Structural Insights into the Mechanism of Base Excision by MBD4

DNA glycosylases remove damaged or modified nucleobases by cleaving the N-glycosyl bond and the correct nucleotide is restored through subsequent base excision repair. In addition to excising threatening lesions, DNA glycosylases contribute to epigenetic regulation by mediating DNA demethylation and perform other important functions. However, the catalytic mechanism remains poorly defined for many glycosylases, including MBD4 (methyl-CpG binding domain IV), a member of the helix-hairpin-helix (HhH) superfamily. MBD4 excises thymine from G·T mispairs, suppressing mutations caused by deamination of 5-methylcytosine, and it removes uracil and modified uracils (e.g., 5-hydroxymethyluracil) mispaired with guanine. To investigate the mechanism of MBD4 we solved high-resolution structures of enzyme-DNA complexes at three stages of catalysis. Using a non-cleavable substrate analog, 2′-deoxy-pseudouridine, we determined the first structure of an enzyme-substrate complex for wild-type MBD4, which confirms interactions that mediate lesion recognition and suggests that a catalytic Asp, highly conserved in HhH enzymes, binds the putative nucleophilic water molecule and stabilizes the transition state. Observation that mutating the Asp (to Gly) reduces activity by 2700-fold indicates an important role in catalysis, but probably not one as the nucleophile in a double-displacement reaction, as previously suggested. Consistent with direct-displacement hydrolysis, a structure of the enzyme-product complex indicates a reaction leading to inversion of configuration. A structure with DNA containing 1-azadeoxyribose models a potential oxacarbenium-ion intermediate and suggests the Asp could facilitate migration of the electrophile towards the nucleophilic water. Finally, the structures provide detailed snapshots of the HhH motif, informing how these ubiquitous metal-binding elements mediate DNA binding.     

Infrared spectroscopy of proteins

This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.     

Cellular Thiol Production and Oxidation of Low-Density Lipoprotein

Compelling evidence suggests that low-density lipoprotein (LDL) is oxidized by cells within the arterial intima and that, once oxidized, it is profoundly atherogenic. The precise mechanism(s) by which cells promote the oxidation of LDL in vivo are not known; in vitro, however, oxidation of LDL can be enhanced by a number of differing mechanisms, including reaction with free and protein-bound metal ions, thiols, reactive oxygen species, lipoxygenase, myeloperoxidase and peroxynitrite. This review is concerned with the mechanisms by which cells enhance the oxidation of LDL in the presence of transition metals; in particular, the regulation, pro- and anti-oxidant consequences, and mechanism of action of cellular thiol production are examined, and contrasted with thiol-independent oxidation of LDL in the presence of transition metals.     

Phase transition kinetics of phosphatidic acid bilayers A stopped-flow study of the electrostatically induced transition

The kinetics of the electrostatically induced phase transition of dimyristoyl phosphatidic acid bilayers was followed using the stopped-flow technique. The phase transition was triggered by a fast change in the pH or the magnesium ion concentration and followed by recording the time dependence of the absorbance. When the phase transition was induced by a pH jump the time course of the absorbance could be described by two exponentials, their time constants displaying the for cooperative processes characteristic maximum at the transition midpoint. The time constants are in the 10 and 100 ms range for the H⁺ triggered transition from the fluid to the ordered state. A third slower process shows no appreciable temperature dependence and is probably caused by vesicle aggregation. For the OH^--induced transition fron the ordered to the fluid state the time constants are in the 100 and 1000 ms range. The fluid-ordered transition could also be triggered by addition of magnesium ions. Of the several observed processes only the fastest in the 10–100 ms time range could definitely be assigned to the fluid-ordered transition while the others are due to aggregation phenomena. The experimental data were compared with results obtained from pressure jump experiments and could be interpreted on the basis of theories for non-equilibrium relaxation.     

Induction of the blue form of bacteriohodopsin by low concentrations of sodium dodecyl sulfate

The effects produced on bacteriorhodopsin by low concentrations of several detergents have been studied by absorption and fourth-derivative spectrophotometry. Sodium dodecyl sulfate induces the appearance of the blue form of bacteriorhodopsin (λ_max = 600 nm) at pH values up to 7.0 in a reversible manner. The apparent pK of the purple-to-blue transition raised with increasing concentration of SDS. Of the other detergents tested, only sodium dodecyl-N-sarcosinate showed a slight red-shift of the absorption band to 580 nm, whereas sodium taurocholate, Triton X-100 and cetyltrimethylammonium bromide did not favour the appearance of the blue form. The effect of SDS was found to be consistent with a localized conformational change that moves away the counter-ion of the protonated Schiff base.     

Functional Casein-Poly saccharide Conjugates Prepared by Controlled Dry Heating

Casein was conjugated with dextran and galactomannan in a controlled dry state at a relative humidity of 79% and at 60°C for 24 hr. The covalent attachment of polysaccharides to casein was confirmed by SDS-PAGE and HPLC. The emulsifying activity of the casein-dextran and casein-galactomannan conjugates was 1.5 times higher than that of casein. The emulsion stability of the casein-dextran and casein-galactomannan conjugates was 10 times higher than that of casein. The improvement in these emulsifying properties reached a steady state when the conjugation of casein with polysaccharide was done for 24 hr in a controlled dry state, suggesting the rapid formation of conjugates through a Maillard reaction in the case of casein. Compared to commercial emulsifiers, the casein-polysaccharide conjugates showed better emulsifying properties in acidic and high-salt concentration systems.     

