Kinetics of proton transfer in a green fluorescent protein: A laser-induced pH jump study

The sub-millisecond protonation dynamics of the chromophore in S65T mutant form of the green fluorescent protein (GFP) was tracked after a rapid pH jump following laser-induced proton release from the caged photolabile compoundo-nitrobenzaldehyde. Following a jump in pH from 8 to 5 (which is achieved within 2 μs), the fluorescence of S65T GFP decreased as a single exponential with a time constant of ∼90 μs. This decay is interpreted as the conversion of the deprotonated fluorescent GFP chromophore to a protonated non-fluorescent species. The protonation kinetics showed dependence on the bulk viscosity of the solvent, and therefore implicates bulk solvent-controlled protein dynamics in the protonation process. The protonation is proposed to be a sequential process involving two steps: (a) proton transfer from solvent to the chromophore, and (b) internal structural rearrangements to stabilize a protonated chromophore. The possible implications of these observations to protein dynamics in general is discussed     

Cooperative Strategies for Solving the Bicriteria Sparse Multiple Knapsack Problem

For hard optimization problems, it is difficult to design heuristic algorithms which exhibit uniformly superior performance for all problem instances. As a result it becomes necessary to tailor the algorithms based on the problem instance. In this paper, we introduce the use of a cooperative problem solving team of heuristics that evolves algorithms for a given problem instance. The efficacy of this method is examined by solving six difficult instances of a bicriteria sparse multiple knapsack problem. Results indicate that such tailored algorithms uniformly improve solutions as compared to using predesigned heuristic algorithms.     

Effects of saturation on optical bistability with coupled surface plasmons

We present exact numerical results for a symmetric layered medium (prism/Ag film/nonlinear dielectric/Ag film/prism) where the middle dielectric slab is assumed to have a saturation-type nonlinearity. We show bistable behaviour in the power dependence of the reflectivity ofp-polarized light under the condition when coupled surface modes are excited in the structure. Moreover, we study the effect of saturation on the bistable behaviour to show that multivalued character is inhibited by saturation effects. The field distributions corresponding to the minimum reflectivity states of the nonlinear structure are also presented.     

Molecular simulation study of effect of molecular association on vapor-liquid interfacial properties

Vapor-liquid interfacial properties of square-well associating fluids are studied via transition-matrix Monte Carlo simulation. Results for one-site and two-site association models are presented. Coexistence properties, surface tension, cluster distribution, density profile, and orientation profile are presented. Molecular association affects the interfacial properties and cluster fractions more than it affects the bulk densities. We observe that the surface tension exhibits a maximum with respect to association strength. This behavior is in agreement with the recent study of Peery and Evans for one site system using a square-gradient approach.     

Molecular simulation study of the effect of pressure on the vapor-liquid interface of the square-well fluid

We examine a model system to study the effect of pressure on the surface tension of a vapor-liquid interface. The system is a two-component mixture of spheres interacting with the square-well (A-A) and hard-sphere (B-B) potentials and with unlike (A-B) interactions ranging (for different cases) from hard sphere to strongly attractive square well. The bulk-phase and interfacial properties are measured by molecular dynamics simulation for coexisting vapor-liquid phases for various mixture compositions, pressures, and temperatures. The variation of the surface tension with pressure compares well to values given by surface-excess formulas derived from thermodynamic considerations. We find that surface tension increases with pressure only for the case of an inert solute (hard-sphere A-B interactions) and that the presence of A-B attractions strongly promotes a decrease of surface tension with pressure. An examination of density and composition profiles is made to explain these effects in terms of surface-adsorption arguments.     

Dielectric studies of binary mixtures of n -propyl alcohol and ethylenediamine

Dielectric constant (ε’) and dielectric loss (ε") of n-propyl alcohol (PA), ethylenediamine (EDA) and their binary mixtures, for different mole fractions of ethylenediamine have been experimentally measured at 11.15 GHz microwave frequency. Values of density (ρ), viscosity (η) and square refractive index (n _D ² ) of binary mixtures as well as those of pure liquids are reported. Excess square refractive index, viscosity and activation energy of viscous flow have also been estimated. These parameters have been used to explain the formation of complexes in the system.     

Spectrophotometric determination of thiourea in microgram quantities

Summary Copper(II) forms a stable colourless complex with thiourea. This property has been utilized to develop a Spectrophotometric method for the determination ofg quantities of thiourea. The complex absorbs in ultraviolet region and the determinations are carried out at 250 nm. The method permits the determination of thiourea from 10–60g with error not exceeding ± 1.0%.

---

Zusammenfassung Kupfer(II) bildet mit Thioharnstoff eine farblosa Komplexverbindung, die sich auf Grund ihrer Absorption bei 250 nm zur spektrophotometrischen Bestimmung von Mikrogrammengen Thioharnstoff eignet. 10 bis 60g Thioharnstoff lassen sieh mit einem Fehler von höchstens ± 1,0% bestimmen.

     

Analytical aspects of some organic acids Part III

Summary m-Phenylenedioxydiacetic acid gives a white precipitate with thorium even in the absence of an electrolyte which is quantitative up toph 4. Be²⁺, Mg²⁺, Ca²⁺, Zn²⁺, Pb²⁺ and Mn²⁺ ions are removed by single precipitation and Al³⁺, UO₂ ²⁺ and trivalent cerite earth ions are removed by double precipitation. Sn²⁺, Sn⁴⁺ and Cr³⁺ ions interfere.Part II: See. Z. analyt. Chem.165, 343 (1959).     

New designs for inhibitors of the NF-κB: DNA binding

We present a series of new inhibitors of the association between nuclear factor kappa B (NF-B) and the corresponding B site in DNA. They were designed using the lead compound 15-deoxy-^12,14 -prostaglandin J₂ (PGJ2), which is a natural product with demonstrated inhibitory efficiency for this system. First, the binding mode of PGJ2 to NF-B was unraveled by GOLD docking calculation. Subsequently, substitutions were made to PGJ2 to optimize its association with NF-B. Care was taken not to strongly increase the reactivity of the new compounds, and to keep the overall shape, size and hydrophilicity of the lead compound, which should render them a similar bioavailability. Molecular mechanics calculations were performed to decide on the suitability of the substitutions, and to evaluate the energies of association with NF-B. Density functional theory calculations were performed also to study the overall reactivity of the substituted drugs towards NF-B. Important general conclusions were obtained, concerning the improvement of these natural inhibitors; namely, a set of rational methodologies were deduced to improve the association between the PGJ2 derivatives and NF-B, and their efficiency demonstrated by generating a set of substituted complexes, some of them with a very much increased affinity for NF-B, opening new doors to enlarge the therapeutic capabilities of this class of drugs.