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.     

Novel ring transformation reactions of xanthine derivatives

The novel ring transformation reactions were found in the reactions of 1,3,7,9-tetra-alkyl-8,9-dihydroxanthines and acetylenic compounds. The reaction of the dihydroxanthine with DMAD gave a propellane type compound and with methyl propiolate afforded the similar type compound and a pyrimido[4,5-b]diazepine derivative. The mechanism of these reactions was also discussed.     

An unusual twist conformation of 2-O-methyl-1,3,4,5-tetrakis-O-tert-butyldiphenylsilyl-myo-inositol

The ring conformation of 2-O-methyl-1,3,4,5-tetrakis-O-tert-butyldiphenylsilyl-myo-inositol was in a twist form both in solid state and in solution. This is the first observation of a stable twist conformer induced by the introduction of bulky silyl protecting groups.     

Interaction of pentoxifylline with human erythrocytes. III. Comparison of fluidity change of erythrocyte membrane caused by S-adenosyl-L-methionine with that by pentoxifylline

The change in fluidity by adding pentoxifylline to erythrocyte membranes was compared with that caused by S-adenosyl-L-methionine (SAM) by the method of electron spin resonance (ESR) spectroscopy. When SAM or pentoxifylline was added externally to the erythrocyte suspension (outside), the fluidity of the membrane bilayer was increased after incubation at 37 degrees C. However, the fluidity change in the inner part of the bilayer was relatively small compared to that in its outer part. These fluidity changes were dependent on the incubation time and the temperature. When the erythrocyte suspension was preincubated overnight at 4 degrees C in the presence of drugs (inside), the fluidity of the inner part of the membrane changed significantly. Nevertheless, that of the outer part of the lipid bilayer was not affected. Such an asymmetric fluidity change in the lipid bilayer was not observed by the addition of other xanthine derivatives such as caffeine, theophylline and theobromine. S-Adenosyl-L-homocysteine suppressed and MgCl2 enhanced the increase of the membrane fluidity by SAM or pentoxifylline. Furthermore, the effects of SAM and pentoxifylline on erythrocyte deformability were determined by a filtering technique method. In increasing order the additive effects of SAM and pentoxifylline on the erythrocyte filterability were SAM (outside) less than pentoxifylline (inside) less than pentoxifylline (outside) less than SAM (inside). These results suggest that pentoxifylline also affects the membrane fluidity through the enzymatic methylation of phospholipids.     

Determination of the change of nuclear charge radius of the119Sn Mössbauer transition by internal conversion

Radioactive¹¹⁹Sb was implanted into six host matrices (CaSnO₃, Pt, Y, Au,-Sn, Pb) and internal conversion electrons of the 23.87 keV transition in¹¹⁹Sn were measured with an iron-free magnetic spectrometer as well as Mössbauer spectra. In the analysis of the conversion spectra of outermost electrons, the overlapping K-LM Auger lines were subtracted using the Auger spectrum of tin measured with another source of^117mSn, and the shake-off effect accompanying the conversion process was considered. From the correlation between the Mössbauer isomer shifts and the intensity ratios of O-shell to N₁-shell conversion electrons, the change of the nuclear charge radius of the 23.87 keV transition of¹¹⁹Sn was deduced to be R/R=(0.87 ± 0.25) × 10^–4 for a uniform charge distribution ofR= 1.2 ×A ^1/3 fm or, equivalently, r²>—=(3.6 ± 1.0) ×10^–3 fm².     

