The structures and proton-coupled behavior of adenine-thymine (A-T) and a modified base pair containing a thymine isostere, adenine-difluorotoluene (A-F), are studied in different solvents by dispersion-corrected density functional theory. The stability of the canonical Watson-Crick base pair and the mismatched pair in various solvents with low and high dielectric constants is analyzed. It is demonstrated that A-F base pairing is favored in solvents with low dielectric constant. The stabilization and conformational changes induced by protonation are also analyzed for the natural as well as the mismatched base pair. DNA sequences capable of changing their sequence conformation on protonation are used in the construction of pH-based molecular switches. An acidic medium has a profound influence in stabilizing the isostere base pair. Such a large gain in stability on protonation leads to an interesting pH-controlled molecular switch, which can be incorporated in a natural DNA tract.
β-Glucosidase (EC 3.2.1.21)
plays an essential role in the
removal of glycosyl residues from disaccharide cellobiose to produce
glucose during the hydrolysis of lignocellulosic biomass. Although
there exist a few β-glucosidase that are tolerant to large concentrations
of glucose, these enzymes are typically prone to glucose inhibition.
Understanding the basis of this inhibition is important for the production
of cheaper biofuels from lignocellulose. In this study, all
-
atom molecular dynamics simulation at different temperatures and
glucose concentrations was used to understand the molecular basis
of glucose inhibition of GH1 β-glucosidase (B8CYA8) from
Halothermothrix orenii
. Our results show that glucose
induces a broadening of the active site tunnel through residues lining
the tunnel and facilitates the accumulation of glucose. In particular,
we observed that glucose accumulates at the tunnel entrance and near
the catalytic sites to block substrate accessibility and inhibit enzyme
activity. The reduction of enzyme activity was also confirmed experimentally
through specific activity measurements in the presence of 0–2.5
M glucose. We also show that the increase in glucose concentrations
leads to a decrease in the number of water molecules inside the tunnel
to affect substrate hydrolysis. Overall, the results help in understanding
the role of residues along the active site tunnel for the engineering
of glucose-tolerant β-glucosidase.
Elucidating the regulation of glucose tolerance through the interaction between the reaction product and 2 active site pocket residues of a β-glucosidase from Halothermothrix orenii
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.