Rapid crack growth in a thermoelastic solid under mixed-mode thermomechanical loading

A two-dimensional steady-sate analysis of semi-infinite brittlecrack growth at a constant subcritical rate in an unboundedfully-coupled thermoelastic solid under mixed-mode thermomechanicalloading is made. The loading consists of normal and shear tractionsand heat fluxes applied as point sources (line loads in theout-of-plane direction). A related problem is solved exactly in an integral transformspace, and robust asymptotic forms used to reduce the originalproblem to a set of integral equations. The equations are partiallycoupled and exhibit operators of both Cauchy and Abel types,yet can be solved analytically. The temperature change field at a distance from the moving crackedge is then constructed, and its dominant term is found tobe controlled by the imposed heat fluxes. The role of this termis, indeed, enhanced if the heat fluxes serve to render thecrack as a net heat source/sink for the solid, as opposed tobeing a transmitter of heat across its plane. More generally,the influence of the thermoelastic coupling on this field, aswell as other functions, is found to increase with crack speed.     

Crystal and molecular structure of 2,5-dimethyl-3,4-diacetylfuran

The crystal and molecular structure of 2,5-dimethyl-3,4-diacetylfuran has been determined by direct methods using CuK. photographic data. Refinement by full-matrix least-squares methods gave a finalR factor of 0·097. The crystals are monoclinic: space groupP2₁/c,a =14·92(2),b = 4·09(1),c =16·68(3) Å and = 109·7(5) °;Z = 4. The furan ring of the molecule is planar, and the exocyclic atoms bound to the atoms of the ring lie close to the ring plane. The planes of the acetyl groups are tilted by 16 ° and 47 ° with respect to the ring plane. The exocyclic bond angles of this compound are significantly different from the equivalent angles in furan.     

Role of entropy in increased rates of intramolecular reactions

The rates of intramolecular condensation of a series of monoesters of dicarboxylic acids have been shown to be highly dependent on the nature of the intervening groups. To understand the origin of this effect, we estimated DeltaS(NAC,S), the entropy difference between the ensemble of accessible ground state conformers and a single ground state conformer having transition-state-like geometry. DeltaS(NAC,S) differs from the activation entropy for the reaction by DeltaS(TS,NAC), the difference in vibrational entropy between the selected ground state conformer and the transition state. The estimated values of DeltaS(NAC,S) correlate well (R(2) = 0.96 and 0.73 using dielectric constant values of 80 and 1, respectively) with experimentally determined reaction rate constants. Normal-mode analysis performed on minimized ground state conformations of each molecule suggests that the change in vibrational entropy makes only a small contribution to the total activation entropy. These results indicate that the conformational entropy difference between the transition and the ground states contributes significantly to the free energy of activation.     

Crystal and molecular structure of 2,5-dimethyl-3,4-diacetylpyrrole

An X-ray crystallographic study of 2,5-dimethyl-3,4-diacetylpyrrole showed that the crystals are monoclinic, space groupP2₁/n,a = 10·01(3),b = 12·93(3),c = 7·41(2) Å and = 91·5(5) °. The crystal structure was solved by direct methods and refined by least squares to a finalR factor of 0·13. The values determined for the bond distances and angles of the pyrrole ring are in good agreement with the values reported in the literature. However, there are significant changes in the exocyclic bond angles of the atoms of the ring. The planes of the acetyl groups are tilted with respect to the ring plane, forming dihedral angles of 22 ° and 40 °.     

Synthetic magnetic opals

We present studies of novel nanocomposites of BiNi impregnated into the structure of opals as well as inverse opals. Atomic force microscopy and high resolution elemental analyses show a highly ordered structure and uniform distribution of the BiNi filler in the matrix. These BiNi-based nanocomposites are found to exhibit distinct ferromagnetic-like ordering with transition temperature of about 675 K. As far as we know there exists no report in literature on any BiNi compound which is magnetic.     

