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Catherine A Peters

Publications and source records attributed to Catherine A Peters.

4 recordsLinked to original sources
PubMed2006

A molecular modeling analysis of polycyclic aromatic hydrocarbon biodegradation by naphthalene dioxygenase.

A theoretical analysis was performed to examine the role of naphthalene dioxygenase (NDO) enzymes in determining differences in biodegradability and biodegradation rates of two- to four-ring polycyclic aromatic hydrocarbons (PAHs) via oxygenation and desaturation reactions. Investigation of the thermodynamics of PAH biodegradation reactions catalyzed by NDO revealed that enthalpies of reaction can explain reaction patterns or regioselectivity of the enzyme in limited cases. Molecular modeling analysis of the size and shape constraints of PAH-enzyme interactions suggests that PAHs bigger than approximately four rings and compounds with alpha substituents or other structural features contributing to increased width at the end of the substrate near the active site are expected to have binding difficulties. This explains some regioselectivity observations, in that thermodynamically favorable sites on some PAH molecules cannot be positioned correctly to be oxidized at the active site. The enzyme fit analysis also suggests that slower biodegradation rates are expected for compounds with larger widths because of the unique positioning that is required for reaction to occur. An inverse relationship between a molecular descriptor of compound width and previously obtained biodegradation rates suggests that this descriptor may be valuable for predicting relative biodegradation rates of PAHs with dioxygenases other than NDO.

Biodegradation, Environmental↗
PubMed2006

Multisubstrate biodegradation kinetics for binary and complex mixtures of polycyclic aromatic hydrocarbons.

Biodegradation kinetics were studied for binary and complex mixtures of nine polycyclic aromatic hydrocarbons (PAHs): Naphthalene, 1-methylnaphthalene, 2-methylnaphthalene, 2-ethylnaphthalene, phenanthrene, anthracene, pyrene, fluorene, and fluoranthene. Discrepancies between the observed biodegradation rates and those predicted by a sole-substrate model indicate that significant substrate interactions occurred in both the binary and complex-mixture experiments. For all compounds except naphthalene, biodegradation was enhanced. The observations were compared to predictions from two multisubstrate biodegradation kinetic models: One that accounts for competitive inhibition, and one that does not. Both models are fully predictive in that parameters had been determined from an independent set of sole-substrate experiments. In the binary experiments, the major multisubstrate effect was biomass enhancement as a result of growth on naphthalene. Substrate interactions were orders of magnitude larger for most compounds in the complex mixtures, but significant competitive inhibition effects counteracted some of the biomass enhancement effect. The present study has demonstrated that the sole-substrate model is inadequate to describe multisubstrate biodegradation kinetics for a broad range of PAH mixtures. Whereas the multisubstrate model without inhibition did an adequate job of predicting the observed effects in some cases, we advocate the use of the multisubstrate model with inhibition for similar modeling efforts in light of the evidence that the model was correct more often than not. Theory supports its use because of the common enzyme pathways for biodegradation of PAHs.

Biomass↗
PubMed2005

Polycyclic aromatic hydrocarbon biodegradation rates: a structure-based study.

This study was designed to examine the role of molecular structure in determining the biodegradation rates of polycyclic aromatic hydrocarbons (PAHs). Laboratory experiments were performed in aqueous systems, and data were analyzed in a manner that allowed determination of first-order biodegradation rates independent of bioavailability limitations from physical-chemical processes. An aerobic mixed culture was used, which had been enriched on a broad range of PAHs. The 22 PAHs included in this study ranged in size from two to four rings and included compounds with 5-carbon rings and alkyl substituents. The range of observed biodegradation rates was only 1 order of magnitude, which is much less than that which is typically observed in the field. This supports the findings of other types of studies, which conclude that most of the observed variation in environmental PAH biodegradation rates comes from processes controlling the bioavailability of the compounds and not processes controlling uptake or biotransformation. Rate differences that were observed were attributable either to the presence of a 5-carbon ring or an alkyl substituent in an alpha position. Various molecular descriptors that might be expected to correlate with rate-limiting steps in the biodegradation process were used in an attemptto develop a quantitative structure-activity relationship for the PAH biodegradation rates. No significant correlations were found, but rate limitation from interactions with the relevant enzymes remains a possibility.

Aerobiosis↗