Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information

The three-dimensional structures of leucine-rich repeat (LRR) -containing proteins from five different families were previously predicted based on the crystal structure of the ribonuclease inhibitor. using an approach that combined homology-based modeling, structure-based sequence alignment of LRRs, and several rational assumptions. The structural models have been produced based on very limited sequence similarity, which, in general. cannot yield trustworthy predictions. Recently, the protein structures from three of these five families have been determined. In this report we estimate the quality of the modeling approach by comparing the models with the experimentally determined structures. The comparison suggests that the general architecture, curvature, interior/exterior orientations of side chains. and backbone conformation of the LRR structures can be predicted correctly. On the other hand. the analysis revealed that, in some cases. it is difficult to predict correctly the twist of the overall super-helical structure. Taking into consideration the conclusions from these comparisons, we identified a new family of bacterial LRR proteins and present its structural model. The reliability of the LRR protein modeling suggests that it would be informative to apply similar modeling approaches to other classes of solenoid proteins.

Structural characterization of the N-terminal autoregulatory sequence of phenylalanine hydroxylase

Phenylalanine hydroxylase (PAH) is activated by its substrate phenylalanine, and through phosphorylation by cAMP-dependent protein kinase at Ser 16 in the N-terminal autoregulatory sequence of the enzyme. The crystal structures of phosphorylated and unphosphorylated forms of the enzyme showed that, in the absence of phenylalanine, in both cases the N-terminal 18 residues including the phosphorylation site contained no interpretable electron density. We used nuclear magnetic resonance (NMR) spectroscopy to characterize this N-terminal region of the molecule in different stages of the regulatory pathway. A number of sharp resonances are observed in PAH with an intact N-terminal region, but no sharp resonances are present in a truncation mutant lacking the N-terminal 29 residues. The N-terminal sequence therefore represents a mobile flexible region of the molecule. The resonances become weaker after the addition of phenylalanine, indicating a loss of mobility. The peptides corresponding to residues 2-20 of PAH have different structural characteristics in the phosphorylated and unphosphorylated forms, with the former showing increased secondary structure. Our results support the model whereby upon phenylalanine binding, the mobile N-terminal 18 residues of PAH associate with the folded core of the molecule; phosphorylation may facilitate this interaction.

Synthesis and structural properties of patellamide a derivatives and their copper(II) compounds

The synthesis, characterization and copper(II) coordination chemistry of three new cyclic peptide ligands, PatJ(1) (cyclo-(Ile -Thr- (Gly)Thz-lle-Thr(Gly)Thz)), PatJ(2) (cyclo-(Ile-Thr(Gly)Thz-(D)-Ile-Thr-(Gly)Thz)), and PatL (cyclo-(Ile-Ser-(Gly)Thz-Ile-Ser(Gly)Thz)) are reported. All of these cyclic peptides and PatN (cyclo-(Ile-Ser(Gly)Thz-Ile-Thr-(Gly)Thz)) are derivatives of patellamide A and have a [24]azacrown-8 macrocyclic structure. All four synthetic cyclic peptides have two thiazole rings but, in contrast to patellamide A, no oxazoline rings. The molecular structure of PatJ1, determined by X-ray crystallography, has a saddle conformation with two close-to-co-parallel thiazole rings, very similar to the geometry of patellamide D. The two coordination sites of PatJ1 with thiazole-N and amide-N donors are each well preorganized for transition metal ion binding. The coordination of copper(II) was monitored by UV/Vis spectroscopy, and this reveals various (meta)stable mono- and dinuclear copper(II) complexes whose stoichiometry was confirmed by mass spectra. Two types of dinuclear copper(II) complexes, [Cu-2(H4L)(OH2)(n)](2+) (n = 6, 8) and [Cu-2(H4L)(OH2)(n)] (n=4, 6; L=PatN, PatL, PatJ1, PatJ2) have been identified and analyzed structurally by EPR spectroscopy and a combination of spectra simulations and molecular mechanics calculations (MM-EPR). The four structures are similar to each other and have a saddle conformation, that is, derived from the crystal structure of PatJ(1) by a twist of the two thiozole rings. The small but significant structural differences are characterized by the EPR simulations.

