Biological roles of prion domains

In vivo amyloid formation is a widespread phenomenon in eukaryotes. Self-perpetuating amyloids provide a basis for the infectious or heritable protein isoforms (prions). At least for some proteins, amyloid-forming potential is conserved in evolution despite divergence of the amino acid (aa) sequences. In some cases, prion formation certainly represents a pathological process leading to a disease. However, there are several scenarios in which prions and other amyloids or amyloid-like aggregates are either shown or suspected to perform positive biological functions. Proven examples include self/nonself recognition, stress defense and scaffolding of other (functional) polymers. The role of prion-like phenomena in memory has been hypothesized. As an additional mechanism of heritable change, prion formation may in principle contribute to heritable variability at the population level. Moreover, it is possible that amyloid-based prions represent by-products of the transient feedback regulatory circuits, as normal cellular function of at least some prion proteins is decreased in the prion state.

Vibratory reaction unit for the rapid analysis of proteins and glycochains

A protein digestion system using immobilized enzymes for protein identification and glycochain analyses has been developed, and a vibration reaction unit for micro-scale sample convection on an enzyme-immobilized solid surface was constructed. BSA as a model substrate was digested by this unit, and was successfully identified by mass spectrometry (MS) analyses. Compared to the conventional liquid-phase digestion, the reaction unit increased the number of matched peptides from 9 to 26, protein score from 455 to 1247, and sequence coverage from 21% to 48%. Glycopeptidase F (NGF), an enzyme that cleaves N-glycans from glycoproteins, was also immobilized and used to remove the glycochains from human immunoglobulin G (IgG). Trypsin and NGF were immobilized on the same solid surface and used to remove glycochains from IgG in single-step. Glycochains were labeled with fluorescent reagent and analyzed by HPLC. Several peaks corresponding to the glycochains of IgG were detected. These results suggested that the single-step digestion system, by immobilized multiple enzymes (trypsin and NGF) would be effective for the rapid structural analysis of glycoproteins.

Effects of surface wettability and contact time on protein adhesion to biomaterial surfaces

Atomic force microscopy (AFM) was used to directly measure the adhesion forces between three test proteins and low density polyethylene (LDPE) surfaces treated by glow discharge plasma to yield various levels of water wettability. The adhesion of proteins to the LDPE substrates showed a step dependence on the wettability of surfaces as measured by the water contact angle (theta). For LDPE surfaces with theta> approximately 60-65 degrees , stronger adhesion forces were observed for bovine serum albumin, fibrinogen and human FXII than for the surfaces with theta<60 degrees . Smaller adhesion forces were observed for FXII than for the other two proteins on all surfaces although trends were identical. Increasing the contact time from 0 to 50s for each protein-surface combination increased the adhesion force regardless of surface wettability. Time varying adhesion data was fit to an exponential model and free energies of protein unfolding were calculated. This data, viewed in light of previously published studies, suggests a 2-step model of protein denaturation, an early stage on the order of seconds to minutes where the outer surface of the protein interacts with the substrate and a second stage involving movement of hydrophobic amino acids from the protein core to the protein/surface interface. Impact statement: The work described in this manuscript shows a stark transition between protein adherent and protein non-adherent materials in the range of water contact angles 60-65 degrees , consistent with known changes in protein adsorption and activity. Time-dependent changes in adhesion force were used to calculate unfolding energies relating to protein-surface interactions. This analysis provides justification for a 2-step model of protein denaturation on surfaces.

Protein metabolism in preterm infants with particular reference to intrauterine growth restriction

There is growing evidence that neonatal and long-term morbidity in preterm infants, particularly those born before 32 weeks' gestation, can be modified by attained growth rate in the neonatal period. Guidelines for optimal growth and the nutritional intakes, particular of protein, required to achieve this are not well defined. Due to delays in postnatal feeding and a lack of energy stores developed in the last trimester of pregnancy, preterm infants often suffer early postnatal catabolism until feeding is established. There are indications that infants born with intrauterine growth restriction have perturbations in protein metabolism. Therefore, they may have different protein requirements than appropriate for gestational age infants. This review summarises what is known about protein requirements and metabolism in the fetus and preterm infant, with particular emphasis on the distinct requirements of the growth-restricted infant.

The proteins and the mechanisms of apoptosis: a mini-review of the fundamentals

Apoptosis or programmed cell death is a physiological mechanism, characterized by specific morphological and biochemical changes such as cell shrinkage, chromatin condensation, protein cleavage, DNA breakdown and phagocytosis. Apoptosis is a significant contributor to the morphologic and functional development of multicellular organisms. It is also involved in the pathogenesis of several diseases including degenerative diseases of the central nervous system (CNS) like Alzheimer's disease or Parkinson's disease, cancer and immune system dysfunction. There are many factors, mainly proteins, which are involved in the activation, regulation and execution of related events. A fairly detailed outline of apoptotic mechanisms has also started to emerge and to be verified. In this short, focused mini-review, we attempt to outline current evidence regarding the mechanisms and the regulation of apoptosis.

