125Te NMR for structural investigations in phase change materials: Optimization of experimental conditions coupled to NMR shift prediction.

Phase Change Materials as those of the Ge-Sb-Te ternary system are of great interest for technological applications. Properties of these compounds are strongly related to presence of vacancies and structural investigations remain challenging. In this paper we evidence that 125Te NMR in natural abundance and using commercial systems at intermediate field (14.1 â€‹T) together with NMR parameters prediction can contribute to improve understanding of electronic structure of such systems. GeTe is a typical phase change material, whose structure contains germanium vacancies, even in its stoichiometric form, giving it metallic properties. Here, we use nominal Ge50Te50 and Ge48Te52 crystalline samples as an example to optimize the WURST-CPMG technique, a powerful technique to record wide NMR spectra which has not yet been used on 125Te. The goal was to minimize the time devoted to experiments as well as maximize the signal-to-noise ratio in order to detect small intensity signals directly linked to vacancies. Virtual Crystal Approximation (VCA) calculations performed with WIEN2K helped to interpret the NMR spectra. For Te-based crystalline conducting samples the best experimental results were obtained using 3.2 â€‹mm thin wall rotors with diluted samples 40 â€‹vol% GeTe-60 â€‹vol% SiO2. In addition to the WURST-CPMG technique, high resolution spectra using MAS as implemented in the pj-MAT technique allowed us to identify the distributions of chemical shift parameters in the high intensity contribution of the 1D spectra. The NMR spectra recorded on the samples showed that an addition of Tellurium in the stoichiometric Ge50Te50 sample leads to an important broadening of the spectrum together with a shift of the lines. According to VCA calculations it could be attributed to a distribution of concentrations of germanium vacancies in the sample and it would appear that Knight Shift but also Chemical Shift could contribute in similar proportion to the NMR line position when metavalent bonding is invoked.

NMR shieldings from density functional perturbation theory: GIPAW versus all-electron calculations.

We present a benchmark of the density functional linear response calculation of NMR shieldings within the gauge-including projector-augmented-wave method against all-electron augmented-plane-wave+local-orbital and uncontracted Gaussian basis set results for NMR shieldings in molecular and solid state systems. In general, excellent agreement between the aforementioned methods is obtained. Scalar relativistic effects are shown to be quite large for nuclei in molecules in the deshielded limit. The small component makes up a substantial part of the relativistic corrections.

Running a 100-km ultra-marathon induces an inflammatory response but does not raise the level of the plasma iron-regulatory protein hepcidin.

AIM: Exercise may induce an inflammatory response that may lead to changes in iron metabolism. The aim of this study was to examine the relationship between the inflammation induced by a 100 km run and the level of hepcidin, which is a hormone regulating iron metabolism. METHODS: Six males, age 44.5±13.5 years, running 100 km. SETTING: the CRP protein, IL-6 and leucocyte count were measured as an index of inflammation. RESULTS: A 100 km run caused a progressive increase in blood IL-6 concentration, which reached the highest values after 75 km. Furthermore, an increase in levels of CRP, a marker of inflammation, was observed after the 100 km run and continued to increase after a 14 h recovery period. Leucocyte number and markers of muscle damage were significantly elevated after the 100 km run. This was accompanied by a decrease in transferrin saturation and an increase in blood haemoglobin and ferritin. Despite all these changes, the 100 km race did not affect blood hepcidin concentration either during the run or after a 14 h recovery period. CONCLUSION: The study shows that a 100 km run induces an inflammatory response but does not trigger changes in the blood hepcidin level. Thus it can be concluded that changes in IL-6 are not sufficient to increase the blood hepcidin level in runners.

Kinematic variables and blood Acid-base status in the analysis of collegiate swimmers' anaerobic capacity.

