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In this paper we report the synthesis of new azabicycloalkane scaffolds, which could be exploited to obtain cRGD-based bioconjugates that may find promising application for targeted drug delivery, theranostic, and general cancer-cell labeling. By exploiting a Hosomi-Sakurai intramolecular allylation reaction we efficiently converted a silylated aldehyde precursor into 7,5-fused lactam scaffolds endowed with an exocyclic double bond. The presence of the vinyl function should make it possible to conjugate bioactive compounds to selectively carry them to tumor sites. The optimized synthetic sequence allows the gram-scale preparation of the target scaffolds in a few steps and good 39% overall yield from readily accessible materials. The high reactivity of the exocyclic olefin moiety was ascertained by performing a Heck coupling reaction with 1-bromo-4-nitrobenzene, which gave the corresponding functionalized derivatives in good (80-91%) yields. [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]

Confinement of reactive chemical species uniquely affects chemical reactivity by restricting the physical space available and by restricting access to interactions with the solvent. In Nature, for example, confined protein binding pockets govern processes following photoisomerization reactions and the isomerizations themselves. Here we describe the first example of a dihydroazulene/vinylheptafulvene (DHA/VHF) photo-switch functioning in water, and we show how its switching behavior is strongly influenced by supramolecular interactions with a series of cucurbit[ n]uril (CB) host molecules. In CB7 inclusion complexes, the kinetics of the thermal VHF-to-DHA back-reaction is accelerated, while in CB8 inclusion complexes, the kinetics is slowed down as compared to the free photo-switch. The effect of the CB encapsulation of the photo-switch can be effectively canceled by introducing a guest that binds the CB more strongly. According to DFT calculations, a stabilization of the reactive s- cis VHF conformer relative to the s- trans VHF appears to be a contributing factor responsible for the accelerated back-reaction when encapsulated in CB7. [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 interfacial properties of solid substrates are of importance for protein adsorption. Herein, we report a reversible protein adsorption switch based on the host-guest interaction of the butoxy pillar[5]arene and adipic acid. By the detector of the contact angle (CA), atomic force microscopy (AFM), and luminoscope on the silicon substrate, the intelligent protein switch exhibits excellent adsorptivity for BSA and switch performance by pH regulation. [ABSTRACT FROM AUTHOR]

The inhibition of the G protein-coupled receptor, relaxin family peptide receptor 1 (RXFP1), by a small LDLa protein may be a potential approach for prostate cancer treatment. However, it is a significant challenge to chemically produce the 41-residue and three-disulfide cross-bridged LDLa module which is highly prone to aspartimide formation due to the presence of several aspartic acid residues. Known palliative measures, including addition of HOBt to piperidine for Nα-deprotection, failed to completely overcome this side reaction. For this reason, an elegant native chemical ligation approach was employed in which two segments were assembled for generating the linear LDLa protein. Acquisition of correct folding was achieved by using either a regioselective disulfide bond formation or global oxidation strategies. The final synthetic LDLa protein obtained was characterized by NMR spectroscopic structural analysis after chelation with a Ca2+ ion and confirmed to be equivalent to the same protein obtained by recombinant DNA production. [ABSTRACT FROM AUTHOR]

The structure of the Hfq protein from Pseudomonas aeruginosa was determined using two different ionic conditions. In both cases the molecules formed identical hexameric rings, but some variations in the crystal packing were revealed. Hfq belongs to the family of Sm/LSm proteins, the members of which can form hexameric as well as heptameric rings. Comparative analysis of known structures of this protein family shows that the fragment of the Sm-fold responsible for oligomerization is strongly structurally conserved. In the heptameric ring, three conserved hydrogen bonds between β-strands of adjacent molecules hold together the monomers, whereas in the hexameric rings of Hfq an additional conserved inaccessible hydrogen bond between neighbouring monomers is observed. [ABSTRACT FROM AUTHOR]

Describes the preparation and crystallization of five different metal-substituted forms of Clostridium pasteurianum rubredoxin. Isomorphism of all five forms of rubredoxin crystallized; Data indicating that a knowledge of these structures contributes to a molecular understanding of the function of the iron-sulfur electron-transport protein.

Details the computation of the profiles of squared normalized structure factors for a large number of proteins and nucleic acids. Data showing that the solvent dip at around 6.3 A resolution is to a large extent a protein secondary-structure effect that is enhanced by the water structure.

Discusses the utility of the ACORN as a comprehensive and efficient phasing procedure for the determination of protein structures when atomic resolution data are available. Automatic structure solution, phasing and refinement for real data at lower resolutions for proteins of various complexities.

Nudix proteins, formerly called MutT homolog proteins, are a large family of proteins that play an important role in reducing the accumulation of potentially toxic compounds inside the cell. They hydrolyze a wide variety of substrates that are mainly composed of a nucleoside diphosphate linked to some other moiety X and thus are called Nudix hydrolases. Here, the crystal structure of a Nudix hydrolase from the hyperthermophilic archaeon Pyrobaculum aerophilum is reported. The structure was determined by the single-wave length anomalous scattering method with data collected at the peak anomalous wavelength of an iridium-derivatized crystal. It reveals an extensive dimer interlace, with each subunit contributing two strands to the β-sheet of the other subunit. Individual subunits consist of a mixed highly twisted and curved β-sheet of 11 β-strands and two α-helices, forming an α-β-α sandwich. The conserved Nudix box signature motif, which contains the essential catalytic residues, is located at the first α-helix and the β-strand and loop preceding it. The unusually short connections between secondary-structural elements, together with the dimer form of the structure, are likely to contribute to the thermostability of the P. aerophilum Nudix protein. [ABSTRACT FROM AUTHOR]

