Structural and mechanistic motifs in membrane proteins: the three-dimensional modelling of rhodopsin, band 3, and the nicotinic acetylcholine receptor

Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, β-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.

Specific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and β-adrenergic receptors.

The nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.

Band 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.

Formation of nanogratings on the surface of a ZnSe crystal irradiated by femtosecond laser pulses

Two collinear femtosecond laser pulses, one at wavelength of 800 nm and the other at 400 nm (double frequency), simultaneously irradiated the surface of ZnSe crystal, which resulted in regular nanograting with period of 180 nm on the whole ablation area. We attribute the formation of the nanograting to be due to the interference between the surface scattered wave of 800 nm lasers and the 400 nm light. The period of the nanograting Lambda is about lambda/2n, where n is refractive index of the sample, and lambda, the laser wavelength. This mechanism is supported by observation of rotation of the nanograting with the polarization of 400 nm light, and by the dependence of Lambda similar to lambda of the nanoripples on the surface of semiconductors and dielectrics.

Design of adjustable superresolving filters based on birefringent crystals

A two-mode adjustable superresolving filter based on a birefringent filter is proposed. This kind of filter has superresolution in two modes of adjustment. One is rotation of the binary pupil filter on the optical axis of the system and the other is the tilt of the filter away from the pupil plane on axis parallel or perpendicular to the optical axis of the crystal. The filters act as complex amplitude filters in the former mode, and as pure phase filters in the latter. By analyzing two superresolving parameters, we obtain the optimal design parameters that ensure a large field of view, a large superresolving range, and a high setting accuracy. This kind of filter can provide more flexibility in practical applications. (c) 2006 Optical Society of America.

Structural and clumped-isotope constraints on the mechanisms of displacement along low-angle detachments

Despite years of research on low-angle detachments, much about them remains enigmatic. This thesis addresses some of the uncertainty regarding two particular detachments, the Mormon Peak detachment in Nevada and the Heart Mountain detachment in Wyoming and Montana.

Constraints on the geometry and kinematics of emplacement of the Mormon Peak detachment are provided by detailed geologic mapping of the Meadow Valley Mountains, along with an analysis of structural data within the allochthon in the Mormon Mountains. Identifiable structures well suited to constrain the kinematics of the detachment include a newly mapped, Sevier-age monoclinal flexure in the hanging wall of the detachment. This flexure, including the syncline at its base and the anticline at its top, can be readily matched to the base and top of the frontal Sevier thrust ramp, which is exposed in the footwall of the detachment to the east in the Mormon Mountains and Tule Springs Hills. The ~12 km of offset of these structural markers precludes the radial sliding hypothesis for emplacement of the allochthon.

The role of fluids in the slip along faults is a widely investigated topic, but the use of carbonate clumped-isotope thermometry to investigate these fluids is new. Faults rocks from within ~1 m of the Mormon Peak detachment, including veins, breccias, gouges, and host rocks, were analyzed for carbon, oxygen, and clumped-isotope measurements. The data indicate that much of the carbonate breccia and gouge material along the detachment is comminuted host rock, as expected. Measurements in vein material indicate that the fluid system is dominated by meteoric water, whose temperature indicates circulation to substantial depths (c. 4 km) in the upper crust near the fault zone.

Slip along the subhorizontal Heart Mountain detachment is particularly enigmatic, and many different mechanisms for failure have been proposed, predominantly involving catastrophic failure. Textural evidence of multiple slip events is abundant, and include multiple brecciation events and cross-cutting clastic dikes. Footwall deformation is observed in numerous exposures of the detachment. Stylolitic surfaces and alteration textures within and around “banded grains” previously interpreted to be an indicator of high-temperature fluidization along the fault suggest their formation instead via low-temperature dissolution and alteration processes. There is abundant textural evidence of the significant role of fluids along the detachment via pressure solution. The process of pressure solution creep may be responsible for enabling multiple slip events on the low-angle detachment, via a local rotation of the stress field.

Clumped-isotope thermometry of fault rocks associated with the Heart Mountain detachment indicates that despite its location on the flanks of a volcano that was active during slip, the majority of carbonate along the Heart Mountain detachment does not record significant heating above ambient temperatures (c. 40-70°C). Instead, cold meteoric fluids infiltrated the detachment breccia, and carbonate precipitated under ambient temperatures controlled by structural depth. Locally, fault gouge does preserve hot temperatures (>200°C), as is observed in both the Mormon Peak detachment and Heart Mountain detachment areas. Samples with very hot temperatures attributable to frictional shear heating are present but rare. They appear to be best preserved in hanging wall structures related to the detachment, rather than along the main detachment.