Comparative influence of forest management and habitat structural factors on the abundances of hollow-nesting bird species in subtropical Australian eucalypt forest

We examined the impact of single-tree selective logging and fuel reduction bums on the abundance of hollow-nesting bird species at a regional scale in southeastern Queensland, Australia. Data were collected on species abundance and habitat structure of dry sclerophyll production forest at 36 sites with known logging and fire histories. Sixteen bird species were recorded with most being resident, territorial, obligate hollow nesters that used hollows that were either small (18 cm diameter). Species densities were typically low, but combinations of two forest management and three habitat structural variables influenced the abundances of eight bird species in different and sometimes conflicting ways. The results suggest that habitat tree management for biodiversity in production forests cannot depend upon habitat structural characteristics alone. Management histories appear to have independent influence (on some bird species) that are distinguishable from their impacts on habitat structure per se. Rather than managing to maximize species abundances to maintain biodiversity, we may be better off managing to avoid extinctions of populations by identifying thresholds of acceptable fluctuations in populations of not only hollow-nesting birds but other forest dependent wildlife relative to scientifically valid forest management and habitat structural surrogates.

Reversible luminescence thermochromism in dipotassiumsodium tris[dicyanoargentate(I)] and the role of structural phase transitions

As a function of temperature, the layered compound K2Na[Ag(CN)213 displays dramatic variations in luminescence thermochromism with major trend changes occurring around 80 K. In order to understand these interesting optical properties, high-resolution neutron diffraction investigations were performed on a polycrystalline sample of this material in the temperature range from 1.5 to 300 K, and previous synchrotron X-ray data of Larochelle et al. (Solid State Commun. 114, 155 (2000)) were reinterpreted. The corresponding significant structural changes were found to be continuous with an anomalous increase of the monoclinic c-lattice parameter with decreasing temperature, associated with slight reorientations of two inequivalent, approximately linear N-C-Ag-C-N units. In the whole temperature range, the crystal structure is monoclinic with the space group C2/m. Based on the structural results, the major luminescence thermochromism changes around 80 K are attributed to the dominance of a back energy transfer process from low- to high-energy excitons at high temperatures. (E) 2002 Elsevier Science (USA).

Copolymers obtained by the radiation-induced grafting of styrene onto poly(tetrafluoroethylene-co-perfluoropropylvinyl ether) substrates. 1. Preparation and structural investigation

A study has been made to investigate the radiation grafting of styrene onto poly(tetrafluoroethylene-co-perfluoropropylvinyl ether) (PFA) substrates, using the simultaneous irradiation method. Two PFA polymers of different comonomer perfluoropropyl vinyl ether (PPVE) content and degree of crystallinity were used. Effects of grafting conditions such as monomer concentrations, type of solvent, dose rate, and irradiation dose on the grafting yield were investigated. Of the six different solvents used, the most efficient in terms of increasing grafting yield were dichloromethane, benzene, and methanol. The degree of grafting increased with increasing radiation dose up to 500 kGy, stabilizing above this dose. However, the grafting yield decreased with an increase in the dose rate. The grafting of styrene onto the PFA substrates was confirmed by FTIR-ATR and micro-Raman spectroscopy, The increase in the overall grafting yield was accompanied by a proportional increase in the penetration depth of the grafts into the substrate.

Location of innervation zones of sternocleidomastoid and scalene muscles - a basis for clinical and research electromyography applications

Objectives: Advances in surface electromyography (sEMG) techniques provide a clear indication that refinement of electrode location relative to innervation zones (IZ) is required in order to optimise the accuracy, relevance and repeatability of the sEMG signals. The aim of this study was to identify the IZ for the sternocleidomastoid and anterior scalene muscles to provide guidelines for electrode positioning for future clinical and research applications. Methods: Eleven volunteer subjects participated in this study. Myoelectric signals were detected from the sternal and clavicular heads of the stemocleidomastoid and the anterior scalene muscles bilaterally using a linear array of 8 electrodes during isometric cervical flexion contractions. The signals were reviewed and the IZ(s) were identified, marked on the subjects' skin and measurements were obtained relative to selected anatomical landmarks. Results: The position of the IZ lay consistently around the mid-point or in the superior portion of the muscles studied. Conclusions: Results suggest that electrodes should be positioned over the lower portion of the muscle and not the mid-point, which has been commonly used in previous studies. Recommendations for sensor placement on these muscles should assist investigators and clinicians to ensure improved validity in future sEMG applications. (C) 2002 Elsevier Science Ireland Ltd. All rights reserved.

