Systems Chemistry on Ribozyme Self‐Construction: Evidence for Anabolic Autocatalysis in a Recombination Network

Hayden, Eric J.; Kiedrowski, Günter von; Lehman, Niles

doi:10.1002/anie.200802177

Cited by 76 publications

(49 citation statements)

References 32 publications

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“…2 for the Fab drug product lots. Such a kinetic profile has been reported for autocatalytic reactions, a mechanism in which at least one of the products acts as a catalyst to further promote the reaction (32)(33)(34)(35).…”

Section: Mechanism and Kinetics Of Trp Oxidation In Fab Drug Product mentioning

confidence: 74%

Site-Specific Tryptophan Oxidation Induced by Autocatalytic Reaction of Polysorbate 20 in Protein Formulation

Lam¹,

Lai²,

Chan³

et al. 2011

Pharm Res

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Section: Mechanism and Kinetics Of Trp Oxidation In Fab Drug Product mentioning

confidence: 74%

Site-Specific Tryptophan Oxidation Induced by Autocatalytic Reaction of Polysorbate 20 in Protein Formulation

Lam¹,

Lai²,

Chan³

et al. 2011

Pharm Res

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“…69,70 ) or they might self-assemble to be a functional ribozyme 71 . Vasas et al 72 analysed the kinetic stability of a simple two-membered autocatalytic loop, where each member catalyses the inclusion of one non-catalytic molecule.…”

Section: I/1 the Combinatorial Approachmentioning

confidence: 99%

The dynamics of the RNA world: insights and challenges

Kun

Szilágyi

Könnyű

et al. 2015

Annals of the New York Academy of Sciences

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The problem of the origin of life is not only one of structure but also that of dynamics. Ever since the seminal result of Manfred Eigen in 1971 showing that early template replication suffers from an error threshold, research has tackled the issue of how early genomes could have been dynamically stable without highly evolved mechanisms such as accurate replication and chromosomes. We review the theory of the origin, maintenance and enhancement of the RNA world as an evolving population of dynamical systems. Investigation of sequence space has revealed how structures are allocated in sequence space and how this affects the nature of the error threshold that sets the selectively maintainable genome length. New applications of old dynamical theory are still possible: the application of Gause's principle of competitive exclusion, based on resource utilisation, to RNA replication predicts that at most four pairs (plus and minus strands) can stably be maintained on four nucleotides. Other mechanisms of early template coexistence should be regarded as additional means to raise the number of coexisting species above the number set by the competitive exclusion principle. One such example is the hypercycle in which templates were postulated to help replication of the next member in a cycle superimposed on individual replication cycles. Although the hypercycle is ecologically unstable it is evolutionarily unstable because it cannot efficiently compete against emerging parasites. Population structure can modify this conclusion but not without further qualification. The simplest form of population structure is limited diffusion on a surface. This simple mechanism can ensure the coexistence of competing ribozymes contributing to surface metabolism as well as the spread of efficient replicases despite the parasite problem. Hypercyclescan only be saved by active compartmentalization when replicators are enclosed in reproducing protocells. Once there are protocells there is no need for internal hypercyclic organization, however. Finally we review two crucial adaptations that enhanced the RNA world: chromosomes and enzymatic metabolism. Interestingly, it was shown that these two have been presumably coevolutionarily linked because protocells harbouring unlinked, competing ribozymes are better off if the ribozymes remain inefficient but generalists. The appearance of chromosomes alleviates intragenomic conflict and is enabling constraint for the emergence of specific and efficient enzymes.The possibility of an RNA world, a period in the origin of life on Earth, when RNA molecules acted both as enzymes and as genetic material, was suggested well before the name was coined by Gilbert in 1986 1 . The history of the research on the origin of life 2 tells us that the potential prebiotic importance of RNA was suggested as early as in the late 50's. When it became established that living cells harbour much more RNA than DNA some biologist have proposed that RNA preceded DNA during evolution 3,4 . The discovery of the details of protein ...

