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Presents a list of articles for publication in future issues of the "European Journal of Biochemistry". Conformation of physalaemin; Association of cross-linked proteins with a specific mRNA in the cytoplasm of HeLa cells; Transport of proteins into chloroplasts.

The article presents information on various research papers which will be published in the forthcoming issue of the "European Journal of Biochemistry". Some of the papers discusses are "Enzymatic Synthesis of Neolactotetraosylceramide by the N-Acctyllactosamine Synthase of Human Serum". "Rate of Transplantation and Kinetics of Processing of Newly Synthesized Molecules of Two Major Outer-Membrane Proteins, the OmpA and OmpF Proteins of Escherichia Coli," by the researchers I. Crowlesmith and K. Gamon.

This article presents a list of some of the forthcoming papers in biochemistry to be published in this journal. Some of the papers listed are "The Organization of the Chloroplast DNA in wheat and maize in the region containing the LS Gene," by B. Koller, H. Delius and T.A. Dyer, "Effect of Carbamination on the Buffering Power of Purified Human Hamoglobins A Solutions At Two Temperatures," by M. Castaing, E. Bursaux and C. Poyart, "The Complete Nucleotide of the Chicken Ovotransferrin mRNA," by J.M. Jeltsch and P. Chambon, "The Primary Structure of Hen Ovotransferrin," by J. Williams, T.C. Elleman, I.B. Kington, A.G. Wilkins and K.A. Kuhn.

The article reports on the application of biological molecules in printing technology. It indicates that usage of printing biological molecules can offer cheap and disposable sensors when conducting food safety testing. It also mentions that paper industries in Canada and Finland show interest in bioactive surfaces.

As biological macromolecules, proteins are involved in important cellular functions ranging from DNA replication and biosynthesis to metabolic signalling and environmental sensing. Protein sequencing can help understand the relationship between protein function and structure, and provide key information for disease diagnosis and new drug design. Nanopore sensors are a novel technology to achieve the goal of label‐free and high‐throughput protein sequencing. In recent years, nanopore‐based biosensors have been widely used in the detection and analysis of biomolecules such as DNA, RNA, and proteins. At the same time, computer simulations can describe the transport of proteins through nanopores at the atomic level. This paper reviews the applications of nanopore sensors in protein sequencing over the past decade and the solutions to key problems from a computer simulation perspective, with the aim of pointing the way to the future of nanopore protein sequencing. [ABSTRACT FROM AUTHOR]

Acquisition of X‐ray crystallographic data is always accompanied by structural degradation owing to the absorption of energy. The application of high‐fluency X‐ray sources to large biomolecules has increased the importance of finding ways to curtail the onset of X‐ray‐induced damage. A significant effort has been under way with the aim of identifying strategies for protecting protein structure. A comprehensive model is presented that has the potential to explain, both qualitatively and quantitatively, the structural changes induced in crystalline protein at ∼100 K. The first step is to consider the qualitative question: what are the radiation‐induced intermediates and expected end products? The aim of this paper is to assist in optimizing these strategies through a fundamental understanding of radiation physics and chemistry, with additional insight provided by theoretical calculations performed on the many schemes presented. [ABSTRACT FROM AUTHOR]

The Adaptive Gain Integrating Pixel Detector (AGIPD) is an X‐ray imager, custom designed for the European X‐ray Free‐Electron Laser (XFEL). It is a fast, low‐noise integrating detector, with an adaptive gain amplifier per pixel. This has an equivalent noise of less than 1 keV when detecting single photons and, when switched into another gain state, a dynamic range of more than 104 photons of 12 keV. In burst mode the system is able to store 352 images while running at up to 6.5 MHz, which is compatible with the 4.5 MHz frame rate at the European XFEL. The AGIPD system was installed and commissioned in August 2017, and successfully used for the first experiments at the Single Particles, Clusters and Biomolecules (SPB) experimental station at the European XFEL since September 2017. This paper describes the principal components and performance parameters of the system. A description of the 1 million pixel AGIPD system in use at the SPB beamline of the European XFEL is given. [ABSTRACT FROM AUTHOR]

1. Sequence analysis of the NADPH domain (residues 158 - 293) and of the interface domain (365 - 478) was based on 12 CNBr fragments, which were isolated using ion-exchange chromatography and paper methods. Fragments with more than 15 residues were digested further with trypsin and chymotrypsin. The isolated peptides were sequenced by automated solid-phase Edman degradation. All sequenced peptides were ordered and overlapped by computerized comparisons with a complete sequence guessed from the electron density map of the protein. In the case of short CNBr fragments, this alignment was confirmed by the sequence analysis of protein fragments resulting from incomplete CNBr cleavage. 2. In the NADPH domain, residue 197, which is involved in an induced-fit mechanism, was identified as a tyrosine. The structure of the NADPH domain is probably homologous with the NAD domain of lipoamide dehydrogenase and with the FAD domain of several proteins, but not with NADPH domains of known chainfold in other proteins. 3. The paper completes the sequence analysis of glutathione reductase so that the enzyme is now known in atomic detail. The numbering scheme of the chemically determined sequence will be used henceforth in crystallographic studies also. As inferred from the sequence data each of the two identical chains contains 478 amino acid residues, the composition being Cys10, Asp21, Asn17, Thr31, Ser31, Glu29, Gln11, Pro24, Gly43, Ala42, Val44, Met15, Ile29, Leu34, Tyr13, Phe14, Lys34. His16, Arg17, and Trp3. From these data an mr of 2 × 51 600 was calculated for the FAD-free apoenzyme and an Mr of 2 × 52400 for the holoenzyme. [ABSTRACT FROM AUTHOR]