Conformational entropy of alanine versus glycine in protein denatured states

The presence of a solvent-exposed alanine residue stabilizes a helix by 0.4-2 kcal.mol(-1) relative to glycine. Various factors have been suggested to account for the differences in helical propensity, from the higher conformational freedom of glycine sequences in the unfolded state to hydrophobic and van der Waals' stabilization of the alanine side chain in the helical state. We have performed all-atom molecular dynamics simulations with explicit solvent and exhaustive sampling of model peptides to address the backbone conformational entropy difference between Ala and Gly in the denatured state. The mutation of Ala to Gly leads to an increase in conformational entropy equivalent to approximately 0.4 kcal.mol(-1) in a fully flexible denatured, that is, unfolded, state. But, this energy is closely counterbalanced by the (measured) difference in free energy of transfer of the glycine and alanine side chains from the vapor phase to water so that the unfolded alanine- and glycine-containing peptides are approximately isoenergetic. The helix-stabilizing propensity of Ala relative to Gly thus mainly results from more favorable interactions of Ala in the folded helical structure. The small difference in energetics in the denatured states means that the Phi-values derived from Ala --> Gly scanning of helices are a very good measure of the extent of formation of structure in proteins with little residual structure in the denatured state.

Conventional energy and macronutrient variables distort the accuracy of children's dietary reports: illustrative data from a validation study of effect of order prompts

OBJECTIVE

Validation-study data are used to illustrate that conventional energy and macronutrient (protein, carbohydrate, fat) variables, which disregard accuracy of reported items and amounts, misrepresent reporting accuracy. Reporting-error-sensitive variables are proposed which classify reported items as matches or intrusions, and reported amounts as corresponding or overreported.

METHODS

58 girls and 63 boys were each observed eating school meals on 2 days separated by > or =4 weeks, and interviewed the morning after each observation day. One interview per child had forward-order (morning-to-evening) prompts; one had reverse-order prompts. Original food-item-level analyses found a sex-x-order prompt interaction for omission rates. Current analyses compared reference (observed) and reported information transformed to energy and macronutrients.

RESULTS

Using conventional variables, reported amounts were less than reference amounts (ps<0.001; paired t-tests); report rates were higher for the first than second interview for energy, protein, and carbohydrate (ps< or =0.049; mixed models). Using reporting-error-sensitive variables, correspondence rates were higher for girls with forward- but boys with reverse-order prompts (ps< or =0.041; mixed models); inflation ratios were lower with reverse- than forward-order prompts for energy, carbohydrate, and fat (ps< or =0.045; mixed models).

CONCLUSIONS

Conventional variables overestimated reporting accuracy and masked order prompt and sex effects. Reporting-error-sensitive variables are recommended when assessing accuracy for energy and macronutrients in validation studies.

Nuclear magnetic resonance structural studies of membrane proteins in micelles and bilayers

Nuclear magnetic resonance (NMR) spectroscopy enables determination of membrane protein structures in lipid environments, such as micelles and bilayers. This chapter outlines the steps for membrane-protein structure determination using solution NMR with micelle samples, and solid-state NMR with oriented lipid-bilayer samples. The methods for protein expression and purification, sample preparation, and NMR experiments are described and illustrated with examples from gamma and CHIF, two membrane proteins that function as regulatory subunits of the Na+- and K+-ATPase.

Transfer of structural elements from compact to extended states in unsolvated ubiquitin

Multidimensional ion mobility spectrometry techniques (IMS-IMS and IMS-IMS-IMS) combined with mass spectrometry are used to study structural transitions of ubiquitin ions in the gas phase. It is possible to select and activate narrow distributions of compact and partially folded conformation types and examine new distributions of structures that are formed. Different compact conformations unfold, producing a range of new partially folded states and three resolvable peaks associated with elongated conformers. Under gentle activation conditions, the final populations of the three elongated forms depend on the initial structures of the selected ions. This requires that some memory of the compact state (most likely secondary structure) is preserved along the unfolding pathway. Activation of selected, partially folded intermediates (formed from specific compact states) leads to elongated state populations that are consistent with the initial selected compact form-evidence that intermediates not only retain elements of initial structure but also are capable of transmitting structure to final states.

A role for shoot protein in shoot-root dry matter allocation in higher plants

BACKGROUND AND AIMS

It is stated in many recent publications that nitrate (NO3-) acts as a signal to regulate dry matter partitioning between the shoot and root of higher plants. Here we challenge this hypothesis and present evidence for the viewpoint that NO3- and other environmental effects on the shoot:root dry weight ratio (S:R) of higher plants are often related mechanistically to changes in shoot protein concentration.

METHODS

The literature on environmental effects on S:R is reviewed, focusing on relationships between S:R, growth and leaf NO3- and protein concentrations. A series of experiments carried out to test the proposal that S:R is dependent on shoot protein concentration is highlighted and new data are presented for tobacco (Nicotiana tabacum). KEY RESULTS/EVIDENCE: Results from the literature and new data for tobacco show that S:R and leaf NO3- concentration are not significantly correlated over a range of environmental conditions. A mechanism involving the relative availability of C and N substrates for growth in shoots can explain how shoot protein concentration can influence shoot growth and hence root growth and S:R. Generally, results in the literature are compatible with the hypothesis that macronutrients, water, irradiance and CO2 affect S:R through changes in shoot protein concentration. In detailed studies on several species, including tobacco, a linear regression model incorporating leaf soluble protein concentration and plant dry weight could explain the greater proportion of the variation in S:R within and between treatments over a wide range of conditions.

CONCLUSIONS

It is concluded that if NO3- can influence the S:R of higher plants, it does so only over a narrow range of conditions. Evidence is strong that environmental effects on S:R are often related mechanistically to their effects on shoot protein concentration.