It is shown that for crystals of large proteins at low diffraction resolution, with N ≃ 10000 independent non-H protein atoms and dmin ≃ 8 Å, a simple bulk-solvent correction yields the Sayre equation in its classical form, Fh = q Σk FkFh-k. In the low-resolution protein case, the proportionality factor becomes q = 1/[〈ρp〉,- ρs)V], where V is the unit-cell volume, ρs is the assumed constant electron density in the solvent regions of the crystal and (ρp) is the average electron density in the protein regions. The classical form of the tangent formula follows from the bulk-solvent-corrected Sayre equation and its validity at low resolution is verified in empirical calculations. [ABSTRACT FROM AUTHOR]

This paper experimentally verifies the idea presented earlier that the contact of nonpolar clusters located on the surface of protein molecules with water destabilizes proteins. It is demonstrated that protein stabilization can be achieved by artificial hydrophilization of the surface area of protein globules by chemical modification. Two experimental systems are studied for the verification of the hydrophilization approach. 1. The surface tyrosine residues of trypsin are transformed to aminotyrosines using a two-step modification procedure: nitration by tetranitromethane followed by reduction with sodium dithionite. The modified enzyme is much more stable against irreversible thermoinactivation: the stabilizing effect increases with the number of aminotyrosine residues in trypsin and the modified enzyme can become even 100 times more stable than the native one. 2. α-Chymotrypsin is covalently modified by treatment with anhydrides or chloroanhydrides of aromatic carboxytic acids. As a result, different numbers of additional carboxylic groups (up to five depending on the structure of the modifying reagent) are introduced into each Lys residue modified. Acylation of all available amino groups of α-chymotrypsin by cyclic anhydrides of pyromellitic and mellitic acids results in a substantial hydrophilization of the protein as estimated by partitioning in an aqueous Ficoll-400/Dextran-70 biphasic system. These modified enzyme preparations are extremely stable against irreversible thermal inactivation at elevated temperatures (65-98 °C); their thermostability is practically equal to the stability of proteolytic enzymes from extremely thermophilic bacteria, the most stable proteinases known to date. [ABSTRACT FROM AUTHOR]

Inhibitor-2, purified by an improved procedure, was used to identify protein phosphatases capable of catalyzing its dephosphorylation. The results showed that, under our experimental conditions, protein phosphatases-1, 2A and 2B were the only significant protein phosphatases in rabbit skeletal muscle extracts acting on this substrate. Protein phosphatase-1 and 2A accounted for all the inhibitor-2 phosphatase activity in the absence of Ca2+ (resting muscle), and the potential importance of these enzymes in vivo is discussed. Protein phosphatase-2B, a Ca2+-calmodulin-dependent enzyme, could account for up to 30% of the inhibitor-2 phosphatase activity in contracting muscle. The Km of protein phosphatase-1 for inhibitor-2 (40 nM) was 100-fold lower than the Km for phosphorylase a (4.8 µM). This finding, coupled with the failure of inhibitor-2 to inhibit its own dephosphorylation, suggests that inhibitor-2 is dephosphorylated at one of the two sites on protein phosphatase-1 involved in preventing the dephosphorylation of other substrates. The dephosphorylation of inhibitor-2 by protein phosphatase-1 was also unaffected by inhibitor-1, suggesting that the phosphorylation state of inhibitor-2 is unlikely to be controlled by cyclic AMP in vivo. [ABSTRACT FROM AUTHOR]

Presents a study which investigates the calcium regulation of the murine homologues of TRPC6 and TRPC7 proteins. Observations in the study; Effects of calcium on TRPC6 currents; Conclusion of the study.

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Affordability of biopharmaceuticals continues to be a challenge, particularly in developing economies. This has fuelled advancements in manufacturing that can offer higher productivity and better economics without sacrificing product quality in the form of an integrated continuous manufacturing platform. While platform processes for monoclonal antibodies have existed for more than a decade, development of an integrated continuous manufacturing process for bacterial proteins has received relatively scant attention. In this study, we propose an end-to-end integrated continuous downstream process (from inclusion bodies to unformulated drug substance) for a therapeutic protein expressed in Escherichia coli as inclusion body. The final process consisted of a continuous refolding in a coiled flow inverter reactor directly coupled to a three-column periodic counter-current chromatography for capture of the product followed by a three-column con-current chromatography for polishing. The continuous bioprocessing train was run uninterrupted for 26 h to demonstrate its capability and the resulting output was analyzed for the various critical quality attributes, namely product purity (>99%), high molecular weight impurities (<0.5%), host cell proteins (<100 ppm), and host cell DNA (<10 ppb). All attributes were found to be consistent over the period of operation. The developed assembly offers smaller facility footprint, higher productivity, fewer hold steps, and significantly higher equipment and resin utilization. The complexities of process integration in the context of continuous processing have been highlighted. We hope that the study presented here will promote development of highly efficient, universal, end-to-end, fully continuous platforms for manufacturing of biotherapeutics. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:998-1009, 2017 [ABSTRACT FROM AUTHOR]

