Transformations of acetates of citronellol, geraniol, and linalool by Aspergillus niger: regiospecific hydroxylation of citronellol by a cell-free system

Incubation of acetates of geraniol, citronellol and linalool with Aspergillus niger resulted in their hydrolysis to corresponding alcohols which were further hydroxylated to their respective 8-hydroxy derivatives. In the case of linalyl acetate, besides linalool and 8-hydroxylinalool, small amounts of geraniol and agr-terpineol were also formed. Microsomes (105 000xg sediment) prepared from induced cells of A. niger were found to convert (1-3H)citronellol to 8-hydroxy citronellol in the presence of NADPH and O2. The pH optimum for the hydroxylase was found to be 7.6.

Volume effects and associations in liquid alloys

The regular associated solution model for binary systems has been modified by incorporating the size of the complex as an explicit variable. The thermodynamic properties of the liquid alloy and the interactions between theA ?B type of complex and the unassociated atoms in anA-B binary have been evaluated as a function of relative size of the complex using the activity coefficients at infinite dilution and activity data at one other composition in the binary. The computational procedure adopted for determining the concentration of clusters and interaction energies in the associated liquid is similar to that proposed by Lele and Rao. The analysis has been applied to the thermodynamic mixing functions of liquid Al-Ca alloys believed to contain Al2Ca associates. It is found that the size of the cluster significantly affects the interaction energies between the complex and the unassociated atoms, while the equilibrium constant and enthalpy change for the association reaction exhibit only minor variation, when the equations are fitted to experimental data. The interaction energy between unassociated free atoms remains virtually unaltered as the size of the complex is varied between extreme values. Accurate data on free energy, enthalpy, and volume of mixing at the same temperature on alloy systems with compound forming tendency would permit a rigorous test of the proposed model.

Enantioselective and Protecting Group-Free Synthesis of 1-Deoxythionojirimycin, 1-Deoxythiomannojirimycin, and 1-Deoxythiotalonojirimycin

1-Deoxythioglyconojirimycins were synthesized by using a protecting group-free strategy, starting from readily available carbohydrates, in good overall yield. Use of benzyl-triethylammonium tetrathiomolybdate, BnEt3N](2)MoS4, as a sulfur transfer reagent and borohydride exchange resin (BER) reduction of a lactone enabled the efficient synthesis of the title compounds.

Thermodynamic partial properties of Na2O in Nasicon solid solution, Na1+xZr2SixP3-xO12

The thermodynamic activity of sodium oxide (Na2O) in the Nasicon solid solution series, Na1+xZr2SixO12, has been measured in the temperature range 700�1100 K using solid state galvanic cells: Pt|CO2 + O2|Na2CO3?Na1+xZr2SixP3-xO12?(Y2O3)ZrO2?In + In2O3|Ta, Pt for 1 = ? = 2.5, and Pt?CO2 + O2?Na2CO3?ß-alumina?Na1+xZr2SixP3-xO12?Ar + O2?Pt for x = 0, 0.5, 2.5, and 3. The former cell, where the Nasicon solid solution is used as an electrolyte along with yttria-stabilized zirconia, is well suited for Nasicon compositions with high ionic conductivity. In the latter cell, ß-alumina is used as an electrolyte and the Nasicon solid solution forms an electrode. The chemical potential of Na2O is found to increase monotonically with x at constant temperature. The partial entropy of Na2O decreases continuously with x. However, the partial enthalpy exhibits a maximum at x = 2. This suggests that the binding energy is minimum at the composition where ionic conductivity and cell volume have maximum values.

Complexation of siRNA with Dendrimer: A Molecular Modeling Approach

This paper reports the structural behavior and thermodynamics of the complexation of siRNA with poly(amidoamine) (PAMAM) dendrimers of generation 3 (G3) and 4 (G4) through fully atomistic molecular dynamics (MD) simulations accompanied by free energy calculations and inherent structure determination. We have also done simulation with one siRNA and two dendrimers (2 x G3 or 2xG4) to get the microscopic picture of various binding modes. Our simulation results reveal the formation of stable siRNA-dendrimer complex over nanosecond time scale. With the increase in dendrimcr generation, the charge ratio increases and hence the binding energy between siRNA and dendrimer also increases in accordance with available experimental measurements. Calculated radial distribution functions of amines groups of various subgenerations in a given generation of dendrimer and phosphate in backbone of siRNA reveals that one dendrimer of generation 4 shows better binding with siRNA almost wrapping the dendrimer when compared to the binding with lower generation dendrimer like G3. In contrast, two dendrimers of generation 4 show binding without siRNA wrapping the den-rimer because of repulsion between two dendrimers. The counterion distribution around the complex and the water molecules in the hydration shell of siRNA give microscopic picture of the binding dynamics. We see a clear correlation between water. counterions motions and the complexation i.e. the water molecules and counterions which condensed around siRNA are moved away from the siRNA backbone when dendrimer start binding to the siRNA back hone. As siRNA wraps/bind to the dendrimer counterions originally condensed onto siRNA (Na-1) and dendrimer (Cl-) get released. We give a quantitative estimate of the entropy of counterions and show that there is gain in entropy due to counterions release during the complexation. Furthermore, the free energy of complexation of IG3 and IG4 at two different salt concentrations shows that increase in salt concentration leads to the weakening of the binding affinity of siRNA and dendrimer.