After CNBr cleavage of p-hydroxybenzoate hydroxylase from Pseudornonas fluorescens, five peptides and free homoserine were isolated (see preceding paper in this journal). The amino acid sequences of the three smallest peptides, viz. CB3, CB4 and CB5, were determined by automated Edman degradation and analysis of enzymatic subdigests. These peptides form a continuous stretch of 110 residues from the N terminus: [This equation can not be represent in ASCII.TXT]. [ABSTRACT FROM AUTHOR]

Brownian motion of Cowpea mosaic virus (CPMV) in water was measured using small-angle X-ray photon correlation spectroscopy (SA-XPCS) at 19.2 ms time resolution. It was found that the decorrelation time (Q) = 1/DQ2 up to Q = 0.091 nm-1. The hydrodynamic radius RH determined from XPCS using Stokes-Einstein diffusion D = kT/(6RH) is 43% larger than the geometric radius R0 determined from SAXS in the 0.007 M K3PO4 buffer solution, whereas it is 80% larger for CPMV in 0.5 M NaCl and 104% larger in 0.5 M (NH4)2SO4, a possible effect of aggregation as well as slight variation of the structures of the capsid resulting from the salt-protein interactions. [ABSTRACT FROM AUTHOR]

This paper is a further study of ion binding to protein surfaces and builds on the studies of the binding of [Crk(CN)6]3- and [Fe(edta)(H2O)]- previously reported [Williams et al. (1982) FEBS Lett. 15, 293-299; Eley et al. (1982) Eur. J. Biochem. 124, 295-303]. In the present paper the binding of polyaminocarboxylate complexes of gadolinium have been studied. Eight ion-binding sites have been identified on the surface of cytochrome c. These exhibit different binding specificities which, in some cases, are not fully understood. However it is clear that simple outer-sphere interactions are not the sole determining factor for the association of metal ion complexes with proteins. The NMR paramagnetic difference spectrum method has been shown to be good at locating binding sites and revealing qualitative differences in their relative affinities for a range of complex types. However the use of relaxation probes is not a good method for the quantitative determination of binding constants; for this, isostructural shift probes must be sought. [ABSTRACT FROM AUTHOR]

The European X‐ray Free‐Electron Laser (FEL) became the first operational high‐repetition‐rate hard X‐ray FEL with first lasing in May 2017. Biological structure determination has already benefitted from the unique properties and capabilities of X‐ray FELs, predominantly through the development and application of serial crystallography. The possibility of now performing such experiments at data rates more than an order of magnitude greater than previous X‐ray FELs enables not only a higher rate of discovery but also new classes of experiments previously not feasible at lower data rates. One example is time‐resolved experiments requiring a higher number of time steps for interpretation, or structure determination from samples with low hit rates in conventional X‐ray FEL serial crystallography. Following first lasing at the European XFEL, initial commissioning and operation occurred at two scientific instruments, one of which is the Single Particles, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument. This instrument provides a photon energy range, focal spot sizes and diagnostic tools necessary for structure determination of biological specimens. The instrumentation explicitly addresses serial crystallography and the developing single particle imaging method as well as other forward‐scattering and diffraction techniques. This paper describes the major science cases of SPB/SFX and its initial instrumentation – in particular its optical systems, available sample delivery methods, 2D detectors, supporting optical laser systems and key diagnostic components. The present capabilities of the instrument will be reviewed and a brief outlook of its future capabilities is also described. [ABSTRACT FROM AUTHOR]

Two papers in this issue of Molecular Microbiology from Carol Gross and colleagues describe experiments that investigate how two alternative Escherichia coliσ proteins recognize target promoter −10 regions. A combination of genetics, biochemistry and bioinformatics is used to show that determinants in two adjacent domains of the σ proteins contact discrete sequence elements in the −10 regions. [ABSTRACT FROM AUTHOR]

The aim of this paper is to relate morphological properties of single biomacromolecules based on molecular enclosing forms indexed by an appropriate form lattice to the symmetry of the crystal where the molecules are periodically packed. Similar to the way in which the 'molécule intégrante' of Haüy permitted a molecular interpretation of the law of rational indices of crystal growth forms, alternative molecular enclosing forms, indexed by a so‐called packing lattice, allow one to bridge the gap between form and crystal lattices. In this first part, selected tutorial examples illustrate the validity of the approach and the crystallographic compatibility between molecular and crystal structures. In particular, integral molecular lattices are shown to imply the observed axial ratios between crystal lattice parameters, leading sometimes to surprising results, like a cubic crystal lattice with a unit cell having a trigonal molecular filling with hexagonal enclosing form. [ABSTRACT FROM AUTHOR]

Sustainable energy development can no longer be met by fossil fuels alone. Hence, electrochemical water splitting containing oxygen and hydrogen evolution reactions is appealing as a clean energy pathway. As respects the water splitting efficiency which is largely determined by the selectivity, durability, and intrinsic activity of the electrocatalysts, one of the most challenging questions when studying these materials is "which category of electrocatalysts will show the best performance in this issue?" The best electrocatalysts for water splitting still come from noble metals. Although these materials show particularly good efficiency, but due to the scarce resources their massive use is limited. Therefore, the noble metal‐free materials due to their stability, efficiency, abundance and variety of reaction sites were introduced as an interesting candidate for electrochemical water splitting reactions. In this review, based on the important above‐mentioned points, our attention was focused on key categories based on transition metals (TMs), metal organic framework derived (MOF‐derived), carbon‐based hybrids, graphitic carbon nitride (g‐C3N4) hybrids, and bio‐assisted electrocatalysts. These compounds have shown significant activity and stability for broad electrocatalysis applications in water splitting reactions and displaying remarkable potential to replace with noble metal‐based catalysts. This comprehensive review identifies rational strategies for designing and synthesizing high‐performance novel noble metal‐free electrocatalysts for water splitting. [ABSTRACT FROM AUTHOR]