BACKGROUND Little attention has been paid on the inherent molecular structural effects among agricultural by-products. In this study, soybean meal ( SM), wheat bran ( WB), corn distillers dried grains with soluble ( DDGS), dry brewer's grain ( DBG), wet brewer's grain ( WBG), and apple pomace ( AP), which are widely used in the animal industry were selected to explore protein and carbohydrate molecular structural conformations. RESULTS All the protein peak heights (including α-helix and β-sheet) and areas were exhibited highest values in SM and lowest in AP. The SM had the highest peak area intensity of cellulosic compounds ( CELC), while the remaining varieties showed the lowest absorbance level. The TSCHO (sum of structural carbohydrate ( SCHO) and CELC area exhibited variations among the samples. Multivariate comparisons showed AP had no molecular structural association with other by-products within the protein amide region. Protein amides I, II and (I+ II) areas, α-helix, β-sheet and area ratio of protein amide and ( TSCHO + TCHO) had strong relationships with CP, NDF, ADF, ADL, SCP, starch, PC, CA, CC and TDN contents. CONCLUSION Inherent molecular structures varied among the selected by-product types and they might be used as potential predictors of nutritive factors, especially for protein structural information. © 2016 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

BACKGROUND Tenderness is one of the most important quality attributes especially for beef and lamb. As protein phosphorylation and dephosphorylation regulate glycolysis, muscle contraction and turnover of proteins within living cells, it may contribute to the conversion of muscle to meat. The changes of myofibrillar protein phosphorylation in post-mortem ovine muscle with different levels of tenderness were investigated in this study. RESULTS The protein phosphorylation level (P/T ratio) of the tender group increased from 0.5 to 12 h post mortem and then decreased. The P/T ratio of tough group increased during 24 h post mortem, increasing faster from 0.5 to 4 h post mortem than from 4 to 24 h post mortem.The global phosphorylation level of tough meat was significantly higher than tender meat at 4, 12 and 24 h post mortem ( P < 0.05). Protein identification revealed that most of the phosphoproteins were proteins with sarcomeric function; the others were involved in glycometabolism, stress response, etc. The phosphorylation levels of myofibrillar proteins, e.g. myosin light chain 2 and actin, were significantly different among groups of different tenderness and at different post-mortem time points ( P < 0.05). CONCLUSION Protein phosphorylation may influence meat rigor mortis through contractile machinery and glycolysis, which in turn affect meat tenderness. © 2015 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Novel multifunctional reagents were applied in combination with a lipid probe for affinity enrichment of myristoylated proteins and direct detection of lipid-modified tryptic peptides by mass spectrometry. This method enables high-confidence identification of the myristoylated proteome on an unprecedented scale in cell culture, and allowed the first quantitative analysis of dynamic changes in protein lipidation during vertebrate embryonic development. [ABSTRACT FROM AUTHOR]

At the time when the first membrane-protein crystal structure was determined, crystallization of these molecules was widely perceived as extremely arduous. Today, that perception has changed drastically, and the process is regarded as routine (or nearly so). On the occasion of the International Year of Crystallography 2014, this review presents a snapshot of the current state of the art, with an emphasis on the role of detergents in this process. A survey of membrane-protein crystal structures published since 2012 reveals that the direct crystallization of protein-detergent complexes remains the dominant methodology; in addition, lipidic mesophases have proven immensely useful, particularly in specific niches, and bicelles, while perhaps undervalued, have provided important contributions as well. Evolving trends include the addition of lipids to protein-detergent complexes and the gradual incorporation of new detergents into the standard repertoire. Stability has emerged as a critical parameter controlling how a membrane protein behaves in the presence of detergent, and efforts to enhance stability are discussed. Finally, although discovery-based screening approaches continue to dwarf mechanistic efforts to unravel crystallization, recent technical advances offer hope that future experiments might incorporate the rational manipulation of crystallization behaviors. [ABSTRACT FROM AUTHOR]

Aqueous two-phase extraction (ATPE) is increasingly considered to be a feasible unit operation, e.g., for the capture of monoclonal antibodies or recombinant proteins. So far, knowledge on the applicability of ATPE in antibody processes has been collected mostly in lab-scale. In contrast, approaches for the integration of ATPE into a downstream process are investigated. A complete process sequence including extraction, washing, ultrafiltration, and ion-exchange chromatography is discussed and suggested for antibody purification. Excellent antibody purities can be achieved. Additionally, a model is applied that allows early-on prediction of a multistage ATPE with high prediction accuracy. Finally, an economic evaluation between ATPE and Protein A chromatography is performed, reaching up to five-fold cost-saving factors. [ABSTRACT FROM AUTHOR]

Tardigrades are microscopic animals found worldwide in aquatic as well as terrestrial ecosystems. They belong to the invertebrate superclade Ecdysozoa, as do the two major invertebrate model organisms: Caenorhabditis elegans and Drosophila melanogaster. We present a brief description of the tardigrades and highlight species that are currently used as models for physiological and molecular investigations. Tardigrades are uniquely adapted to a range of environmental extremes. Cryptobiosis, currently referred to as a reversible ametabolic state induced by e.g. desiccation, is common especially among limno-terrestrial species. It has been shown that the entry and exit of cryptobiosis may involve synthesis of bioprotectants in the form of selective carbohydrates and proteins as well as high levels of antioxidant enzymes and other free radical scavengers. However, at present a general scheme of mechanisms explaining this phenomenon is lacking. Importantly, recent research has shown that tardigrades even in their active states may be extremely tolerant to environmental stress, handling extreme levels of ionizing radiation, large fluctuation in external salinity and avoiding freezing by supercooling to below −20 °C, presumably relying on efficient DNA repair mechanisms and osmoregulation. This review summarizes the current knowledge on adaptations found among tardigrades, and presents new data on tardigrade cell numbers and osmoregulation. [ABSTRACT FROM AUTHOR]