Differential reactivity between two copper sites in peptidylglycine α-hydroxylating monooxygenase

Peptidylglycine α-hydroxylating monooxygenase (PHM) catalyzes the stereospecific hydroxylation of the Cα of C-terminal glycine-extended peptides and proteins, the first step in the activation of many peptide hormones, growth factors, and neurotransmitters. The crystal structure of the enzyme revealed two nonequivalent Cu sites (Cu(M) and Cu(H)) separated by ～11 ?. In the resting state of the enzyme, Cu(M) is coordinated in a distorted tetrahedral geometry by one methionine, two histidines, and a water molecule. The coordination site of the water molecule is the position where external ligands bind. The Cu(H) has a planar T-shaped geometry with three histidines residues and a vacant position that could potentially be occupied by a fourth ligand. Although the catalytic mechanism of PHM and the role of the metals are still being debated, Cu(M) is identified as the metal involved in catalysis, while Cu(H) is associated with electron transfer. To further probe the role of the metals, we studied how small molecules such as nitrite (NO(2)(-)), azide (N(3)(-)), and carbon monoxide (CO) interact with the PHM copper ions. The crystal structure of an oxidized nitrite-soaked PHMcc, obtained by soaking for 20 h in mother liquor supplemented with 300 mM NaNO(2), shows that nitrite anion coordinates Cu(M) in an asymmetric bidentate fashion. Surprisingly, nitrite does not bind Cu(H), despite the high concentration used in the experiments (nitrite/protein > 1000). Similarly, azide and carbon monoxide coordinate Cu(M) but not Cu(H) in the PHMcc crystal structures obtained by cocrystallization with 40 mM NaN(3) and by soaking CO under 3 atm of pressure for 30 min. This lack of reactivity at the Cu(H) is also observed in the reduced form of the enzyme: CO binds Cu(M) but not Cu(H) in the structure of PHMcc obtained by exposure of a crystal to 3 atm CO for 15 min in the presence of 5 mM ascorbic acid (reductant). The necessity of Cu(H) to maintain its redox potential in a narrow range compatible with its role as an electron-transfer site seems to explain the lack of coordination of small molecules to Cu(H); coordination of any external ligand will certainly modify its redox potential.     

Direct activation of Epac by sulfonylurea is isoform selective

Commonly used as a treatment for Type II diabetes, sulfonylureas (SUs) stimulate insulin secretion from pancreatic β cells by binding to sulfonylurea receptors. Recently, SUs have been shown to also activate exchange protein directly activated by cAMP 2 (Epac2), however, little is known about this molecular action. Using biosensor imaging and biochemical analysis, we show that SUs activate Epac2 and the downstream signaling via direct binding to Epac2. We further identify R447 of Epac2 to be critically involved in SU binding. This distinct binding site from cAMP points to a new mode of allosteric activation of Epac2. We also show that SUs selectively activate Epac2 isoform, but not the closely related Epac1, further establishing SUs as a new class of isoform-selective enzyme activators.     

The catalytic mechanism of peptidylglycine alpha-hydroxylating monooxygenase investigated by computer simulation

The molecular basis of the hydroxylation reaction of the Calpha of a C-terminal glycine catalyzed by peptidylglycine alpha-hydroxylating monooxygenase (PHM) was investigated using hybrid quantum-classical (QM-MM) computational techniques. We have identified the most reactive oxygenated species and presented new insights into the hydrogen abstraction (H-abstraction) mechanism operative in PHM. Our results suggest that O(2) binds to Cu(B) to generate Cu(B)(II)-O(2)(.-) followed by electron transfer (ET) from Cu(A) to form Cu(B)(I)-O(2)(.-). The computed potential energy profiles for the H-abstraction reaction for Cu(B)(II)-O(2)(.-), Cu(B)(I)-O(2)(.-), and [Cu(B)(II)-OOH](+) species indicate that none of these species can be responsible for abstraction. However, the latter species can spontaneously form [Cu(B)O](+2) (which consists of a two-unpaired-electrons [Cu(B)O](+) moiety ferromagnetically coupled with a radical cation located over the three Cu(B) ligands, in the quartet spin ground state) by abstracting a proton from the surrounding solvent. Both this monooxygenated species and the one obtained by reduction with ascorbate, [Cu(B)O](+), were found to be capable of carrying out the H-abstraction; however, whereas the former abstracts the hydrogen atom concertedly with almost no activation energy, the later forms an intermediate that continues the reaction by a rebinding step. We propose that the active species in H-abstraction in PHM is probably [Cu(B)O](+2) because it is formed exothermically and can concertedly abstract the substrate HA atom with the lower overall activation energy. Interestingly, this species resembles the active oxidant in cytochrome P450 enzymes, Compound I, suggesting that both PHM and cytochrome P450 enzymes may carry out substrate hydroxylation by using a similar mechanism.     

