Role of structural water molecule in HIV protease-inhibitor complexes: a QM/MM study

Structural water molecule 301 found at the interface of HIV protease-inhibitor complexes function as a hydrogen bond (H-bond) donor to carbonyl groups of the inhibitor as well as H-bond acceptor to amide/amine groups of the flap region of the protease. In this study, six systems of HIV protease-inhibitor complexes were analyzed, which have the presence of this "conserved" structural water molecule using a two-layer QM/MM ONIOM method. The combination of QM/MM and QM method enabled the calculation of strain energies of the bound ligands as well as the determination of their binding energies in the ligand-water and ligand-water-protease complexes. Although the ligand experiences considerable strain in the protein bound structure, the H-bond interactions through the structural water overcomes this strain effect to give a net stability in the range of 16-24 kcal/mol. For instance, in 1HIV system, the strain energy of the ligand was 12.2 kcal/mol, whereas the binding energy associated with the structural water molecule was 20.8 kcal/mol. In most of the cases, the calculated binding energy of structural water molecule showed the same trend as that of the experimental binding free energy values. Further, the classical MD simulations carried out on 1HVL system with and without structural water 301 showed that this conserved water molecule enhances the H-bond dynamics occurring at the Asp-bound active site region of the protease-inhibitor system, and therefore it will have a direct influence on the mechanism of drug action.     

A computational study of ultrafast acid dissociation and acid-base neutralization reactions. II. The relationship between the coordination state of solvent molecules and concerted versus sequential acid dissociation

We investigate the role played by the coordination state of pre-existing water wires during the dissociation of moderately strong acids by means of first-principles molecular dynamics calculations. By preparing 2,4,6-tricyanophenol (calc. pKa～0.5) in two different initial states, we are able to observe sequential as well as concerted trajectories of dissociation: On one hand, equilibrium dissociation takes place on a ～50 ps timescale; proton conduction occurs through three-coordinated water wires in this case, by means of sequential Grotthus hopping. On the other hand, by preparing 2,4,6-tricyanophenol in a hydration state inherited from that of equilibrated phenol (calc. pKa=7.6), the moderately strong acid finds itself in a presolvated state from which dissociation can take place on a ～1 ps timescale. In this case, concerted dissociation trajectories are observed, which consist of proton translocation through two intervening, four-coordinated, water molecules in 0.1-1.0 ps. The present results suggest that, in general, the mechanism of proton translocation depends on how the excess proton is injected into a hydrogen bond network. In particular, if the initial conditions favour proton release to a fourfold H-bonded water molecule, proton translocation by as much as 6-8 A? can take place on a sub-picosecond timescale.     

Methanogenesis mediated by methylotrophic mixed culture

Enrichment of methanogenic cultures on methanol from the microbial population in the anaerobic digesters operated on agricultural wastes revealed a high rate of biomethanation efficiency. Routine maintenance of this enrichment in a minimal basal medium at room temperature resulted in maximal growth in 40–50 d, and indicated pigment production toward the end of the growth phase. The cultures grown in three different media, with different substrates under light and dark conditions, were analyzed for protein, pigment, and gaseous products, and morphological studies were carried out by light, phase-contrast, fluorescence, and electron microscopy. In different media with methanol as substrate, growth and pigment production were maximal for the light-grown cells, decreasing in the order: phototrophic (PS(m)) > mineral > basal medium. Methanation and phototrophic growth were inversely correlated under lightgrown conditions. In contrast, growth in the dark was predominently methanogenic in the decreasing order: mineral > basal > PS (m). Among other growth conditions tested, utilization of phototrophic substrates under light and dark conditions indicated the following:

1. Basal and mineral media were supportive of methanogenic growth under both light and dark conditions, although methane yields under light-grown conditions were low;
2. Among the different substrates tested, methanol-grown cells gave the highest methane yield in the dark and;
3. Phototrophic growth in PS medium with succinate, malate, and pyruvate was better than that with methanol.

Absorption spectra of light-grown cells indicated the presence of bacteriochlorophyll a (Bchl a), as a doublet in the 800–0 nm region, which was absent in the dark-grown cells. Spectra of extracted pigments confirmed the presence of Bchl a with a 770-nm peak and carotenoid absorption bands in the 400–500 nm region indicative of the presence of a pigment of the spirilloxanthin type. Collective evidence for the predominant growth of a phototrophic organism under lightgrown conditions and microscopic examination under all conditions indicated the possible presence in the mixed culture of purple nonsulfur bacteria of theRhodopseudomonas type. In addition, the enrichment culture was found to contain other morphological forms, such as short and long rods, both individually and in clusters and coccoid cells. The presence of such different forms of microbial population in a methylotrophic enrichment along with phototrophic bacteria is interesting and is of ecological significance. Considering the uphill task of methanol oxidation under anaerobic conditions, the studies on the present enrichment signify metabolic partnerships in the methylotrophic biochemical mechanisms operative toward energy recovery.     

Fluorescence Imaging of Stem Cells,Cancer Cells and Semi-Thin Sections of Tissues using Silica-Coated CdSe Quantum Dots

Trioctylphosphine oxide capped cadmium selenide quantum dots, synthesized in organic media were rendered water soluble by silica overcoating. Silanisation was done by a simple reverse microemulsion method using aminopropyl silane as the silica precursor. Further, the strong photoluminescence of the silica-coated CdSe quantum dots has been utilized to visualize rabbit adipose tissue-derived mesenchymal stem cells (RADMSCs) and Daltons lymphoma ascites (DLA) cancerous cells in vitro. Subsequently the in vivo fluorescence behaviours of QDs in the tissues were also demonstrated by intravenous administration of the QDs in Swiss albino mice. The fluorescence microscopic images in the stem cells, cancer cells and semi-thin sections of mice organs proved the strong luminescence property of silica-coated quantum dots under biological systems. These results establish silica-coated CdSe QDs as extremely useful tools for molecular imaging and cell tracking to study the cell division and metastasis of cancer and other diseases.