Poly(ethylene glycol) (PEG) is a widely used polymer employed to increase the circulating half-life of proteins in blood and to decrease their immunogenicity and antigenicity. PEG attaches to free amines, typically at lysine residues or at the N-terminal amino acid. This lack of selectivity can present problems when a PEGylated protein therapeutic is being developed, because predictability of activity and manufacturing reproducibility are needed for regulatory approval. Enzymatic modification of proteins is one route to overcome this limitation. Bacterial transglutaminases are enzyme candidates for site-specific modification, but they also have rather broad specificity. The need arises to be able to predict a priori potential PEGylation sites on the protein of interest and, especially, to be able to design mutants where unique PEGylation sites can be introduced when needed. We investigated the feasibility of a computational approach to the problem, using human granulocyte colony-stimulating factor as a test case. The selected protein is therapeutically relevant and represents a challenging problem, as it contains 17 potential PEGylation sites. Our results show that a combination of computational methods allows the identification of the specific glutamines that are substrates for enzymatic PEGylation by a microbial transglutaminase, and that it is possible to rationally modify the protein and introduce PEG moieties at desired sites, thus allowing the selection of regions that are unlikely to interfere with the biological activity of a therapeutic protein. [ABSTRACT FROM AUTHOR]

Aspergillus nidulans switches from vegetative growth to conidiation when aerial hyphae make contact with the atmosphere, or are subjected to specific environmental stress. The activation of the central conidiation pathway led by the transcription factor brlA is a critical milestone in this morphogenetic transition. A number of upstream developmental activators ( UDAs), expressed in vegetative cells, are required for this process to occur in conjunction with cessation of vegetative growth. Mutants affected in these factors remain aconidial ( fluffy) with low brlA expression levels ( flb). In this report, we describe FlbE as a UDA containing two conserved but hitherto uncharacterized domains, which functions in close association with putative transcription factor FlbB. Both UDAs are functionally interdependent, and colocalize at the hypha tip in an actin cytoskeleton-dependent manner. Moreover, bimolecular fluorescence studies show that they physically interact in vivo. These findings add evidence in favour of the existence of a signalling complex at or near the Spitzenkörper as an important part of the machinery controlling the morphogenetic transition between vegetative growth and conidiation. [ABSTRACT FROM AUTHOR]

Organic residue analysis utilizes analytical organic chemical techniques to identify the nature and origins of organic remains that cannot be characterized using traditional techniques of archaeological investigation (because they are either amorphous or invisible). The field is founded upon the principle that the biomolecular, or biochemical, components of organic materials associated with human activity survive in a wide variety of locations and deposits at archaeological sites. The archaeological information contained in organic residues is represented by the biomolecular components of the natural products that contribute to the formation of a given residue. By applying appropriate separation (chromatographic) and identification (mass spectrometric) techniques, the preserved, and altered, biomolecular components of such residues can be revealed. Once identified, the Archaeological Biomarker Concept can be applied, wherein the structure and even isotopic composition(s) of a given biomolecule or suite of biomolecules (the ‘chemical fingerprint’) can be related to the compositions of organisms exploited by humans in the past. As the organic residue field emerges from its pre-paradigmatic phase, and the organic residue revolution gathers pace, the way is open for challenging many long-held archaeological hypotheses and offering new perspectives on the study of human activity in the past. [ABSTRACT FROM AUTHOR]

The article reports on the biochemical and molecular aspects of microbial oxidation of inorganic sulfur compounds. It mentions that microorganisms play a role on the oxidation of inorganic sulfur compounds to sulfate. The microorganisms produce several enzymes including hydrolases and oxidoreductases. Microorganisms can be studied to produce desirable enzymes which can be used in biotechnological applications. The article provides a review of the inorganic sulfur compound-oxidizing microorganisms and their potential for sulfur metabolism.

Two fully hydrated pure-species phospholipids bilayers, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dioleoyl-sn-glycero-3-phosphorylcholine (DOPC), in the fluid phase and explicit solvent have been studied using molecular dynamics simulation. Atom interactions were modeled using recently developed force fields based on AMBER with full atomistic details. Several representative liquid phase properties for the structure and dynamics of lipids with different length of hydrocarbon chains and different level of saturation have been reproduced without artificially biasing the system in order to match experimental data. In particular, as the new GAFF (General Amber Force Field) has not been explicitly developed to reproduce lipid characteristics and is naturally compatible with standard AMBER nucleic acids and proteins parameters, it is here proven a promising tool to study mixed lipid–protein processes as protein activity dependence on membrane composition, permeation of solute across membranes, and other cellular processes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [ABSTRACT FROM AUTHOR]

AAA+ adenosine triphosphatases (ATPases) are molecular machines that perform a wide variety of cellular functions. For instance, they can act in vesicle transport, organelle assembly, membrane dynamics and protein unfolding. In most cases, the ATPase domains of these proteins assemble into active ring-shaped hexamers. As AAA+ proteins have a common structure, a central issue is determining how they use conserved mechanistic principles to accomplish specific biological actions. Here, we review the features and motifs that partially define AAA+ domains, describe the cellular activities mediated by selected AAA+ proteins and discuss the recent work, suggesting that various AAA+ machines with very different activities employ a common core mechanism. The importance of this mechanism to human health is demonstrated by the number of genetic diseases caused by mutant AAA+ proteins. [ABSTRACT FROM AUTHOR]