Influence of PEG architecture on protein adsorption and conformation

Poly(L-lysine)-g-poly(ethylene glycol) (PLL-g-PEG) copolymers with various grafting ratios were adsorbed to niobium pentoxide-coated silicon wafers and characterized before and after protein adsorption using X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). Three proteins of different sizes, myoglobin (16 kD), albumin (67 kD), and fibrinogen (340 kD), were studied. XPS was used to quantify the amount of protein adsorbed to the bare and PEGylated surfaces. ToF-SIMS and principal component analysis (PCA) were used to study protein conformational changes on these surfaces. The smallest protein, myoglobin, generally adsorbed in higher numbers than the much larger fibrinogen. Protein adsorption was lowest on the surfaces with the highest PEG chain surface density and increased as the PEG layer density decreased. The highest adsorption was found on lysine-coated and bare niobium surfaces. ToF-SIMS and PCA data evaluation provided further information on the degree of protein denaturation, which, for a particular protein, were found to decrease with increasing PEG surface density and increase with decreasing protein size.

Dietary supplements and sports performance: amino acids

This is the third in a series of six articles to discuss the major classes of dietary supplements (vitamins; minerals; amino acids; herbs or botanicals; metabolites, constituents/extracts, or combinations). The major focus is on efficacy of such dietary supplements to enhance exercise or sport performance.

Complete MALDI-ToF MS analysis of cross-linked peptide-RNA oligonucleotides derived from nonlabeled UV-irradiated ribonucleoprotein particles

Protein-RNA cross-linking combined with mass spectrometry is a powerful tool to elucidate hitherto non-characterized protein-RNA contacts in ribonucleoprotein particles, as, for example, within spliceosomes. Here, we describe an improved methodology for the sequence analysis of purified peptide-RNA oligonucleotide cross-links that is based solely on MALDI-ToF mass spectrometry. The utility of this methodology is demonstrated on cross-links isolated from UV-irradiated spliceosomal particles; these were (1) [15.5K-61 K-U4 atac] small nuclear ribonucleoprotein (snRNP) particles prepared by reconstitution in vitro, and (2) U1 snRNP particles purified from HeLa cells. We show that the use of 2',4',6'-trihydroxyacetophenone (THAP) as MALDI matrix allows analysis of cross-linked peptide-RNA oligonucleotides in the reflectron mode at high resolution, enabling sufficient accuracy to assign unambiguously cross-linked RNA sequences. Most important, post-source decay (PSD) analysis under these conditions was successfully applied to obtain sequence information about the cross-linked peptide and RNA moieties within a single spectrum, including the identification of the actual cross-linking site. Thus, in U4 atac snRNA we identified His 270 in the spliceosomal U4/U6 snRNP-specific protein 61 K (hPrp31p) cross-linked to U 44; in the U1 snRNP we show that Leu175 of the U1 snRNP-specific 70K protein is cross-linked to U 30 of U1 snRNA. This type of analysis is applicable to any type of RNP complex and may be expected to pave the way for the further analysis of protein-RNA complexes in much lower abundance and/or of cross-links that are obtained in low yield.

Assessment of some tools for the characterization of the human osteoarthritic cartilage proteome

Since the proteome of osteoarthritic articular cartilage has been poorly investigated as yet, we adapted proteomic technologies to the study of the proteins secreted or released by fresh human osteoarthritic cartilage in culture. Fresh cartilage explants were obtained from three donors undergoing surgery for knee joint replacement. The explants were dissected out, minced, and incubated in serum-free culture medium. After 48 h, proteins in the medium were identified by two-dimensional or off-gel electrophoresis coupled to tandem mass spectrometry, or by using an antibody-based protein microarray designed to detect angiogenic factors, growth factors, chemokines, and cytokines. We identified a series of 43 proteins. Some of these proteins were already described as secretion products of chondrocytes, such as YKL-39 or osteoprotegerin, while several other were known proteins but have never been reported previously in cartilage, such as the serum amyloid P-component, the vitamin D binding protein, the pigment epithelium derived factor, the pulmonary and activation-regulated chemokine, lyl-1, thrombopoietin, fibrinogen, angiogenin, gelsolin, and osteoglycin/mimecan. While this study enabled the identification of novel proteins secreted or released by human osteoarthritic cartilage, the goal of the present work was essentially to describe the technical approach necessary for a systematic study of osteoarthritic cartilages from a large population of donors, in order to be able to select the good markers and/or targets for this poorly explored disease.

Fractal intermediates in the self-assembly of silicatein filaments

Silicateins are proteins with catalytic, structure-directing activity that are responsible for silica biosynthesis in certain sponges; they are the constituents of macroscopic protein filaments that are found occluded within the silica needles made by Tethya aurantia. Self-assembly of the silicatein monomers and oligomers is shown to form fibrous structures by a mechanism that is fundamentally different from any previously described filament-assembly process. This assembly proceeds through the formation of diffusion-limited, fractally patterned aggregates on the path to filament formation. The driving force for this self-assembly is suggested to be entropic, mediated by the interaction of hydrophobic patches on the surfaces of the silicatein subunits that are not found on highly homologous congeners that do not form filaments. Our results are consistent with a model in which silicatein monomers associate into oligomers that are stabilized by intermolecular disulfide bonds. These oligomeric units assemble into a fractal network that subsequently condenses and organizes into a filamentous structure. These results represent a potentially general mechanism for protein fiber self-assembly.

