Structural effects of a dimer interface mutation on catalytic activity of triosephosphate isomerase.The role of conserved residues and complementary mutations

The active site of triosephosphate isomerase (TIM, EC: 5.3.1.1), a dimeric enzyme, lies very close to the subunit interface. Attempts to engineer monomeric enzymes have yielded well-folded proteins with dramatically reduced activity. The role of dimer interface residues in the stability and activity of the Plasmodium falciparum enzyme, PfTIM, has been probed by analysis of mutational effects at residue 74. The PfTIM triple mutant W11F/W168F/Y74W (Y74W*) has been shown to dissociate at low protein concentrations, and exhibits considerably reduced stability in the presence of denaturants, urea and guanidinium chloride. The Y74W* mutant exhibits concentration-dependent activity, with an approximately 22-fold enhancement of kcat over a concentration range of 2.5–40 μm, suggesting that dimerization is obligatory for enzyme activity. The Y74W* mutant shows an approximately 20-fold reduction in activity compared to the control enzyme (PfTIM WT*, W11F/W168F). Careful inspection of the available crystal structures of the enzyme, together with 412 unique protein sequences, revealed the importance of conserved residues in the vicinity of the active site that serve to position the functional K12 residue. The network of key interactions spans the interacting subunits. The Y74W* mutation can perturb orientations of the active site residues, due to steric clashes with proximal aromatic residues in PfTIM. The available crystal structures of the enzyme from Giardia lamblia, which contains a Trp residue at the structurally equivalent position, establishes the need for complementary mutations and maintenance of weak interactions in order to accommodate the bulky side chain and preserve active site integrity.

Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site

Plasmodium falciparum TIM (PfTIM) is unique in possessing a Phe residue at position 96 in place of the conserved Ser that is found in TIMs from the majority of other organisms. In order to probe the role of residue 96, three PfTIM mutants, F96S, F96H and F96W, have been biochemically and structurally characterized. The three mutants exhibited reduced catalytic efficiency and a decrease in substrate-binding affinity, with the most pronounced effects being observed for F96S and F96H. The k(cat) values and K-m values are (2.54 +/- 0.19) x 10(5) min(-1) and 0.39 +/- 0.049 mM, respectively, for the wild type; (3.72 +/- 0.28) x 10(3) min(-1) and 2.18 +/- 0.028 mM, respectively, for the F96S mutant;(1.11 +/- 0.03) x 10(4) min(-1) and 2.62 +/- 0.042 mM, respectively, for the F96H mutant; and (1.48 +/- 0.05) x 10(5) min(-1) and 1.20 +/- 0.056 mM, respectively, for the F96W mutant. Unliganded and 3-phosphoglycerate (3PG) complexed structures are reported for the wild-type enzyme and the mutants. The ligand binds to the active sites of the wild-type enzyme (wtPfTIM) and the F96W mutant, with a loop-open state in the former and both open and closed states in the latter. In contrast, no density for the ligand could be detected at the active sites of the F96S and F96H mutants under identical conditions. The decrease in ligand affinity could be a consequence of differences in the water network connecting residue 96 to Ser73 in the vicinity of the active site. Soaking of crystals of wtPfTIM and the F96S and F96H mutants resulted in the binding of 3PG at a dimer-interface site. In addition, loop closure at the liganded active site was observed for wtPfTIM. The dimer-interface site in PfTIM shows strong electrostatic anchoring of the phosphate group involving the Arg98 and Lys112 residues of PfTIM.

Nuclear Magnetic-Resonance Spectra Of Oriented Biologically Important Molecules - The Structure Of And The Internal-Rotation In N,N-Dimethyluracil

From the proton NMR spectra of Nfl-dimethyluracil oriented in two different nematic solvents, the internal rotation of the methyl groups about the N-C bonds is studied. It has been observed that the preferred conformation of the methyl group having one carbonyl in the vicinity is the one where a C-H bond is in the ring plane pointing toward the carbonyl group. The results are not sensitive to the mode of rotation of the other methyl group. These data are interpreted in terms of the bond polarizations.