Electron transferring flavoproteins (ETFs) are soluble heterodimeric FAD-containing proteins that function primarily as soluble electron carriers between various flavoprotein dehydrogenases. ETF is positioned at a key metabolic branch point, responsible for transferring electrons from up to 10 primary dehydrogenases to the membrane-bound respiratory chain. Clinical mutations of ETF result in the often fatal disease glutaric aciduria type II. Structural and biophysical studies of ETF in complex with partner proteins have shown that ETF partitions the functions of partner binding and electron transfer between (a) a ‘recognition loop’, which acts as a static anchor at the ETF–partner interface, and (b) a highly mobile redox-active FAD domain. Together, this enables the FAD domain of ETF to sample a range of conformations, some compatible with fast interprotein electron transfer. This ‘conformational sampling’ enables ETF to recognize structurally distinct partners, whilst also maintaining a degree of specificity. Complex formation triggers mobility of the FAD domain, an ‘induced disorder’ mechanism contrasting with the more generally accepted models of protein–protein interaction by induced fit mechanisms. We discuss the implications of the highly dynamic nature of ETFs in biological interprotein electron transfer. ETF complexes point to mechanisms of electron transfer in which ‘dynamics drive function’, a feature that is probably widespread in biology given the modular assembly and flexible nature of biological electron transfer systems. [ABSTRACT FROM AUTHOR]

Pyridoxamine has been found to inhibit protein glycation and to avoid the formation of advanced glycation end-products (AGEs). One of the mechanisms by which pyridoxamine can inhibit glycation involves the scavenger of carbonyl groups with glycation capacity. In this work, we conducted a kinetic study of the reactions of pyridoxamine with various carbohydrates under physiological pH and temperature. The reactions involving hexoses were found to give a tricyclic compound (5) in addition to pyridoxal and pyridoxine. Such a tricyclic compound inhibits the Amadori rearrangement and the formation of other carbonyl compounds with glycating properties. The reactions involving pentoses gave compound 7 and pyridoxal—by transamination of the Schiff base. The transamination reaction enhances the inhibitory action of pyridoxamine. The formation rate constants for the Schiff base, k3, were found to be similar to those for the reactions of D-glucose with amino acids, which suggests competition between pyridoxamine and terminal amino residues in proteins for glycating sites in sugars. These constants are dependent on the electrophilic character of the carbonyl carbon in the carbohydrate. © 2007 Wiley Periodicals, Inc. 39: 154–167, 2007 [ABSTRACT FROM AUTHOR]

We tested to what extent differences in construction costs (CC) and chemical composition of woody species are attributed to leaf habit. Eight evergreen and eight deciduous species belonging to six families were selected to form eight phylogenetic independent contrasts (PICs). The plants were grown from seed in a glasshouse. Differences in leaf, stem and root CC between evergreen and deciduous species were minor, the proportion of variance explained by leaf habit generally being less than 6%. Surprisingly, differences in leaf chemical composition between deciduous and evergreen species were small as well. Variation in CC and chemical composition among families was substantial, the factor ‘family’ explaining 50–85% of variance. We therefore conclude that in this case, phylogeny is a more important factor than functional group. Leaves of the fast-growing species in this experiment showed high levels of minerals, organic acids, proteins and lipids, whereas leaves of the slow-growing species had higher concentrations of soluble phenolics, lignin as well as higher carbon/nitrogen (C/N) ratio. These relationships suggest a trade-off between growth and defence. In contrast, CC of leaves, stems, roots or whole plants showed no or only a weak correlation with relative growth rate (RGR). The C/N ratio of the leaves is an easily measured parameter that correlated strongly in a negative way with the RGR of the plants and reflected better the balance between investment in structure and physiological functioning than CC. [ABSTRACT FROM AUTHOR]

The article focuses on the role of advances in technology and algorithms in facilitating development in protein structure prediction. There are three categories of structure prediction methods namely comparative modelling, fold recognition and ab initio. The methods may combine more than one approach.

The article focuses on the functions of prion proteins. Prions could have both beneficial and harmful effects on cells. There is a need to study mammalian model systems to study the pathogenesis of clinical prion disease. A method has been devised to identify new anti-prion drugs using a yeast-based screen.

The volume fraction occupied by the dry matter of the cell can be as large as 40%, of which more than half (∼60%) are proteins. Thus, cellular proteins and protein assemblies occupy a large volume that can have a profound effect on their own native-state stabilities and on their unfolding/refolding rates. In addition, macromolecular crowding can change the properties of a significant fraction of the water in the cell. We review features of the molecular crowding effect which are relevant for describing the microscopic mechanism of thermal injuries. [ABSTRACT FROM AUTHOR]

The review discusses the molecular origins of the forces and free energies that determine several things about proteins, and how experiment and theory reveal this information. The first subject is the stability of the folded, native structures. The second is the range of molecular mechanisms by which proteins find their way to those folded structures in laboratory environments. The third is the much more complex problem of how folding occurs in the cellular environment. This topic includes a discussion of crowding and of the roles of chaperone molecules. The review concludes with a discussion of protein aggregation and fibril formation and of misfolding and therapies associated with it. [ABSTRACT FROM AUTHOR]

14-3-3 proteins form a family of highly conserved proteins capable of binding to more than 200 different mostly phosphorylated proteins. They are present in all eukaryotic organisms investigated, often in multiple isoforms, up to 13 in some plants. 14-3-3 binding partners are involved in almost every cellular process and 14-3-3 proteins play a key role in these processes. 14-3-3 proteins interact with products encoded by oncogenes, with filament forming proteins involved in Alzheimer'ss disease and many other proteins related to human diseases. Disturbance of the interactions with 14-3-3 proteins may lead to diseases like cancer and the neurological Miller-Dieker disease. The molecular consequences of 14-3-3 binding are diverse and only partly understood. Binding of a protein to a 14-3-3 protein may result in stabilization of the active or inactive phosphorylated form of the protein, to a conformational alteration leading to activation or inhibition, to a different subcellular localization or to the interaction with other proteins. Currently genome- and proteome-wide studies are contributing to a wider knowledge of this important family of proteins. IUBMB Life , 57: 623–629, 2005 [ABSTRACT FROM AUTHOR]