Non-linear changes of lower extremity kinetics prior to gait transition

IntroductionThe purpose of this study was to examine the changes of lower extremity kinetics during walk-to-run (WR) transition and if the changes would follow a non-linear trend within the five strides before WR transition using a constant acceleration protocol.MethodsFourteen participants performed gait transition on the instrumented treadmill at a constant acceleration. Peak, time to peak, and movement and power of hip, knee and ankle joints were recorded and analyzed in sagittal plane for five strides before gait transition. Three Two-way MANOVA were employed to examine the differences of kinetic measures among the five strides. Univariate analysis and Post-Hoc Tukey’s test would be applied if needed. Also, Post hoc polynomial trend analyses were used to examine the trend of the kinetic measures that significantly changed during the five strides.ResultsCompared to the first four strides, significant differences were observed for peaks moments, joint powers, and time to peaks in the last stride before running at ankle, knee, and hip joints respectively. In general, the changes of kinetic variables were following a quadratic trend during the five strides before running.ConclusionJoint kinetic measures actively change in non-linear patterns during the five strides before running to prepare for the gait transition, indicating that the gait transition is an active reorganization rather than a passive reaction.     

Partition of lindane in synthetic and native membranes

Partition coefficients of the insecticide γ-1,2,3,4,5,6-hexachlorocyclohexane (trivially, lindane) were determined in model and native membranes. Partition in egg phosphatidylcholine bilayers decreases linearly with temperature, over a range (10–40°C) at which the lipid is in the liquid-crystalline state. Addition of 50 mol% cholesterol dramatically decreases partition (2100 falls to 100, at 10°C) and abolishes the temperature dependence. First-order phase transitions of dimyristoyl-, dipalmitoyl- and distearoylphosphatidylcholines (DMPC, DPPC and DSPC) are accompanied by a sharp increase in lindane partition. Apparently, the insecticide is easily accommodated in bilayers of short-aliphatic-chain lipids, since the partitions were 2450, 600 and 50 in DMPC, DPPC and DSPC, respectively, at temperatures 10 Cdeg below the midpoint of their transitions. The lindane partition sequence in native membranes is as follows: mitochondria, sarcoplasmic reticulum, myelin, brain microsomes and erythrocytes. This sequence correlates reasonably well with the relative content of cholesterol and is similar in liposomes of total extracted lipids, although the absolute partitions showed decreased values. Therefore, the presence of proteins in native membranes contributes to the insecticide partition, probably by favouring its interaction with lipids.     

Reversible effects of moderately elevated temperature on the distribution of excitation energy between the two photosystems of photosynthesis in intact avocado leaves

Initial (F_o), maximum (F_m) and steady-state (F_s) levels of modulated chlorophyll fluorescence were measured in intact avocado leaves (Persea americana Mill.) during state 1-state 2 transitions using a combination of modulated and non-modulated lights with synchronized detection. Under normal temperature conditions (20°C), transition from state 2 to state 1 was associated with a substantial increase (about 20%) in F_m and F_o whereas the F_m/F_o ratio remained constant, reflecting increased absorption cross-section of PS II. On the contrary, at moderately elevated temperature (35°C), these fluorescence changes were very limited, indicating marked inhibition of the state regulation. The fraction of light distributed to PS II () was calculated from the F_o, F_m and F_s levels for both types of leaves. In control leaves, varied from 48% (in state 2) to values as high as 58% (in state 1). In contrast, mild heat treatment resulted in values close to 50% in both states, indicating the inability of heated leaves to reach extreme state 1. The results suggested that avocado leaves under moderately elevated temperature conditions are blocked in a state close to state 2. This effect was shown to occur in a non-injurious temperature range (as shown by the preservation of the (photoacoustically monitored) oxygen evolution activity) and to be rapidly reversed upon lowering of the temperature. Thermally induced development of state 2 (independent on the light spectral quality) could possibly be a protective mechanism to avoid photodamage of the heat-labile PS II by high light intensities which usually accompany heat stress in the field.     

Involvement of a Ca2+-calmodulin interaction in the yeast-mycelial (Y-M) transition of Candida albicans

A yeast-mycelium (Y-M) transition of Candida albicans (3153A) was induced by 1.5 mM CaCl₂ · 2H₂O in defined liquid medium, pH 7, at 25 °C. Germ tube formation was detected after approximately 8 h and peaks of maximum germination occurred at approximately 20 h in all experimental treatments. Non-toxic concentrations of the calmodulin inhibitor R24571 almost completely suppressed germ tube formation whereas trifluoperazine (TFP) and the Ca²⁺ ionophore A23187 were only about half as effective. Further Ca²⁺ addition failed to reverse the inhibitory effect of R24571 and induced only about 10% of the cells inhibited by TFP or A23187 to germinate.