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After its discovery in 1669, phosphorus (P) was named Phosphorus mirabilis ("the miraculous bearer of light"), arising from the chemoluminescence when white P is exposed to the atmosphere. The metaphoric association between P and light resonates through history: from the discovery of P at the start of the Enlightenment period to the vital role of P in photosynthetic capture of light in crop and food production through to new technologies, which seek to capitalize on the interactions between novel ultrathin P allotropes and light, including photocatalysis, solar energy production, and storage. In this introduction to the Journal of Environmental Quality special section "Celebrating the 350th Anniversary of Discovering Phosphorus—For Better or Worse," which brings together 22 paper contributions, we shine a spotlight on the historical and emerging challenges and opportunities in research and understanding of the agricultural, environmental, and societal significance of this vital element. We highlight the role of P in water quality impairment and the variable successes of P mitigation measures. We reflect on the need to improve P use efficiency and on the kaleidoscope of challenges facing efficient use of P. We discuss the requirement to focus on place‐based solutions for developing effective and lasting P management. Finally, we consider how cross‐disciplinary collaborations in P stewardship offer a guiding light for the future, and we explore the glimmers of hope for reconnecting our broken P cycle and the bright new horizons needed to ensure future food, water, and bioresource security for growing global populations. Core Ideas: This special section comprises 22 papers celebrating the 350th anniversary of P discovery.Historical and emerging challenges and opportunities exist in P research and understanding.Authors address P use efficiency and a kaleidoscope of challenges for efficient P use.Focusing on place‐based solutions is required for effective P management.Cross‐disciplinary collaborations in P stewardship are needed for food and water security. [ABSTRACT FROM AUTHOR]

With more than 40 countries currently proposing to boost their national bioeconomies, there is no better time for a clarion call for a "new" bioeconomy, which, at its core, tackles the current disparities and inequalities in phosphorus (P) availability. Existing biofuel production systems have widened P inequalities and contributed to a linear P economy, impairing water quality and accelerating dependence on P fertilizers manufactured from finite nonrenewable phosphate rock reserves. Here, we explore how the emerging bioeconomy in novel, value‐added, bio‐based products offers opportunities to rethink our stewardship of P. Development of integrated value chains of new bio‐based products offers opportunities for codevelopment of "P refineries" to recover P fertilizer products from organic wastes. Advances in material sciences are exploiting unique semiconductor and opto‐electrical properties of new "two‐dimensional" (2D) P allotropes (2D black phosphorus and blue phosphorus). These novel P materials offer the tantalizing prospect of step‐change innovations in renewable energy production and storage, in biomedical applications, and in biomimetic processes, including artificial photosynthesis. They also offer a possible antidote to the P paradox that our agricultural production systems have engineered us into, as well as the potential to expand the future role of P in securing sustainability across both agroecological and technological domains of the bioeconomy. However, a myriad of social, technological, and commercialization hurdles remains to be crossed before such an advanced circular P bioeconomy can be realized. The emerging bioeconomy is just one piece of a much larger puzzle of how to achieve more sustainable and circular horizons in our future use of P. Core Ideas: Society's vision for a more circular economy must go beyond the C cycle to include P.Some biofuel systems have widened P inequalities and contributed to a linear P economy.New bioeconomy in bio‐based products offers an opportunity to rethink P stewardship.A circular bioeconomy requires efficient P reuse, recovery, and recycling from waste.New 2D P allotrope technologies offer a potential antidote to our current P "paradox." [ABSTRACT FROM AUTHOR]

Aortic smooth muscle cells (SMCs) have an intrinsic role in regulating vessel homeostasis and pathological remodelling. In two-dimensional (2D) cell culture formats, however, SMCs are not embedded in their physiological extracellular matrix (ECM) environment. To overcome the limitations of conventional 2D SMC cultures, we established a 3D in vitro model of engineered vascular smooth muscle cell tissues (EVTs). EVTs were casted from primary murine aortic SMCs by suspending a SMC-fibrin master mix between two flexible silicon-posts at day 0 before prolonged culture up to 14 days. Immunohistochemical analysis of EVT longitudinal sections demonstrated that SMCs were aligned, viable and secretory. Mass spectrometry-based proteomics analysis of murine EVT lysates was performed and identified 135 matrisome proteins. Proteoglycans, including the large aggregating proteoglycan versican, accumulated within EVTs by day 7 of culture. This was followed by the deposition of collagens, elastin-binding proteins and matrix regulators up to day 14 of culture. In contrast to 2D SMC controls, accumulation of versican occurred in parallel to an increase in versikine, a cleavage product mediated by proteases of the A Disintegrin and Metalloproteinase with Thrombospondin motifs (ADAMTS) family. Next, we tested the response of EVTs to stimulation with transforming growth factor beta-1 (TGFβ-1). EVTs contracted in response to TGFβ-1 stimulation with altered ECM composition. In contrast, treatment with the pharmacological activin-like kinase inhibitor (ALKi) SB 431542 suppressed ECM secretion. As a disease stimulus, we performed calcification assays. The ECM acts as a nidus for calcium phosphate deposition in the arterial wall. We compared the onset and extent of calcification in EVTs and 2D SMCs cultured under high calcium and phosphate conditions for 7 days. Calcified EVTs displayed increased tissue stiffness by up to 30 % compared to non-calcified controls. Unlike the rapid calcification of SMCs in 2D cultures, EVTs sustained expression of the calcification inhibitor matrix Gla protein and allowed for better discrimination of the calcification propensity between independent biological replicates. In summary, EVTs are an intuitive and versatile model to investigate ECM synthesis and turnover by SMCs in a 3D environment. Unlike conventional 2D cultures, EVTs provide a more relevant pathophysiological model for retention of the nascent ECM produced by SMCs., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)