The clinical requirements for wound care are increasing daily, and the global wound dressing market is expanding; however, the research and development of new wound dressings are imminent. Natural biomolecules such as polyphenols, have been widely used in this field of vision. Owing to their unique anti‐oxidative, adhesive, antibacterial and other bioactive functions, researchers have developed a series of wound dressings with excellent performance and applied them to a variety of biomaterials, such as hydrogels, nanofibers, films and scaffolds. They can effectively promote angiogenesis and fibroblast migration and proliferation, scavenge active oxygen free radicals, inhibit excessive inflammatory reactions at wound sites and ultimately accelerate wound healing. The authors summarise the latest progress in polyphenol‐derived biomaterials in skin wound repair to provide inspiration for future wound dressing research. [ABSTRACT FROM AUTHOR]

This is a series of papers (three reviews and five regular papers) focused on Mitochondria from authors contributing to two FEBS courses on Mitochondria held in 2012. These papers focus on: (i) mitochondrial biogenesis (regulation by phosphorylation, import of SOD1 and Mia40, mitophagy and tRNA variants) or (ii) mitochondrial pathology (ischaemia, obesity and Parkinson's disease). [ABSTRACT FROM AUTHOR]

WHAT IS ALREADY KNOWN ABOUT THE SUBJECT • Ciclosporin's nephrotoxicity initially targets the proximal tubule and is, at least in part, driven by increased formation of oxygen radicals. • 1H-nuclear magnetic resonance spectroscopy (NMR)- and mass spectrometry (MS)-based biochemical profiling (metabolomics) allows for the sensitive detection of metabolite pattern changes in urine. • In systematic studies in rats we showed that ciclosporin caused urine metabolite pattern changes typical for proximal tubule damage and that these pattern changes seemed to be more sensitive than established clinical kidney function markers such as serum creatinine concentrations. WHAT THIS PAPER ADDS • This study showed that urine metabolite pattern changes as assessed by 1H-NMR and HPLC-MS are sensitive enough to detect the effect of ciclosporin as early as 4 h after a single oral dose. • In our previous rat studies, changes in urine metabolite pattern in response to ciclosporin translated into healthy humans, indicating the involvement of the same toxicodynamic mechanisms. • The results provide proof of concept for further development of this combination molecular marker strategy into diagnostic tools for the detection and monitoring of drug nephrotoxicity. AIMS The immunosuppressant ciclosporin is an efficient prophylaxis against transplant organ rejection but its clinical use is limited by its nephrotoxicity. Our previous systematic studies in the rat indicated urine metabolite pattern changes to be sensitive indicators of the negative effects of ciclosporin on the kidney. To translate these results, we conducted an open label, placebo-controlled, crossover study assessing the time-dependent toxicodynamic effects of a single oral ciclosporin dose (5 mg kg−1) on the kidney in 13 healthy individuals. METHODS In plasma and urine samples, ciclosporin and 15- F2t-isoprostane concentrations were assessed using HPLC-MS and metabolite profiles using 1H-NMR spectroscopy. RESULTS The maximum ciclosporin concentrations were 1489 ± 425 ng ml−1 (blood) and 2629 ± 1308 ng ml−1 (urine). The increase in urinary 15- F2t-isoprostane observed 4 h after administration of ciclosporin indicated an increase in oxidative stress. 15- F2t-isoprostane concentrations were on average 2.9-fold higher after ciclosporin than after placebo (59.8 ± 31.2 vs. 20.9 ± 19.9 pg mg−1 creatinine, P < 0.02). While there were no conclusive changes in plasma 15- F2t-isoprostane concentrations or metabolite patterns, non-targeted metabolome analysis using principal components analysis and partial least square fit analysis revealed significant changes in urine metabolites typically associated with negative effects on proximal tubule cells. The major metabolites that differed between the 4 h urine samples after ciclosporin and placebo were citrate, hippurate, lactate, TMAO, creatinine and phenylalanine. CONCLUSION Changes in urine metabolite patterns as a molecular marker are sufficiently sensitive for the detection of the negative effects of ciclosporin on the kidney after a single oral dose. [ABSTRACT FROM AUTHOR]

Many biological molecules carry a net surface charge and have the potential to be monitored in drinking water by electrodepositing them on an optical sensing element and measuring their spectroscopic fingerprints in the infrared (IR) spectral region. In this detection scheme, glasses with high conductivity and excellent IR transmitting property are essential. Therefore, it is necessary to develop suitable materials that combine these properties. In this paper, a series of high-conductivity IR transmitting glasses in Ge–As–Te and Ge–As–Te–Cu systems are reported. The conductivity, thermal stability, IR transmitting property, as well as chemical durability are studied. Their suitability for bio-optical detection applications is also evaluated. Some glasses in these two systems have relatively high conductivities (near 10−4 (Ω·cm)−1), and exhibit superior thermal stability, excellent IR transmitting property, as well as good chemical durability. The electro-deposition and spectroscopic tests of protein molecules indicate that these glasses are promising materials for bio-optical detection applications. [ABSTRACT FROM AUTHOR]