Evidence is presented for the prevalence of relatively cold, meteoric fluids along both shallow crustal detachments studied, and for protracted histories of slip along both detachments. Frictional heating is evident from both areas, but is a minor component of the preserved fault rock record. Pressure solution is evident, and might play a role in initiating slip on the Heart Mountain fault, and possibly other low-angle detachments.

The Molecular Basis of Lysine Acetylation: Addition, Removal, and Recognition

Acetyltransferases and deacetylases catalyze the addition and removal, respectively, of acetyl groups to the epsilon-amino group of protein lysine residues. This modification can affect the function of a protein through several means, including the recruitment of specific binding partners called acetyl-lysine readers. Acetyltransferases, deacetylases, and acetyl-lysine readers have emerged as crucial regulators of biological processes and prominent targets for the treatment of human disease. This work describes a combination of structural, biochemical, biophysical, cell-biological, and organismal studies undertaken on a set of proteins that cumulatively include all steps of the acetylation process: the acetyltransferase MEC-17, the deacetylase SIRT1, and the acetyl-lysine reader DPF2. Tubulin acetylation by MEC-17 is associated with stable, long-lived microtubule structures. We determined the crystal structure of the catalytic domain of human MEC-17 in complex with the cofactor acetyl-CoA. The structure in combination with an extensive enzymatic analysis of MEC-17 mutants identified residues for cofactor and substrate recognition and activity. A large, evolutionarily conserved hydrophobic surface patch distal to the active site was shown to be necessary for catalysis, suggesting that specificity is achieved by interactions with the alpha-tubulin substrate that extend outside of the modified surface loop. Experiments in C. elegans showed that while MEC-17 is required for touch sensitivity, MEC-17 enzymatic activity is dispensible for this behavior. SIRT1 deacetylates a wide range of substrates, including p53, NF-kappaB, FOXO transcription factors, and PGC-1-alpha, with roles in cellular processes ranging from energy metabolism to cell survival. SIRT1 activity is uniquely controlled by a C-terminal regulatory segment (CTR). Here we present crystal structures of the catalytic domain of human SIRT1 in complex with the CTR in an apo form and in complex with a cofactor and a pseudo-substrate peptide. The catalytic domain adopts the canonical sirtuin fold. The CTR forms a beta-hairpin structure that complements the beta-sheet of the NAD^+-binding domain, covering an essentially invariant, hydrophobic surface. A comparison of the apo and cofactor bound structures revealed conformational changes throughout catalysis, including a rotation of a smaller subdomain with respect to the larger NAD^+-binding subdomain. A biochemical analysis identified key residues in the active site, an inhibitory role for the CTR, and distinct structural features of the CTR that mediate binding and inhibition of the SIRT1 catalytic domain. DPF2 represses myeloid differentiation in acute myelogenous leukemia. Finally, we solved the crystal structure of the tandem PHD domain of human DPF2. We showed that DPF2 preferentially binds H3 tail peptides acetylated at Lys14, and binds H4 tail peptides with no preference for acetylation state. Through a structural and mutational analysis we identify the molecular basis of histone recognition. We propose a model for the role of DPF2 in AML and identify the DPF2 tandem PHD finger domain as a promising novel target for anti-leukemia therapeutics.

Electro-optic modulation of light propagating near the optic axis with any polarization in uniaxial crystals

The electro-optic effect in uniaxial crystals for light propagating near the optic axis with any polarization has been analyzed. The passive and the electrically induced birefringences and the rotation of polarization direction in crystals have been calculated, and the conoscopic interference figures under orthogonal polariscopes for different polarizer directions have been plotted. The extinction areas caused by the rotation of polarization direction in crystals change with the polarizer direction, but the two heads of the induced optical axes do not vary, which are always on the induced principal axis with bigger refractive index. The directions of polariscopes are always extinction, and the +/- 45 degrees directions with polarizer are always complete transmission. The conoscopic interference figures for LiNbO3 crystals have been demonstrated experimentally by rotating polariscopes directions, which accord with the theoretically calculating plots. (c) 2006 Elsevier GmbH. All rights reserved.

The production of freshwater fish for food

It has been estimated that in England and Wales fresh water covers some 340 square miles of which about one quarter is inhabited mainly by salmon and trout; in Scotland the lakes cover an area of 340 square miles. The principal object of this publication is to make available in handy form some of the methods, especially those involving the use of manures, by which crops of fish from water can be increased. The cultivation of water which this implies may be compared directly to the cultivation of farm land: the conditions for growth are made as favourable as possible, the seed is sown in the form of young fish, and after one or perhaps two growing seasons the crop is harvested. There are however many waters about the country where marketable fish are already available and can be removed without prejudice to, and indeed to the advantage of, sporting fisheries. In such cases it is necessary only to remove the fish and to rely on the natural processes of reproduction of those which are left to repopulate the water. Farming waters in the true sense is the concern of the greater part of this publication; the removal of crops of otherwise unwanted fish is considered in the last two sections on perch trapping and eel fisheries.