Local and long-range stability in tandemly arrayed tetratricopeptide repeats

The tetratricopeptide repeat (TPR) is a 34-aa alpha-helical motif that occurs in tandem arrays in a variety of different proteins. In natural proteins, the number of TPR motifs ranges from 3 to 16 or more. These arrays function as molecular scaffolds and frequently mediate protein-protein interactions. We have shown that correctly folded TPR domain proteins, exhibiting the typical helix-turn-helix fold, can be designed by arraying tandem repeats of an idealized TPR consensus motif. To date, three designed proteins, CTPR1, CTPR2, and CTPR3 (consensus TPR number of repeats) have been characterized. Their high-resolution crystal structures show that the designed proteins indeed adopt the typical TPR fold, which is specified by the correct positioning of key residues. Here, we present a study of the thermodynamic properties and folding kinetics of this set of designed proteins. Chemical denaturation, monitored by CD and fluorescence, was used to assess the folding and global stability of each protein. NMR-detected amide proton exchange was used to investigate the stability of each construct at a residue-specific level. The results of these studies reveal a stable core, which defines the intrinsic stability of an individual TPR motif. The results also show the relationship between the number of tandem repeats and the overall stability and folding of the protein.

Microcalorimetric studies of the effects on the interactions of human recombinant interferon-alpha2a

The applicability of the physical stability of protein solution monitored by isothermal titration calorimetry (ITC) was evaluated. The second virial coefficient, b2, derived from the dilution enthalpies of protein solution measured by ITC under various experimental conditions was studied. The protein applied in this work is human recombinant interferon-alpha2a (hrIFN-alpha2a), which is a commercial drug applied for the treatment of virus-infected diseases. The results obtained were used to predict the possibility of hrIFN-alpha2a aggregation, and the prediction can be further confirmed by size-exclusion chromatography (SEC). Various factors affecting the stability of protein solution were investigated, for example, temperature, salts, surfactants, and mechanical stress. Specifically, the results show that the dilution enthalpy of hrIFN-alpha2a increased with increasing temperature and NaCl concentration, while b2 decreased, indicating that the attraction between hrIFN-alpha2a molecules was enhanced under these conditions. On studying the effect of mechanical stress, the data obtained reveals that the introduction of centrifugal or vortex force strengthened the attractive forces between hrIFN-alpha2a molecules. These implications were supported by SEC data, demonstrating that the amount of aggregated hrIFN-alpha2a was increased. As a consequence, the methodologies presented in this investigation offer a possibility of monitoring the physical stability of protein solution at various stages of recovery, purification as well as the development of appropriate drug storage formulations.

Molecular characterization and phylogenetic evaluation of the hsp90 gene from selected nematodes

While multiple genes are optimal for corroborating nematode phylogenies, only a few are commonly used. Here we examine the phylogenetic potential of the nuclear Hsp90 chaperone gene. We used degenerate primers to obtain partial Hsp90 sequences from several plant-parasitic and free-living nematodes. Hsp90 was single-copy in Heterodera glycines and Meloidogyne javanica, similar to the situation for Caenorhabditis elegans. The full-length H. glycines Hsp90 protein sequence showed homology to sequences from C. elegans and Brugia pahangi and to other eukaryotes, and contains several functionally important regions common to cytoplasmic Hsp90 proteins. The Hsp90 amino acid phylogeny supported the Coelomata hypothesis for metazoan evolution. Phylogenetic trees, substitution scatter plots, and statistics for phylogenetic signal were made for Hsp90, 18S small subunit (SSU), and 28S large subunit (LSU) over a limited but broad sampling of nematode taxa. Only the LSU data set failed to recover any of the expected topology and showed extensive substitution saturation. In an intensive sampling of plant-parasitic nematode taxa, the Hsp90 tree topologies were generally congruent with rDNA results and alignments were unambiguous. Hsp90 sequences may help strengthen branch support or clarify tree topologies when other molecules show ambiguous alignments, greater branch-length heterogeneity, or codon bias in certain taxonomic groups.

Ultrasonic drug delivery--a general review

Ultrasound has an ever-increasing role in the delivery of therapeutic agents, including genetic material, protein and chemotherapeutic agents. Cavitating gas bodies, such as microbubbles, are the mediators through which the energy of relatively non-interactive pressure waves is concentrated to produce forces that permeabilise cell membranes and disrupt the vesicles that carry drugs. Thus, the presence of microbubbles enormously enhances ultrasonic delivery of genetic material, proteins and smaller chemical agents. Numerous reports show that the most efficient delivery of genetic material occurs in the presence of cavitating microbubbles. Attaching the DNA directly to the microbubbles, or to gas-containing liposomes, enhances gene uptake even further. Ultrasonic-enhanced gene delivery has been studied in various tissues, including cardiac, vascular, skeletal muscle, tumour and even fetal tissue. Ultrasonic-assisted delivery of proteins has found most application in transdermal transport of insulin. Cavitation events reversibly disrupt the structure of the stratus corneum to allow transport of these large molecules. Other hormones and small proteins could also be delivered transdermally. Small chemotherapeutic molecules are delivered in research settings from micelles and liposomes exposed to ultrasound. Cavitation appears to play two roles: it disrupts the structure of the carrier vesicle and releases the drug; and makes cell membranes and capillaries more permeable to drugs. There remains a need to better understand the physics of cavitation of microbubbles and the impact that such cavitation has on cells and drug-carrying vesicles.

Amino acids composition of Teucrium nutlet proteins and their systematic significance

BACKGROUND AND AIMS

Plant species are considered as a good source of dietary proteins, although the nutritional quality of proteins depends on their amino acid composition. In this work the protein content and amino acid composition of nutlets of 21 Teucrium taxa (Lamiaceae) from Spain were analysed and their nutritional quality was compared with the minimum values established by the Food and Agriculture Organization of the United Nations (FAO). In addition, the amino acid composition was evaluated as a chemical character to clarify the taxonomic complexity in this genus.

METHODS

Amino acid content of nutlets was determined after derivatization with diethyl ethoxymethylenemalonate by high-performance liquid chromatography. Previously, nutlets samples were hydrolysed and incubated in an oven at 110 degrees C for 24 h.