Prediction of bubble growth rates and departure volumes in nucleate boiling at isolated sites

A model has been developed to predict heat transfer rates and sizes of bubbles generated during nucleate pool boiling. This model assumes conduction and a natural convective heat transfer mechanism through the liquid layer under the bubble and transient conduction from the bulk liquid. The temperature of the bulk liquid in the vicinity of the bubble is obtained by assuming a turbulent natural convection process from the hot plate to the liquid bulk. The shape of the bubble is obtained by equilibrium analysis. The bubble departure condition is predicted by a force balance equation. Good agreement has been found between the bubble radii predicted by the present theory and the ones obtained experimentally.

Laser Raman spectroscopic study of ferroelastic LiCsSO4

Lithium caesium sulphate has been reported to undergo a phase transition from the room temperature orthorhombic phase with space groupP cmn to a final phase with space groupP 22/n. Though a sharp anomaly in its physical properties has been found at 202.0;K, it was found that there was a need for careful investigations in the vicinity of 240 and 210.0;K. Since the changes in the crystal structure involve primarily a rotation of the SO4 tetrahedron about thec-axis and as this may be reflected both in the intensity and polarisation of the internal as well as external phonon modes, the laser Raman spectra of oriented single crystals of LiCsSO4 at different temperatures were investigated. For correlation and definite identification of the spectral features, its infrared absorption spectrum was also studied. An analysis of the intensities and polarizations of the internal modes of the sulphate ions reveals the change in symmetry of the crystal. The integrated intensity and peak height of thev 1 line, plotted against temperature show anomalous peaks in the region of the phase transition. Differential scanning calorimetric study gives the enthalpy change ΔH across the phase transition to be 0.213 kJ/mol.

Peptide models for the bacteriorhodopsin chromophore. Retinylidene-lysine systems containing aspartic acid and serine residues

The retinylidene Schiff base derivative of seven lysine containing peptides have been prepared in order to investigate solvent and neighboring group effects, on the absorption maximum of the protonated Schiff base chromophore. The peptides studied are Boc-Aib-Lys-Aib-OMe (1), Boc-Ala-Aib-Lys-OMe (2), Boc-Ala-Aib-Lys-Aib-OMe (3), Boc-Aib-Asp-Aib-Aib-Lys-Aib-OMe (4), Boc-Aib-Asp-Aib-Ala-Aib-Lys-Aib-OMe (5), Boc-Lys-Val-Gly-Phe-OMe (6) and Boc-Ser-Ala-Lys-Val-Gly-Phe-OMe (7). In all cases protonation shifts the absorption maxima to the red by 3150–8450 cm-1. For peptides 1–3 the protonation shifts are significantly larger in nonhydrogen bonding solvents like CHCl3 or CH2Cl2 as compared to hydrogen bonding solvents like CH3OH. The presence of a proximal Asp residue in 4 and 5 results in pronounced blue shift of the absorption maximum of the protonated Schiff base in CHCl3, relative to peptides lacking this residue. Peptides 6 and 7 represent small segments of the bacteriorhodopsin sequence in the vicinity of Lys-216. The presence of Ser reduces the magnitude of the protonation shift.

Dielectric studies of As-Se glasses

Dielectric constants and loss tangents of As-Se glasses have been measured between 300 K and the respective glass transition temperatures and between 1 kHz and 20 kHz. The variation of dielectric constants has been interpreted in terms of both heteropolarity of bonds and average bond energies employing a chemically ordered network model. Various contributions to total molar polarizations have been estimated. Rapid rise of loss tangent in the vicinity of glass transitions has been interpreted in terms of rapid increase; of d.c. conductivity.