Sources of variability in the free-ball micro-scale abrasion test

In the 'free-ball' version of the micro-scale abrasion or ball-cratering test the rotating ball rests against a tilted sample and a grooved drive shaft. Tests under nominally identical conditions with different apparatus commonly show small but significant differences in measured wear rate. An indirect method has been developed and demonstrated for continuous on-line measurement of the coefficient of friction in the free-ball test. Experimental investigation of the effects of sample tilt angle and drive shaft groove width shows that both these factors influence the stability of the rotation of the ball, and the shape of the abrasive slurry pool, which in turn affect the coefficient of friction in the wear scar area and the measured wear rate. It is suggested that in order to improve the reproducibility of this method the geometry of the apparatus should be specified. For the apparatus used in this work with a steel ball of 25 mm diameter, a sample tilt angle of 60-75° and a shaft groove width of about 10mm provided the most stable ball motion and a wear rate which showed least variability. © 2004 Elsevier B.V. All rights reserved.

Flexoelectro-optic properties of chiral nematic liquid crystals in the uniform standing helix configuration.

The flexoelectro-optic effect describes the rotation of the optic axis of a short-pitch chiral nematic liquid crystal under the application of an electric field. We investigate the effect in the uniform standing helix, or "Grandjean" configuration. An in-plane electric field is applied. The director profile is determined numerically using a static one-dimensional continuum model with strong surface anchoring. The Berreman method is used to solve for plane-wave solutions to Maxwell's equations, and predict the optical properties of the resulting structure in general cases. By using a chiral nematic with short pitch between crossed polarizers an optical switch may be generated. With no applied field the configuration is nontransmissive at normal incidence, but becomes transmissive with an applied field. For this case, numerical results using the Berreman method are supplemented with an analytic theory and found to be in good agreement. The transmitted intensity as a function of tilt, the contrast ratio, and the tilt required for full intensity modulation are presented. The angular dependence of the transmission is calculated and the isocontrast curves are plotted. For typical material and cell parameters a switching speed of 0.017 ms and contrast ratio of 1500:1 at normal incidence are predicted, at a switch-on tilt of 41.5 degrees. Experimental verification of the analytic and numerical models is provided.

Effects of rotating inlet distortion on multistage compressor stability

In multi-spool engines, rotating stall in an upstream compressor will impose a rotating distortion on the downstream compressor, thereby affecting its stability margin. In this paper experiments are described in which this effect was simulated by a rotating screen upstream of several multistage low-speed compressors. The measurements are complemented by, and compared with, a theoretical model of multistage compressor response to speed and direction of rotation of an inlet distortion. For co-rotating distortions (i.e., distortions rotating in the same direction as rotor rotation), experiments show that the compressors exhibited significant loss in stability margin and that they could be divided into two groups according to their response. The first group exhibited a single peak in stall margin degradation when the distortion speed corresponded to roughly 50% of rotor speed. The second group showed two peaks in stall margin degradation corresponding to distortion speeds of approximately 25-35% and 70-75% of rotor speed. These new results demonstrate that multistage compressors can have more than a single resonant response. Detailed measurements suggest that the two types of behavior are linked to differences between the stall inception processes observed for the two groups of compressors and that a direct connection thus exists between the observed forced response and the unsteady flow phenomena at stall onset. For counter-rotational distortions, all the compressors tested showed minimal loss of stability margin. The results imply that counter-rotation of the fan and core compressor, or LP and HP compressors, could be a worthwhile design choice. Calculations based on the two-dimensional theoretical model show excellent agreement for the compressors which had a single peak for stall margin degradation. We take this first-of-a-kind comparison as showing that the model, though simplified, captures the essential fluid dynamic features of the phenomena. Agreement is not good for compressors which had two peaks in the curve of stall margin shift versus distortion rotation speed. The discrepancy is attributed to the three-dimensional and short length scale nature of the stall inception process in these machines; this includes phenomena that have not yet been addressed in any model.