KEY RESULTS

The protein content was variable, ranging from 6.4 % in T. dunense to 43.8 % in T. algarbiense. According to the FAO values all taxa contain satisfactory amounts of leucine, threonine and valine and are deficient in lysine. The similarity analysis of Teucrium taxa using amino acid composition data did not clearly reflect the infrageneric classification of this genus.

CONCLUSIONS

Annual species, such as T. spinosum, T. aristatum and T. resupinatum showed a better balanced amino acid composition. The dendrogram partly matched with the karyological complexity of Teucrium. No correlation between amino acid composition and habitat has been observed, showing that Teucrium nutlet amino acid composition may not be strongly influenced by the environment.

Net digestive absorption and adaptive hyperphagia in adult short bowel patients

BACKGROUND AND AIMS

Intestinal adaptation after small bowel resection in humans is debated. We have quantified in adult short bowel (remnant small bowel length <2 m) patients oral intake and net digestive absorption and their evolution over time.

PATIENTS AND METHODS

Oral intake and faecal output were studied over three days in 90 patients (39 and 51 without or with parenteral nutrition, respectively) and in 14 patients in early (<6 months) and late (>6 months) periods after digestive continuity. Nitrogen and fat output were measured using chemiluminescence and Van de Kamer techniques, respectively.

RESULTS

In the whole group, 81% of patients had hyperphagia (spontaneous oral intake >1.5 x resting energy expenditure), independently and negatively related to fat absorption (p<0.01) and body mass index (p<0.001) but not braked by the presence of parenteral nutrition. Protein and fat absorption were related to small bowel length. We observed, in the late in comparison with the early period after digestive continuity: an increase in oral intake (1.6 v 2.3 resting energy expenditure), decrease in stool weight/oral intake ratio, no reduction in per cent fat absorption, and protein absorption improvement associated with a significant increase in the amount of protein absorbed (40 v 64 g/day; p<0.05), both being correlated with remnant small bowel length (p<0.01).

CONCLUSIONS

This study confirms an adaptive hyperphagia in adult short bowel patients. Over time, hyperphagia and amount of protein absorbed increased, the latter being related to remnant small bowel length, indicating a behavioural adaptation that allows expression of intestinal absorptive adaptation.

H-bonding in protein hydration revisited

H-bonding between protein surface polar/charged groups and water is one of the key factors of protein hydration. Here, we introduce an Accessible Surface Area (ASA) model for computationally efficient estimation of a free energy of water-protein H-bonding at any given protein conformation. The free energy of water-protein H-bonds is estimated using empirical formulas describing probabilities of hydrogen bond formation that were derived from molecular dynamics simulations of water molecules at the surface of a small protein, Crambin, from the Abyssinian cabbage (Crambe abyssinica) seed. The results suggest that atomic solvation parameters (ASP) widely used in continuum hydration models might be dependent on ASA for polar/charged atoms under consideration. The predictions of the model are found to be in qualitative agreement with the available experimental data on model compounds. This model combines the computational speed of ASA potential, with the high resolution of more sophisticated solvation methods.

Metabolic profiling of the Arabidopsis pkl mutant reveals selective derepression of embryonic traits

Embryos express several unique differentiation characteristics, including the accumulation of a number of metabolites that are generally considered to be unique to seeds. PICKLE (PKL) codes for a CHD3-chromatin remodeling factor that is necessary for repression of embryonic traits in seedlings of Arabidopsis thaliana (L.) Heynh. In pkl mutants, primary roots are capable of expressing many embryonic traits after germination and are referred to as "pickle roots". In an attempt to examine the breadth of PKL-dependent repression of embryo-specific differentiation pathways, we determined the extent to which a variety of embryo-specific compounds accumulate in pickle roots. We found that pickle roots accumulate triacylglycerol with a fatty acid composition that is similar to that found in seeds. The major seed storage proteins are also present in pickle roots. In addition to these two well-characterized seed storage compounds, we observed that pickle roots accumulate phytate, a form of stored phosphate that is preferentially accumulated in seeds. Seeds of members of the Brassicaceae also accumulate a variety of unique secondary metabolites, including sinapate esters and glucosinolates. Surprisingly, the levels of secondary metabolites in pickle roots were not suggestive of an embryonic differentiation state, but did reveal that a mutation in PKL results in substantial changes in root secondary metabolism. Taken together, these data suggest that PKL is responsible for regulating some but not all aspects of the embryonic program as it relates to the accumulation of embryo-specific metabolites.

Pseudopollen in Dendrobium unicum Seidenf. (Orchidaceae): reward or deception?

BACKGROUND AND AIMS

In 1987, Kjellsson and Rasmussen described the labellar trichomes of Dendrobium unicum Seidenf. and proposed that these hairs function as pseudopollen. Pseudopollen is a mealy material that superficially resembles pollen, is usually laden with food substances and is formed when labellar hairs either fragment into individual cells or become detached from the labellum. However, the trichomes of D. unicum are very different from pseudopollen-forming hairs found in other orchid genera such as Maxillaria and Polystachya. Moreover, Kjellsson and Rasmussen were unable to demonstrate the presence of food substances within these trichomes and argued that even in the absence of food substances, the hairs, in that they superficially resemble pollen, can still attract insects by deceit. The aim of this paper is to investigate whether the labellar trichomes of D. unicum contain food reserves and thus reward potential pollinators or whether they are devoid of foods and attract insects solely by mimicry.

METHODS

Light microscopy, histochemistry and transmission electron microscopy.

