Insight into the Interactions of Amyloid β-Sheets with Graphene Flakes: Scrutinizing the Role of Aromatic Residues in Amyloids that Interact with Graphene.

The interaction of amyloid β-sheet segments with graphene-flake models is investigated by using DFT calculations. The structure of β-sheets of selected amyloid segments is based on crystal structures obtained from the Protein Data Bank. Our study, based on DFT calculations for model systems, indicates that the interaction in amyloid-graphene aggregates can be stronger than the interaction in the respective amyloid-amyloid aggregates.

Metaproteogenomic analysis of a sulfate-reducing enrichment culture reveals genomic organization of key enzymes in the m-xylene degradation pathway and metabolic activity of proteobacteria.

This study aimed to ascertain the functional and phylogenetic relationships within an m-xylene degrading sulfate-reducing enrichment culture, which had been maintained for several years in the laboratory with m-xylene as the sole source of carbon and energy. Previous studies indicated that a phylotype affiliated to the Desulfobacteraceae was the main m-xylene assimilating organism. In the present study, genes and gene products were identified by a metaproteogenomic approach using LC-MS/MS analysis of the microbial community, and 2426 peptides were identified from 576 proteins.

Functional analysis of an anaerobic m-xylene-degrading enrichment culture using protein-based stable isotope probing.

A sulfate-reducing consortium maintained for several years in the laboratory with m-xylene as sole source of carbon and energy was characterized by terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of PCR-amplified 16S rRNA genes and stable isotope probing of proteins (Protein-SIP). During growth upon m-xylene or methyl-labeled m-xylene (1,3-dimethyl-(13)C(2)-benzene), a phylotype affiliated to the family Desulfobacteriaceae became most abundant. A second dominant phylotype was affiliated to the phylum Epsilonproteobacteria.

Crystal structures of intermediates in the nitroalkane oxidase reaction.

The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.

Mechanistic and structural analyses of the roles of Arg409 and Asp402 in the reaction of the flavoprotein nitroalkane oxidase.

The flavoprotein nitroalkane oxidase (NAO) catalyzes the oxidation of primary and secondary nitroalkanes to the corresponding aldehydes and ketones. The enzyme is a homologue of acyl-CoA dehydrogenase. Asp402 in NAO has been proposed to be the active site base responsible for removing the substrate proton in the first catalytic step; structurally it corresponds to the glutamate which acts as the base in medium chain acyl-CoA dehydrogenase.