Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition

Sequence dependence of DNA conformation plays a crucial role in its recognition by proteins and ligands. To clarify the relationship between sequence and conformation, it is necessary to quantify the conformational energy and specificity of DNA. Here, we make a systematic analysis of dodecamer DNA structures including all the 136 unique tetranucleotide sequences at the center by molecular dynamics simulations. Using a simplified conformational model with six parameters to describe the geometry of adjacent base pairs and harmonic potentials along these coordinates, we estimated the equilibrium conformational parameters and the harmonic potentials of mean force for the central base-pair steps from many trajectories of the simulations. This enabled us to estimate the conformational energy and the specificity for any given DNA sequence and structure. We tested our method by using sequence-structure threading to estimate the conformational energy and the Z-score as a measure of specificity for many B-DNA and A-DNA crystal structures. The average Z-scores were negative for both kinds of structures, indicating that the potential of mean force from the simulation is capable of predicting sequence specificity for the crystal structures and that it may be used to study the sequence specificity of both types of DNA. We also estimated the positional distribution of conformational energy and Z-score within DNA and showed that they are strongly position dependent. This analysis enabled us to identify particular conformations responsible for the specificity. The presented results will provide an insight into the mechanisms of DNA sequence recognition by proteins and ligands.     

Thermal and FTIR spectroscopic analysis of the interactions of aniline adsorbed on to MCM-41 mesoporous material

The adsorption of aniline on Na-AlMCM-41 synthesized by us has been characterized by infrared spectroscopy, temperature programmed desorption (TPD), and differential thermal analysis methods. Aniline would be mostly bound to the mesostructure through weak pi interactions. On the mesostructure containing adsorbed water, the co-adsorption of aniline could occur by weak hydrogen bonding through surface water molecules. For water, two possible modes of adsorption have been identified. Different associations between aniline and hydrated and nonhydrated mesostructures have been evaluated in order to favor the posterior in situ polymerization of adsorbed aniline.     

Kinetic determination of selenium, based on inhibition of the Pd(II)-catalysed reaction between pyronine G and hypophosphite

A new kinetic method for determination of selenium is based on its inhibitory effect on the Pd(II)-catalysed reaction between Pyronine G and hypophosphite. Under the optimum experimental conditions (6 x 10(-5)M Pyronine G, 0.4M hypophosphite, 0.4 mug/ml Pd(II), pH 2.8, temperature 22.0 +/- 0.2 degrees ), Se can be determined in the concentration range 0.033-0.50 mug/ml. The method suffers from numerous interferences and is thus limited in application. It has been applied to the determination of selenium in spring waters and pharmaceutical preparations.     

Investigating the possibility of simultaneously finding an electron-hole and an electron-pair in a molecule: Delocalization,competition of ionic vs. covalent character,and related effects in push–pull ethylenes

This work examines the possibility of finding an electron-hole and an electron-pair simultaneously in a π-system substituted by an electron-donating (NH₂) and/or electron-withdrawing (NO₂) group. The contributions of various ionic [(+), ( ↑ ↓ )] structures are calculated from ab initio SCF –CI wave functions, using a recently developed general multielectron population analysis. The molecules studied are two monosubstituted ethylenes, aminoethylene and nitroethylene, and a disubstituted ethylene, the 2-nitroethenamine (push–pull ethylene) in its two configurational forms. The influence of the NH₂ and/or NO₂ group in delocalization and ionic (vs. covalent) character of the C?C double bond are investigated, along with examining the experimental chemist formalism of electron-pair “displacements” in several resonance structures. Analysis of mutual dependence of an electron-hole and an electron-pair, at short and long distances, leads to the conclusion that a push–pull π-system can stimulate the simultaneous existence of an electronhole and an electron-pair even for nonvicinal positions. The relationship between the electronpair distributions and contributions of the corresponding structures are also examined; the effects of electronic correlation are analyzed as well. © 1992 John Wiley & Sons, Inc.     