Short duration repeated maximal efforts are often used in swimming training to improve lactate tolerance, which gives swimmers the ability to maintain a high work rate for a longer period of time. The aim of the study was to examine the kinematics of swimming and its relation to the changes in blood acid-base status and potassium level. Seven collegiate swimmers, with at least 6 years of training experience, volunteered to participate in the study. The test consisted of 8 x 25 m front crawl performed with maximum effort. The rest period between repetitions was set to five seconds. Blood samples were taken from the fingertip at rest, after warm-up and in the 3rd minute after completion of the test. The swimming was recorded with a video recorder, for later analysis of time, velocity and technique (stroke index). Based on the swimming velocity results, the obtained curve can be divided into rapid decrease of velocity and relatively stable velocities. The breaking point of repetition in swimming velocity was assumed as the swimming velocity threshold and it was highly correlated with the decrease of the blood acid-base status (pH r=0.82, BE r=0.87, HCO3 (-) r=0.76; p<0.05 in all cases). There was no correlation between stroke index or fatigue index and blood acid-base status. Analysis of the swimming speed in the 8 x 25 m test seems to be helpful in evaluation of lactate tolerance (anaerobic capacity) in collegiate swimmers.

A single oral intake of arginine does not affect performance during repeated Wingate anaerobic test.

AIM: The ergogenic effect of arginine has been demonstrated in research focusing on its intake before exercise. However, in these studies, the effect of arginine in combination with other various metabolites were assessed. The aim of this study was to determine whether a single oral intake of arginine, without any other compounds, 60 minutes prior to exercise, modifies performance and exercise metabolism during a repeated Wingate anaerobic test. METHODS: Six healthy, active, but not highly trained volunteers participated in the study. Subjects performed three 30s all-out supramaximal Wingate Anaerobic Tests (WAnTs) with 4 minute-interval rest periods between WAnTs. RESULTS: Arginine ingestion before exercise did not influence physical performance. Triple WAnTs resulted in a marked increase in white blood cell (WBC) count, lactate and ammonia concentrations, however there were no differences between arginine and the placebo trials. CONCLUSION: Our data indicated that 2 g of arginine ingested in a single dose, neither induced nitrite/nitrate (NOx) concentrations changes, nor improved physical performance.

Density functional theory simulations of B K and N K NEXAFS spectra of h-BN/transition metal(111) interfaces.

The electronic structure and the corresponding B K and N K near-edge x-ray fine structure (NEXAFS) spectra of epitaxially grown h-BN on Ni(111), Pt(111), and Rh(111) surfaces are investigated by density functional theory. The calculations are carried out using the WIEN2k program package applying the augmented-plane-wave+local orbitals (APW+lo) method. The NEXAFS spectra are simulated using a 3 × 3 × 1 super cell and considering the final state rule by means of a (partial) core hole for the corresponding atom. The influence of a full or partial core hole is shown for the h-BN/Ni(111) system, for which the best agreement with the experimental spectra is found when half a core hole is assumed. All characteristic features of the experimental spectra are well reproduced by theory, including the angular dependences. The bonding effects are investigated by comparing the spectra of bulk h-BN with those of the h-BN/Ni(111) system. An analysis of both the density of states and charge densities reveals strong N-p(z)-Ni-d(z(2)) bonding/antibonding interactions. In the case of Pt(111) and Rh(111) surfaces, we discuss the effects of the nanomesh structures in terms of simple 1 × 1 commensurate models.

Unraveling the structure of the h-BN/Rh(111) nanomesh with ab initio calculations.

The properties of a single layer of h-BN on top of a Rh(111) surface are discussed in terms of an ab initio generated force field approach as well as by direct ab initio density-functional theory (DFT) calculations. A single-layer model for the h-BN/Rh(111) nanomesh, in contrast to a previously considered (incomplete) double-layer model of h-BN, can explain the experimental data. The main focus of this work is to compare a force field approach described earlier in (Laskowski et al 2007 Phys. Rev. Lett. 98 106802) with direct ab initio calculations. The calculated geometry of the h-BN layer is very similar to the structure predicted by the force field approach. The ab initio calculated density of states projected on N-p(x,y) of BN corresponding to 'low' and 'high' regions with respect to the Rh surface shows a 1 eV splitting and thus explains the observed σ-band splitting. Moreover, we find good agreement between calculated and experimental scanning tunneling microscope (STM) images of this system.

Changes in cardiac structure and function among elite judoists resulting from long-term judo practice.