This paper summarises how scaffold proteins affects and regulate the JNK signalling pathway. We believe that some of these scaffold proteins, by virtue of their anchoring and catalytic properties contribute to a high degree of specificity of intra cellular signalling pathways that regulate the progression through the cell cycle. [ABSTRACT FROM AUTHOR]

The potent immunomodulatory, anti-inflammatory and procoagulant properties of protein no. 4 secreted from the rat seminal vesicle epithelium (SV-IV) have previously been found to be modulated by a supramolecular monomer–trimer equilibrium. More structural details that integrate experimental data into a predictive framework have recently been reported. Unfortunately, homology modelling and fold-recognition strategies were not successful in creating a theoretical model of the structural organization of SV-IV. It was inferred that the global structure of SV-IV is not similar to that of any protein of known three-dimensional structure. Reversing the classical approach to the sequence–structure–function paradigm, in this paper we report novel information obtained by comparing the physicochemical parameters of SV-IV with two datasets composed of intrinsically unfolded and ideally globular proteins. In addition, we analyse the SV-IV sequence by several publicly available disorder-oriented predictors. Overall, disorder predictions and a re-examination of existing experimental data strongly suggest that SV-IV needs large plasticity to efficiently interact with the different targets that characterize its multifaceted biological function, and should therefore be better classified as an intrinsically disordered protein. [ABSTRACT FROM AUTHOR]

The ability ofEntamoeba histolyticaTATA binding protein (EhTBP) to interact with different TATA boxes in gene promoters may be one of the key factors to perform an efficient transcription in this human parasite. In this paper we used several TATA variants to study thein vitroEhTBP DNA-binding activity and to determine the TATA-EhTBP dissociation constants. The presence of EhTBP in complexes formed by nuclear extracts (NE) and the TATTTAAA oligonucleotide, which corresponds to the canonical TATA box forE. histolytica, was demonstrated by gel-shift assays. In these experiments a single NE-TATTTAAA oligonucleotide complex was detected. Complex was retarded by anti-EhTBP Igs in supershift experiments and antibodies also recognized the cross-linked complex in Western blot assays. Recombinant EhTBP formed specific complexes with TATA variants found inE. histolyticagene promoters and other TATA variants generated by mutation of TATTTAAA sequence. The dissociation constants of recombinant EhTBP for TATA variants ranged between 1.04 (±0.39) × 10−11 and 1.60 (±0.37) × 10−10 m. TATTTAAA and TAT_ _AAA motifs presented the lowestKD values. Intriguingly, the recombinant EhTBP affinity for TATA variants is stronger than other TBPs reported. In addition, EhTBP is more promiscuous than human and yeast TBPs, probably due to modifications in amino acids involved in TBP-DNA binding. [ABSTRACT FROM AUTHOR]

This paper presents information about the complexity of biological networks. Complex systems are often networked and biology is no exception. The follow-up experiments to the genome sequencing projects, such as those using microarrays or the yeast two-hybrid system, show that molecules in living organisms are also highly connected. This interconnectivity helps to explain how such great complexity can be achieved by acomparatively small set of molecules either in a single organism or in nature as a whole.

In this paper, we studied the fate of endocytosed glycosyiphosphatidyl inositol anchored proteins (GPI-APs) in mammalian cells, using aerolysin, a bacterial toxin that binds to the GPI anchor, as a probe. We find that GPI-APs are transported down the endocytic pathway to reducing late endosomes in BHK cells, using biochemical, morphological and functional approaches. We also find that this transport correlates with the association to raft-like membranes and thus that lipid rafts are present in late endosomes (in addition to the Golgi and the plasma membrane). In marked contrast, endocytosed GPI-APs reach the recycling endosome in CHO cells and this transport correlates with a decreased raft association. GPI-APs are, however, diverted from the recycling endosome and routed to late endosomes in CHO cells, when their raft association is increased by clustering seven or less GPI-APs with an aerolysin mutant. We conclude that the different endocytic routes followed by GPI-APs in different cell types depend on the residence time of GPI-APs in lipid rafts, and hence that raft partitioning regulates GPI-APs sorting in the endocytic pathway. [ABSTRACT FROM AUTHOR]

SUMMARY: Adaptation to different soil conditions is a well‐regulated process vital for plant life. AtHB23 is a homeodomain‐leucine zipper I transcription factor (TF) that was previously revealed as crucial for plant survival under salinity conditions. We wondered whether this TF has partners to perform this essential function. Therefore, TF cDNA library screening, yeast two‐hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays were complemented with expression analyses and phenotypic characterization of silenced, mutant, overexpression, and crossed plants in normal and salinity conditions. We revealed that AtHB23, AtPHL1, and AtMYB68 interact with each other, modulating root development and the salinity response. The encoding genes are coexpressed in specific root tissues and at specific developmental stages. In normal conditions, amiR68 silenced plants have fewer initiated roots, the opposite phenotype to that shown by amiR23 plants. AtMYB68 and AtPHL1 play opposite roles in lateral root elongation. Under salinity conditions, AtHB23 plays a crucial positive role in cooperating with AtMYB68, whereas AtPHL1 acts oppositely by obstructing the function of the former, impacting the plant's survival ability. Such interplay supports the complex interaction between these TF in primary and lateral roots. The root adaptation capability is associated with the amyloplast state. We identified new molecular players that through a complex relationship determine Arabidopsis root architecture and survival in salinity conditions. Significance Statement: Root plasticity, which is crucial to soil adaptation, is fine‐tuned by multiple biomolecules, including transcription factors and phytohormones. We revealed that the regulatory proteins AtHB23, AtMYB68, and AtPHL1 interact which each other in primary and lateral roots, playing essential roles in development and the stress response. Their cooperative and opposite functions vary depending on the root tissue and developmental stage. [ABSTRACT FROM AUTHOR]