The GLUT4-regulating protein, TUG, functions to retain GLUT4-containing membrane vesicles intracellularly and, in response to insulin stimulation, releases these vesicles to the cellular exocytic machinery for translocation to the plasma membrane. As part of our on going effort to describe the molecular basis for TUG function, we have determined the tertiary structure and characterized the backbone dynamics for an N-terminal ubiquitin-like domain (TUG-UBL1) using NMR spectroscopy. A well-ordered conformation is observed for residues 10-83 of full-length TUG, and confirms a β-grasp or ubiquitin-like topology. Although not required for in vitro association with GLUT4, the functional role of the TUG-UBL1 domain has not yet been described. We undertook a limited literature review of similar N-terminal UBL domains and noted that a majority participate in protein-protein interactions, generally functioning as adaptor modules to physically associate the over all activity of the protein with a specific cellular process, such as the ubiquitin-proteasome pathway. In consistent fashion, TUG-UBL1 is not expected to participate in a covalent protein modification reaction as it lacks the characteristic C-terminal diglycine ('GG') motif required for conjugation to an acceptor lysine, and also lacks the three most common acceptor lysine residues involved in polyubiquitination. Additionally, analysis of the TUG-UBL1 molecular surface reveals a lack of conservation of the 'Ile-44 hydrophobic face' typically involved in ubiquitin recognition. Instead, we speculate on the possible significance of a concentrated area of negative electrostatic potential with increased backbone mobility, both of which are features suggestive of a potential protein-protein interaction site. [ABSTRACT FROM AUTHOR]

CFE88 is a conserved essential gene product from Streptococcus pneumoniae. This 227-residue protein has minimal sequence similarity to proteins of known 3Dstructure. Sequence alignment models and computational protein threading studies suggest that CFE88 is a methyltransferase. Characterization of the conformation and function of CFE88 has been performed by using several techniques. Backbone atom and limited side-chain atom NMR resonance assignments have been obtained. The data indicate that CFE88 has two domains: an N-terminal domain with 163 residues and a C-terminal domain with 64 residues. The C-terminal domain is primarily helical, while the N-terminal domain has a mixed helical/extended (Rossmann) fold. By aligning the experimentally observed elements of secondary structure, an initial unrefined model of CFE88 has been constructed based on the X-ray structure of ErmC′ methyltransferase (Protein Data Bank entry 1QAN). NMR and biophysical studies demonstrate binding of S-adenosyl-L-homocysteine (SAH) to CFE88; these interactions have been localized by NMR to the predicted active site in the N-terminal domain. Mutants that target this predicted active site (H26W, E46R, and E46W) have been constructed and characterized. Overall, our results both indicate that CFE88 is a methyltransferase and further suggest that the methyltransferase activity is essential for bacterial survival. [ABSTRACT FROM AUTHOR]

The interaction of bovine microsomal ferricytochrome b5 with yeast iso-1-ferri and ferrocytochrome c has been investigated using heteronuclear NMR techniques. Chemical-shift perturbations for 1H and 15N nuclei of both cytochromes, arising from the interactions with the unlabeled partner proteins, were used for mapping the interacting surfaces on both proteins. The similarity of the binding shifts observed for oxidized and reduced cytochrome c indicates that the complex formation is not influenced by the oxidation state of the cytochrome c. Protein-protein docking simulations have been performed for the binary cytochrome b5-cytochrome c and ternary (cytochrome b5)-(cytochrome c)2 complexes using a novel HADDOCK approach. The docking procedure, which makes use of the experimental data to drive the docking, identified a range of orientations assumed by the proteins in the complex. It is demonstrated that cytochrome c uses a confined surface patch for interaction with a much more extensive surface area of cytochrome b5. Taken together, the experimental data suggest the presence of a dynamic ensemble of conformations assumed by the proteins in the complex. [ABSTRACT FROM AUTHOR]

Knowledge about the functional impact of the topological organization of DNA sequences within interphase chromosome territories is still sparse. Of the few analyzed single copy genomic DNA sequences, the majority had been found to localize preferentially at the chromosome periphery or to loop out from chromosome territories. By means of dual-color fluorescence in situ hybridization (FISH), immunolabeling, confocal microscopy, and three-dimensional (3D) image analysis, we analyzed the intraterritorial and nuclear localization of 10 genomic fragments of different sequence classes in four different human cell types. The localization of three muscle-specific genes FLNA, NEB, and TTN, the oncogene BCL2, the tumor suppressor gene MADH4, and five putatively nontranscribed genomic sequences was predominantly in the periphery of the respective chromosome territories, independent from transcriptional status and from GC content. In interphase nuclei, the noncoding sequences were only rarely found associated with heterochromatic sites marked by the satellite III DNA D1Z1 or clusters of mammalian heterochromatin proteins (HP1α, HP1β, HP1γ). However, the nontranscribed sequences were found predominantly at the nuclear periphery or at the nucleoli, whereas genes tended to localize on chromosome surfaces exposed to the nuclear interior. [Copyright &y& Elsevier]