AIM: The aim of this study was to investigate the character of changes in cardiac structure and function among elite judoists due to long-term judo practice. METHODS: A group of male (N = 20, average age: 22.1) and female (N = 15, average age: 19.4) athletes practising judo for about 10 years was subjected to echocardiographic tests carried out during rest (aorta diameter [AoD], diastolic dimension of the left ventricle [Dd], thickness of the interventricular septum [IVST], the thickness of the posterior wall of the left ventricle [LVPWT]), and to measurement of cardiovascular system's action parameters (heart rate [HR], stroke volume [SV], cardiac output [Q], blood pressure [BP]). Moreover, control non trained subjects were also studied, women (N = 30, average age: 19.1) and men (N = 30, average age: 21.4). In order to determine aerobic efficiency, the authors measured the maximal oxygen uptake (VO2max) using the direct method. The anaerobic capacity was estimated on the basis of the maximal anaerobic power, and the volume of the performed work was calculated by means of the 30s Wingate test. RESULTS: Echocardiographic test values imply that changes in heart morphology induced by long term judo training, such as increase diastolic dimension of the left ventricle, thickness of the interventricular septum and left ventricular posterior wall, resemble more the changes observed in endurance athletes than changes observed in strength athletes. CONCLUSION: The obtained data indicated that judo training improves both aerobic and anerobic performance and these changes were associated with changes in heart structure and function as compared to non trained control.

Validation of protein models derived from experiment.

The growing number of protein structures solved at atomic resolution holds the promise of further improvements in geometry-based validation parameters. Additionally, the estimated standard uncertainties of the atomic coordinates have been computed for a number of X-ray structures, providing a measure of the coordinate precision. In NMR spectroscopy, a measure analogous to the crystallographic R-factor has been developed.

PDBsum: summaries and analyses of PDB structures.

PDBsum is a web-based database providing a largely pictorial summary of the key information on each macromolecular structure deposited at the Protein Data Bank (PDB). It includes images of the structure, annotated plots of each protein chain's secondary structure, detailed structural analyses generated by the PROMOTIF program, summary PROCHECK results and schematic diagrams of protein-ligand and protein-DNA interactions. RasMol scripts highlight key aspects of the structure, such as the protein's domains, PROSITE patterns and protein-ligand interactions, for interactive viewing in 3D. Numerous links take the user to related sites. PDBsum is updated whenever any new structures are released by the PDB and is freely accessible via http://www.biochem.ucl.ac.uk/bsm/pdbsum.

Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.

To assess whether there are universal rules that govern amino acid-base recognition, we investigate hydrogen bonds, van der Waals contacts and water-mediated bonds in 129 protein-DNA complex structures. DNA-backbone interactions are the most numerous, providing stability rather than specificity. For base interactions, there are significant base-amino acid type correlations, which can be rationalised by considering the stereochemistry of protein side chains and the base edges exposed in the DNA structure. Nearly two-thirds of the direct read-out of DNA sequences involves complex networks of hydrogen bonds, which enhance specificity. Two-thirds of all protein-DNA interactions comprise van der Waals contacts, compared to about one-sixth each of hydrogen and water-mediated bonds. This highlights the central importance of these contacts for complex formation, which have previously been relegated to a secondary role. Although common, water-mediated bonds are usually non-specific, acting as space-fillers at the protein-DNA interface. In conclusion, the majority of amino acid-base interactions observed follow general principles that apply across all protein-DNA complexes, although there are individual exceptions. Therefore, we distinguish between interactions whose specificities are 'universal' and 'context-dependent'. An interactive Web-based atlas of side chain-base contacts provides access to the collected data, including analyses and visualisation of the three-dimensional geometry of the interactions.

On the molecular discrimination between adenine and guanine by proteins.

The molecular recognition and discrimination of adenine and guanine ligand moieties in complexes with proteins have been studied using empirical observations on carefully selected crystal structures. The distribution of protein folds that bind these purines has been found to differ significantly from that across the whole PDB, but the most populated architectures and folds are also the most common in three genomes from the three different domains of life. The protein environments around the two nucleic acid bases were significantly different, in terms of the propensities of amino acid residues to be in the binding site, as well as their propensities to form hydrogen bonds to the bases. Plots of the distribution of protein atoms around the two purines clearly show different clustering of hydrogen bond donors and acceptors opposite complimentary acceptors and donors in the rings, with hydrophobic areas below and above the rings. However, the clustering pattern is fuzzy, reflecting the variety of ways that proteins have evolved to recognise the same molecular moiety. Furthermore, an analysis of the conservation of residues in the protein chains binding guanine shows that residues in contact with the base are in general better conserved than the rest of the chain.

