There is potential for flight time based DNA sequencing involving disassembly into individual nucleotides which would pass through a nanochannel with two or more detectors. We performed molecular dynamics simulations of electrophoretic motion of single DNA nucleotides through 3 nm wide hydrophobic slits with both smooth and rough walls. The electric field (E) varied from 0.0 to 0.6 V/nm. The nucleotides adsorb and desorb from walls multiple times during their transit through the slit. The nucleotide–wall interactions differed due to nucleotide hydrophobicities and wall roughness which determined duration and frequency of nucleotide adsorptions and their velocities while adsorbed. Transient association of nucleotides with one, two, or three sodium ions occurred, but the mean association numbers (ANs) were weak functions of nucleotide type. Nucleotide–wall interactions contributed more to separation of nucleotide flight time distributions than ion association and thus indicate that nucleotide–wall interactions play a defining role in successfully discriminating between nucleotides on the basis of their flight times through nanochannels/slits. With smooth walls, smaller nucleotides moved faster, but with rough walls larger nucleotides moved faster due to fewer favorable wall adsorption sites. This indicates that roughness, or surface patterning, might be exploited to achieve better time-of-flight based discrimination between nucleotides.
The enzyme biotin carboxylase (BC) uses adenosine triphosphate (ATP) to carboxylate biotin and is involved in fatty acid synthesis. Structural evidence suggests that the B domain of BC undergoes a large hinge motion of ∼45° when binding and releasing substrates. Escherichia coli BC can function as a natural homodimer and as a mutant monomer. Using molecular dynamics simulations, we evaluate the free energy profile along a closure angle of the B domain of E. coli BC for three cases: a monomer without bound Mg2ATP, a monomer with bound Mg2ATP, and a homodimer with bound Mg2ATP in one subunit. The simulation results show that a closed state is the most probable for the monomer with or without bound Mg2ATP. For the dimer with Mg2ATP in one of its subunits, communication between the two subunits was observed. Specifically, in the dimer, the opening of the subunit without Mg2ATP caused the other subunit to open, and hysteresis was observed upon reclosing it. The most stable state of the dimer is one in which the B domain of both subunits is closed; however, the open state for the B domain without Mg2ATP is only approximately 2kBT higher in free energy than the closed state. A simple diffusion model indicates that the mean times for opening and closing of the B domain in the monomer with and without Mg2ATP are much smaller than the overall reaction time, which is on the order of seconds.
Mohammad Hossein Mirjalili, Elisabeth Moyano, Mercedes Bonfill, Rosa M. Cusido, Javier Palazón
Published: Jul 2009
Since vitanolides are likely to be derived from cholesterol, this is an appropriate starting point for discussing their biosynthesis. The first step in cholesterol biosynthesis is the activation of acetate by converting it to acetyl coenzyme A, abbreviated acetylCoA.
The hydrolyzed sheep and alpaca skins had a high content of macronutrients with an acceptable apparent digestibility of nutrients, making them a viable alternative to improve the nutritive value of more economical feeds for rainbow trout feed.
Although initiation of ART during Fiebig stages I - II AHI reversed the cytokine storm caused by HIV, these people in the acute phase still had significant eosinophil, basophil, and lymphocyte depletion and a temporary increase in monocytes before the onset of the disease. initiation of ART, which suggests that even ART, started during the onset of viremia, does not reverse all immune changes caused by HIV.