Active control of sound radiated by a submarine hull in bending vibration using inertial actuators

Submarines are efficient sources of low frequency radiated noise due to the vibrations induced by the rotation of the propeller in a non uniform wake. In this work the possibility of using inertial actuators to reduce the far field sound pressure is investigated. The submerged vessel is modelled as a cylindrical shell with two conical end caps. Complicating effects such as ring stiffeners, bulkheads and the fluid loading are taken into account. A harmonic radial force is transmitted from the propeller to the hull through the stern end cone and it is tonal at the blade passing frequency (rotational speed of the shaft multiplied by the number of blades). The actuators are attached at the inside of the prow end cone to form a circumferential array. Both Active Vibration Control (AVC) and Active Structural Acoustic Control (ASAC) are analysed and it is shown that the inertial actuators can significantly reduce the far field sound pressure.

Impact assessment of Farakka barrage on environmental issues at Bheramara Upazila, Bangladesh

Different problems have been created on the downstream territory, especially on Bheramara on the bank of mighty river Padma. The study is preferred to assess the impacts on river flow of Ganges water, and on fisheries, agriculture, irrigation, groundwater, livelihood, and biodiversity because of Farakka Barrage. Information were collected from various respondents among which 42% is farmer, 12% is fisherman, 36% is businessman and 10% is service holder. It is evident from this study that 65% of crops production were directly affected by Farakka Barrage, in which 34% crops were damaged due to scarcity of water, lowering the ground water level, less access to rainwater, etc. and 66% crops were invent for increasing char land, increasing soil fertility for the use of agrochemicals. Irrigation has been adversely affected because of 35% insufficient flow of water and 65% lowering the ground water level.

Potential risks of contaminants with specific reference to mercury

Fresh water and fish are important to the people who live in the Lake Victoria region therefore the quality of the water and fish is of major importance (Johnson & Odada, 1996). It is well known that dirty water and spoilt fish can lead to poor health and lower standards of living, and that quality can be affected by the pollution in the environment. Even though Lake Victoria is very large, it is relatively shallow and the water remains in the lake basin for a long time (Bootsma & Hecky, 1993). There are a number of environmental issues in Lake Victoria, including water hyacinth~over-population and increased farming causing problems with the lake ecosystem. All these factors combine to keep contaminants within the lake for long time, which will lead to gradually increasing concentrations in the lake. Pollution is a term that covers a wide variety of chemicals and physical changes and their adverse effects on the environment. Here we focus on contaminants, which are unwanted chemicals introduced to the environment. Contaminants include a very wide variety of chemicals, both man-made and natural, for example, mercury, pesticides and herbicides, heavy metals, and natural plant and algae toxins. Many contaminants do not always lead to adverse effects immediately, but can gradually induce long-term problems leading to chronic illnesses and physical damage. A few contaminants have very rapid impacts resulting in immediately obvious changes such as death or injury. Sources of contaminants are varied. Contaminants can get in the lake by the way of agricultural treatment of crops near the lake, industrial effluent, intentional introduction such as fish poisoning byfishermen, natural sources such as heavy metals from particular types of rocks, and even some plants naturally release their toxins. Contaminant sources are not always found near Lake Victoria.

Discrete dislocation plasticity analysis of size effects in single crystals

The effect of size and slip system configuration on the tensile stress-strain response of micron-sized planar crystals as obtained from discrete dislocation plasticity simulations is presented. The crystals are oriented for either single or symmetric double slip. With the rotation of the tensile axis unconstrained, there is a strong size dependence, with the flow strength increasing with decreasing specimen size. Below a certain specimen size, the flow strength of the crystals is set by the nucleation strength of the initially present Frank-Read sources. The main features of the size dependence are the same for both the single and symmetric double slip configurations.

Finite element modelling of the sismic behaviour of water front structures

Water front structures have suffered significant damage in many of the recent earthquakes. These include gravity type quay walls, vertically composite walls, cantilever retaining walls, anchored bulkheads and similar structures. One of the primary causes for the poor performance of these classes of structures is the liquefaction of the foundation soil and in some instances liquefaction of the backfill soil. The liquefaction of the soil in-front of the quay wall tends to cause large lateral displacements and rotation of the wall. Often such gravity walls are placed on rubble mound deposited onto the sea bed.This paper presents finite element analyses of such a problem in which strength degradation of the foundation soil and the backfill material will be modelled using PZ mark III constitutive model. The performance of the wall in terms of its lateral displacement, vertical settlement and/or the rotation suffered by the wall will be presented. In addition, the contours of the horizontal and vertical effective stresses and the excess pore pressure ratio will be presented at different time instants together with hyrdraulic gradients. Immediately after the earthquake, the hydraulic gradients indicate migration of pore water into the region below the wall, suggesting further softening of the foundation soil below the wall.