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Conceptual similarities between zeolites and artificial enzymes.

ABSTRACT: By using a Diels-Alder (DA) reaction as a base case, we show that a pure silica zeolite acting as an entropy-trapping scaffold can be synthesized with an organic structure directing agent (OSDA) analogue of the transition state (TS) of the DA reaction. A cavity stabilization of the TS is observed with the corresponding decrease in the activation energy of the reaction. A lower enthalpy of activation and a larger decrease in entropy are obtained with the zeolite synthesized with the analogue of the DA TS when compared with other zeolitic structures. Those differences are maintained, while catalytic activity is increased, when active sites are introduced in the zeolite. The catalytic zeolitic system synthesized with the OSDA analogue of the TS shows conceptual similarities with "de novo design" of an artificial enzyme to perform DA reactions, in where a suitable scaffold of existing proteins is chosen, and computationally designed active sites able to catalyze the cycloaddition reaction are introduced.

SUBMITTER: Gallego EM

PROVIDER: S-EPMC6837030 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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Conceptual similarities between zeolites and artificial enzymes.

Gallego Eva M EM Paris Cecilia C Cantín Ángel Á Moliner Manuel M Corma Avelino A

Chemical science 20190717 34

By using a Diels-Alder (DA) reaction as a base case, we show that a pure silica zeolite acting as an entropy-trapping scaffold can be synthesized with an organic structure directing agent (OSDA) analogue of the transition state (TS) of the DA reaction. A cavity stabilization of the TS is observed with the corresponding decrease in the activation energy of the reaction. A lower enthalpy of activation and a larger decrease in entropy are obtained with the zeolite synthesized with the analogue of t ...[more]

PMID: 31853356

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Project description:Background. Neuropeptides are important regulators of physiological processes and behavior. Although they tend to be generally well conserved, recent results using trancriptome sequencing on decapod crustaceans give the impression of significant differences between species, raising the question whether such differences are real or artefacts. Methods. The BLAST+ program was used to find short reads coding neuropeptides and neurohormons in publicly available short read archives. Such reads were then used to find similar reads in the same archives, and the DNA assembly program Trinity was employed to construct contigs encoding the neuropeptide precursors as completely as possible. Results. The seven decapod species analyzed in this fashion, the crabs Eriocheir sinensis, Carcinus maenas and Scylla paramamosain, the shrimp Litopenaeus vannamei, the lobster Homarus americanus, the fresh water prawn Macrobrachium rosenbergii and the crayfish Procambarus clarkii had remarkably similar neuropeptidomes. Although some neuropeptide precursors could not be assembled, in many cases individual reads pertaining to the missing precursors show unambiguously that these neuropeptides are present in these species. In other cases, the tissues that express those neuropeptides were not used in the construction of the cDNA libraries. One novel neuropeptide was identified: elongated PDH (pigment dispersing hormone), a variation on PDH that has a two-amino-acid insertion in its core sequence. Hyrg is another peptide that is ubiquitously present in decapods and is likely a novel neuropeptide precursor. Discussion. Many insect species have lost one or more neuropeptide genes, but apart from elongated PDH and hyrg all other decapod neuropeptides are present in at least some insect species, and allatotropin is the only insect neuropeptide missing from decapods. This strong similarity between insect and decapod neuropeptidomes makes it possible to predict the receptors for decapod neuropeptides that have been deorphanized in insects. This includes the androgenic insulin-like peptide that seems to be homologous to drosophila insulin-like peptide 8.

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Conceptual similarities between zeolites and artificial enzymes.

Publications

Conceptual similarities between zeolites and artificial enzymes.

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