Modelling of Lamb waves in composite laminated plates excited by interdigital transducers

The technique of permanently attaching interdigital transducers (IDT) to either flat or curved structural surfaces to excite single Lamb wave mode has demonstrated great potential for quantitative non-destructive evaluation and smart materials design, In this paper, the acoustic wave field in a composite laminated plate excited by an IDT is investigated. On the basis of discrete layer theory and a multiple integral transform method, an analytical-numerical approach is developed to evaluate the surface velocity response of the plate due to the IDTs excitation. In this approach, the frequency spectrum and wave number spectrum of the output of IDT are obtained directly. The corresponding time domain results are calculated by applying a standard inverse fast Fourier transformation technique. Numerical examples are presented to validate the developed method and show the ability of mode selection and isolation. A new effective way of transfer function estimation and interpretation is presented by considering the input wave number spectrum in addition to the commonly used input frequency spectrum. The new approach enables the simple physical evaluation of the influences of IDT geometrical features such as electrode finger widths and overall dimension and excitation signal properties on the input-output characteristics of IDT. Finally, considering the convenience of Mindlin plate wave theory in numerical computations as well as theoretical analysis, the validity is examined of using this approximate theory to design IDT for the excitation of the first and second anti-symmetric Lamb modes. (C) 2002 Elsevier Science Ltd. All rights reserved.

Negative ion electrospray mass spectra of caerulein peptides: an aid to structural determination

MS/MS data derived from the [M-H](-) ions of desulfated caerulein peptides provide (i) sequencing information from a combination of alpha, beta and gamma backbone cleavages, and (ii) identification of specific amino acid side chains by side-chain cleavages [e.g. Ser (-CH2O), Thr (-CH3CHO) and Asp (-H2O)] (fragmentations having no counterparts in positive ion spectra). In addition, delta and/or gamma backbone cleavage ions from Asp residues identify the position of these residues in the peptide. In contrast, neither delta nor gamma cleavage ions are observed from either the Gln2 residue nor from Phe residues. Full structural information can be obtained from a consideration of the positive and negative ion MS/MS data in concert. Copyright (C) 2002 John Wiley Sons, Ltd.

Structural changes in mixed Langmuir-Blodgett films upon nanoparticle formation

The formation of CdS nanoparticles by reacting mixed Langmuir-Blodgett films of arachidic acid and either octadecylamine or dimethyldioctadecylammonium nitrate on a cadmium-containing subphase with hydrogen sulfide gas has resulted in the identification of a number of structural changes, observed using grazing incidence X-ray diffraction. In the case of octadecylamine, the structure after reaction is a hexagonal close-packed array of surfactant-stabilized nanoclusters, with a lattice constant of a = 17.65 Angstrom. In both octadecylamine and dimethyldioctadecylammonium nitrate films, the presence of a unit cell tilted at 38degrees to the plane of the substrate was found. Despite these changes, the average nanoparticle size was unaffected by the addition of either second component to the film.

Comparisons between bone and cementum compositions and the possible basis for their layered appearances

In humans, age estimation from the adult skeleton represents an attempt to determine chronological age based on growth and maturational events. In teeth, such events can be characterized by appositional growth layers in midroot cementum. The purpose of this study was to determine the underlying cause of the layered microstructure of human midroot cementum. Whether cementum growth layers are caused by changes in relative mineralization, collagen packing and/or orientation, or by variations in organic matrix apposition was investigated by subjecting midroot sections of human canine teeth to analysis using polarized light and scanning electron microscopy (SEM). Polarized light was used to examine transverse midroot sections in both mineralized and demineralized states. Mineralized sections were also reexamined following subsequent decollagenization. Polarized light was additionally used in the examination of mineralized sections taken transversely, longitudinally, and obliquely from the same tooth root. From the birefringence patterns it was concluded that collagen orientation does not change with varying section plane. Instead, the mineral phase was most responsible for the birefringence of the cementum. SEM studies suggested that neither collagen packing nor collagen orientation change across the width of the cementum, confirming and validating the results of the polarized light examination. Also, SEM analysis using electron backscatter and the electron probe suggested no changes in the mean atomic number density, calcium, phosphate, and sulfur levels across the width of the cementum. Therefore, we conclude that crystalline orientation and/or size is responsible for the layered appearance of cementum. (Bone 30:386-392; 2002) (C) 2002 by Elsevier Science Inc. All rights reserved.