The zebrafish is a popular vertebrate model organism with similar organ systems and gene sequences to humans. Zebrafish embryos are optically transparent enabling organ visualisation, which can be complemented with gene expression analysis at the transcript and protein levels. Furthermore, zebrafish can be treated with small molecules and drugs in a microtitre plate format for high-throughput analysis and for the identification and validation of drugs. High-throughput methodologies for use in zebrafish include phenotype-based visualisation, transcript studies using low-density DNA microarrays and proteomic analysis. These technologies offer significant whole-organism biological value in the drug discovery and drug development pipeline. [Copyright &y& Elsevier]

The classical Zn finger contains a phenylalanine at the crux of its three architectural elements: a β-hairpin, an α-helix, and a Zn2+-binding site. Surprisingly, phenylalanine is not required for high-affinity Zn2+ binding, but instead contributes to the specification of a precise DNA-binding surface. Substitution of phenylalanine by leucine leads to a floppy but native-like structure whose Zn affinity is maintained by marked entropy-enthalpy compensation (Δ Δ H −8.3 kcal/mol and − TΔ Δ S 7.7 kcal/mol). Phenylalanine and leucine differ in shape, size, and aromaticity. To distinguish which features correlate with dynamic stability, we have investigated a nonstandard finger containing cyclohexanylalanine at this site. The structure of the nonstandard finger is similar to that of the native domain. The cyclohexanyl ring assumes a chair conformation, and conformational fluctuations characteristic of the leucine variant are damped. Although the nonstandard finger exhibits a lower affinity for Zn2+ than does the native domain (Δ Δ G −1.2 kcal/mol), leucine-associated perturbations in enthalpy and entropy are almost completely attenuated (Δ Δ H −0.7 kcal/mol and − TΔ Δ S −0.5 kcal/mol). Strikingly, global changes in entropy (as inferred from calorimetry) are in each case opposite in sign from changes in configurational entropy (as inferred from NMR). This seeming paradox suggests that enthalpy-entropy compensation is dominated by solvent reorganization rather than nominal molecular properties. Together, these results demonstrate that dynamic and thermodynamic perturbations correlate with formation or repair of a solvated packing defect rather than type of physical interaction (aromatic or aliphatic) within the core. [ABSTRACT FROM AUTHOR]

This study was designed to define the current role of coronary magnetic resonance angiography (CMRA) for the diagnosis of coronary artery disease (CAD).Coronary magnetic resonance angiography has been proposed as a promising noninvasive method for diagnosis of CAD, but individual studies evaluating its clinical value have been of limited sample size.We identified all studies (MEDLINE and EMBASE) that evaluated CAD by both CMRA and conventional angiography in ≥10 subjects during the period 1991 to January 2004. We recorded true and false positive and true and false negative CMRA assessments for detection of CAD using X-ray angiography as the reference standard. Analysis was done at segment, vessel, and subject level.We analyzed 39 studies (41 separate comparisons). Across 25 studies (27 comparisons) with data on 4,620 segments (993 subjects), sensitivity and specificity for detection of CAD were 73% and 86%, respectively. Vessel-level analyses (16 studies, 2,041 vessels) showed sensitivity 75% and specificity 85%. Subject-level analyses (13 studies, 607 subjects) showed sensitivity 88% and specificity 56%. At the segment level, sensitivity was 69% to 79% for all but the left circumflex (61%) coronary artery; specificity was 82% to 91%. There was considerable between-study heterogeneity, but weighted summary receiver-operating characteristic curves agreed with these estimates. There were no major differences between subgroups based on technical or population characteristics, year of publication, reported blinding, or sample size.In evaluable segments of the native coronary arteries, CMRA has moderately high sensitivity for detecting significant proximal stenoses and may have value for exclusion of significant multivessel CAD in selected subjects considered for diagnostic catheterization. [Copyright &y& Elsevier]

This study was designed to predict the response and prognosis after cardiac resynchronization therapy (CRT) in patients with end-stage heart failure (HF).Cardiac resynchronization therapy improves HF symptoms, exercise capacity, and left ventricular (LV) function. Because not all patients respond, preimplantation identification of responders is needed. In the present study, response to CRT was predicted by the presence of LV dyssynchrony assessed by tissue Doppler imaging. Moreover, the prognostic value of LV dyssynchrony in patients undergoing CRT was assessed.Eighty-five patients with end-stage HF, QRS duration >120 ms, and left bundle-branch block were evaluated by tissue Doppler imaging before CRT. At baseline and six months follow-up, New York Heart Association functional class, quality of life and 6-min walking distance, LV volumes, and LV ejection fraction were determined. Events (death, hospitalization for decompensated HF) were obtained during one-year follow-up.Responders (74%) and nonresponders (26%) had comparable baseline characteristics, except for a larger dyssynchrony in responders (87 ± 49 ms vs. 35 ± 20 ms, p < 0.01). Receiver-operator characteristic curve analysis demonstrated that an optimal cutoff value of 65 ms for LV dyssynchrony yielded a sensitivity and specificity of 80% to predict clinical improvement and of 92% to predict LV reverse remodeling. Patients with dyssynchrony ≥65 ms had an excellent prognosis (6% event rate) after CRT as compared with a 50% event rate in patients with dyssynchrony <65 ms (p < 0.001).Patients with LV dyssynchrony ≥65 ms respond to CRT and have an excellent prognosis after CRT. [Copyright &y& Elsevier]

