Antioxidant potential of the root of Vetiveria zizanioides (L.) Nash.

Vetiveria zizanioides, an aromatic plant commonly known as vetiver has been used for various ailments. The essential oil of vetiver root has been shown to possess antioxidant activity. However, antioxidant potential of spent root extract has not been reported. Hence, in the present study, ferric reducing, free radical scavenging and antioxidant activity of two genotypes namely KS1 and gulabi of V. zizanioides L. Nash root were investigated using in vitro assays - the ferric reducing antioxidant power (FRAP), 1,1-diphenyl-2-picrylhydrazyl (DPPH), total phenolic content (TPC), total antioxidant capacity (TAC) and reducing power (RP). KS1 genotype showed higher FRAP values, DPPH inhibition, TPC and RP potential compared to gulabi and the antioxidant activity increased with the concentration of the extract (10-1000 microg/mL). A significant protective effect of cv KS1 (100 microg/mL) extract was also observed in reduced glutathione (GSH) and malondialdehyde (MDA) concentrations of erythrocytes subjected to oxidative stress by tert-butyl hydroperoxide (t-BHP) and hydrogen peroxide (H202). The cv KS1 showed better antioxidant activity, compared to cv gulabi indicating the possibility of exploring the presence of different phytoconstituents in the two varieties.

Impact of the access tunnel engineering on catalysis is strictly ligand-specific.

The traditional way of rationally engineering enzymes to change their biocatalytic properties utilizes the modifications of their active sites. Another emerging approach is the engineering of structural features involved in the exchange of ligands between buried active sites and the surrounding solvent. However, surprisingly little is known about the effects of mutations that alter the access tunnels on the enzymes' catalytic properties, and how these tunnels should be redesigned to allow fast passage of cognate substrates and products. Thus, we have systematically studied the effects of single-point mutations in a tunnel-lining residue of a haloalkane dehalogenase on the binding kinetics and catalytic conversion of both linear and branched haloalkanes. The hotspot residue Y176 was identified using computer simulations and randomized through saturation mutagenesis, and the resulting variants were screened for shifts in binding rates. Strikingly, opposite effects of the substituted residues on the catalytic efficiency toward linear and branched substrates were observed, which was found to be due to substrate-specific requirements in the critical steps of the respective catalytic cycles. We conclude that not only the catalytic sites, but also the access pathways must be tailored specifically for each individual ligand, which is a new paradigm in protein engineering and de novo protein design. A rational approach is proposed here to address more effectively the task of designing ligand-specific tunnels using computational tools.

Kinetics of binding of fluorescent ligands to enzymes with engineered access tunnels.

Molecular recognition mechanisms and kinetics of binding of ligands to buried active sites via access tunnels are not well understood. Fluorescence polarization enables rapid and non-destructive real-time quantification of the association between small fluorescent ligands and large biomolecules. In this study, we describe analysis of binding kinetics of fluorescent ligands resembling linear halogenated alkanes to haloalkane dehalogenases. Dehalogenases possess buried active sites connected to the surrounding solvent by access tunnels. Modification of these tunnels by mutagenesis has emerged as a novel strategy to tailor the enzyme properties. We demonstrate that the fluorescence polarization method can sense differences in binding kinetics originating from even single mutations introduced to the tunnels. The results show, strikingly, that the rate constant of the dehalogenase variants varied across seven orders of magnitude, and the type of ligand used strongly affected the binding kinetics of the enzyme. Furthermore, fluorescence polarization could be applied to cell-free extracts instead of purified proteins, extending the method's application to medium-throughput screening of enzyme variant libraries generated in directed evolution experiments. The method can also provide in-depth kinetic information about the rate-determining step in binding kinetics and reveals the bottlenecks of enzyme accessibility. Assuming availability of appropriate fluorescent ligand, the method could be applied for analysis of accessibility of tunnels and buried active sites of enzymes forming a covalent alkyl-enzyme intermediate during their catalytic cycle, such as α/ß-hydrolases containing > 100 000 protein sequences based on the Pfam database.

Exploring residues crucial for nitrilase function by site directed mutagenesis to gain better insight into sequence-function relationships.

Nitrilases represent a very important class of enzymes having an array of applications. In the present scenario, where the indepth information about nitrilases is limited, the present work is an attempt to shed light on the residues crucial for the nitrilase activity. The nitrilase sequences demonstrating varying degree of identity with P. putida nitrilase were explored. A stretch of residues, fairly conserved throughout the range of higher (96%) to lower (27%) sequence identity among different nitrilases was selected and investigated for the possible functional role in nitrilase enzyme system. Subsequently, the alanine substitution mutants (T48A, W49A, L50A, P51A, G52A, Y53A and P54A) were generated. Substitution of the rationally selected conserved residues altered the substrate recognition ability, catalysis and affected the substrate specificity but had very little impact on enantioselectivity and pattern of nitrile hydrolysis.