The development of rapid, selective, and sensitive fluorescent sensors is essential for visualizing and quantifying biological molecules and processes in vitro, ex vitro, and in vivo, which is important for not only fundamental biological studies but the accurate diagnosis of diseases. The emerging field of activity-based sensing (ABS), a sensing method that utilizes molecular reactivity for analyte detection possesses many advantages including high specificity, sensitivity and accuracy. The aggregation caused quenching phenomenon which occurs in most conventional fluorophores results in reduced labeling efficiency of the target analytes and low photobleaching resistance, therefore limiting the applications of the ABS strategy. In contrast, aggregation induced emission (AIE) active luminogens (AIEgens) provide exceptional molecular frameworks for ABS. Of the many reaction classes utilized in the AIEgen ABS approach, click chemistry has become increasing popular. In this review, the sensing concepts of the ABS approach with AIEgens and the principles of click chemistry are discussed, followed by a systematic summary of the application of specific click chemistry reactions in AIEgen ABS protocols for the detection of an array of target analytes. Furthermore, the utility of click chemistry in the construction of AIEgens for bioimaging will also be showcased throughout the review. [ABSTRACT FROM AUTHOR]

Precise and highly regulated flow of biomolecules and ions through complex cellular networks is crucial for communication and information processing in living systems. In contrast, human‐made electronics rely on the flow of electrons and holes through well‐defined semiconductor networks for processing. Ion channels play vital roles in regulating the flow of ions and biomolecules across the cell membrane with a complexity unmatched in any semiconductor device. To enable biotic–abiotic communication and leverage this complexity, supported lipid bilayers (SLBs) create a planar cell membrane for integration with bioelectronics. This review discusses the integration of ion channels in bioelectronic devices for biotic–abiotic communication with enhanced functionality. This review begins with an introduction of natural and artificial ion channels across SLBs, continues with a description of bioelectronic devices integrating SLBs, and concludes with examples of functional ion channel bioelectronics. [ABSTRACT FROM AUTHOR]

A 64-kDa membrane-bound glycoprotein (gp64) of the cellular slime mold Polysphondylium pallidum, is a putative cell/cell adhesion protein identified by adhesion-blocking antibody fragments (Fab). gp64 is expressed on the cell surface of growth-phase cells and seems to mediate cell/cell adhesion. This paper describes an improved purification method based on the lipophilic nature of this protein. A critical step in the purification method is to collect an insoluble top layer appearing during ammonium sulfate precipitation. The sequence of cDNA encoding gp64 and its deduced amino acid sequence have been determined previously. Based on cDNA sequence data, the structure of gp64 protein was analyzed: almost all amino acid compositions and partial amino acid sequences of lysyl-endopeptidase-digested peptides of gp64 were determined by protein analysis; all six asparagine- linked glycosylation sites (Asn-Xaa-Ser/Thr) in fact contain carbohydrates, and all 36 cysteine residues were involved in forming disulfide bridges. From these data, gp64 seems to be a unique protein among cell/cell adhesion proteins. [ABSTRACT FROM AUTHOR]

Detailed biophysical studies have been carried out on echistatin, a member of the disintegrin family of small, cysteine-rich, RGD-containing proteins, isolated from the venom of the saw-scaled viper Echis carinatus. Analysis of circular-dichroism spectra indicates that, at 20 °C, echistatin contains no α-helix but contains mostly β-turns and β-sheet. Two isobestic points are observed as the temperature is raised, the conformational changes associated with that observed between 40 °C and 72 °C being irreversible. Raman spectra also indicate considerable β-turn and β-sheet (20%) structure and an absence of α-helical structure. Three of the four disulphide bridges are shown to be in an all-gauche conformation, while the fourth adopts a trans-gauche-gauche conformation. The 1H-NMR spectrum of echistatin has been almost fully assigned. A single conformation was observed at 27 °C with the four proline residues adopting only the trans conformation. A large number of backbone amide protons were found to exchange slowly, but no segments of the backbone were found to be in either α-helical or β-sheet conformation. A number of turns could be characterised. An irregular β-hairpin contains the RGD sequence in a mobile loop at its tip. Two of the four disulphide cross-links have been identified from the NMR spectra. The data presented in this paper will serve to define the structure of echistatin more closely in subsequent studies. [ABSTRACT FROM AUTHOR]

Proton-nuclear-magnetic-resonance spectroscopy is a powerful tool for investigating the solution structure of biopolymers provided that a substantial number of proton resonances are assigned in the spectrum. For large proteins the assignments have usually been made by the comparative one-dimensional NMR investigations of the parent and derivative proteins in different physicochemical conditions. In this paper, we show that the more powerful two-dimensional methods could be successfully applide to proteins of the size of human adult hemoglobin (Mr = 64 500). J-Correlated and NOE-correlated spectroscopy, together with topological relationships in the known crystalline structure, enabled us to assign a large number of resonances. The majority of the assigned resonances correspond to the heine substituents and to amino acids in the heme pockets of the two subunits. These results thus provide an extensive set of intrinsic probes for mapping the conformation of the ligand-binding site and its functional changes. Comparison of the observed ring-current shifts of the assigned resonances with those calculated from the known crystallographic coordinates suggests a close similarity between the heme-pocket tertiary conformation in solution and in the crystalline state. A significant difference was noted for Leu141 in β subunits which, in solution, appears to have stronger contacts with the heine groups than in the crystalline form. The present results also demonstrate that two-dimensional-NMR methods could be successfully applied to the investigation of the structure of large biomolecules in solution (Mr ≤ 65 000). [ABSTRACT FROM AUTHOR]