The paper is focused on recent accomplishments in basic and applied research on pulse detonation engines (PDE) and various PDE design concepts. Current understanding of gas and sprary detonations, thermodynamic grounds for detonation-based propulsion, principles of practical implementation of the detonation-based thermodynamic cycle, and various operational constraints of PDEs are discussed. [Copyright &y& Elsevier]

Syndecan-1 was overexpressed in T47D, MCF-7, or Hs578t human breast carcinoma cell lines, mimicking overexpression observed in carcinomas in vivo. Overexpression of syndecan-1, or its ectodomain alone fused to a glycosylphosphatidylinositol anchor (GPI-mS1ED), promotes cell rounding in 2D culture. Deletions within the syndecan-1 ectodomain (S1ED) implicate an active site within the core protein between the glycosaminoglycan attachment region and the transmembrane domain. Polyclonal antibodies directed against the ectodomain, or treatment with the tyrosine kinase inhibitor genistein, block activity and revert GPI-mS1ED overexpressing cells to a normal morphology. Extracellular matrix (ECM)-dependent signaling appears to be targeted, as GPI-mS1ED cells attach and spread similarly to control cells in response to E-cadherin engagement, but fail to spread on integrin-dependent ligands. However, integrin-dependent cell attachment, and integrin activation and subsequent FAK phosphorylation are unaffected, suggesting that the syndecan regulates the integration of signaling following matrix adhesion. In 3D culture, where syndecan-1 may have a more critical role in cell behavior, the disrupted signaling leads to poorly cohesive, invasive colonies. Thus, altered matrix-dependent signaling due to increased levels of cell surface syndecan-1 may lead to epithelial cell invasion during early stages of tumorigenesis. [Copyright &y& Elsevier]

The repair of early tooth enamel lesions has been recently demonstrated by tryptic phosphopeptides derived from milk caseins that associate with amorphous calcium phosphate (ACP) forming stable complexes. These casein phosphopeptides (CPP), containing the cluster sequence–Ser(P)–Ser(P)–Ser(P)–Glu–Glu–, form calcium phosphate delivery vehicles that retard enamel demineralization and promote remineralization. Recently, we have shown that these peptides also stabilize calcium fluoride phosphate as soluble complexes. These complexes designated CPP–ACFP, have the potential to provide superior clinical efficacy in preventing dental caries and treating and repairing early stages of disease. In an approach to determine the ultrastructure of the casein phosphopeptide–amorphous calcium fluoride phosphate complexes, we have studied the structure of the predominant peptide αS1-CN(59–79) bound to ACFP using nuclear magnetic resonance (NMR) spectroscopy and X-ray diffraction. The αS1-CN(59–79) peptide stabilized calcium fluoride phosphate as amorphous nanocomplexes with a hydrodynamic radius of 2.12±0.26 nm. The nanocomplexes exhibited stoichiometry of one peptide to 15 calcium, nine phosphate and three fluoride ions. Sequence-specific resonance assignments were determined for the peptide αS1-CN(59–79) complexed to the ACFP. The secondary structure of the peptide αS1-CN(59–79) was characterized by sequential (i, i+1), medium-range (i, i+2) nOes and Hα chemical shifts. The spectral data were compared with that of the peptide αS1-CN(59–79) bound to calcium ions, revealing that the structurally significant secondary NH and α-chemical shifts were similar. [Copyright &y& Elsevier]

The HIV-1 Gag polyprotein contains a segment called p2, located between the capsid (CA) and nucleocapsid (NC) domains, that is essential for ordered virus assembly and infectivity. We subcloned, overexpressed, and purified a 156-residue polypeptide that contains the C-terminal capsid subdomain (CACTD) through the NC domain of Gag (CACTD-p2-NC, Gag residues 276-431) for NMR relaxation and sedimentation equilibrium (SE) studies. The CACTD and NC domains are folded as expected, but residues of the p2 segment, and the adjoining thirteen C-terminal residues of CACTD and thirteen N-terminal residues of NC, are flexible. Backbone NMR chemical shifts of these 40 residues deviate slightly from random coil values and indicate a small propensity toward an α-helical conformation. The presence of a transient coil-to-helix equilibrium may explain the unusual and necessarily slow proteolysis rate of the CA-p2 junction. CACTD-p2-NC forms dimers and self-associates with an equilibrium constant ( Kd = 1.78 ± 0.5 μM) similar to that observed for the intact capsid protein ( Kd = 2.94 ± 0.8 μM), suggesting that Gag self-association is not significantly influence by the P2 domain. [ABSTRACT FROM AUTHOR]