The heat capacity of liquid carbon disulfide + acetonitrile, especially near the upper critical solution temperature

The heat capacity Cp of the binary liquid system CS2 + CH3CN has been studied. This system has an upper critical solution temperature To ≈ 323.4 K and a critical mole fraction of CS2xo ≈ 0.5920. Measurements were made both for mixtures close to and far away from the critical region. The heat capacity of the mixture with x = xo exhibits a symmetric logarithmic anomaly around Tc, which is apparently preserved even for compositions in the immediate vicinity of xc. For compositions far away from xc, only a normal rise in Cp over the covered temperature range is observed.

Unsteady laminar boundary layers in a compressible stagnation flow

The unsteady laminar compressible boundary-layer flow in the immediate vicinity of a two-dimensional stagnation point due to an incident stream whose velocity varies arbitrarily with time is considered. The governing partial differential equations, involving both time and the independent similarity variable, are transformed into new co-ordinates with finite ranges by means of a transformation which maps an infinite interval into a finite one. The resulting equations are solved by converting them into a matrix equation through the application of implicit finite-difference formulae. Computations have been carried out for two particular unsteady free-stream velocity distributions: (1) a constantly accelerating stream and (2) a fluctuating stream. The results show that in the former case both the skin-friction and the heat-transfer parameter increase steadily with time after a certain instant, while in the latter they oscillate thus responding to the fluctuations in the free-stream velocity.

Inhibition of Human Two-Pore Domain K+ Channel TREK1 by Local Anesthetic Lidocaine: Negative Cooperativity and Half-of-Sites Saturation Kinetics

TWIK-related K+ channel TREK1, a background leak K+ channel, has been strongly implicated as the target of several general and local anesthetics. Here, using the whole-cell and single-channel patch-clamp technique, we investigated the effect of lidocaine, a local anesthetic, on the human (h) TREK1 channel heterologously expressed in human embryonic kidney 293 cells by an adenoviral-mediated expression system. Lidocaine, at clinical concentrations, produced reversible, concentration-dependent inhibition of hTREK1 current, with IC50 value of 180 mu M, by reducing the single-channel open probability and stabilizing the closed state. We have identified a strategically placed unique aromatic couplet (Tyr352 and Phe355) in the vicinity of the protein kinase A phosphorylation site, Ser348, in the C-terminal domain (CTD) of hTREK1, that is critical for the action of lidocaine. Furthermore, the phosphorylation state of Ser348 was found to have a regulatory role in lidocaine-mediated inhibition of hTREK1. It is interesting that we observed strong intersubunit negative cooperativity (Hill coefficient = 0.49) and half-of-sites saturation binding stoichiometry (half-reaction order) for the binding of lidocaine to hTREK1. Studies with the heterodimer of wild-type (wt)-hTREK1 and Delta 119 C-terminal deletion mutant (hTREK1(wt)-Delta 119) revealed that single CTD of hTREK1 was capable of mediating partial inhibition by lidocaine, but complete inhibition necessitates the cooperative interaction between both the CTDs upon binding of lidocaine. Based on our observations, we propose a model that explains the unique kinetics and provides a plausible paradigm for the inhibitory action of lidocaine on hTREK1.

Korteweg-De Vries Equation for Non-Linear Ion-Acoustic Waves in a Plasma with Negative Ions

The theoretical analysis, based on the perturbation technique, of ion-acoustic waves in the vicinity of a Korteweg-de Vries (K-dV) equation derived in a plasma with some negative ions has been made. The investigation shows that the negative ions in plasma with isothermal electrons introduced a critical concentration at which the ion-acoustic wave plays an important role of wave-breaking and forming a precursor while the plasma with non-isothermal electrons has no such singular behaviour of the wave. These two distinct features of ion waves lead to an overall different approach of present study of ion-waves. A distinct feature of non-uniform transition from the nonisothermal case to isothermal case has been shown. Few particular plasma models have been chosen to show the characteristics behaviour of the ion-waves existing in different cases