Measuring intracellular calcium fluxes in high throughput mode

The measurement of intracellular calcium fluxes in real time is widely applied within the pharmaceutical industry to measure the activation of G-protein coupled receptors (GPCRhyp;s), either for pharmacological characterisation or to screen for new surrogate ligands. Initially restricted to G(q) coupled GPCRs, the introduction of promiscuous and chimeric G-proteins has further widened the application of these assays. The development of new calcium sensitive dyes and assays has provided sensitive, homogeneous assays which can be readily applied to high throughput screening (HTS). In this paper we describe the full automation of this assay type using a fluorometric imaging plate reader (FLIPR ) integrated into a Beckman/Sagian system to establish a simple robotic system that is well suited for the current medium throughput screening in this area of lead discovery. Using a recently completed HTS we discuss important determinants for FLIPR based screening, highlight some limitations of the current approach, and look at the requirements for future automated systems capable of keeping up with expanding compound files.     

Studies of surface properties of Na- and La-montmorillonites

This paper presents possible applications of thermal analysis, sorptometry and porosimetry to study physico-chemical properties of Na- and La-montmorillonite samples, especially for determination of total surface heterogeneity. The quasi-isothermal thermogravimetric (Q-TG) mass loss and its first derivative (Q-DTG) curves with respect to temperature and time obtained during programmed liquid thermodesorption under quasi-isothermal conditions have been used to study adsorbed layers and heterogeneous properties of the Na- and La-montmorillonites. Calculations of the desorption energy distribution functions by analytical procedure using mass loss Q-TG and differential mass loss Q-DTG curves of thermodesorption under quasi-isothermal conditions of polar and non-polar liquid vapours preadsorbed on a material surface are presented. Parameters relating to porosity of samples were determined by sorptometry, mercury porosimetry and atomic force microscopy (AFM). From nitrogen sorption isotherms from sorptometry and porosimetry methods, the fractal dimensions of montmorillonites have been calculated. Moreover, a new approach is proposed to calculate fractal dimensions of materials obtained from Q-TG curve; this is compared with values obtained by the above methods. The total heterogeneous properties (energy distribution function and pore-size distribution functions) of samples studied were estimated. The radius and pore volume of the tested samples calculated on the basis of thermogravimetry, sorptometry and porosimetry techniques were compared and good correlations obtained.     

On eigenvalue calculations for radiative transfer models that include polarization effects

Several representations of the dispersion matrix (z) basic to analytical solutions for a theory of radiative transfer that includes the effects of polarization are reported, and a method for computing the zeros of det (z) is discussed. Numerical results are given for several specific models.

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Zusammenfassung Verschiedene Darstellungen der Dispersionsmatrix (z), welche grundlegende Bedeutung für die analytischen Lösungen der Theorie der Strahlungsübertragung mit Polarisation hat, werden angegeben. Eine Methode zur Berechnung der Nullstellen von det (z) wird diskutiert. Es werden numerische Ergebnisse für verschiedene Modelle angegeben.

     

Combined Dynamic Model for the Kinetics of Electron Transfer from Cytochrome to a Bacteriochlorophill Dimer in Reaction Centers of Rps. Sulfoviridis

The electron transfer from the heme of cytochrome c to the bacteriochlorophill dimer in reaction centers of photosynthetic purple bacteria Rps. sulfoviridis is studied by laser flash photolysis at 40–296 K in conditions where one, two, or three cytochrome hemes are chemically reduced. In the model used for the electron transfer kinetics, the protein relaxation is described with a temperature-independent oscillatory coordinate and a temperature-dependent diffusion coordinate, with the protein dielectric relaxation times widely distributed along the diffusion coordinate. It is found that all the protein complexes can be divided into proteins with fast (k _et = 10⁷ to 10^–4 s^–1) and slow (k _et 100 s^–1) electron transfer. These populations presumably differ by the protonation state of the functional group. The contribution of the oscillatory and diffusion coordinates alters, which severely affects k _et. Parameters V _ab, G, , ₀, and for these reactions are determined.     

Directed evolution of the dioxygenase complex for the synthesis of furanone flavor compounds

Herein we report a new preparation of 4-hydroxy-2,5-dimethyl-2,3-dihydrofuran-3-one, the flavor compound strawberry furanone, based on a ‘green’ approach with a minimum number of steps. The first step is an enzymatic dioxygenation of p-xylene to form cyclohexadiene-cis-diol, followed by ring opening via ozonolysis, and ring closure to form the furanone. In efforts to improve the efficiency of the enzymatic step, a directed evolution approach was taken to increase the substrate specificity and selectivity of the toluene dioxygenase enzyme system.