A comparative study on the solution structures of bovine microsomal cytochrome b5 (T b5) and the mutant V45H has been achieved by 1D and 2D 1H-NMR spectroscopy to clarify the differences in the solution conformations between these two proteins. The results reveal that the global folding of the V45H mutant in solution is unchanged, but the subtle changes exist in the orientation of the axial ligand His39, and heme vinyl groups. The side chain of His45 in V45H mutant extends to the outer edge of the heme pocket leaving a cavity at the site originally occupied by the inner methyl group of Val45 residue. In addition, the imidazole ring of axial ligand His39 rotates counterclockwise by ∼3° around the His-Fe-His axis, and the 4-heme vinyl group turns to the space vacated by the removed side chain due to the mutation. Furthermore, the helix III of the heme pocket undergoes outward displacement, while the linkage between helix II and III is shifted leftward. These observations are not only consistent with the pattern of the pseudocontact shifts of the heme protons, but also well account for the lower stability of V45H mutant against heat and urea. [ABSTRACT FROM AUTHOR]

Hepatitis B virus core antigen (HBcAg) gene (C gene) was expressed in Saccharomyces cerevisiae and the products (rHBcAg or core particles) were purified from a crude lysate of the yeast by three steps: Sephrose CL-4B chromatography, Sucrose step-gradient ultracentrifugation and CsCl-isopycnic ultracentrifugation. It has been observed that HBcAg was synthesized in yeast cells as a particle consisting of polypeptides with a molecular weight of 21.5 kDa (p21.5). Results of ELISA test and density analysis of CsCl-isopycnic ultracentrifugation indicated that the purified products (rHBcAg particles) with HBcAg antigenicity mainly located at the densities of 1.27 and 1.40 g ml−1, respectively. Observation and analysis of the purified rHBcAg products by TEM indicated that rHBcAg peptides could mainly self-assemble into two size classes of core particles. The larger particles were ∼30.1 nm and the smaller were ∼21.5 nm in mean diameter. Further observation and analysis of the same rHBcAg (core) particles by AFM also indicated that rHBcAg (core) particles were similar to the native HBcAg (core) particles from infected human hepatocytes and mainly composed of two size classes of partides core. The larger particles were ∼31.3 nm and the smaller were ∼22.5 nm in mean diameter which was similar to the results obtained by TEM. All results from both TEM and AFM suggested that core particles (capsids) produced in S. cerevisiae possessed dimorphism. [Copyright &y& Elsevier]

Several recombinant proteins in inclusion bodies expressed in Escherichia coli have been measured by Fourier transform infrared and solid-state nuclear magnetic resonance spectra to provide the secondary structural characteristics of the proteins from hyperthermophilic archaeon Pyrococcus horikoshii OT3 (hyperthermophilic proteins) in inclusion bodies. The β-strand-rich single chain Fv fragment (scFv) and α-helix-rich interleukin (IL)-4 lost part of the native-like secondary structure in inclusion bodies, while the inclusion bodies composed of the hyperthermophilic proteins of which the native form is α-helix rich, are predominated by α-helix structure. Further, the secondary structure of the recombinant proteins solubilized from inclusion bodies by detergent or denaturant was observed by circular dichroism (CD) spectra. The solubilization induced the denaturation of the secondary structure for scFv and IL-4, whereas the solubilized hyperthermophilic proteins have retained the α-helix structure with the CD properties resembling those of their native forms. This indicates that the hyperthermophilic proteins form native-like secondary structure in inclusion bodies. Refolding of several hyperthermophilic proteins from in vivo aggregated form without complete denaturation could be accomplished by solubilization with lower concentration (e.g. 2 M) of guanidine hydrochloride and removal of the denaturant via stepwise dialysis. This supports the existence of proteins with native-like structure in inclusion bodies and suggests that non-native association between the secondary structure elements leads to in vivo aggregation. We propose a refolding procedure on the basis of the structural properties of the aggregated archaeon proteins. [Copyright &y& Elsevier]

Background: The hand-carried cardiac ultrasound (HCU) device is a recently introduced imaging device, which may be potentially useful in the primary care setting.Aim: To test the screening potential of a HCU for the detection of left ventricular (LV) dysfunction by evaluating LV ejection fraction (LVEF) and inferior vena cava (IVC) collapse. Standard echocardiographic system (SE) and plasma brain natriuretic peptide (BNP) measurements were used as a reference.Methods: Eighty-eight consecutive patients (56 male, aged 59+/-12 years) with suspected LV dysfunction were enrolled in the study. The HCU-LVEF was visually estimated and the SE-LVEF was derived by the Simpson's biplane method. A LVEF <40% represented LV dysfunction. An IVC collapse of <50% and BNP levels > or =15 pmol/l were considered abnormal. The correlation of HCU-LVEF, HCU-IVC and BNP to the SE-LVEF and SE-IVC was analysed independently using 2x2 tables.Results: Six patients were excluded because of poor echo images. 19/82 patients had LV dysfunction. The HCU and BNP could identify 17 and 18 out of these 19 patients, respectively. The agreement for LVEF and IVC collapse between SE and HCU was 96% for both parameters. The sensitivity of IVC collapse, HCU-LVEF and BNP in identifying patients with LV dysfunction was 26, 89 and 94%, respectively.Conclusion: A HCU device can reliably be used as a screening tool for LV dysfunction. [ABSTRACT FROM AUTHOR]