Thermodynamic properties of RhO2

A solid-state electrochemical cell, with yttria-stabilized zirconia as the electrolyte and pure O-2 gas at 0.1 MPa as the reference electrode, has been used to measure the oxygen chemical potential corresponding to the equilibrium between beta-Rh2O3 and RhO2 in the temperature range from 850 to 1050K. Using standard Gibbs energy of formation of beta-Rh2O3 available in the literature and the measured oxygen potential, the standard Gibbs free energy of formation of RhO2 is derived as a function of temperature: Delta G(f)degrees(RhO2)(+/- 71)/J mol(-1) = 238,418 + 179.89T Using an estimated value of Delta C-p degrees; for the formation reaction of RhO2 from its elements, the standard enthalpy of formation, standard entropy and isobaric heat capacity of RhO2 at 298.15 K are evaluated: Delta H-f degrees (298.15 K)(+/- 164)/kJ mol(-1) = -244.94, S degrees (298.15 K)(+/- 3.00)/J mol(-1) K-1 = 45.11 and C-p degrees(298.15 K)(+/- 2.6)1mol(-1) K-1 =64.28. (C) 2010 Elsevier B.V. All rights reserved.

PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes

Background: Signal transduction events often involve transient, yet specific, interactions between structurally conserved protein domains and polypeptide sequences in target proteins. The identification and validation of these associating domains is crucial to understand signal transduction pathways that modulate different cellular or developmental processes. Bioinformatics strategies to extract and integrate information from diverse sources have been shown to facilitate the experimental design to understand complex biological events. These methods, primarily based on information from high-throughput experiments, have also led to the identification of new connections thus providing hypothetical models for cellular events. Such models, in turn, provide a framework for directing experimental efforts for validating the predicted molecular rationale for complex cellular processes. In this context, it is envisaged that the rational design of peptides for protein-peptide binding studies could substantially facilitate the experimental strategies to evaluate a predicted interaction. This rational design procedure involves the integration of protein-protein interaction data, gene ontology, physico-chemical calculations, domain-domain interaction data and information on functional sites or critical residues. Results: Here we describe an integrated approach called ``PeptideMine'' for the identification of peptides based on specific functional patterns present in the sequence of an interacting protein. This approach based on sequence searches in the interacting sequence space has been developed into a webserver, which can be used for the identification and analysis of peptides, peptide homologues or functional patterns from the interacting sequence space of a protein. To further facilitate experimental validation, the PeptideMine webserver also provides a list of physico-chemical parameters corresponding to the peptide to determine the feasibility of using the peptide for in vitro biochemical or biophysical studies. Conclusions: The strategy described here involves the integration of data and tools to identify potential interacting partners for a protein and design criteria for peptides based on desired biochemical properties. Alongside the search for interacting protein sequences using three different search programs, the server also provides the biochemical characteristics of candidate peptides to prune peptide sequences based on features that are most suited for a given experiment. The PeptideMine server is available at the URL: http://caps.ncbs.res.in/peptidemine

X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures

The crystal structures of two forms of Mycobacterium leprae single-stranded DNA-binding protein (SSB) have been determined at 2.05 and 2.8 A resolution. Comparison of these structures with the structures of other eubacterial SSBs indicates considerable variation in their quaternary association, although the DNA-binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but could be related to variation in protein stability. Molecular-dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype Escherichia coli SSB and the individual subunits of both proteins. Together, the X-ray studies and molecular-dynamics simulations yield information on the relatively rigid and flexible regions of the molecule and on the effect of oligomerization on flexibility. The simulations provide insight into the changes in subunit structure on oligomerization. They also provide insight into the stability and time evolution of the hydrogen bonds/water bridges that connect the two pairs of monomers in the tetramer.