Abstract: We developed a new method based on quasimolecular
modeling to simulate the cavity flow in three cavity
shapes: rectangular, half-circular and bucket beer in cgs units. Each
quasi-molecule was a group of particles that interacted in a fashion
entirely analogous to classical Newtonian molecular interactions.
When a cavity flow was simulated, the instantaneous velocity vector
fields were obtained by using an inverse distance weighted
interpolation method. In all three cavity shapes, fluid motion was
rotated counter-clockwise. The velocity vector fields of the three
cavity shapes showed a primary vortex located near the upstream
corners at time t ~ 0.500 s, t ~ 0.450 s and t ~ 0.350 s, respectively.
The configurational kinetic energy of the cavities increased as time
increased until the kinetic energy reached a maximum at time t ~
0.02 s and, then, the kinetic energy decreased as time increased. The
rectangular cavity system showed the lowest kinetic energy, while
the half-circular cavity system showed the highest kinetic energy.
The kinetic energy of rectangular, beer bucket and half-circular
cavities fluctuated about stable average values 35.62 x 103, 38.04 x
103 and 40.80 x 103 ergs/particle, respectively. This indicated that the
half-circular shapes were the most suitable shape for a shrimp pond
because the water in shrimp pond flows best when we compared with
rectangular and beer bucket shape.
Abstract: In this study, a synthetic pathway was created by
assembling genes from Clostridium butyricum and Escherichia coli
in different combinations. Among the genes were dhaB1 and dhaB2
from C. butyricum VPI1718 coding for glycerol dehydratase (GDHt)
and its activator (GDHtAc), respectively, involved in the conversion
of glycerol to 3-hydroxypropionaldehyde (3-HPA). The yqhD gene
from E.coli BL21 was also included which codes for an NADPHdependent
1,3-propanediol oxidoreductase isoenzyme (PDORI)
reducing 3-HPA to 1,3-propanediol (1,3-PD). Molecular modeling
analysis indicated that the conformation of fusion protein of YQHD
and DHAB1 was favorable for direct molecular channeling of the
intermediate 3-HPA. According to the simulation results, the yqhD
and dhaB1 gene were assembled in the upstream of dhaB2 to express
a fusion protein, yielding the recombinant strain E. coliBL21
(DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP41Y3). Strain
BP41Y3 gave 10-fold higher 1,3-PD concentration than E. coliBL21
(DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP31Y2) expressing
the recombinant enzymes simultaneously but in a non-fusion mode.
This is the first report using a gene fusion approach to enhance the
biological conversion of glycerol to the value added compound 1,3-
PD.
Abstract: Every 2-3 years the influenza B virus serves
epidemics. Neuraminidase (NA) is an important target for influenza
drug design. Although, oseltamivir, an oral neuraminidase drug, has
been shown good inhibitory efficiency against wild-type of influenza
B virus, the lower susceptibility to the R152K mutation has been
reported. Better understanding of oseltamivir efficiency and
resistance toward the influenza B NA wild-type and R152K mutant,
respectively, could be useful for rational drug design. Here, two
complex systems of wild-type and R152K NAs with oseltamivir
bound were studied using molecular dynamics (MD) simulations.
Based on 5-ns MD simulation, the loss of notable hydrogen bond and
decrease in per-residue decomposition energy from the mutated
residue K152 contributed to drug compared to those of R152 in wildtype
were found to be a primary source of high-level of oseltamivir
resistance due to the R152K mutation.
Abstract: Owing to the stringent environmental legislations,
CO2 capture and sequestration is one of the viable solutions to reduce
the CO2 emissions from various sources. In this context, Ionic liquids
(ILs) are being investigated as suitable absorption media for CO2
capture. Due to their non-evaporative, non-toxic, and non-corrosive
nature, these ILs have the potential to replace the existing solvents
like aqueous amine solutions for CO2 separation technologies. Thus,
the present work aims at studying the important aspects such as the
interactions of CO2 molecule with different anions (F-, Br-, Cl-, NO3
-,
BF4
-, PF6
-, Tf2N-, and CF3SO3
-) that are commonly used in ILs
through molecular modeling. In this, the minimum energy structures
have been obtained using Ab initio based calculations at MP2
(Moller-Plesset perturbation) level. Results revealed various degrees
of distortion of CO2 molecule (from its linearity) with the anions
studied, most likely due to the Lewis acid-base interactions between
CO2 and anion. Furthermore, binding energies for the anion-CO2
complexes were also calculated. The implication of anion-CO2
interactions to the solubility of CO2 in ionic liquids is also discussed.
Abstract: Certain tRNA synthetases have developed highly accurate molecular machinery to discriminate their cognate amino acids. Those aaRSs achieve their goal via editing reaction in the Connective Polypeptide 1 (CP1). Recently mutagenesis studies have revealed the critical importance of residues in the CP1 domain for editing activity and X-ray structures have shown binding mode of noncognate amino acids in the editing domain. To pursue molecular mechanism for amino acid discrimination, molecular modeling studies were performed. Our results suggest that aaRS bind the noncognate amino acid more tightly than the cognate one. Finally, by comparing binding conformations of the amino acids in three systems, the amino acid binding mode was elucidated and a discrimination mechanism proposed. The results strongly reveal that the conserved threonines are responsible for amino acid discrimination. This is achieved through side chain interactions between T252 and T247/T248 as well as between those threonines and the incoming amino acids.