Proteome analysis in the pI 4–7 range of aqueous extracts from whole barley seeds results in complex 2D-gel spot patterns that represent proteins from all seed tissues. Proteins were extracted from dissected aleurone layer, embryo and endosperm for separate analysis of these components and comparison with single seed extracts. The analysis showed that while the starchy endosperm comprises approximately 85% of the mature seed dry weight, it contributes less than 50% of the soluble protein to seed extracts. Although the aleurone layer and embryo are minor components of the seed in terms of dry weight, their proteins contribute significantly to the 2D-gel pattern. Distinct but overlapping patterns were observed for the dissected tissues. While whole seed gels contained about 850 spots, endosperm, aleurone layer and embryo gels had about 575, 850 and 1000 spots, respectively, representing a total increase of at least 15%. Protein patterns were also reduced in complexity and this enrichment of subsets of proteins facilitated identification by mass spectrometry of proteins of interest in mature seed tissues and developing endosperm. These techniques can therefore be used with advantage to describe the proteomes of dissected seed tissues. [Copyright &y& Elsevier]

The N-terminal large fragments of staphylococcal nuclease (SNase), SNase110 (1–110 residues), SNase121 (1–121 residues), and SNase135 (1–135 residues), and the fragment mutants G88W110, G88W121, V66W110 and V66W121 were studied by heteronuclear multidimensional NMR spectroscopy. Ensembles of co-existent native-like partially folded and unfolded states were observed for fragments. The persistent native-like tertiary interaction drives fragments to be in partially folded states, which reveal native-like β-barrel conformations. G88W and V66W mutations modulate the extent of inherent native-like tertiary interaction in fragment molecules, and in consequence, fragment mutants fold into native-like β-subdomain conformations. In cooperation with the inherent tertiary interaction, 2 M TMAO (trimethylamine N-oxide) can promote the folding reaction of fragments through the changes of unfolding free energy, and a native-like β-subdomain conformation is observed when the chain length contains 135 residues. Heterogeneous partially folded conformations of 1–121 and 1–135 fragments due to cis and trans X-prolyl bond of Lys116–Pro117 make a non-unique folding pathway of fragments. The folding reaction of fragments can be characterized as a hierarchical process. [Copyright &y& Elsevier]

The fusion of a protein of interest to a large-affinity tag, such as the maltose-binding protein (MBP), thioredoxin (TRX), or glutathione- S-transferase (GST), can be advantageous in terms of increased expression, enhanced solubility, protection from proteolysis, improved folding, and protein purification via affinity chromatography. Unfortunately, crystal growth is hindered by the conformational heterogeneity induced by the fusion tag, requiring that the tag is removed by a potentially problematic cleavage step. The first three crystal structures of fusion proteins with large-affinity tags have been reported recently. All three structures used a novel strategy to rigidly fuse the protein of interest to MBP via a short three- to five-amino acid spacer. This strategy has the potential to aid structure determination of proteins that present particular experimental challenges and are not conducive to more conventional crystallization strategies (e.g., membrane proteins). Structural genomics initiatives may also benefit from this approach as a way to crystallize problematic proteins of significant interest. [ABSTRACT FROM AUTHOR]

p38, which has been suggested to be a scaffold protein for the assembly of a macromolecular tRNA synthetase complex, contains a leucine zipper-like motif. To understand the importance of the leucine zipper-like motif of p38 (p38LZ) in macromolecular assembly, the p38LZ solution structure was investigated by circular dichroism and nuclear magnetic resonance spectroscopy. The solution structure of p38LZ showed an amphipathic α-helical structure and characteristics similar to a coiled-coil motif. The protein–protein interaction mediated by p38LZ was examined by an in vitro binding assay. The p43 protein, another non-synthetase component of the complex, could bind to p38LZ via its N-terminal domain, which is also predicted to have a potential coiled-coil motif. Thus, we propose that the p38–p43 complex would be formed by coiled-coil interactions, and the formation of the binary complex would facilitate the macromolecular assembly of aminoacyl-tRNA synthetases. [Copyright &y& Elsevier]

We report the effects of peptide binding on the 15N relaxation rates and chemical shifts of the C-SH3 of Sem-5. 15N spin-lattice relaxation time (T1), spin-spin relaxation time (T2), and {1H}-15N NOE were obtained from heteronuclear 2D NMR experiments. These parameters were then analyzed using the Lipari-Szabo model free formalism to obtain parameters that describe the internal motions of the protein. High-order parameters (S2 > 0.8) are found in elements of regular secondary structure, whereas some residues in the loop regions show relatively low-order parameters, notably the RT loop. Peptide binding is characterized by a significant decrease in the 15N relaxation in the RT loop. Concomitant with the change in dynamics is a cooperative change in chemical shifts. The agreement between the binding constants calculated from chemical shift differences and that obtained from ITC indicates that the binding of Sem-5 C-SH3 to its putative peptide ligand is coupled to a cooperative conformational change in which a portion of the binding site undergoes a significant reduction in conformational heterogeneity. [ABSTRACT FROM AUTHOR]