Hydrogen bonding in the mechanism of GDP-mannose mannosyl hydrolase

GDP-mannose mannosyl hydrolase (GDPMH) from E. coli catalyzes the hydrolysis of GDP-α-d-sugars to GDP and β-d-sugars by nucleophilic substitution with inversion at the anomeric C1 of the sugar, with general base catalysis by His-124. The 1.3 Å X-ray structure of the GDPMH-Mg²⁺-GDP complex was used to model the complete substrate, GDP-mannose into the active site. The substrate is linked to the enzyme by 12 hydrogen bonds, as well as by the essential Mg²⁺. In addition, His-124 was found to participate in a hydrogen bonded triad: His-124-NδHTyr-127-OHPro-120(CO). The contributions of these hydrogen bonds to substrate binding and to catalysis were investigated by site-directed mutagenesis. The hydrogen bonded triad detected in the X-ray structure was found to contribute little to catalysis since the Y127F mutation of the central residue shows only 2-fold decreases in both k_cat and K_m. The GDP leaving group is activated by the essential Mg²⁺ which contributes at least 10⁵-fold to k_cat, and by nine hydrogen bonds, including those from Tyr-103, Arg-37, Arg-52, and Arg-65 (via an intervening water), each of which contribute factors to k_cat ranging from 24- to 309-fold. Both Arg-37 and Tyr-103 bind the β-phosphate of the leaving GDP and are only 5.0 Å apart. Accordingly, the R37Q/Y103F double mutant shows partially additive effects of the two single mutants on k_cat, indicating cooperativity of Arg-37 and Tyr-103 in promoting catalysis. The extensive activation of the GDP leaving group suggests a mechanism with dissociative character with a cationic oxocarbenium-like transition state and a half-chair conformation of the sugar ring, as found with glycosidase enzymes. Accordingly, Asp-22 which contributes 10^2.1- to 10^2.6-fold to k_cat, is positioned to both stabilize a developing cationic center at C1 and to accept a hydrogen bond from the C2–OH of the mannosyl group, and His-88, which contributes 10^2.3-fold to k_cat, is positioned to accept a hydrogen bond from the C3–OH of the mannose facilitating its distortion to a half-chair conformation. Also, the fluorinated substrate GDP-2-fluoro-α-d-mannose, for which the oxocarbenium ion-like transition state centered at C1 would be destabilized by electron withdrawal, shows a 16-fold lower k_cat and a 2.5-fold greater K_m than does GDP-α-d-mannose. The product of the contributions to catalysis of Arg-37 and Tyr-103 (taking their cooperativity into account), Arg-52, Arg-65, Mg²⁺, Asp-22, His-124, and His-88 is ≥10¹⁹, which exceeds the 10¹²-fold rate acceleration produced by GDPMH by a factor ≥10⁷. Hence, additional pairs or groups of catalytic residues must act cooperatively to promote catalysis.     

Functional neural network analysis in frontotemporal dementia and Alzheimer's disease using EEG and graph theory

Background  

Although a large body of knowledge about both brain structure and function has been gathered over the last decades, we still have a poor understanding of their exact relationship. Graph theory provides a method to study the relation between network structure and function, and its application to neuroscientific data is an emerging research field. We investigated topological changes in large-scale functional brain networks in patients with Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) by means of graph theoretical analysis of resting-state EEG recordings. EEGs of 20 patients with mild to moderate AD, 15 FTLD patients, and 23 non-demented individuals were recorded in an eyes-closed resting-state. The synchronization likelihood (SL), a measure of functional connectivity, was calculated for each sensor pair in 0.5–4 Hz, 4–8 Hz, 8–10 Hz, 10–13 Hz, 13–30 Hz and 30–45 Hz frequency bands. The resulting connectivity matrices were converted to unweighted graphs, whose structure was characterized with several measures: mean clustering coefficient (local connectivity), characteristic path length (global connectivity) and degree correlation (network 'assortativity'). All results were normalized for network size and compared with random control networks.