Structural and surface property changes of macadamia nut-shell char upon activation and high temperature treatment

Structural and surface property changes of macadamia nut-shell (MNS) char upon activation and high temperature treatment (HTT) were studied by high-resolution nitrogen adsorption, diffuse reflectance infra-red Fourier transform spectroscopy, X-ray photoelectron spectroscopy, and temperature-programmed desorption. It is found that activation of MNS char can be divided into the low extent activation which may involve the reactions of internal oxygen-containing groups and leads to the formation of comparatively uniform micropores, and the high extent activation which induces reactions between carbon and activating gas and produces a large amount of micropores. The surface functional groups (SFGs) basically increase with the increase of activation extent, but high extent activation preferentially increases the amount of -C-O and -C=O. HTT in air for a short tithe at a high temperature (1173 K) greatly increases the micropore volume and the amounts of SFGs. By appropriately choosing the activation and HTT conditions, it is possible to control both the textural structure and the type and amounts of SFG. (C) 2002 Published by Elsevier Science Ltd.

Effect of a control burn on lizards and their structural environment in a eucalypt open-forest

The composition of an open-forest lizard assemblage in eastern Australia was examined before and after a low-intensity controlled fire and concurrently compared with that in an adjoining unburnt area. The effect of fire on the available structural environment and the habitat used by two focal species, Carlia vivax and Lygisaurus foliorum, was also examined. Lizard species richness was unaffected by the controlled burn as was the abundance of most species. C. vivax was the only species to display a significant reduction in abundance after fire. While the low-intensity fire resulted in significant changes to the available structural environment, there were no compensatory shifts in the habitat preferences of either C. vivax or L. foliorum. The reduction in abundance of C. vivax was congruent with this species' avoidance of burnt areas. C. vivax displayed a non-random preference for ground cover and litter cover, which were reduced in burnt areas. Changes in the availability of preferred structural habitat features are likely to contribute to changes in the abundance of some lizard species. Therefore, even low-intensity disturbances can have an impact on lizard assemblages if critical habitat features are lost or become limiting.

Structural ordering of coal char during heat treatment and its impact on reactivity

The effect of heat treatment on the structure of an Australian semi-anthracite char was studied in detail in the 850-1150degreesC temperature range using XRD, HRTEM, and electrical resistivity techniques. It was found that the carbon crystallite size in the char does not change significantly during heat treatment in the temperature range studied, for both the raw coal and its ash-free derivative obtained by acid treatment. However, the fraction of the organized carbon in the raw coal chars, determined by XRD, increased with increase of heat treatment time and temperature, while that for the ash-free coal chars remained almost unchanged. This suggests the occurrence of catalytic ordering during heat treatment, supported by the observation that the electrical resistivity of the raw coal chars decreased with heat treatment, while that of the ash-free coal chars did not vary significantly. Further confirmatory evidence was provided by high resolution transmission electron micrographs depicting well-organized carbon layers surrounding iron particles. It is also found that the fraction of organized carbon does not reach unity, but attains an apparent equilibrium value that increases with increase in temperature, providing an apparent heat of ordering of 71.7 kJ mol(-1) in the temperature range studied. Good temperature-independent correlation was found between the electrical resistivity and the organized carbon fraction, indicating that electrical resistivity is indeed structure sensitive. Good correlation was also found between the electrical resistivity and the reactivity of coal char. All these results strongly suggest that the thermal deactivation is the result of a crystallite-perfecting process, which is effectively catalyzed by the inorganic matter in the coal char. Based on kinetic interpretation of the data it is concluded that the process is diffusion controlled, most likely involving transport of iron in the inter-crystallite nanospaces in the temperature range studied. The activation energy of this transport process is found to be very low, at about 11.8 kJ mol(-1), which is corroborated by model-free correlation of the temporal variation of organized carbon fraction as well as electrical resistivity data using the superposition method, and is suggestive of surface transport of iron. (C) 2002 Elsevier Science Ltd. All rights reserved.