Protein phosphorylation is a very important posttranslational modification the role of which is practically unexplored in mitochondria. Using two-dimensional gel electrophoresis followed by mass spectrometry, 14 new phosphoproteins are identified in potato tuber mitochondria, all household proteins also present in mammalian and fungal mitochondria. Seven of the new phosphoproteins are involved in the tricarboxylic acid cycle or associated reactions, four are subunits of respiratory complexes and involved in electron transport, ATP synthesis and protein processing, two are heat shock proteins and one is involved in defence against oxidative stress. These findings open up entirely new possibilities for the regulation and signal integration of mitochondrial processes. [Copyright &y& Elsevier]

Polyproline II (PPII) is reported to be a dominant conformation in the unfolded state of peptides, even when no prolines are present in the sequence. Here we use isothermal titration calorimetry (ITC) to investigate the PPII bias in the unfolded state by studying the binding of the SH3 domain of SEM-5 to variants of its putative PPII peptide ligand, Sos. The experimental system is unique in that it provides direct access to the conformational entropy change of the substituted amino acids. Results indicate that the denatured ensemble can be characterized by at least two thermodynamically distinct states, the PPII conformation and an unfolded state conforming to the previously held idea of the denatured state as a random collection of conformations determined largely by hard-sphere collision. The probability of the PPII conformation in the denatured states for Ala and Gly were found to be significant, ∼30% and ∼10%, respectively, resulting in a dramatic reduction in the conformational entropy of folding. [ABSTRACT FROM AUTHOR]

The solution NMR structure is reported for Ca2+-loaded S100B bound to a 12-residue peptide, TRTK-12, from the actin capping protein CapZ (α1 or α2 subunit, residues 265–276: TRTKIDWNKILS). This peptide was discovered by Dimlich and co-workers by screening a bacteriophage random peptide display library, and it matches exactly the consensus S100B binding sequence ((K/R)(L/I)XWXXIL). As with other S100B target proteins, a calcium-dependent conformational change in S100B is required for TRTK-12 binding. The TRTK-12 peptide is an amphipathic helix (residues W7 to S12) in the S100B–TRTK complex, and helix 4 of S100B is extended by three or four residues upon peptide binding. However, helical TRTK-12 in the S100B–peptide complex is uniquely oriented when compared to the three-dimensional structures of other S100–peptide complexes. The three-dimensional structure of the S100B–TRTK peptide complex illustrates that residues in the S100B binding consensus sequence (K4, I5, W7, I10, L11) are all involved in the S100B–peptide interface, which can explain its orientation in the S100B binding pocket and its relatively high binding affinity. A comparison of the S100B–TRTK peptide structure to the structures of apo- and Ca2+-bound S100B illustrates that the binding site of TRTK-12 is buried in apo-S100B, but is exposed in Ca2+-bound S100B as necessary to bind the TRTK-12 peptide. [Copyright &y& Elsevier]

The dihydropyridine receptors (DHPR) are L-type voltage-gated calcium channels that regulate the flux of calcium ions across the cell membrane. Here we present the three-dimensional (3D) structure at ∼27 A˚ resolution of purified skeletal muscle DHPR, as determined by electron microscopy and single particle analysis. Here both biochemical and 3D structural data indicate that DHPR is dimeric. DHPR dimers are composed of two arch-shaped monomers ∼210 A˚ across and ∼75 A˚ thick, that interact very tightly at each end of the arch. The roughly toroidal structure of the two monomers encloses a cylindrical space of ∼80 A˚ diameter, which is then closed on each side by two dome-shaped protein densities reaching over from each monomer arch. The dome-shaped domains have a length of ∼80–90 A˚ and a maximum height of ∼45 A˚. Small orifices punctuate their exterior surface. The 3D structure disclosed here may have important implications for the understanding of DHPR Ca2+ channel function. We also propose a model for its in vivo interactions with the calcium release channel at the junctional sarcoplasmic recticulum. [Copyright &y& Elsevier]

To monitor the fast compaction process during protein folding, we have used a stopped-flow small-angle X-ray scattering technique combined with a two-dimensional charge-coupled device-based X-ray detector that makes it possible to improve the signal-to-noise ratio of data dramatically, and measured the kinetic refolding reaction of α-lactalbumin. The results clearly show that the radius of gyration and the overall shape of the kinetic folding intermediate of α-lactalbumin are the same as those of the molten globule state observed at equilibrium. Thus, the identity between the kinetic folding intermediate and the equilibrium molten globule state is firmly established. The present results also suggest that the folding intermediate is more hydrated than the native state and that the hydrated water molecules are dehydrated when specific side-chain packing is formed during the change from the molten globule to the native state. [Copyright &y& Elsevier]

