Efficient free energy calculation of water across lipid membranes

An efficient free energy (FE) calculation of a water molecule to go across lipid membranes is presented. Both overlapping distribution and cavity insertion Widom methods are complementarily used. The former is useful for a dense region where water molecules are found, i.e., from the interfacial to bulk water region, while the latter works well in the low density region, i.e., the hydrocarbon region. Since both methods evaluate the excess chemical potential of water, the obtained FE profile is free from the fitting problem usually arisen when a FE difference method is used. A diphytanyl phosphatidylcholine bilayer is used for our test calculations. An excellent and fast convergence of the chemical potential is obtained when each method is applied for the appropriate region. The estimated FE barrier using the Ewald method for the electrostatic interaction is approximately 7.2 kcal/mol, which is higher than that using the interaction cutoff of 20 A by about 0.9 kcal/mol.     

Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation

A statistical-mechanical treatment of the molecular binding into lipid membrane is presented in combination with molecular simulation. The membrane solution is viewed as an inhomogeneous, mixed solvent system, and the free energy of solvation of a solute in membrane is computed with a realistic set of potential functions by the method of energy representation. Carbon monoxide, carbon dioxide, benzene, and ethylbenzene are adopted as model solutes to analyze the binding into 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) membrane. It is shown that the membrane inside is more favorable than bulk water and that the solute distribution is diffuse throughout the membrane inside. The membrane-water partition coefficient is then constructed with the help of the Kirkwood-Buff theory from the solvation free energy obtained separately in the hydrophobic, glycerol, headgroup, and aqueous regions. To discuss the role of repulsive and attractive interactions, the solvation free energy is partitioned into the DMPC and water contributions and the effect of water to stabilize the benzene and ethylbenzene solutes within the membrane is pointed out.     

Dendrimer container for anion-responsive lanthanide complexation and "on-off" switchable near-infrared luminescence

A new dendrimer-type ligand dynamically switched the lanthanide complexation and luminescence profiles in response to external anions.     

Biosynthesis of violacein: a genuine intermediate, protoviolaceinic acid, produced by VioABDE, and insight into VioC function

A biosynthetic intermediate of violacein produced by the mixed enzymes of VioABDE was elucidated to be 5-(5-hydroxy-1H-indol-3-yl)-3-(1H-indol-3-yl)-1H-pyrrole-2-carboxylic acid, named protoviolaceinic acid, indicating that VioC, responsible for the final biosynthetic step, works to oxygenate at the 2-position of the right side indole ring, and that the oxygenation reaction to form the central pyrrolidone core proceeds in a non-enzymatic fashion.     

"Pocket dendrimers" as nanoscale receptors for bimolecular guest accommodation

A new series of dendrimer receptors was prepared by combining a (tetraphenylporphinato)zinc(II) core and benzyl ether type dendritic substituents. Since one direction of the (tetraphenylporphinato)zinc(II) was not substituted by a dendritic residue, the resulting unsymmetrical dendrimers have "pockets" available for access of external substrates. Molecular modeling, NMR measurements, and zinc-coordination experiments revealed that the third-generation dendrimer of this type exhibited characteristic inclusion of coordinative pyridine guests. When diamidopyridine moiety was introduced into the dendrimer pocket, a thymine derivative was bound through complementary hydrogen bonding. Two different kinds of substrates, pyridine and thymine derivatives, were simultaneously accommodated in the nanoscale pocket and bimolecular guest accommodation was realized with the designed dendrimer receptor.     

Synthesis and Characterization of Amphiphilic Biodegradable Copolymer,Poly(aspartic acid‐co‐lactic acid)

An amphiphilic biodegradable polymer, poly(aspartic acid‐co‐lactic acid) (PAL), was synthesized by simply heating a mixture of aspartic acid (Asp) and L ‐lactide without additional catalysts or solvents. The unique branched architecture comprising succinimide units and lactic acid units was confirmed by IR and NMR spectroscopy. A copolymer of sodium aspartate and lactic acid (PALNa) was prepared by reacting PAL with an aqueous sodium hydroxide solution. The PAL was soluble in many organic solvents, while the PALNa was soluble in methanol and water. The hydrolytic degradation behavior of PAL varied with the copolymer composition. A higher Asp content resulted in a faster molecular weight decrease, and introducing glycolic acid units accelerated the degradation rate.

Microphotograph of microsphere of PAL‐1/5.     

Calculating the surface tension between a flat solid and a liquid: a theoretical and computer simulation study of three topologically different methods

We discuss three topologically different methods for calculating the surface tension between a flat solid and a liquid from theoretical and computer simulation viewpoints. The first method, commonly used in experiments, measures the contact angle at which a static droplet of liquid rests on a solid surface. We present a new analysis algorithm for this method and explore the effects of line tension on the contact angle. The second method, commonly used computer simulations, uses the pressure tensor through the virial in a system where a thick, infinitely extended slab of liquid rests on a solid surface. The third method, which is original to this paper and is closest to the thermodynamic definition of surface tension, applies to a spherical solid in contact with liquid in which the flat solid is recovered by extrapolating the sphere radius to infinity. We find that the second and third methods agree with each other, while the first method systematically underestimates surface tension values.     

Multidimensional cluster stability analysis from a Brazilian Bradyrhizobium sp. RFLP/PCR data set

The taxonomy of the N₂-fixing bacteria belonging to the genus Bradyrhizobium is still poorly refined, mainly due to conflicting results obtained by the analysis of the phenotypic and genotypic properties. This paper presents an application of a method aiming at the identification of possible new clusters within a Brazilian collection of 119 Bradyrhizobium strains showing phenotypic characteristics of B. japonicum and B. elkanii. The stability was studied as a function of the number of restriction enzymes used in the RFLP-PCR analysis of three ribosomal regions with three restriction enzymes per region. The method proposed here uses clustering algorithms with distances calculated by average-linkage clustering. Introducing perturbations using sub-sampling techniques makes the stability analysis. The method showed efficacy in the grouping of the species B. japonicum and B. elkanii. Furthermore, two new clusters were clearly defined, indicating possible new species, and sub-clusters within each detected cluster.