Studies on steroids. CCXXXXV. Determination of 5 beta-cholestanoic acids in human urine by gas chromatography-mass spectrometry with negative ion chemical ionization detection

A method for the determination of 3 alpha,7 alpha-dihydroxy-5 beta-cholestanoic acid (DHCA) and 3 alpha,7 alpha,12 alpha-trihydroxy-5 beta-cholestanoic acid (THCA) in human urine by gas chromatography (GC) in combination with negative ion chemical ionization (NICI) mass spectrometry is described. Unconjugated, glycine- and taurine-conjugated DHCA and THCA labelled with 18O and 2H were used as internal standards. 5 beta-Cholestanoic acids in urine were extracted with a Sep-Pak C18 cartridge, separated into the unconjugated, glycine- and taurine-conjugated fractions by ion-exchange chromatography on piperidinohydroxypropyl Sephadex LH-20 and, following alkaline hydrolysis of conjugated forms, derivatization into the pentafluorobenzyl ester-dimethylethylsilyl ethers. Subsequent resolution of each fraction into DHCA and THCA was attained by GC on a cross-linked 5% phenylmethylsilicone fused-silica capillary column where 5 beta-cholestanoic acids were monitored with a characteristic carboxylate anion [M-181]- in the NICI mode using isobutane as a reagent gas. The method was applied to separation and determination of 5 beta-cholestanoic acids in urine from a patient with Zellweger syndrome and from healthy volunteers.     

Stereoblock poly(lactic acid): synthesis via solid-state polycondensation of a stereocomplexed mixture of poly(L-lactic acid) and poly(D-lactic acid)

Stereoblock poly(lactic acid) consisting of D- and L-lactate stereosequences can be successfully synthesized by solid-state polycondensation of a 1:1 mixture of poly(L-lactic acid) and poly(D-lactic acid). In the first step, melt-polycondensation of L- and D-lactic acids is conducted to synthesize poly(L-lactic acid) and poly(D-lactic acid) with a medium-molecular-weight, respectively. In the next step, these poly(L-lactic acid) and poly(D-lactic acid) are melt-blended in 1:1 ratio to allow formation of their stereocomplex. In the last step, this melt-blend is subjected to solid-state polycondensation at temperature where the dehydrative condensation is allowed to promote chain extension in the amorphous phase with the stereocomplex crystals preserved. Finally, stereoblock poly(lactic acid) having high-molecular-weight is obtained. The stereoblock poly(lactic acid) synthesized by this way shows a higher melting temperature in consequence of the controlled block lengths and the resulting higher-molecular-weight. The product characterization as well as the optimization of the polymerization conditions is described. Changes in M(w) of stereoblock poly(lactic acid) (sb-PLA) as a function of the reaction time.     

Broad spectrum and mode of action of an antibiotic produced byScytonema sp. TISTR 8208 in a seaweed-type bioreactor

A photobioreactor was constructed using anchored polyurethane foam strips (1 x 1 x 40 cm) fixed onto a stainless-steel ring to prevent flotation, as a biomass support material (BSM). This type of reactor was named a seaweed-type bioreactor. A filamentous cyanobacterium, Scytonema sp. TISTR 8208, which produces a novel cyclic dodecapeptide antibiotic, was immobilized in seaweed-type photobioreactor and cultivated with air containing 5% CO₂ sparged at a gas flow rate of 250 mL/min under illumination at a light intensity of 200 μmol photon m^-2s^-1. The antibiotic produced in the seaweed-type photobioreactor was purified by HPLC and examined regarding its spectrum and mode of action. The antibiotic effectively inhibited the growth of Gram-positive bacteria, pathogenic yeasts, and filamentous fungi, but it had only a weak effect on Gram-negative bacteria. Scanning electron micrograph analysis showed that the most characteristic change was swelling of the cells after exposure to the antibiotic. The antibiotic seems to alter the conformation of the microbial cell membrane, thereby changing its permeability, leading to osmotic shock.     

Cross-coupling of alkenyl,aryl or allylic selenides and grignard reagents catalyzed by nickel-phosphine complexes

Alkenyl, aryl or allylic selenides smoothly couple with Grignard reagents in the presence of Ni(II)-phosphine complexes as catalysts to afford the corresponding unsaturated compounds in good yields. The reactivity order of coupling reaction with BuMgBr catalyzed by NiCl₂ [Ph₂PCH₂CH₂CH₂PPh₂] was found to be PhSeMe « PhCl > PhSMe by the competitive reactions.