The modification of RNA nucleotide bases, a fundamental process in all cells, alters the chemical and physical properties of RNA molecules and broadly impacts the physiological properties of cells. tRNA molecules are by far the most diverse-modified RNA species within cells, containing as a group >80% of the known 96 chemically unique nucleic acid modifications. The greatest varieties of modifications are located on residue 37 and play a role in ensuring fidelity and efficiency of protein synthesis. The enzyme dimethylallyl (Δ2-isopentenyl) diphosphate:tRNA transferase catalyzes the addition of a dimethylallyl group to the exocyclic amine nitrogen (N6) of A37 in several tRNA species. Using a 17 residue oligoribonucleotide corresponding to the anticodon arm of Escherichia coli tRNAPhe, we have investigated the structural and dynamic changes introduced by the dimethylallyl group. The unmodified RNA molecule adopts stem-loop conformation composed of seven base-pairs and a compact three nucleotide loop. This conformation is distinctly different from the U-turn motif that characterizes the anticodon arm in the X-ray crystal structure of the fully modified yeast tRNAPhe. The adoption of the tri-nucleotide loop by the purine-rich unmodified tRNAPhe anticodon arm suggests that other anticodon sequences, especially those containing pyrimidine bases, also may favor a tri-loop conformation. Introduction of the dimethylallyl modification increases the mobility of nucleotides of the loop region but does not dramatically alter the RNA conformation. The dimethylallyl modification may enhance ribosome binding through multiple mechanisms including destabilization of the closed anticodon loop and stabilization of the codon–anticodon helix. [Copyright &y& Elsevier]

A novel antibacterial peptide, moricin, isolated from the silkworm Bombyx mori, consists of 42 amino acids. It is highly basic and the amino acid sequence has no significant similarity to those of other antibacterial peptides. The 20 structures of moricin in methanol have been determined from two-dimensional 1H-nuclear magnetic resonance spectroscopic data. The solution structure reveals an unique structure comprising of a long α-helix containing eight turns along nearly the full length of the peptide except for four N-terminal residues and six C-terminal residues. The electrostatic surface map shows that the N-terminal segment of the α-helix, residues 5–22, is an amphipathic α-helix with a clear separation of hydrophobic and hydrophilic faces, and that the C-terminal segment of the α-helix, residues 23–36, is a hydrophobic α-helix except for the negatively charged surface at the position of Asp30. The results suggest that the amphipathic N-terminal segment of the α-helix is mainly responsible for the increase in permeability of the membrane to kill the bacteria. [Copyright &y& Elsevier]

The stylet secretions produced by plant parasitic root-knot nematodes are thought to be pathogenicity factors involved in the invasion of the root tissue and in the induction and maintenance of feeding cells. A new procedure was established that allowed the direct qualitative analysis of proteins secreted by Meloidogyne incognita infective juveniles. Purified proteins whose isoelectric point (pI) ranged from 5.0 to 7.5 were separated by two-dimensional (2D) electrophoresis and the seven most abundant proteins were identified by micro-sequencing. A calreticulin (CRT) was isolated and transcription of its gene in infective juveniles and adults was demonstrated. Moreover, evidence for expression of the CRT in the subventral oesophageal glands of infective juveniles was obtained. The potential roles of this secreted protein in pathogenesis and the advantages of developing this strategy to obtain new insights into plant-nematode interactions are discussed. [Copyright &y& Elsevier]

Experimental studies employing surface science methods indicate that kinetic oscillations, chaos, and pattern formation in heterogeneous catalytic reactions often result from the interplay of rapid chemical reaction steps and relatively slow complementary processes such as oxide formation or adsorbate-induced surface restructuring. In general, the latter processes should be analysed in terms of theory of phase transitions. Therefore, the conventional mean-field reaction–diffusion equations widely used to describe oscillations in homogeneous reactions are strictly speaking not applicable. Under such circumstances, application of the Monte Carlo method becomes almost inevitable. In this review, we discuss the advantages and limitations of employing this technique and show what can be achieved in this way. Attention is focused on Monte Carlo simulations of CO oxidation on (1 0 0) and (1 1 0) single-crystal Pt and polycrystal Pt, Pd and Ir surfaces and of NO reduction by CO and H2 on Pt(1 0 0). CO oxidation on supported nanometre-sized catalyst particles and NO reduction on composite catalysts are also discussed. The results show that with current computer facilities the MC technique has become an effective tool for analysing temporal oscillations and pattern formation on the nanometre scale in catalytic reactions occurring on both single crystals and supported particles. [Copyright &y& Elsevier]

Surface roughness evaluation is very important for many fundamental problems such as friction, contact deformation, heat and electric current conduction, tightness of contact joints and positional accuracy. For this reason surface roughness has been the subject of experimental and theoretical investigations for many decades. The real surface geometry is so complicated that a finite number of parameters cannot provide a full description. If the number of parameters used is increased, a more accurate description can be obtained. This is one of the reasons for introducing new parameters for surface evaluation. Surface roughness parameters are normally categorised into three groups according to its functionality. These groups are defined as amplitude parameters, spacing parameters, and hybrid parameters. This paper illustrates the definitions and the mathematical formulae for about 59 of the roughness parameters. This collection of surface roughness parameter was used in a new software computer vision package called SurfVision developed by the authors. In the package, these definitions were extended to calculate the 3D surface topography of different specimens. [Copyright &y& Elsevier]