The growth is observed to switch periodically between the vertical and horizontal directions.</p><p><strong>Conclusion: </strong>A structure grown in a dish is observed to have many similarities to other hierarchical systems such as biological organisms or cities. This system may provide a simple model system to search for universal laws governing the growth of complex hierarchical structures. Graphical AbstractSide view of the chemical structure made from many vertical cones to form a chemical metropolis. The tallest structure is 17 cm high.</p>","PeriodicalId":90244,"journal":{"name":"Journal of systems chemistry","volume":"6 1","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13322-015-0007-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33183087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the divide between animate and inanimate.","authors":"Arto Annila,&nbsp;Erkki Kolehmainen","doi":"10.1186/s13322-015-0008-8","DOIUrl":"https://doi.org/10.1186/s13322-015-0008-8","url":null,"abstract":"<p><p>Vitalism was abandoned already for a long time ago, yet the impression that animate beings differ in some fundamental way from inanimate objects continues to thrive. Here, we argue that scale free patterns, found throughout nature, present convincing evidence that this demarcation is only imaginary. Therefore, all systems ought to be regarded alike, i.e., all are consuming free energy in least time. This way evolutionary processes can be understood as a series of changes from one state to another, so that flows of energy themselves naturally select those ways and means, such as species and societies or gadgets and galaxies to consume free energy in the least time in quest of attaining thermodynamic balance in respective surroundings. This holistic worldview, albeit an accurate account of nature, was shelved soon after its advent at the turn of the 18^th century, because the general tenet did not meet that time expectations of a deterministic law, but now it is time to reconsider the old universal imperative against observations rather than expectations.</p>","PeriodicalId":90244,"journal":{"name":"Journal of systems chemistry","volume":"6 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13322-015-0008-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33243536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Autocatalytic sets in <i>E. coli</i> metabolism.","authors":"Filipa L Sousa, Wim Hordijk, Mike Steel, William F Martin","doi":"10.1186/s13322-015-0009-7","DOIUrl":"10.1186/s13322-015-0009-7","url":null,"abstract":"<p><strong>Background: </strong>A central unsolved problem in early evolution concerns self-organization towards higher complexity in chemical reaction networks. In theory, autocatalytic sets have useful properties to help model such transitions. Autocatalytic sets are chemical reaction systems in which molecules belonging to the set catalyze the synthesis of other members of the set. Given an external supply of starting molecules - the food set - and the conditions that (i) all reactions are catalyzed by at least one molecule, and (ii) each molecule can be constructed from the food set by a sequence of reactions, the system becomes a reflexively autocatalytic food-generated network (RAF set). Autocatalytic networks and RAFs have been studied extensively as mathematical models for understanding the properties and parameters that influence self-organizational tendencies. However, despite their appeal, the relevance of RAFs for real biochemical networks that exist in nature has, so far, remained virtually unexplored.</p><p><strong>Results: </strong>Here we investigate the best-studied metabolic network, that of <i>Escherichia coli</i>, for the existence of RAFs. We find that the largest RAF encompasses almost the entire <i>E. coli</i> cytosolic reaction network. We systematically study its structure by considering the impact of removing catalysts or reactions. We show that, without biological knowledge, finding the minimum food set that maintains a given RAF is NP-complete. We apply a randomized algorithm to find (approximately) smallest subsets of the food set that suffice to sustain the original RAF.</p><p><strong>Conclusions: </strong>The existence of RAF sets within a microbial metabolic network indicates that RAFs capture properties germane to biological organization at the level of single cells. Moreover, the interdependency between the different metabolic modules, especially concerning cofactor biosynthesis, points to the important role of spontaneous (non-enzymatic) reactions in the context of early evolution. Graphical Abstract<i>E. coli</i> metabolic network in the context of autocatalytic sets.</p>","PeriodicalId":90244,"journal":{"name":"Journal of systems chemistry","volume":"6 1","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429071/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33321737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transition to diversification by competition for multiple resources in catalytic reaction networks.","authors":"Atsushi Kamimura,&nbsp;Kunihiko Kaneko","doi":"10.1186/s13322-015-0010-1","DOIUrl":"https://doi.org/10.1186/s13322-015-0010-1","url":null,"abstract":"<p><strong>Background: </strong>All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which the use of a great variety of components, and the coexistence of diverse cell-types with different compositions are achieved is as yet unknown.</p><p><strong>Results: </strong>Here we show that coexistence of such diverse compositions and cell-types is the result of competitions for a variety of limited resources. We find that a transition to diversity occurs both in chemical compositions and in protocell types, as the resource supply is decreased, when the maximum inflow and consumption of resources are balanced.