KEY RESULTS

Dendrobium unicum produces pseudopollen. Pseudopollen here, however, differs from that previously described for other orchid genera in that the pseudopollen-forming trichomes consist of a stalk cell and a 'head' of component cells that separate at maturity, in contrast to Maxillaria and some Polystachya spp. where pseudopollen is formed by the fragmentation of moniliform hairs. Moreover, the pseudopollen of Maxillaria and Polystachya largely contains protein, whereas in D. unicum the main food substance is starch.

CONCLUSIONS

Flowers of D. unicum, rather than attracting insects solely by deceit may also reward potential pollinators.

Intravenous insulin decreases protein breakdown in infants on extracorporeal membrane oxygenation

BACKGROUND/PURPOSE

Infants requiring extracorporeal membrane oxygenation (ECMO) have the highest rates of protein catabolism ever reported. Recent investigations have found that such extreme protein breakdown is refractory to conventional nutritional management. In this pilot study, the authors sought to use the anabolic hormone insulin to reduce the profound protein degradation in this cohort.

METHODS

Four parenterally fed infants on ECMO were enrolled in a prospective, randomized, crossover trial. Subjects were administered an insulin infusion using a 4-hour hyperinsulinemic euglycemic clamp followed by a control saline infusion on consecutive days in random order. Whole-body protein flux and breakdown were quantified using a primed continuous infusion of the stable isotope L-[1-13C]leucine. Statistical analyses were performed using paired t tests.

RESULTS

Serum insulin levels were increased 15-fold during the insulin clamp compared with the saline control (407 +/- 103 v 26 +/- 12 microU/mL; P <.05). During the insulin infusion, infants had decreased rates of total leucine flux (214 +/- 25 v 298 +/- 38 micromol/kg/h; P <.05) and leucine flux derived from protein breakdown (156 +/- 40 v 227 +/- 54 micromol/kg/h; P <.05) when compared with saline control. Overall, insulin administration produced a 32% reduction in protein breakdown (P <.05).

CONCLUSIONS

In this pilot study, the anabolic hormone insulin markedly reduced protein breakdown in critically ill infants on ECMO. Because elevated protein breakdown correlates with mortality and morbidity, the administration of intravenous insulin may ultimately have broad applicability to the metabolic management of critically ill infants.

ABRF-ESRG'03: analysis of a PVDF-bound known protein with a homogeneous amino-terminus

The Association of Biomolecular Resource Facilities 2003 Edman Sequencing Research Group (ABRF-ESRG'03) sample is the 15th in a series of studies designed to allow participating members to evaluate their abilities to analyze the N-terminus of a protein or peptide using automated Edman degradation chemistry. It is a follow-up study to the ESRG'02 sample, which was a single protein with a heterogeneous N-terminus. Both the 2002 and 2003 samples were obtained from the same protein complex and were resolved by SDS-PAGE followed by electrophoretic transfer to PVDF membrane. The ABRF-ESRG'03 sample had an apparent molecular weight of 49 kDa and a single N-terminus, with initial yields of approximately 2 pmol. Participants were asked to sequence 25 residues and return their results to the ESRG for analysis along with two completed surveys and an area/pmol table for repetitive and initial yield calculations. Data for 46 responses are presented which include initial yields, repetitive yields, sequencer performance, and ability to identify the protein.

Improvement of automatic in-gel digestion by in situ alkylation of proteins

We have recently improved the automation of an in-gel digestion system, DigestPro 96, using in situ alkylation of proteins with acrylamide, conducted during one-dimensional (ID) SDS-PAGE. The improved method included the processes of destaining, dehydration, trypsin digestion, and extraction but excluded the reduction and alkylation steps following staining of proteins with CBB. The extracted peptide mixtures were directly loaded onto a micro C18 LC column of the mass spectrometer. The resultant spectra were processed with "Mascot" search engine to estimate the sequence coverage of the bovine serum albumin (BSA). The original method, designed for Laemmli ID SDS gel applications, consisted of reduction and post-alkylation with iodoacetamide, which produced carboxyamidemethyl (CAM; -S-CH2CONH2) derivatives. The original method also included a desalting step essential for mass spectrometry, especially matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. We compared the original and improved methods using BSA (3 pmol loaded to the gel, one third of digested peptide mixture injected into LC-MS). The original method yielded both CAM and propionicamide (PAM;-S-CH2CH2CONH2) derivatives. The source of PAM derivatives is the unpolymerized acrylamide formed during electrophoresis. The sequence coverage of CAM derivatives of BSA by the original method was 10% with desalting and 19% without desalting. The sequence coverage of PAM derivative by the improved method was 32%. Our results clearly show the advantage of our improved automated in-gel digestion method for in situ PAM alkylated protein with respect to peptide recovery, compared with the original method with CAM post-alkylation.

Rapid amyloid fiber formation from the fast-folding WW domain FBP28

The WW domains are small proteins that contain a three-stranded, antiparallel beta-sheet. The 40-residue murine FBP28 WW domain rapidly formed twirling ribbon-like fibrils at physiological temperature and pH, with morphology typical of amyloid fibrils. These ribbons were unusually wide and well ordered, making them highly suitable for structural studies. Their x-ray and electron-diffraction patterns displayed the characteristic amyloid fiber 0.47-nm reflection of the cross-beta diffraction signature. Both conventional and electron cryomicroscopy showed clearly that the ribbons were composed of many 2.5-nm-wide subfilaments that ran parallel to the long axis of the fiber. There was a region of lower density along the center of each filament. Lateral association of these filaments generated twisted, often interlinked, sheets up to 40 nm wide and many microns in length. The pitch of the helix varied from 60 to 320 nm, depending on the width of the ribbon. The wild-type FBP28 fibers were formed under conditions in which multiexponential folding kinetics is observed in other studies and which was attributed to a change in the mechanism of folding. It is more likely that those phases result from initial events in the off-pathway aggregation observed here.

MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences

BACKGROUND

The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization has become a major goal for many laboratories. To aid in this categorization, there is a need for non-commercial software that is able to both align sequences and also calculate pairwise levels of similarity/identity.

RESULTS

We have developed MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data.

CONCLUSIONS

The advantages of this program over other software are that it is open-source freeware, can analyze a large number of sequences simultaneously, can visualize both sequence alignment and similarity/identity values concurrently, employs global alignment in calculations, and has been formatted to run under both the Unix and the Microsoft Windows Operating Systems. We are presently completing the Macintosh-based version of the program.

A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex

NMR studies of the binding of a substrate to an inactive HIV-1 protease construct, containing an active site mutation PR(D25N), are reported. Substrate titration measurements monitored by HSQC spectra and a (15)N-edited NOESY experiment show that the chromogenic substrate analog of the capsid/p2 cleavage site binds to PR(D25N) with an equilibrium dissociation constant, K(D), of 0.27 +/- 0.05 mM, and upper limits of the association and dissociation rate constants, 2 x 10(4) M(-1)s(-1) and 10 s(-1), respectively, at 20 degrees C, pH 5.8. This association rate constant is not in the diffusion limit, suggesting that association is controlled by a rare event, such as opening of the protease flaps. Analysis of (15)N relaxation experiments reveals a slight reduction of S(2) values in the flap region, indicating a small increase in the amplitude of internal motion on the sub-nsec timescale. In addition, several residues in the flap region are mobile on the conformational exchange timescale, msec-microsec. Flap dynamics of the protease-substrate complex are compared with those of protease-inhibitor complexes, and the implications of these results for substrate-binding models are discussed.

Effect of thiazide drug compound on the testicular protein and cholesterol contents of albino rat

In this study the effect of thiazide diuretic compound on the protein and cholesterol contents in the testes of albino rats as the experimental model. The drug thiazide was administered orally daily for 10,20 and 30 days at the dose of 100mg/kg body weight. Total protein decrease in the testes of rats were evidenced may be due to the side effects of thiazide drug compound which is linked with the hyponatremia and protein metabolism. An elevated level of cholesterol contents observed in thiazide treated rats also revealed that the side effect of drug compound thiazide and also may be due to the stimulation of catecholamine which is stimulated therefore, the biochemical estimation such as protein and cholesterol in the testes after the thiazide treatment determined the effectiveness of diuretic drug compound would provide clinical evidences of their side effects.

Growth, nutrient utilization, and body composition of dairy calves fed milk replacers containing different amounts of protein

Male Holstein calves < 1 wk of age were allowed a 2-wk adaptation period after purchase, and then were blocked by BW and assigned randomly within block to either a baseline slaughter group or one of four experimental groups (n = 8 to 9 per group). Treatments were isocaloric milk replacers (12.5% solids) fed at 12% of BW that contained 16.1, 18.5, 22.9, or 25.8% CP (DM basis) from whey protein sources. After a 6-wk feeding period, all calves were slaughtered and the weights and chemical composition of the viscera-free carcasses (VFC; including head, hide, feet, and tail) were determined. Gain of BW (0.38, 0.45, 0.56, and 0.62 kg/d) and gain:feed ratio (0.51, 0.59, 0.71, and 0.78) increased linearly (P < 0.001) as dietary CP increased; rate of change in body length, wither height, and heart girth also increased linearly (P < or = 0.05). Balance measurements conducted during wk 3 and 4 of the experimental period showed that both absorbed N (16.9, 20.0, 25.8, and 30.6 g/d) and retained N (7.6, 9.0, 13.2, and 15.6 g/d) increased linearly (P < 0.001) as dietary CP increased. Retained N as a percentage of absorbed N increased linearly (P < 0.01) as dietary CP increased (44.3, 44.7, 50.7, and 50.9%), whereas biological value was unaffected (71.1, 68.7, 69.5, and 67.3%; P = 0.26). Digestible energy and ME represented 94.5 and 89.7% of intake energy, respectively, and were not affected by dietary CP content. Plasma urea N concentration increased linearly (2.9, 3.3, 4.6, and 6.0 mg/dL) as dietary CP increased. Contents of water (68.2, 69.1, 70.2, and 70.5%; P < 0.001) and protein (19.6, 20.0, 20.0, and 20.2%; P < 0.10) in VFC increased linearly, whereas contents of fat (7.2, 6.2, 5.5, and 5.2%; P < 0.001) and ash (5.1, 5.2, 4.8, and 4.7%; P < 0.02) decreased linearly as dietary CP increased. Trends in visceral tissue composition were similar to those for VFC. The content of water in VFC tissue gain increased, whereas contents of fat and energy decreased, as dietary CP increased. Final VFC energy and gain of energy in VFC were not affected by dietary CP. At similar initial ME intakes, increasing dietary CP (i.e., increasing protein: energy) linearly increased ADG, gain:feed, N retention, and deposition of lean tissue in VFC, demonstrating that diet composition can markedly affect components of body growth in preruminant dairy calves.

