scholarly journals Protoenzymes: the case of hyperbranched polyesters

2017 ◽  
Vol 375 (2109) ◽  
pp. 20160357 ◽  
Author(s):  
Irena Mamajanov ◽  
George D. Cody
Keyword(s):  
Reaction Mechanisms ◽  
Metabolic Pathways ◽  
Hyperbranched Polymers ◽  
Specific Substrate ◽  
Complex Structures ◽  
Elimination Reaction ◽  
Globular Structure ◽  
Hyperbranched Polyesters ◽  
Methylsuccinic Acid ◽  
Polymeric Structures

Enzymes are biopolymeric complexes that catalyse biochemical reactions and shape metabolic pathways. Enzymes usually work with small molecule cofactors that actively participate in reaction mechanisms and complex, usually globular, polymeric structures capable of specific substrate binding, encapsulation and orientation. Moreover, the globular structures of enzymes possess cavities with modulated microenvironments, facilitating the progression of reaction(s). The globular structure is ensured by long folded protein or RNA strands. Synthesis of such elaborate complexes has proven difficult under prebiotically plausible conditions. We explore here that catalysis may have been performed by alternative polymeric structures, namely hyperbranched polymers. Hyperbranched polymers are relatively complex structures that can be synthesized under prebiotically plausible conditions; their globular structure is ensured by virtue of their architecture rather than folding. In this study, we probe the ability of tertiary amine-bearing hyperbranched polyesters to form hydrophobic pockets as a reaction-promoting medium for the Kemp elimination reaction. Our results show that polyesters formed upon reaction between glycerol, triethanolamine and organic acid containing hydrophobic groups, i.e. adipic and methylsuccinic acid, are capable of increasing the rate of Kemp elimination by a factor of up to 3 over monomeric triethanolamine. This article is part of the themed issue ‘Reconceptualizing the origins of life’.

scholarly journals Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

2019 ◽  
Author(s):  
Waldeyr Silva ◽  
Jakob Andersen ◽  
Maristela Holanda ◽  
Maria Emília Walter ◽  
Marcelo Brigido ◽  
...  
Keyword(s):  
Reaction Mechanisms ◽  
Metabolic Pathways ◽  
Software Package ◽  
Farnesyl Diphosphate ◽  
Graph Database ◽  
Simulation Results ◽  
Biological Evidence

Plants produce a diverse portfolio of sesquiterpenes that are important in their response to herbivores and the interaction with other plants. Their biosynthesis from farnesyl diphosphate depends on the sesquiterpene synthases. Here, we investigate to what extent metabolic pathways can be reconstructed just from knowledge of the final product and the reaction mechanisms catalyzed by sesquiterpene synthases. We use the software package MedØlDatschgerl (MØD) to generate chemical networks and elucidate pathways contained in them. As examples, we successfully consider the reachability of the important plant sesquiterpenes β-caryophyllene, α-humulene, and β-farnesene. We also introduce a graph database to integrate simulation results with experimental biological evidence for selected predicted sesquiterpenes biosynthesis.

Low Temperature Synthesis of Plasma Teos SiO2

1996 ◽  
Vol 446 ◽  
Author(s):  
T. Itani ◽  
S. Fukuyama
Keyword(s):  
Reaction Mechanisms ◽  
Plasma Reactor ◽  
Substrate Surface ◽  
Condensation Reaction ◽  
Excitation Frequency ◽  
Elimination Reaction ◽  
Film Properties ◽  
Low Temperature Synthesis ◽  
Temperature Synthesis ◽  
Precursor Molecules

AbstractIn this study, we investigated the deposition temperature's affect on TEOS based Si02 properties and reaction mechanisms while changing the excitation frequency. We used a parallel-plate plasma reactor, and either 100 kHz or 13.56 MHz radio frequency to generate plasma. We found that 100 kHz plasma promotes SiO formation and improves the film properties at low deposition temperatures. We assume this to be due to the supplement of higher energy ions to the substrate surface in 100 kHz plasma. This in turn promotes the elimination reaction (condensation reaction) of OH that links to Si atoms as a terminator of surface SiO networks or precursor molecules.

scholarly journals A nematode sterol C4α-methyltransferase catalyzes a new methylation reaction responsible for sterol diversity

2019 ◽  
Vol 61 (2) ◽  
pp. 192-204 ◽  
Author(s):  
Wenxu Zhou ◽  
Paxtyn M. Fisher ◽  
Boden H. Vanderloop ◽  
Yun Shen ◽  
Huazhong Shi ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Fossil Record ◽  
Sedimentary Rock ◽  
Amino Acid Sequence Identity ◽  
Dietary Cholesterol ◽  
Specific Substrate ◽  
Metabolism Pathway ◽  
Sequence Identity ◽  
Binding Domains ◽  
Methyl Sterols