Polypurine/polypyrimidine sequences as cis-acting transcriptional regulators

Genome sequence information has generated increasing evidence for the claim that repetitive DNA sequences present within and around genes could play a important role in the regulation of gene expression. Polypurine/polypyrimidine sequences [poly(Pu/Py)] have been observed in the vicinity of promoters and within the transcribed regions of many genes. To understand whether such sequences influence the level of gene expression, we constructed several prokaryotic and eukaryotic expression vectors incorporating poly(Pu/Py) repeats both within and upstream of a reporter gene, lacZ (encoding β-galactosidase), and studied its expression in vivo. We find that, in contrast to the situation in Escherichia coli, the presence of poly(Pu/Py) sequences within the gene does not significantly inhibit gene expression in mammalian cells. On the other hand, the presence of such sequences upstream of lacZ leads to a several-fold reduction of gene expression in mammalian cells. Similar down-regulation was observed when a structural cassette containing poly(Pu/Py) sequences upstream of lacZ was integrated into yeast chromosome V. Sequence analysis of the nine totally sequenced yeast chromosomes shows that a large number of such sequences occur upstream of ORFs. On the basis of our experimental results and DNA sequence analysis, we propose that these sequences can function as cis-acting transcriptional regulators.

Steady mixed convection stagnation-point flow of upper convected Maxwell fluids with magnetic field

The steady MHD mixed convection flow of a viscoelastic fluid in the vicinity of two-dimensional stagnation point with magnetic field has been investigated under the assumption that the fluid obeys the upper-convected Maxwell (UCM) model. Boundary layer theory is used to simplify the equations of motion. induced magnetic field and energy which results in three coupled non-linear ordinary differential equations which are well-posed. These equations have been solved by using finite difference method. The results indicate the reduction in the surface velocity gradient, surface heat transfer and displacement thickness with the increase in the elasticity number. These trends are opposite to those reported in the literature for a second-grade fluid. The surface velocity gradient and heat transfer are enhanced by the magnetic and buoyancy parameters. The surface heat transfer increases with the Prandtl number, but the surface velocity gradient decreases.

2,6-Bis(3-methoxyphenyl)-3-methylpiperidin-4-one

In the molecule of the title compound, C20H23NO3, the bulky methoxyphenyl substituents at the equatorial 2,6-positions crowd the vicinity of the equatorial amino H atom and prevent it from forming intermolecular hydrogen bonds. The piperidine ring adopts a distorted chair conformation.

On the Average Case Communication Complexity for Detection in Sensor Networks

The problem of sensor-network-based distributed intrusion detection in the presence of clutter is considered. It is argued that sensing is best regarded as a local phenomenon in that only sensors in the immediate vicinity of an intruder are triggered. In such a setting, lack of knowledge of intruder location gives rise to correlated sensor readings. A signal-space viewpoint is introduced in which the noise-free sensor readings associated to intruder and clutter appear as surfaces $\mathcal{S_I}$ and $\mathcal{S_C}$ and the problem reduces to one of determining in distributed fashion, whether the current noisy sensor reading is best classified as intruder or clutter. Two approaches to distributed detection are pursued. In the first, a decision surface separating $\mathcal{S_I}$ and $\mathcal{S_C}$ is identified using Neyman-Pearson criteria. Thereafter, the individual sensor nodes interactively exchange bits to determine whether the sensor readings are on one side or the other of the decision surface. Bounds on the number of bits needed to be exchanged are derived, based on communication complexity (CC) theory. A lower bound derived for the two-party average case CC of general functions is compared against the performance of a greedy algorithm. The average case CC of the relevant greater-than (GT) function is characterized within two bits. In the second approach, each sensor node broadcasts a single bit arising from appropriate two-level quantization of its own sensor reading, keeping in mind the fusion rule to be subsequently applied at a local fusion center. The optimality of a threshold test as a quantization rule is proved under simplifying assumptions. Finally, results from a QualNet simulation of the algorithms are presented that include intruder tracking using a naive polynomial-regression algorithm.