</p><p><strong>Conclusions: </strong>Our results indicate that a simple physical principle of competition for a variety of limiting resources can be a strong driving force to diversify intracellular dynamics of a catalytic reaction network and to develop diverse protocell types in a primitive stage of life.</p>","PeriodicalId":90244,"journal":{"name":"Journal of systems chemistry","volume":"6 1","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13322-015-0010-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33290916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Autocatalytic sets and boundaries.","authors":"Wim Hordijk,&nbsp;Mike Steel","doi":"10.1186/s13322-014-0006-2","DOIUrl":"https://doi.org/10.1186/s13322-014-0006-2","url":null,"abstract":"<p><p>Autopoietic systems, chemotons, and autogens are models that aim to explain (the emergence of) life as a functionally closed and self-sustaining system. An essential element in these models is the notion of a boundary containing, maintaining, and being generated by an internal reaction network. The more general concept of collectively autocatalytic sets, formalized as RAF theory, does not explicitly include this notion of a boundary. Here, we argue that (1) the notion of a boundary can also be incorporated in the formal RAF framework, (2) this provides a mechanism for the emergence of higher-level autocatalytic sets, (3) this satisfies a necessary condition for the evolvability of autocatalytic sets, and (4) this enables the RAF framework to formally represent and analyze (at least in part) the other models. We suggest that RAF theory might thus provide a basis for a unifying formal framework for the further development and study of such models. Graphical abstractThe emergence of an autocatalytic (super)set of autocatalytic (sub)sets.</p>","PeriodicalId":90244,"journal":{"name":"Journal of systems chemistry","volume":"6 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13322-014-0006-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33087825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serial transfer can aid the evolution of autocatalytic sets.","authors":"Wim Hordijk,&nbsp;Nilesh Vaidya,&nbsp;Niles Lehman","doi":"10.1186/1759-2208-5-4","DOIUrl":"https://doi.org/10.1186/1759-2208-5-4","url":null,"abstract":"<p><strong>Background: </strong>The concept of an autocatalytic set of molecules has been posited theoretically and demonstrated empirically with catalytic RNA molecules. For this concept to have significance in a realistic origins-of-life scenario, it will be important to demonstrate the evolvability of such sets. Here, we employ a Gillespie algorithm to improve and expand on previous simulations of an empirical system of self-assembling RNA fragments that has the ability to spontaneously form autocatalytic networks. We specifically examine the role of serial transfer as a plausible means to allow time-dependent changes in set composition, and compare the results to equilibrium, or \"batch\" scenarios.</p><p><strong>Results: </strong>We show that the simulation model produces results that are in close agreement with the original experimental observations in terms of generating varying autocatalytic (sub)sets over time. Furthermore, the model results indicate that in a \"batch\" scenario the equilibrium distribution is largely determined by competition for resources and stochastic fluctuations. However, with serial transfer the system is prevented from reaching such an equilibrium state, and the dynamics are mostly determined by differences in reaction rates. This is a consistent pattern that can be repeated, or made stronger or weaker by varying the reaction rates or the duration of the transfer steps. Increasing the number of molecules in the simulation actually strengthens the potential for selection.</p><p><strong>Conclusions: </strong>These simulations provide a more realistic emulation of wet lab conditions using self-assembling catalytic RNAs that form interaction networks. In doing so, they highlight the potential evolutionary advantage to a prebiotic scenario that involves cyclic dehydration/rehydration events. We posit that such cyclicity is a plausible means to promote evolution in primordial autocatalytic sets, which could later lead to the establishment of individual-based biology.</p>","PeriodicalId":90244,"journal":{"name":"Journal of systems chemistry","volume":"5 ","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2014-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1759-2208-5-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32384767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The nature and mathematical basis for material stability in the chemical and biological worlds","authors":"R. Pascal, A. Pross","doi":"10.1186/1759-2208-5-3","DOIUrl":"https://doi.org/10.1186/1759-2208-5-3","url":null,"abstract":"","PeriodicalId":90244,"journal":{"name":"Journal of systems chemistry","volume":"5 1","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2014-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1759-2208-5-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65808312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Autocatalytic sets in a partitioned biochemical network.","authors":"Joshua I Smith,&nbsp;Mike Steel,&nbsp;Wim Hordijk","doi":"10.1186/1759-2208-5-2","DOIUrl":"https://doi.org/10.1186/1759-2208-5-2","url":null,"abstract":"<p><strong>Background: </strong>In previous work, RAF theory has been developed as a tool for making theoretical progress on the origin of life question, providing insight into the structure and occurrence of self-sustaining and collectively autocatalytic sets within catalytic polymer networks. We present here an extension in which there are two \"independent\" polymer sets, where catalysis occurs within and between the sets, but there are no reactions combining polymers from both sets. Such an extension reflects the interaction between nucleic acids and peptides observed in modern cells and proposed forms of early life.