Primitive sterol evolution plays an important role in fossil record interpretation and offers potential therapeutic avenues for human disease resulting from nematode infections. Recognizing that C4-methyl stenol products [8(14)-lophenol] can be synthesized in bacteria while C4-methyl stanol products (dinosterol) can be synthesized in dinoflagellates and preserved as sterane biomarkers in ancient sedimentary rock is key to eukaryotic sterol evolution. In this regard, nematodes have been proposed to convert dietary cholesterol to 8(14)-lophenol by a secondary metabolism pathway that could involve sterol C4 methylation analogous to the C2 methylation of hopanoids (radicle-type mechanism) or C24 methylation of sterols (carbocation-type mechanism). Here, we characterized dichotomous cholesterol metabolic pathways in Caenorhabditis elegans that generate 3-oxo sterol intermediates in separate paths to lophanol (4-methyl stanol) and 8(14)-lophenol (4-methyl stenol). We uncovered alternate C3-sterol oxidation and Δ7 desaturation steps that regulate sterol flux from which branching metabolite networks arise, while lophanol/8(14)-lophenol formation is shown to be dependent on a sterol C4α-methyltransferse (4-SMT) that requires 3-oxo sterol substrates and catalyzes a newly discovered 3-keto-enol tautomerism mechanism linked to S-adenosyl-l-methionine-dependent methylation. Alignment-specific substrate-binding domains similarly conserved in 4-SMT and 24-SMT enzymes, despite minimal amino acid sequence identity, suggests divergence from a common, primordial ancestor in the evolution of methyl sterols. The combination of these results provides evolutionary leads to sterol diversity and points to cryptic C4-methyl steroidogenic pathways of targeted convergence that mediate lineage-specific adaptations.­­

scholarly journals Polyglycerol Hyperbranched Polyesters: Synthesis, Properties and Pharmaceutical and Biomedical Applications

2019 ◽  
Vol 20 (24) ◽  
pp. 6210 ◽  
Author(s):  
Alexandra Zamboulis ◽  
Eirini A. Nakiou ◽  
Evi Christodoulou ◽  
Dimitrios N. Bikiaris ◽  
Eleana Kontonasaki ◽  
...  
Keyword(s):  
Biomedical Applications ◽  
Degradation Products ◽  
Low Cost ◽  
Dicarboxylic Acids ◽  
Hyperbranched Polymers ◽  
Molar Ratio ◽  
Poly Lactic Acid ◽  
Hyperbranched Polyesters ◽  
Synthesis Properties ◽  
Potential Applications

In a century when environmental pollution is a major issue, polymers issued from bio-based monomers have gained important interest, as they are expected to be environment-friendly, and biocompatible, with non-toxic degradation products. In parallel, hyperbranched polymers have emerged as an easily accessible alternative to dendrimers with numerous potential applications. Glycerol (Gly) is a natural, low-cost, trifunctional monomer, with a production expected to grow significantly, and thus an excellent candidate for the synthesis of hyperbranched polyesters for pharmaceutical and biomedical applications. In the present article, we review the synthesis, properties, and applications of glycerol polyesters of aliphatic dicarboxylic acids (from succinic to sebacic acids) as well as the copolymers of glycerol or hyperbranched polyglycerol with poly(lactic acid) and poly(ε-caprolactone). Emphasis was given to summarize the synthetic procedures (monomer molar ratio, used catalysts, temperatures, etc.,) and their effect on the molecular weight, solubility, and thermal and mechanical properties of the prepared hyperbranched polymers. Their applications in pharmaceutical technology as drug carries and in biomedical applications focusing on regenerative medicine are highlighted.

scholarly journals Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

Processes ◽  
2019 ◽  
Vol 7 (4) ◽  
pp. 240 ◽  
Author(s):  
Waldeyr M. C. da Silva ◽  
Jakob L. Andersen ◽  
Maristela T. Holanda ◽  
Maria Emília M. T. Walter ◽  
Marcelo M. Brigido ◽  
...  
Keyword(s):  
Reaction Mechanisms ◽  
Metabolic Pathways ◽  
Software Package ◽  
Farnesyl Diphosphate ◽  
Graph Database ◽  
Simulation Results ◽  
Biological Evidence

Plants produce a diverse portfolio of sesquiterpenes that are important in their response to herbivores and the interaction with other plants. Their biosynthesis from farnesyl diphosphate depends on the sesquiterpene synthases that admit different cyclizations and rearrangements to yield a blend of sesquiterpenes. Here, we investigate to what extent sesquiterpene biosynthesis metabolic pathways can be reconstructed just from the knowledge of the final product and the reaction mechanisms catalyzed by sesquiterpene synthases. We use the software package MedØlDatschgerl (MØD) to generate chemical networks and to elucidate pathways contained in them. As examples, we successfully consider the reachability of the important plant sesquiterpenes β -caryophyllene, α -humulene, and β -farnesene. We also introduce a graph database to integrate the simulation results with experimental biological evidence for the selected predicted sesquiterpenes biosynthesis.

Kinetic correlations for H2 addition and elimination reaction mechanisms during silicon hydride pyrolysis

2010 ◽  
Vol 12 (39) ◽  
pp. 12676 ◽  
Author(s):  
Andrew J. Adamczyk ◽  
Marie-Françoise Reyniers ◽  
Guy B. Marin ◽  
Linda J. Broadbelt
Keyword(s):  
Reaction Mechanisms ◽  
Elimination Reaction ◽  
Silicon Hydride ◽  
H2 Addition
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