Retention index calculation without n-alkanes—the virtual carbon number

Harangi, János

doi:10.1016/s0021-9673(03)00320-0

Cited by 19 publications

(18 citation statements)

References 9 publications

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“…Compounds were identified by comparison of their individual mass spectra and chromatographic retention indices with those of authentic compounds using the MassFinder 4.0 Program and Database. 19 …”

Section: Methodsmentioning

confidence: 99%

Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi-Isozizaene Synthase

et al. 2014

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The class I terpenoid cyclase epi-isozizaene synthase (EIZS) utilizes the universal achiral isoprenoid substrate, farnesyl diphosphate, to generate epi-isozizaene as the predominant sesquiterpene cyclization product and at least five minor sesquiterpene products, making EIZS an ideal platform for the exploration of fidelity and promiscuity in a terpenoid cyclization reaction. The hydrophobic active site contour of EIZS serves as a template that enforces a single substrate conformation, and chaperones subsequently formed carbocation intermediates through a well-defined mechanistic sequence. Here, we have used the crystal structure of EIZS as a guide to systematically remold the hydrophobic active site contour in a library of 26 site-specific mutants. Remolded cyclization templates reprogram the reaction cascade not only by reproportioning products generated by the wild-type enzyme but also by generating completely new products of diverse structure. Specifically, we have tripled the overall number of characterized products generated by EIZS. Moreover, we have converted EIZS into six different sesquiterpene synthases: F96A EIZS is an (E)-β-farnesene synthase, F96W EIZS is a zizaene synthase, F95H EIZS is a β-curcumene synthase, F95M EIZS is a β-acoradiene synthase, F198L EIZS is a β-cedrene synthase, and F96V EIZS and W203F EIZS are (Z)-γ-bisabolene synthases. Active site aromatic residues appear to be hot spots for reprogramming the cyclization cascade by manipulating the stability and conformation of critical carbocation intermediates. A majority of mutant enzymes exhibit only relatively modest 2–100-fold losses of catalytic activity, suggesting that residues responsible for triggering substrate ionization readily tolerate mutations deeper in the active site cavity.

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Section: Methodsmentioning

confidence: 99%

Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi-Isozizaene Synthase

et al. 2014

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“…Samples were then concentrated under vacuum in an ice water bath using a rotary evaporator and analyzed by GC-MS. Mixtures of diterpene hydrocarbons were detected at m / z 272, some of which were directly identified by comparison of their individual mass spectra and chromatographic retention indices with those of authentic compounds using the MassFinder 4.0 Program and Database. 37 Sesterterpene hydrocarbons were detected at m/z 340.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Exploring the Influence of Domain Architecture on the Catalytic Function of Diterpene Synthases

et al. 2017

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Terpenoid synthases catalyze isoprenoid cyclization reactions underlying the generation of more than 80,000 natural products. Such dramatic chemodiversity belies the fact that these enzymes generally consist of only three domain folds designated α, β, and γ. Catalysis by class I terpenoid synthases occurs exclusively in the α domain, which is found with α, αα, αβ, and αβγ domain architectures. Here, we explore the influence of domain architecture on catalysis by taxadiene synthase from Taxus brevifolia (TbTS, αβγ), fusicoccadiene synthase from Phomopsis amygdali (PaFS, (αα)6), and ophiobolin F synthase from Aspergillus clavatus (AcOS, αα). We show that the cyclization fidelity and catalytic efficiency of the α domain of TbTS are severely compromised by deletion of the βγ domains; however, retention of the β domain preserves significant cyclization fidelity. In PaFS, we previously demonstrated that one α domain similarly influences catalysis by the other α domain [Chen, M., Chou, W. K. W., Toyomasu, T., Cane, D. E., Christianson, D. W. (2016) ACS Chem. Biol. 11, 889–899]. Here, we show that the hexameric quaternary structure of PaFS enables cluster channeling. We also show that the α domains of PaFS and AcOS can be swapped so as to make functional chimeric αα synthases. Notably, both cyclization fidelity and catalytic efficiency are altered in all chimeric synthases. Twelve newly formed and uncharacterized C20 diterpene products and three C25 sesterterpene products are generated by these chimeras. Thus, engineered αβγ and αα terpenoid cyclases promise to generate chemodiversity in the greater family of terpenoid natural products.

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“…25 The virtual carbon number was a further proposal studied for the identification of compounds without applying any index calculation, but using solely the retention behaviour. 9 According to this system, an homologous series is not necessary for the calculation of retention indices, since the analysed matrix certainly contains a series of compounds with well-known retention indices; the latter, which do not necessarily belong to a homologous series, could be used as index references. The index of the other compounds shall then be calculated as with n-alkanes, although instead of the carbon numbers of the n-alkanes, virtual carbon numbers of the reference compounds should be used.…”

Section: Retention Index Theoriesmentioning

confidence: 99%

“…With time, numerous linear relationships between the retention index and other fundamental properties, such as boiling point, 8 carbon number 9 and molecular weight 10,11 were derived. The prediction of programmed temperature retention indices is also an in-depth discussed subject, 12 involving the calculation and theoretical determination of the elution order of many compounds.…”

Section: Introductionmentioning

confidence: 99%

Linear retention indices in gas chromatographic analysis: a review

Zellner

Bicchi

Dugo

et al. 2008

Flavour & Fragrance J

210

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ABSTRACT:The main purpose of any chromatographic analysis is to resolve mixtures of compounds into less complex mixtures or ultimately into pure components. In addition to this function, the chromatographic system can provide retention data which serve as complementary information for the positive identification of resolved components. The need to express gas chromatographic retention data in a standardized system has long been recognized and retention index values presented to be a valuable parameter. Those values are mainly calculated by applying the equations proposed by Kováts, for isothermal analysis, and van den Dool and Kratz, for programmed gas chromatographic runs. In general, these indices denote the retention behaviour of the compounds of interest according to a uniform scale determined by a series of closely related standard substances. The use of retention indices in the flavour and fragrance field is well-documented, and they are widely applied for the comparison of results between laboratories, as well as to characterize stationary phases.

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Retention index calculation without n-alkanes—the virtual carbon number

Cited by 19 publications

References 9 publications

Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi-Isozizaene Synthase

Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi-Isozizaene Synthase

Exploring the Influence of Domain Architecture on the Catalytic Function of Diterpene Synthases

Linear retention indices in gas chromatographic analysis: a review

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