</p><p><strong>Results: </strong>We present theoretical work and simulations which suggest that the occurrence of autocatalytic sets is robust to the partitioned structure of the network. We also show that autocatalytic sets remain likely even when the molecules in the system are not polymers, and a low level of inhibition is present. Finally, we present a kinetic extension which assigns a rate to each reaction in the system, and show that identifying autocatalytic sets within such a system is an NP-complete problem.</p><p><strong>Conclusions: </strong>Recent experimental work has challenged the necessity of an RNA world by suggesting that peptide-nucleic acid interactions occurred early in chemical evolution. The present work indicates that such a peptide-RNA world could support the spontaneous development of autocatalytic sets and is thus a feasible alternative worthy of investigation.</p>","PeriodicalId":90244,"journal":{"name":"Journal of systems chemistry","volume":"5 ","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2014-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1759-2208-5-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32384766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Testing for adaptive signatures of amino acid alphabet evolution using chemistry space","authors":"Melissa Ilardo, S. Freeland","doi":"10.1186/1759-2208-5-1","DOIUrl":"https://doi.org/10.1186/1759-2208-5-1","url":null,"abstract":"","PeriodicalId":90244,"journal":{"name":"Journal of systems chemistry","volume":"5 1","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2014-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1759-2208-5-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65808298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design and synthesis of nucleolipids as possible activated precursors for oligomer formation via intramolecular catalysis: stability study and supramolecular organization.","authors":"Kishore Lingam Gangadhara,&nbsp;Puneet Srivastava,&nbsp;Jef Rozenski,&nbsp;Henri-Philippe Mattelaer,&nbsp;Volker Leen,&nbsp;Wim Dehaen,&nbsp;Johan Hofkens,&nbsp;Eveline Lescrinier,&nbsp;Piet Herdewijn","doi":"10.1186/s13322-014-0005-3","DOIUrl":"https://doi.org/10.1186/s13322-014-0005-3","url":null,"abstract":"<p><strong>Background: </strong>Fatty acid vesicles are an important part of protocell models currently studied. As protocells can be considered as pre-biological precursors of cells, the models try to contribute to a better understanding of the (cellular) origin of life and emphasize on 2 major aspects: compartmentalization and replication. It has been demonstrated that lipid-based membranes are amenable to growth and division (shell replication). Furthermore compartmentalization creates a unique micro-environment in which biomolecules can accumulate and reactions can occur. Pioneering research by Sugawara, Deamer, Luisi, Szostak and Rasmussen gave more insight in obtaining autocatalytic, self-replicating vesicles capable of containing and reproducing nucleic acid sequences (core replication). Linking both core and shell replication is a challenging feat requiring thorough understanding of membrane dynamics and (auto)catalytic systems. A possible solution may lie in a class of compounds called nucleolipids, who combine a nucleoside, nucleotide or nucleobase with a lipophilic moiety. Early contributions by the group of Yanagawa mentions the prebiotic significance (as a primitive helical template) arising from the supramolecular organization of these compounds. Further contributions, exploring the supramolecular scope regarding phospoliponucleosides (e.g. 5'-dioleylphosphatidyl derivatives of adenosine, uridine and cytidine) can be accounted to Baglioni, Luisi and Berti. This emerging field of amphiphiles is being investigated for surface behavior, supramolecular assembly and even drug ability.</p><p><strong>Results: </strong>A series of α/β-hydroxy fatty acids and α-amino fatty acids, covalently bound to nucleoside-5'-monophosphates via a hydroxyl or amino group on the fatty acid was examined for spontaneous self-assembly in spherical aggregates and their stability towards intramolecular cleavage. Staining the resulting hydrophobic aggregates with BODIPY-dyes followed by fluorescent microscopy gave several distinct images of vesicles varying from small, isolated spheres to higher order aggregates and large, multimicrometer sized particles. Other observations include rod-like vesicle precursors. NMR was used to assess the stability of a representative sample of nucleolipids. 1D ³¹P NMR revealed that β-hydroxy fatty acids containing nucleotides were pH-stable while the α-analogs are acid labile. Degradation products identified by [¹H-³¹P] heteroTOCSY revealed that phosphoesters are cleaved between sugar and phosphate, while phosphoramidates are also cleaved at the lipid-phosphate bond. For the latter compounds, the ratio between both degradation pathways is influenced by the nucleobase moiety. However no oligomerization of nucleotides was observed; nor the formation of 3'-5'-cyclic nucleotides, possible intermediates for oligonucleotide synthesis.</p><p><strong>Conclusions: </strong>The nucleolipids with a deoxyribo","PeriodicalId":90244,"journal":{"name":"Journal of systems chemistry","volume":"5 ","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13322-014-0005-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32950165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}