• We examined whether nitrogen (N) and carbohydrates reserves allowVeratrum album, an alpine forb, to start spring growth earlier than the neighbouring vegetation and to survive unpredictable disturbances resulting in loss of above-ground biomass.• Seasonal dynamics of plant reserves, soil N availability and vegetation growth were monitored.Veratrum albumshoots were experimentally removed when carbohydrate reserves were at a seasonal minimum and the subsequent changes in biomass and reserves were compared with those in control plants.• Reserves did not giveV. albuma competitive advantage in spring; however, they did function as a buffer against the impact of calamities. Shoot removal resulted in significantly lower root dry weight, higher N concentration in rhizome and roots and lower starch concentrations in rhizome and roots but no plant mortality was observed.• Veratrum albumused stored N reserves to supplement N uptake and establish high leaf N concentrations, which facilitated a rapid refilling of depleted carbohydrate reserves. The primary function of N reserves appears to be to allowV. albumto complete the growing cycle in as short a period as possible, thus minimizing exposure to above-ground risks.New Phytologist(2005)doi: 10.1111/j.1469-8137.2005.01321.x© New Phytologist(2005) [ABSTRACT FROM AUTHOR]

Phosphorylase kinase (PhK) is a large hexadecameric enzyme consisting of four copies of four subunits: (αβγδ)4. An intrinsic calmodulin (CaM, theδ subunit) binds directly to theγ protein kinase chain. The interaction site of CaM onγ has been localized to a C-terminal extension of the kinase domain. Two 25-mer peptides derived from this region, PhK5 and PhK13, were identified previously as potential CaM-binding sites. Complex formation between Ca2+/CaM with these two peptides was characterized using analytical gel filtration and NMR methods. NMR chemical shift perturbation studies showed that while PhK5 forms a robust complex with Ca2+/CaM, no interactions with PhK13 were observed.15N relaxation characteristics of Ca2+/CaM and Ca2+/CaM/PhK5 complexes were compared with the experimentally determined structures of several Ca2+/CaM/peptide complexes. Good fits were observed between Ca2+/CaM/PhK5 and three structures: Ca2+/CaM complexes with peptides from endothelial nitric oxide synthase, with smooth muscle myosin light chain kinase and CaM kinase I. We conclude that the PhK5 site is likely to have a direct role in Ca2+-regulated control of PhK activity through the formation of a classical‘compact’ CaM complex. [ABSTRACT FROM AUTHOR]

Purpureofilum apyrenoidigerumgen et sp. nov. was obtained from a mangrove habitat in New South Wales, Australia. It had unbranched uniseriate to multiseriate filaments less than 1 mm tall, with a unicellular base. Each cell had a single multilobed parietal chloroplast without a pyrenoid. During reproduction vegetative cells were discharged directly as monospores that remained motile for several hours after release. Spores with long tails moved more slowly (0.053–0.195 µm s−1) than spores without tails (0.43–1.76 µm s−1). Phylogenetic analysis of sequences of the small subunit of the nuclear-encoded rRNA and plastid-encoded ribulose bisphosphate carboxylase/oxygenase genes revealed thatPurpureofilumis a member of the Stylonematales and is most closely related to the filamentous genusBangiopsis.Bangiopsisdiffers fromPurpureofilumby having longer (to 5 mm) multiseriate filaments, cells containing a stellate chloroplast, a conspicuous central pyrenoid, and monospores often formed in packets. Monospores ofBangiopsiswere also motile. Transmission electron microscopy investigation ofPurpureofilumandBangiopsisrevealed that the Golgi complexes are associated only with rough endoplasmic reticulum and that the plastid contains a peripheral thylakoid; this combination of features being the same as in all other multicellular members of the Stylonematales. The low molecular weight carbohydrates ofPurpureofilumandBangiopsiswere digeneaside and sorbitol, which were present in most other Stylonematales. [ABSTRACT FROM AUTHOR]

High-pressure NMR experiments performed on the histidine-containing phosphocarrier protein (HPr) fromStaphylococcus carnosushave shown that residue Ile14, which is located in the active-centre loop, exhibits a peculiarly small pressure response. In contrast, the rest of the loop shows strong pressure effects as is expected for typical protein interaction sites. To elucidate the structural role of this residue, the mutant protein HPr(I14A), in which Ile14 is replaced by Ala, was produced and studied by solution NMR spectroscopy. On the basis of 1406 structural restraints including 20 directly detected hydrogen bonds, 491HN-15N, and 251HN-1Hα residual dipolar couplings, a well resolved three-dimensional structure could be determined. The overall fold of the protein is not influenced by the mutation but characteristic conformational changes are introduced into the active-centre loop. They lead to a displacement of the ring system of His15 and a distortion of the N-terminus of the first helix, which supports the histidine ring. In addition, the C-terminal helix is bent because the side chain of Leu86 located at the end of this helix partly fills the hydrophobic cavity created by the mutation. Xenon, which is known to occupy hydrophobic cavities, causes a partial reversal of the mutation-induced structural effects. The observed structural changes explain the reduced phosphocarrier activity of the mutant and agree well with the earlier suggestion that Ile14 represents an anchoring point stabilizing the active-centre loop in its correct conformation. [ABSTRACT FROM AUTHOR]