Eosinophils interact with extracellular matrix proteins and endothelial cells through adhesion proteins belonging to the β1 and β2 subfamilies of integrins. Extending previous observations, we found that tumour necrosis factor (TNF) and granulocyte-macrophage colony-stimulating factor stimulated generation of superoxide anion by eosinophils plated on fibronectin-coated surfaces. As studies with adherent neutrophils indicated that TNF might act as activating leucocyte integrins to deliver signals involved in activation of cell functions, we investigated the effects of monoclonal antibodies (mAb) directed against VLA-4 (CD49d/CD29), LFA-I (CD1 la/CDI8), CR3 (CDI lb/ CD 18) or the common β2 subunit (CD 18) on generation of eosinophil toxic oxygen molecules and spreading. We show that cross-linking of members of both the β and the β2 integrin subfamilies triggers eosinophil respiratory burst and spreading. Evidence for the selectivity of anti-integrin mAb effects is derived from thc findings that isotype-matched mAb of other specificities (anti-class I MHC Ag, anti-β2-microglobulin, anti-CD4) did not trigger eosinophil functions. The findings presented in this paper suggest that integrin-dependent, cosinophil adhesion in sites of allergic reaction may be accompanied by release of toxic oxygen molecules involved in tissue damage. [ABSTRACT FROM AUTHOR]

Shigella flexneri, a Gram-negative bacillus belonging to the family Enterobacteriaceae, causes bacillary dysentery in humans by invading colonic epithelial cells. Processes by which epithelial cells, which are not professional phagocytes, may limit the spread of the invading microorganisms are poorly understood. This paper shows that IcsA (VirG), a 120kDa bacterial outer membrane protein responsible for intracellular and cell-to-cell spread through polymerization of actin, is a major substrate for phosphorylation by cyclic-dependent protein kinases. Site-directed mutagenesis of a sequence encoding phosphorylation consensus motif SSRRASS, located at residues 754-760, almost completely abolished the ability of this protein to be phosphorylated by protein kinase A. Such mutants expressed a 'super lcs' phenotype, characterized by an increased capacity to spread from cell-to-cell during the first three hours of infection in the HeLa cell infection assay. These data suggest that host-cell phosphorylation of key virulence proteins located on the bacterial surface may represent a significant host defence mechanism during the invasion process. [ABSTRACT FROM AUTHOR]

In this paper we describe the reduction of corticosteroid metabolites containing the 17β-aldol side chain (isocorticosteroids) by aldose and aldehyde reductase from human tissues. Aldose reductase catalyzed the reduction of the aldehydes derived from cortisol and corticosterone at about the same rate, whereas aldehyde reductase preferentially acted on the aldehydes derived Irom 1 7-deoxycorticosteroids. At comparable rates of reduction the Michaelis constants for the best steroid aldehydes were one order of magnitude lower than for the hitherto best substrates. We propose that aldose and aldehyde reductase participate in the conversion of the corticosteroid ketol side chain to the glycol side chain via an aldol intermediate by the `long loop' pathway proposed by Monder and Bradlow [(1977) J. Steroid Biochem. 8. 897 - 908]. [ABSTRACT FROM AUTHOR]

The complete primary structure of the constant part of the μ-chain-disease protein, BOT, was established. It includes the whole CH2, CH3 and CH4 domains. Two amino acid changes were found, at positions 309 (Ser ↵ Gly) and 333 (Val ↵ Gly) (GAL numbering). In two additional monoclonal n chains (SCO and CO), the same positions showed an amino acid variability. From these data it may be concluded that four types of μ chains exist in the human: (1) GAL type with Ser-309 and Val-333; (2) OU type with Gly-309 and Val-333; (3) SCO type with Ser-309 and Gly-333; (4) BOT/CO type with Gly-309 and Gly-333. The meaning of this molecular polymorphism is discussed. [ABSTRACT FROM AUTHOR]

In this paper the mode of action of IF-1 in 40-S initiation complex formation was studied with MS 2 RNA as messenger. Using initiation factors IF-2 and IF-3 labeled in vitro it appeared that IF-I did not influence the binding of these factors in the absence of fMet-tRNA. However, in the presence of fMet-tRNA it was found that the enhancement of the fMet-tRNA binding by IF-1 was accompanied with an equimolar increase in binding of IF-2. Moreover, it appeared that also in absence of IF-I, fMet-tRNA binding is coupled with an equimolar enhancement of the IF-2 binding, which suggests the existence of a preribosomal complex between IF-2 and fMet-tRNA. The apparent K,, values for both the binding of fMet-tRNA and IF-2 to 30-S subunits were determined and appeared to be equal, which makes a functioning of such a preribosomal complex in protein initiation very likely. The participation of GTP in this complex will be discussed. Functions of IF-I in dissociation and recycling of IF-2, described by others, and the stimulation on the 30-S subunit level might well be explained as pleiotropic effects of one basic action of IF-1, i.e. a conformational change of 30-S subunits. [ABSTRACT FROM AUTHOR]