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“…Apesar do avanço teórico e experimental, apenas recentemente foi demonstrado que a comunicação intercelular via difusão é responsável pela diferenciação na composição química, seguida pela diferenciação 11 O desenvolvimento da biologia sintética na construção de estruturas supramoleculares com atividades biológicas específi-cas [108][109][110] apresenta-se como uma vertente interessante na utilização do controle da estruturação espacial ao conduzir o sistema para um estado desejado.…”

Section: Futuras Direçõesunclassified

Turing Patterns in Chemical Systems

Nagao¹,

Varela²

2016

Química Nova

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publicado na web em 18/02/2016 TURING PATTERNS IN CHEMICAL SYSTEMS. Spontaneous pattern formation in reaction-diffusion systems was theoretically proposed by Alan M. Turing in 1952. His breakthrough conceptions of chemical self-organization were able to explain how patterns emerge in nature and the symmetry breaking, which are of utmost importance, for instance, in the context of origin of life. Along with the experimental observations in the Belousov-Zhabotinsky reaction and the development of the nonequilibrium thermodynamics by Prigogine and co-workers, Turing predictions are considered the foundation of the field of Nonlinear Chemical Dynamics. This review aims to describe the basis of Turing structures with their consequent scientific achievements and to provide future directions in the development of this field. Keywords: Turing patterns; self-organization; nonlinear dynamics; pattern formation; oscillations. INTRODUÇÃOA prevalência de padrões auto-organizados em seres vivos é um resultado característico da seleção natural.1 Ao longo do tempo, o padrão que melhor se adapta ao ambiente externo é selecionado e transmitido para as gerações seguintes. Pode-se citar como um exemplo recorrente desta estruturação, a formação de moléculas de ácido desoxirribonucleico (deoxyribonucleic acid, DNA) capazes de carregar informações codificadas estritamente necessárias para a concepção de estruturas complexas em escala supramolecular. 2A autorreplicação dessas moléculas é regida por uma maquinaria reprodutiva de divisão celular que, em determinadas condições, desencadeia um processo de diferenciação e, consequentemente, um conjunto de células ou órgãos com funcionalidades específicas. Este desenvolvimento celular seletivo é conhecido por morfogênese. A primeira descrição químico-matemática desse processo foi formulada por Turing em 1952 em seu trabalho: The Chemical Basis of Morphogenesis. 3Alan Mathison Turing (23/06/1912 -7/06/1954) foi um matemá-tico britânico e criptoanalista conhecido sobretudo pela fundação da ciência da computação, criando o conceito de algoritmo e computação com a "Máquina de Turing".6 Trabalhou durante a Segunda Guerra Mundial à serviço do comando militar britânico no Government Code and Cypher School em Bletchley Park como decifrador de mensagens encriptadas por uma máquina desenvolvida pelos alemães chamada de "Enigma". Além da sua contribuição na ciência da computação, outro grande legado foi concebido dois anos antes do seu falecimento.Turing acreditava que padrões complexos encontrados em diversos aspectos na natureza poderiam ser descritos por meio da combinação de leis físicas simples. Basicamente, ele sugere que a formação desses padrões é regida pelo acoplamento entre os parâ-metros cinéticos da reação com fenômenos de transporte de massa de espécies químicas presentes no meio reacional. Essa descrição, ainda que simplificada, serviu como um passo inicial importante para o melhor entendimento da segregação espontânea de espécies químicas ao longo do espaço observada em diversos sistema...

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Systems Chemistry on Ribozyme Self‐Construction: Evidence for Anabolic Autocatalysis in a Recombination Network

Cited by 76 publications

References 32 publications

Site-Specific Tryptophan Oxidation Induced by Autocatalytic Reaction of Polysorbate 20 in Protein Formulation

Site-Specific Tryptophan Oxidation Induced by Autocatalytic Reaction of Polysorbate 20 in Protein Formulation

The dynamics of the RNA world: insights and challenges

Turing Patterns in Chemical Systems

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