Ubiquitination, a modification in which single or multiple ubiquitin molecules are attached to a protein, serves as a signalling function that controls a wide variety of cellular processes. To date, two major forms of polyubiquitin chain have been functionally characterized, in which the isopeptide bond linkages involve Lys48 or Lys63. Lys48-linked polyubiquitin tagging is mostly used to target proteins for degradation by the proteasome, whereas Lys63-linked polyubiquitination has been linked to numerous cellular events that do not rely on degradative signalling via the proteasome. Apparently linkage-specific conformations of polyubiquitin chains are important for these cellular functions, but the structural bases distinguishing Lys48- and Lys63-linked chains remain elusive. Here, we report NMR and small-angle X-ray scattering (SAXS) studies on the intersubunit interfaces and conformations of Lys63- and Lys48-linked di- and tetraubiquitin chains. Our results indicate that, in marked contrast to Lys48-linked chains, Lys63-linked chains are elongated molecules with no stable non-covalent intersubunit interfaces and thus adopt a radically different conformation from that of Lys48-linked chains. [ABSTRACT FROM AUTHOR]

Hermansky–Pudlak syndrome (HPS) defines a group of at least seven autosomal recessive disorders characterized by albinism and prolonged bleeding due to defects in the lysosome-related organelles, melanosomes and platelet-dense granules, respectively. Most HPS genes, including HPS3, HPS5 and HPS6, encode ubiquitously expressed novel proteins of unknown function. Here, we report the biochemical characterization of a stable protein complex named Biogenesis of Lysosome-related Organelles Complex-2 (BLOC-2), which contains the HPS3, HPS5 and HPS6 proteins as subunits. The endogenous HPS3, HPS5 and HPS6 proteins from human HeLa cells coimmunoprecipitated with each other from crude extracts as well as from fractions resulting from size-exclusion chromatography and density gradient centrifugation. The native molecular mass of BLOC-2 was estimated to be 340 ± 64 kDa. As inferred from the biochemical properties of the HPS6 subunit, BLOC-2 exists in a soluble pool and associates to membranes as a peripheral membrane protein. Fibroblasts deficient in the BLOC-2 subunits HPS3 or HPS6 displayed normal basal secretion of the lysosomal enzyme β-hexosaminidase. Our results suggest a common biological basis underlying the pathogenesis of HPS-3, -5 and -6 disease. [ABSTRACT FROM AUTHOR]

The human I1-imidazoline receptor candidate gene, iras, has previously been cloned and mapped to locus 3p21.1-9 (also known as Nischarin; accession #AC006208). By comparison to a database of expressed sequence tags (ESTs), three alternatively spliced transcripts have been deduced. A map of 21 exons was constructed for the medium-length transcript (IRAS-M) containing 5,232 base pairs (bp) and encoding 1,504 amino acids (aas). Introns 13B and 13C are inserted into the two alternative transcripts, forming IRAS-S and IRAS-L mRNA (short and long isoforms). Northern blots confirmed the existence of these mRNA isoforms. In most brain regions the order of mRNA abundance was IRAS-M > IRAS-L > IRAS-S mRNA. Although aas 1 through 510 are theoretically identical, truncated proteins could be derived from IRAS-S (2,678 bp transcript yields 515 aas) and IRAS-L (9,457 bp transcript yields 583 aas). Because exon-16 of the iras gene has been proposed to encode the functional domains of imidazoline and a-5 integrin binding, only IRAS-M is expected to possess I1 receptor properties. Subtype-selective cDNA expression constructs were therefore generated and used to transfect CHO cells. High-affinity I1 binding was endowed by IRAS-M and IRAS-L, but not by IRAS-S transfection. [ABSTRACT FROM AUTHOR]

The penicillin-binding proteins (PBPs) are ubiquitous bacterial enzymes involved in cell wall biosynthesis, and are the targets of the β-lactam antibiotics. The low molecular mass Neisseria gonorrhoeae PBP 4 (NG PBP 4) is the fourth PBP revealed in the gonococcal genome. NG PBP 4 was cloned, overexpressed, purified, and characterized for β-lactam binding, dd-carboxypeptidase activity, acyl-donor substrate specificity, transpeptidase activity, inhibition by a number of active site directed reagents, and pH profile. NG PBP 4 was efficiently acylated by penicillin (30 000 m−1·s−1). Against a set of five α- and ε-substituted l-Lys- d-Ala- d-Ala substrates, NG PBP 4 exhibited wide variation in specificity with a preference for Nε-acylated substrates, suggesting a possible preference for crosslinked pentapeptide substrates in the cell wall. Substrates with an Nε-Cbz group demonstrated pronounced substrate inhibition. NG PBP 4 showed 30-fold higher activity against the depsipeptide Lac-ester substrate than against the analogous peptide substrate, an indication that k2 (acylation) is rate determining for carboxypeptidase activity. No transpeptidase activity was apparent in a model transpeptidase reaction. Among a number of active site-directed agents, N-chlorosuccinimide, elastinal, iodoacetamide, iodoacetic acid, and phenylglyoxal gave substantial inhibition, and methyl boronic acid gave modest inhibition. The pH profile for activity against Ac2- l-Lys- d-Ala- d-Ala ( kcat/ Km) was bell-shaped, with p Ka values at 6.9 and 10.1. Comparison of the enzymatic properties of NG PBP 4 with other dd-carboxypeptidases highlights both similarities and differences within these enzymes, and suggests the possibility of common mechanistic roles for the two highly conserved active site lysines in Class A and C low molecular mass PBPs. [ABSTRACT FROM AUTHOR]

