Dataset Information

3-Ishwarone, a rare ishwarane sesquiterpene from Peperomia scandens Ruiz & Pavon: structural elucidation through a joint experimental and theoretical study.

ABSTRACT: 3-Ishwarone, (1), a sesquiterpene with a rare ishwarane skeleton, was isolated from Peperomia scandens Ruiz & Pavon (Piperaceae). Its structure was unambiguously determined by 1D- and 2D-NMR and infrared analyses, as well as by comparative theoretical studies which involved calculations of 13C-NMR chemical shifts, using the Density Functional Theory (DFT) with the mPW1PW91 hybrid functional and Pople's 6-31G(d) basis set, and of vibrational frequencies, using the B3LYP hybrid functional and triple ? Dunning's correlation consistent basis set (cc-pVTZ), of (1) and three of its possible diastereomers, compounds 2-4.

SUBMITTER: Junior FM

PROVIDER: S-EPMC6269709 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

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3-Ishwarone, a rare ishwarane sesquiterpene from Peperomia scandens Ruiz & Pavon: structural elucidation through a joint experimental and theoretical study.

Junior Fernando M dos S FM Velozo Leosvaldo S M LS de Carvalho Erika M EM Marques André M AM Borges Ricardo M RM Trindade Ana Paula F AP dos Santos Maria Isabel S MI de Albuquerque Ana Carolina F AC Costa Fabio L P FL Kaplan Maria Auxiliadora C MA de Amorim Mauro B MB

Molecules (Basel, Switzerland) 20131031 11

3-Ishwarone, (1), a sesquiterpene with a rare ishwarane skeleton, was isolated from Peperomia scandens Ruiz & Pavon (Piperaceae). Its structure was unambiguously determined by 1D- and 2D-NMR and infrared analyses, as well as by comparative theoretical studies which involved calculations of 13C-NMR chemical shifts, using the Density Functional Theory (DFT) with the mPW1PW91 hybrid functional and Pople's 6-31G(d) basis set, and of vibrational frequencies, using the B3LYP hybrid functional and trip ...[more]

PMID: 24184821

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Project description:Time-resolved Fourier transform infrared (FTIR) spectroscopy is a powerful tool to elucidate label-free the reaction mechanisms of proteins. After assignment of the absorption bands to individual groups of the protein, the order of events during the reaction mechanism can be monitored and rate constants can be obtained. Additionally, structural information is encoded into infrared spectra and can be decoded by combining the experimental data with biomolecular simulations. We have determined recently the infrared vibrations of GTP and guanosine diphosphate (GDP) bound to Gαi1, a ubiquitous GTPase. These vibrations are highly sensitive for the environment of the phosphate groups and thereby for the binding mode the GTPase adopts to enable fast hydrolysis of GTP. In this study we calculated these infrared vibrations from biomolecular simulations to transfer the spectral information into a computational model that provides structural information far beyond crystal structure resolution. Conformational ensembles were generated using 15 snapshots of several 100 ns molecular-mechanics/molecular-dynamics (MM-MD) simulations, followed by quantum-mechanics/molecular-mechanics (QM/MM) minimization and normal mode analysis. In comparison with other approaches, no time-consuming QM/MM-MD simulation was necessary. We carefully benchmarked the simulation systems by deletion of single hydrogen bonds between the GTPase and GTP through several Gαi1 point mutants. The missing hydrogen bonds lead to blue-shifts of the corresponding absorption bands. These band shifts for α-GTP (Gαi1-T48A), γ-GTP (Gαi1-R178S), and for both β-GTP/γ-GTP (Gαi1-K46A, Gαi1-D200E) were found in agreement in the experimental and the theoretical spectra. We applied our approach to open questions regarding Gαi1: we show that the GDP state of Gαi1 carries a Mg2+, which is not found in x-ray structures. Further, the catalytic role of K46, a central residue of the P-loop, and the protonation state of the GTP are elucidated.

Dataset Information

3-Ishwarone, a rare ishwarane sesquiterpene from Peperomia scandens Ruiz & Pavon: structural elucidation through a joint experimental and theoretical study.

Publications

3-Ishwarone, a rare ishwarane sesquiterpene from Peperomia scandens Ruiz & Pavon: structural elucidation through a joint experimental and theoretical study.

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