Protein folds and functions.

BACKGROUND: The recent rapid increase in the number of available three-dimensional protein structures has further highlighted the necessity to understand the relationship between biological function and structure. Using structural classification schemes such as SCOP, CATH and DALI, it is now possible to explore global relationships between protein fold and function, something which was previously impractical. RESULTS: Using a relational database of CATH data we have generated fold distributions for arbitrary selections of proteins automatically. These distributions have been examined in the light of protein function and bound ligand. Different enzyme classes are not clearly reflected in distributions of protein class and architecture, whereas the type of bound ligand has a much more dramatic effect. CONCLUSIONS: The availability of structural classification data has enabled this novel overview analysis. We conclude that function at the top level of the EC number enzyme classification is not related to fold, as only a very few specific residues are actually responsible for enzyme activity. Conversely, the fold is much more closely related to ligand type.

Conformational analysis of pentapeptide sequences matching a proposed recognition motif for lysosomal degradation.

A selective pathway for the degradation of specific long-lived cytosolic proteins is activated in response to starvation in vivo or to serum withdrawal from cultured cells. It involves recognition of a targeting motif by a member of the hsp70 family. A 5-residue targeting motif has been proposed on the basis of sequence comparisons. We investigate whether there is any structural basis for this motif being the true recognition signal. We examine the conformations of four motif peptides in proteins that are either known to be serum regulated or are from related vertebrate species, and two equivalent peptides in bacterial proteins that closely resemble other regulated proteins. Our studies show that all the motif sequences are located near the ends of surface helices with one or more of the residues buried in the structure, yet it is known that members of the hsp70 family tend to interact with extended peptide chains. Furthermore, recognition by these proteins generally requires a specific ordering of key residues, yet the motif implies a largely order-independent sequence characterized by residue type only. We conclude that the proposed motif is unlikely to be the true targeting signal for lysosomal degradation unless additional factors apply.

X-SITE: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins.

A new empirically based method for predicting favourable interaction regions within the binding sites of proteins is presented. The method uses spatial distributions of atomic contact preferences derived from a non-homologous dataset of 83 high-resolution protein structures. The contact preferences are obtained for 26 different atom types relative to 163 different types of three-atom fragments. Each fragment consists of a triplet of bonded atoms, 1-2-3, which defines a reference frame for the three-dimensional distributions. In this way, directional, as well as distance, information is retained. Once derived, the distribution can be applied in a predictive manner. Given a protein's binding site, each distribution is transformed on to the three-atom fragments of the constituent residues and, when combined, can identify the favourable interaction regions for each different atom type. These predicted regions can then form the basis either for the modification of known inhibitors or for the search and design of new ones. Five known protein-ligand complexes are used to demonstrate the validity and usefulness of the approach. The results show that the method provides a powerful tool both in understanding how a given ligand exploits the interactions available to it in an active site and in helping to design improved, or novel, protein ligands.

Main-chain bond lengths and bond angles in protein structures.

The main-chain bond lengths and bond angles of protein structures are analysed as a function of resolution. Neither the means nor standard deviations of these parameters show any correlation with resolution over the resolution range investigated. This is as might be expected as bond lengths and bond angles are likely to be heavily influenced by the geometrical restraints applied during structure refinement. The size of this influence is then investigated by performing an analysis of variance on the mean values across the five most commonly used refinement methods. The differences in means are found to be highly statistically significant, suggesting that the different target values used by the different methods leave their imprint on the structures they refine. This has implications concerning the actual target values used during refinement and stresses the importance of the values being not only accurate but also consistent from one refinement method to another.

Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases.

It is well established that sequence templates (e.g., PROSITE) and databases are powerful tools for identifying biological function and tertiary structure for an unknown protein sequence. Here we describe a method for automatically deriving 3D templates from the protein structures deposited in the Brookhaven Protein Data Bank. As an example, we describe a template derived for the Ser-His-Asp catalytic triad found in the serine proteases and triacylglycerol lipases. We find that the resultant template provides a highly selective tool for automatically differentiating between catalytic and noncatalytic Ser-His-Asp associations. When applied to nonproteolytic proteins, the template picks out two "non-esterase" catalytic triads that may be of biological relevance. This suggests that the development of databases of 3D templates, such as those that currently exist for protein sequence templates, will help identify the functions of new protein structures as they are determined and pinpoint their functionally important regions.