Extracellular vesicles (EVs) are natural vehicles carrying and transferring bioactive molecules for intercellular communication and play key roles in physiological and pathological processes. EVs are promising biomarkers for disease diagnosis due to their rich biological information and minimally invasive sampling. In this review, we summarize the current methods for isolating EVs from the body fluids and the techniques for analyzing EVs' biomolecules including the proteins, nucleic acids, and lipids. The advantages, feasibility, and challenges of EV‐based in vitro diagnosis toward clinical application are discussed. Finally, an outlook on the marketing and routine clinical application of EV‐based in vitro diagnosis is provided. [ABSTRACT FROM AUTHOR]

Surface‐enhanced Raman spectroscopy (SERS) has shown strength in non‐invasive, rapid, trace analysis and has been used in many fields in medicine. Machine learning (ML) is an algorithm that can imitate human learning styles and structure existing content with the knowledge to effectively improve learning efficiency. Integrating SERS and ML can have a promising future in the medical field. In this review, we summarize the applications of SERS combined with ML in recent years, such as the recognition of biological molecules, rapid diagnosis of diseases, developing of new immunoassay techniques, and enhancing SERS capabilities in semi‐quantitative measurements. Ultimately, the possible opportunities and challenges of combining SERS with ML are addressed. [ABSTRACT FROM AUTHOR]

Mass spectrometry imaging (MSI) is a powerful analytical technique that generates maps of hundreds of molecules in biological samples with high sensitivity and molecular specificity. Advanced MSI platforms with capability of high‐spatial resolution and high‐throughput acquisition generate vast amount of data, which necessitates the development of computational tools for MSI data analysis. In addition, computation‐driven MSI experiments have recently emerged as enabling technologies for further improving the MSI capabilities with little or no hardware modification. This review provides a critical summary of computational methods and resources developed for MSI data analysis and interpretation along with computational approaches for improving throughput and molecular coverage in MSI experiments. This review is focused on the recently developed artificial intelligence methods and provides an outlook for a future paradigm shift in MSI with transformative computational methods. [ABSTRACT FROM AUTHOR]

Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this study suggests that they can play the same rôle in the modelling, analysis and synthesis of biomolecular systems. The particular structure of bond graphs arising from biomolecular systems is established and used to elucidate the relation between thermodynamically closed and open systems. Block diagram representations of the dynamics implied by these bond graphs are used to reveal implicit feedback structures and are linearised to allow the application of control-theoretical methods. Two concepts of modularity are examined: computational modularity where physical correctness is retained and behavioural modularity where module behaviour (such as ultrasensitivity) is retained. As well as providing computational modularity, bond graphs provide a natural formulation of behavioural modularity and reveal the sources of retroactivity. A bond graph approach to reducing retroactivity, and thus inter-module interaction, is shown to require a power supply such as that provided by the ATP⇌ADP + Pi reaction. The mitogen-activated protein kinase cascade (Raf-MEK-ERK pathway) is used as an illustrative example. [ABSTRACT FROM AUTHOR]

Inspired by the recognition mechanism of biological molecules, molecular imprinting techniques (MITs) are imparted with numerous merits like excellent stability, recognition specificity, adsorption properties, and easy synthesis processes, and thus broaden the avenues for convenient fabrication protocol of bio‐inspired molecularly imprinted polymers (MIPs) with desirable functions to satisfy the extensive demands of biomedical applications. Herein, the recent research progress made with respect to bio‐inspired imprinting materials is discussed in this review. First, the underlying mechanism and basic components of a typical molecular imprinting procedure are briefly explored. Then, emphasis is put on the introduction of diverse MITs and novel bio‐inspired imprinting materials. Following these two sections, practical applications of MIPs in the field of biomedical science are focused on. Last but not least, perspectives on the remaining challenges and future development of bio‐inspired imprinting materials are presented. [ABSTRACT FROM AUTHOR]

Pump-probe experiments at X-ray free-electron laser (XFEL) facilities are a powerful tool for studying dynamics at ultrafast and longer timescales. Observing the dynamics in diverse scientific cases requires optical laser systems with a wide range of wavelength, flexible pulse sequences and different pulse durations, especially in the pump source. Here, the pump-probe instrumentation available for measurements at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of the European XFEL is reported. The temporal and spatial stability of this instrumentation is also presented. [ABSTRACT FROM AUTHOR]

The Implication and Inhibition Boolean logic gates were realized using NAD+/NADH‐dependent dehydrogenases combined with hexokinase competing for biomolecule input signals. Both logic gates operated with the same enzyme composition and their reconfiguration was achieved simply by redefining the input signals. The output signals produced by the logic gates were analyzed optically and electrochemically, particularly using enzyme‐modified electrodes. The logically processed input signals were used to switch operation of a biofuel cell and activate a molecule release process. [ABSTRACT FROM AUTHOR]

Histopathological hallmarks of Alzheimer's disease (AD) are intracellular neurofibrillary tangles and extracellular formation of senile plaques composed of the aggregated amyloid‐beta peptide along with metal ions (copper, iron or zinc). In addition, oxidative stress is considered as an important factor in the etiology of AD and a multitude of metalloproteins and transporters is affected, leading to metal ion misregulation. Redox‐active metal ions (e.g., copper) can catalyze the production of reactive oxygen species (ROS) in the presence of molecular oxygen and a reductant such as ascorbate. The ROS thus produced, in particular the hydroxyl radical which is the most reactive one, may contribute to oxidative stress conditions. Thus, detecting ROS in vivo or in biological models of AD is of interest for better understanding AD etiology. The use of biocompatible and highly specific and sensitive probes is needed for such a purpose, since ROS are transient species whose steady‐state concentrations are very low. Luminescent lanthanide complexes are sensitive probes that can meet these criteria. The present review focuses on the recent advances in the use of luminescent lanthanide complexes for ROS biosensing. It shows why the use of luminescent lanthanide complexes is of particular interest for selectively detecting ROS (O2·‐, HO•, 1O2, H2O2, etc.) in biological samples in the µM‐nM range. It particularly focuses on the most recent strategies and discusses what could be expected with the use of luminescent lanthanide complexes for better understanding some of the molecular mechanisms underlying the development of Alzheimer's disease. [ABSTRACT FROM AUTHOR]