A large number of proteins, found experimentally to have different optimum pH of maximal stability, were studied to reveal the basic principles of their preferenence for a particular pH. The pH-dependent free energy of folding was modeled numerically as a function of pH as well as the net charge of the protein. The optimum pH was determined in the numerical calculations as the pH of the minimum free energy of folding. The experimental data for the pH of maximal stability (experimental optimum pH) was reproducible (rmsd = 0.73). It was shown that the optimum pH results from two factors – amino acid composition and the organization of the titratable groups with the 3D structure. It was demonstrated that the optimum pH and isoelectric point could be quite different. In many cases, the optimum pH was found at a pH corresponding to a large net charge of the protein. At the same time, there was a tendency for proteins having acidic optimum pHs to have a base/acid ratio smaller than one and vice versa. The correlation between the optimum pH and base/acid ratio is significant if only buried groups are taken into account. It was shown that a protein that provides a favorable electrostatic environment for acids and disfavors the bases tends to have high optimum pH and vice versa. [ABSTRACT FROM AUTHOR]

A biomonitoring campaign was conducted in the Belgian North Sea and in the Western Scheldt (The Netherlands) with the primary goal to assess perfluorooctane sulfonic acid (PFOS) contamination and distribution in different biota. This study covers the results obtained for bib (Trisopterus luscus) and plaice (Pleuronectes platessa) and includes the assessment of some stress-related biochemical endpoints. Analysis of liver and muscle PFOS concentrations of both species provided evidence for the existence of a PFOS pollution gradient along the Western Scheldt with higher levels at the upstream locations and a lower degree of PFOS pollution at the marine locations. Cellular necrosis was studied by measuring aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels in the serum. Serum ALT but not serum AST was shown to correlate positively with the PFOS liver concentration in bib (r = 0.44, p < 0.05), indicating that PFOS might contribute to the induction of hepatic damage in bib in the area of study. Analysis of total carbohydrate, lipid, and protein content of bib liver tissue revealed a positive correlation between the protein content and the PFOS liver concentration (r = 0.55, p < 0.01). Whether this is due to induction of compensatory mechanisms, detoxification, or repair processes remains unclear. [ABSTRACT FROM AUTHOR]

The total, protein, and nonprotein nitrogen, 3 amino acids (lysine, histidine, and tyrosine), available lysine, and in vitro protein digestibility in enteral formulas were determined. Available lysine and protein digestibility were lower in the liquid formulas tested than in the powdered formulas. The protein quality of the formula made from soy protein isolate (soy) was lower than that of the formulas made from casein, and the protein quality of a low-protein formula was lower than that of the standard formulas. There was a statistically significant correlation between the available lysine content and protein digestibility in the polymeric formulas. New methods are required for assessing the protein quality of formulas containing hydrolyzed proteins. [ABSTRACT FROM AUTHOR]

The aim of this work was to examine whether carbohydrates are involved in signalling N deficiency through source:sink imbalance. Photosynthetic metabolism in tobacco was studied over 8 d during the withdrawal of N from previously N-sufficient plants in which the source:sink ratio was manipulated by shading leaves on some of the plants. In N-sufficient plants over this timescale, there was a small decline in photosynthetic rate, Rubisco protein and amino acid content, with a larger decrease in carbohydrate content. Withdrawal of N from the growing medium induced a large decrease in the rate of photosynthesis (35% reduction after 8 d under the growing conditions, with a reduction also apparent at high and low measuring CO2), which was caused by a large decrease in the amount of Rubisco protein (62% after 8 d) and Rubisco activity. Higher amounts of hexoses preceded the loss of photosynthetic activity and sucrose and starch accumulation. Reduction of the source:sink ratio by shading prevented the loss of photosynthetic activity and the increase in hexoses and other carbohydrates. These data indicate that the reduction of photosynthesis that accompanies N deficiency in intact plants has the characteristics of sugar repression of photosynthesis observed in model systems, but that the accumulation of hexose prior to the decline in photosynthesis is small. The possibility that sugar repression of photosynthesis under physiological conditions depends more crucially on the C:N status of leaves than the carbohydrate status alone is discussed. [ABSTRACT FROM AUTHOR]

Lycopersicon esculentum and L. chmielewskii are respectively susceptible and resistant to the potato tuber moth (Phthorimaea operculella Zeller) in the field. Feeding bioassays were conducted with the herbivore caterpillars reared on callus derived from both tomato species and grown in vitro, and the influence of carbohydrate supplements to the callus culture medium, on the insect's feeding behavior was investigated. Newly-hatched larvae fed with L. esculentum or L. chmielewskii callus raised on a medium with 88 mM sucrose, reached a weight of 12-15 mg and 1.5-3.0 mg, respectively, within 9 days. Restriction of larval weight increase in insects reared on L. chmielewskii callus, disappeared when the host tissue was transferred 24 h prior to the callus-insect assay to a medium supplemented with 264 mM of either sucrose, glucose, fructose or mannose. The capability of L. chmielewskii callus to restrict growth of larvae was restored in host tissue retransferred from a medium with 264 mM sucrose to a 24-h incubation on one supplemented with 264 mM of either mannitol, sorbitol, glycerol or myo-inositol, before the callus-insect bioassay. The larval growth response remained unaltered by callus incubated on a medium with 264 mM xylose. The ameliorating effect on insect growth of high sucrose in the callus medium was not due to sucrose as an ingredient of the insect's diet. The diverse response of L. chmielewskii callus, and its dependence on the type of carbohydrate in the medium, rule out effects of these substances as nonspecific medium osmotica. The swift callus responses to carbohydrates (within hours of a change in medium composition), as reflected in the insect's growth, were not accompanied by visible morphological variations in the host tissue. We suggest that suppression by high levels of exogenously applied saccharides and derepression by exogenous polyols and myo-inositol of the impedement to growth of the potato tuber moth larva, reflect the existence in L. chmielewskii of a carbon metabolic control mechanism of gene expression whose products affect insect growth. [ABSTRACT FROM AUTHOR]