Protein clefts in molecular recognition and function.

One of the primary factors determining how proteins interact with other molecules is the size of clefts in the protein's surface. In enzymes, for example, the active site is often characterized by a particularly large and deep cleft, while interactions between the molecules of a protein dimer tend to involve approximately planar surfaces. Here we present an analysis of how cleft volumes in proteins relate to their molecular interactions and functions. Three separate datasets are used, representing enzyme-ligand binding, protein-protein dimerization and antibody-antigen complexes. We find that, in single-chain enzymes, the ligand is bound in the largest cleft in over 83% of the proteins. Usually the largest cleft is considerably larger than the others, suggesting that size is a functional requirement. Thus, in many cases, the likely active sites of an enzyme can be identified using purely geometrical criteria alone. In other cases, where there is no predominantly large cleft, chemical interactions are required for pinpointing the correct location. In antibody-antigen interactions the antibody usually presents a large cleft for antigen binding. In contrast, protein-protein interactions in homodimers are characterized by approximately planar interfaces with several clefts involved. However, the largest cleft in each subunit still tends to be involved.

Comparative in vitro activity of gatifloxacin, grepafloxacin, levofloxacin, moxifloxacin and trovafloxacin against 4151 Gram-negative and Gram-positive organisms.

Gatifloxacin, grepafloxacin, moxifloxacin and trovafloxacin are fluoroquinolones with enhanced Gram-positive activity while retaining broad-spectrum activity against Gram-negative pathogens. Levofloxacin and ciprofloxacin are older quinolones with broad activity against Gram-negative pathogens and borderline activity against some Gram-positive organisms. We compared the in vitro activity of these compounds against 4151 Gram-negative and -positive organisms. Gatifloxacin, grepafloxacin, moxifloxacin and trovafloxacin were highly active against penicillin sensitive and resistant Streptococcus pneumoniae, Staphylococcus aureus, Streptococcus pyogenes and Streptococcus agalactiae. Ciprofloxacin and levofloxacin were active but less potent. All compounds were highly active (overall) against Gram-negative pathogens with ciprofloxacin being the most active agent against Pseudomonas aeruginosa. Our data indicate that the advanced fluoroquinolones will be important compounds for treating infections caused by Gram-positive and Gram-negative pathogens.

Susceptibility of Canadian isolates of Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pneumoniae to oral antimicrobial agents.

We measured the susceptibility of Canadian isolates of three respiratory tract pathogens (Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pneumoniae) to several currently approved antimicrobial agents by two different methods. We also measured the susceptibility of isolates to seven fluoroquinolones. Beta-lactamase was produced by 123/566 (21.7%) of H. influenzae isolates compared with 178/200 (89%) of M. catarrhalis isolates. For S. pneumoniae 83/374 (22.2%) isolates were penicillin resistant and of these 2.1% (8/374) showed high level resistance (MIC > or = 2 mg/l). Regardless of methodology, all fluoroquinolones were highly active against H. influenzae (MIC(90) < or = 0.031 mg/l) and M. catarrhalis (MIC(90) < or = 0.064 mg/l) isolates. Susceptibility of H. influenzae to cefuroxime and amoxycillin/clavulanic acid was 99-100% whereas 84-85.5% were susceptible to cefaclor and cefprozil. Azithromycin susceptibility ranged from 82.6 to 99.2% depending on the method. M. catarrhalis isolates were uniformly susceptible to all agents tested except amoxycillin. Cross-resistance in S. pneumoniae to all non-quinolone agents was concurrent with increasing penicillin resistance as shown by increasing MIC90 values. For the fluoroquinolones tested, the rank order of potency based on MIC(90) values was as follows: gemifloxacin (0.031-0.063 mg/l), trovafloxacin (0.125 mg/l), moxifloxacin (0.125-0.25 mg/l), grepafloxacin (0.125-0.25 mg/l), gatifloxacin (0.5 mg/l), levofloxacin (1 mg/l) and ciprofloxacin (2 mg/l). Our study confirms either a high or increasing prevalence of antimicrobial resistant respiratory pathogens in Canada and also compares the new and old fluoroquinolones and their potential role as therapy for community-acquired infections. The prevalence of beta-lactamase positive H. influenzae may have decreased from levels reported in previous studies.