Small-angle X-ray scattering (SAXS) is an experimental technique that allows structural information on biomolecules in solution to be gathered. High-quality SAXS profiles have typically been obtained by manual merging of scattering profiles from different concentrations and exposure times. This procedure is very subjective and results vary from user to user. Up to now, no robust automatic procedure has been published to perform this step, preventing the application of SAXS to high-throughput projects. Here, SAXS Merge, a fully automated statistical method for merging SAXS profiles using Gaussian processes, is presented. This method requires only the buffer-subtracted SAXS profiles in a specific order. At the heart of its formulation is non-linear interpolation using Gaussian processes, which provides a statement of the problem that accounts for correlation in the data. [ABSTRACT FROM AUTHOR]

Single-particle coherent X-ray diffraction imaging using an X-ray free-electron laser has the potential to reveal the three-dimensional structure of a biological supra-molecule at sub-nanometer resolution. In order to realise this method, it is necessary to analyze as many as 1 × 106 noisy X-ray diffraction patterns, each for an unknown random target orientation. To cope with the severe quantum noise, patterns need to be classified according to their similarities and average similar patterns to improve the signal-to-noise ratio. A high-speed scalable scheme has been developed to carry out classification on the K computer, a 10PFLOPS supercomputer at RIKEN Advanced Institute for Computational Science. It is designed to work on the real-time basis with the experimental diffraction pattern collection at the X-ray free-electron laser facility SACLA so that the result of classification can be feedback for optimizing experimental parameters during the experiment. The present status of our effort developing the system and also a result of application to a set of simulated diffraction patterns is reported. About 1 × 106 diffraction patterns were successfully classificatied by running 255 separate 1 h jobs in 385-node mode. [ABSTRACT FROM AUTHOR]

Recent experiments at free-electron laser X-ray sources have been able to resolve the intensity distributions about Bragg peaks in nanocrystals of large biomolecules. Information derived from small shifts in the peak positions augment the Bragg samples of the particle intensity with samples of its gradients. Working on the assumption that the nanocrystal is entirely generated by lattice translations of a particle, an algorithm is developed that reconstructs the particle from intensities and intensity gradients. Unlike traditional direct phasing methods that require very high resolution data in order to exploit sparsity of the electron density, this method imposes no constraints on the contrast other than positivity and works well at low resolution. Successful reconstructions are demonstrated with simulated P1 lysozyme nanocrystal data down to a signal-to-noise ratio of 2 in the intensity gradients. [ABSTRACT FROM AUTHOR]

Migraine is one of the most common of neurological disorders with a global prevalence of up to 15%. One in five migraineurs have frequent episodic or chronic migraine requiring prophylactic treatment. In recent years, specific pharmacological treatments targeting calcitonin gene‐related peptide (CGRP) signalling molecules have provided safe and effective treatments, monoclonal antibodies for prophylaxis and gepants for acute therapy. Albeit beneficial, it is important to understand the molecular mechanisms of these new drugs to better understand migraine pathophysiology and improve therapy. Here, we describe current views on the role of the CGRP family of peptides ‐ CGRP, calcitonin, adrenomedullin, amylin ‐ and their receptors in the trigeminovascular system. All these molecules are present within the trigeminovascular system but differ in expression and localization. It is likely that they have different roles, which can be utilized in providing additional drug targets. LINKED ARTICLES: This article is part of a themed issue on Advances in Migraine and Headache Therapy (BJP 75th Anniversary). To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v179.3/issuetoc [ABSTRACT FROM AUTHOR]

Ultrashort X-ray pulses from free-electron laser X-ray sources make it feasible to conduct small- and wide-angle scattering experiments on biomolecular samples in solution at sub-picosecond timescales. During these so-called fluctuation scattering experiments, the absence of rotational averaging, typically induced by Brownian motion in classic solution-scattering experiments, increases the information content of the data. In order to perform shape reconstruction or structure refinement from such data, it is essential to compute the theoretical profiles from three-dimensional models. Based on the three-dimensional Zernike polynomial expansion models, a fast method to compute the theoretical fluctuation scattering profiles has been derived. The theoretical profiles have been validated against simulated results obtained from 300 000 scattering patterns for several representative biomolecular species. [ABSTRACT FROM AUTHOR]

Synthetic biology is first represented in terms of two complementary aspects, the bio-engineering one, based on the genetic manipulation of extant microbial forms in order to obtain forms of life which do not exist in nature; and the chemical synthetic biology, an approach mostly based on chemical manipulation for the laboratory synthesis of biological structures that do not exist in nature. The paper is mostly devoted to shortly review chemical synthetic biology projects currently carried out in our laboratory. In particular, we describe: the minimal cell project, then the “Never Born Proteins” and lastly the Never Born RNAs. We describe and critically analyze the main results, emphasizing the possible relevance of chemical synthetic biology for the progress in basic science and biotechnology. [ABSTRACT FROM AUTHOR]

Announces the need for abstracts and articles relevant to biomolecular technologies for the conference organized by the European Society for Philosophy of Medicine and Healthcare in Reykjavik, Iceland in August 2004. Topics for the conference; Details about the conference; Contact information.