MD simulations

Mustard oil is one of the main edible oil consumed in Bangladesh which market is entirely controlled by local producers. However, no study has been reported to assess the actual quality of these products yet. To evaluate this situation, an experimental study has been performed to detect the degree of different types of adulteration and to establish their relative contamination level in different brands of commercial mustard oil. Qualitative tests were performed for twelve samples of which eleven were arbitrarily chosen commercial samples and the rest was a raw sample produced from seed. These were investigated to find five common adulterants in mustard oil. Unfortunately, the presence of argemone oil and mineral oil were found in all the samples, however, the concentration of argemone oil was ten folds higher in some of the commercial oils compared to the raw oil. The appearance of turbidity in the case of mineral oil detection was quantified with the help of spectrophotometer and they varied from 74 to 1165 FAU. A wide range of variation in these values attributes to the variations in the processing steps of commercial mustard oil. Castor oil was present in some of the samples in varying amount. Of twelve samples, two contained remarkably high amount of castor oil, five contained trace amount and the rest was free from this contamination. Prohibited color was not found in any of the samples. HAZEN, pH and density data for all the oil samples were determined which ranged from 310 to 926 H,3.62 to 5.5 and 843.33 to 910 kg/m 3 respectively which might be attributed to different refining techniques. The results are very alarming as the presence of these adulterants endanger public health.

Besides four Bcl-2 homology (BH1, BH2, BH3 and BH4)
domains, the fl exible loop domain (FLD) of Bcl-2 is also
important in regulating apoptosis. The FLD regulates
apoptosis by interacting with JNK-1, PKC, PP2A
phosphatase caspase-3, MAPKinase, Ubiquitin, PS1
and FKBP38 proteins. In addition, mutations in FLD at
ASP34, Thr56, Thr69, Ser70, Thr74 and Ser87 disrupt
Bcl-2 anti-apoptotic function. Therefore to predict the
FLD behavior, it is essential to elucidate its folding and
consequent effect on the overall Bcl-2 protein through
simulations. We have predicted fl exibility and stability
behavior of FLD by Molecular Dynamics (MD) simulations.
The simulated improved quality average structure
(ID: PM0076467) and ensemble of 23 structures (ID:
PM0077081-PM0077103) were submitted in protein
model database (PMDB). The optimized FLD was used
to predict the collective motions and essential subspace
relevant for Bcl-2 protein functions which revealed that
conformational changes in FLD likely affect BH3 cleft.
These results provide a possible reason for difference
between BH3 cleft of 1GJH (NMR) and 2XA0 (X-ray)
models. Our study would facilitate understanding of the
structural basis of Bcl-2 anti-apoptotic activity regulation
upon binding with other proteins through FLD.

A B S T R A C T Understanding of the molecular interaction between asphaltenes and other molecules, which may act as its solvents , provides insights into the nature of its stability in petroleum fluids and its phase transitions. Molecular dynamics simulations were performed and reported here on systems consisting of a single asphaltene molecule and pure solvents. Three types of asphaltenes with different architectures, molecular weights, and heteroatoms content were investigated. Water and ortho-xylene were selected to be the interacting solvents. All simulations were performed by using GROMACS software. OPLS_AA potential model for hydrocarbons and SPC/E potential model for water were used in simulations. It was shown that the polar functional groups in asphaltenes were responsible for generating hydrogen bonds (HBs) between asphaltenes and water. It was also demonstrated that both electrostatic (ES) and van der Waals (vdW) interaction energies between asphaltenes and water had important roles. On the contrary, ES between asphaltenes and ortho-xylene had a minor effect as compared with the vdW. In all cases, potential energies increased rather slightly when the pressure was boosted. Moreover, they decreased noticeably when the temperature was raised. HBs between asphaltenes and water were not influenced by pressure change. Additionally, they increased slightly when the temperature was dropped.

Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the ‘wobble’ 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level. Hence, 50ns multiple molecular dynamics (MD) simulations of various anticodon stem loop (ASL) models of tRNALeu in presence and absence of τm5U34 along with UUG and UUA codons were performed to explore the dynamic behaviour of τm5U34 during codon recognition process. The MD simulation results revealed that τm5U34 recognizes G/A ending codons by ‘wobble’ as well as a novel ‘single’ hydrogen bonding interactions. RMSD and RMSF values indicate the comparative stability of the ASL models containing τm5U34 modification over the other models, lacking τm5U34. Another MD simulation study of 55S mammalian mitochondrial rRNA with tRNALeu showed crucial interactions between the A-site residues, A918, A919, G256 and codon-anticodon bases. Thus, these results could improve our understanding about the decoding efficiency of human mt tRNALeu with τm5U34 to recognize UUG and UUA codons.