Expression of cyclin D1, D3, E, and p27 in human renal cell carcinoma analysed by tissue microarray

Aberrations in the G1/S transition of the cell cycle have been observed in many malignancies and seem to be critical in the transformation process. Few studies have delineated the presence of G1/S regulatory defects and their clinical relevance in renal cell carcinoma (RCC). Therefore, we have examined the protein contents of cyclin D1, D3, E, and p27 in 218 RCCs, using tissue microarray and immunohistochemistry. The results from a subset of tumours were confirmed by Western blotting and immunohistochemical staining of regular tissue sections. Interestingly, low protein contents of cyclin D1 and p27 were associated with high nuclear grade, large tumour size, and poor prognosis for patients with conventional tumours. We further observed substantial differences in the pattern of G1/S regulatory defects between the different RCC subtypes. The majority of both conventional and papillary cases expressed p27; however, chromophobe tumours generally lacked p27 staining. In addition, conventional RCCs often expressed high cyclin D1 protein levels, while papillary RCCs exhibited high cyclin E. In summary, we have shown that G1/S regulatory defects are present in RCC and are associated with clinico-pathological parameters. The pattern of cell cycle regulatory defects also differed between RCC subtypes.

Development of a multidose formulation for a humanized monoclonal antibody using experimental design techniques

The purpose of this study was to identify optimal preservatives for a multidose formulation of a humanized monoclonal antibody using experimental design techniques. The effect of antimicrobial parenteral preservatives (benzyl alcohol, chlorobutanol, methylparaben, propylparaben, phenol, and m-cresol) on protein stability was assessed using size-exclusion chromatography, differential scanning calorimetry, right-angle light scattering, UV spectroscopy, and potency testing using a cell-based fluorescence-activated cell sorting method. A quick, cost-effective preservative screening test was designed. Combinations of preservatives were examined using an I-optimal experimental design. The protein was most stable in the presence of methylparaben and propylparaben, and was compatible with benzyl alcohol and chlorobutanol at low concentrations. Phenol and m-cresol were not compatible with the protein. The I-optimal experimental design indicated that as an individual preservative, benzyl alcohol was promising. The model also indicated several effective combinations of preservatives that satisfied the antimicrobial efficacy and physical stability constraints. The preservative screening test and the experimental design approach were effective in identifying optimal concentrations of antimicrobial preservatives for a multidose protein formulation; (1) benzyl alcohol, and (2) the combination of methylparaben and chlorobutanol were screened as potential candidates to satisfy the regulatory requirements of various preservative efficacy tests.

Advances in therapy for osteoporosis

The current status of detection and treatment of osteoporosis is reviewed. Despite substantial advances in the past ten years, most patients with osteoporotic fractures are still not being treated for the underlying bony cause of the fracture, and most people at risk for fracture are not being offered known protective regimens. The foundation of any therapeutic program is adequate nutrition--specifically protein, calcium, phosphorus and vitamin D. Current anti-resorptive agents reduce vertebral fracture risk by 30% to 50% and teriparatide, a newly approved anabolic agent, reduces risk by up to 80+%. Effective treatments for chronic bony pain that occurs in some patients with spine fractures is affored by two minimally invasive procedures, kyphoplasty and vertebroplasty. Some of these chronically painful fractures represent instances of previously unrecognized non-union, and in them low-pressure vertebroplasty produces prompt and lasting relief. Fracture risk reductions with current anti-resorptive agents are at least twice as great as can be explained by drug effects on bone mass. Moreover, risk is reduced within a few months of starting therapy. These observations focus attention on bone remodeling and point to the need for improvement of biomarker technology, since it seems likely that reduction in remodeling activity underlies much of the fracture risk reduction and can therefore be used to monitor therapy.

Identification of novel components of Trypanosoma brucei editosomes

The editosome is a multiprotein complex that catalyzes the insertion and deletion of uridylates that occurs during RNA editing in trypanosomatids. We report the identification of nine novel editosome proteins in Trypanosoma brucei. They were identified by mass spectrometric analysis of functional editosomes that were purified by serial ion exchange/gel permeation chromatography, immunoaffinity chromatography specific to the TbMP63 editosome protein, or tandem affinity purification based on a tagged RNA editing ligase. The newly identified proteins have ribonuclease and/or RNA binding motifs suggesting nuclease function for at least some of these. Five of the proteins are interrelated, as are two others, and one is related to four previously identified editosome proteins. The implications of these findings are discussed.

Self-assembly of proteins and their nucleic acids

We have developed an artificial protein scaffold, herewith called a protein vector, which allows linking of an in-vitro synthesised protein to the nucleic acid which encodes it through the process of self-assembly. This protein vector enables the direct physical linkage between a functional protein and its genetic code. The principle is demonstrated using a streptavidin-based protein vector (SAPV) as both a nucleic acid binding pocket and a protein display system. We have shown that functional proteins or protein domains can be produced in vitro and physically linked to their DNA in a single enzymatic reaction. Such self-assembled protein-DNA complexes can be used for protein cloning, the cloning of protein affinity reagents or for the production of proteins which self-assemble on a variety of solid supports. Self-assembly can be utilised for making libraries of protein-DNA complexes or for labelling the protein part of such a complex to a high specific activity by labelling the nucleic acid associated with the protein. In summary, self-assembly offers an opportunity to quickly generate cheap protein affinity reagents, which can also be efficiently labelled, for use in traditional affinity assays or for protein arrays instead of conventional antibodies.

An assessment of the ability of the stay-green phenotype in lolium species to provide an improved protein supply for ruminants

The stay-green phenotype results from a naturally occurring mutation in which senescent leaves retain their chlorophyll and the associated apoprotein, LHCPII. Protection of this protein pool could deliver grass with enhanced protein content and could decrease the extent of protein degradation by plant proteases in the rumen. This would enhance the efficiency of protein utilization in livestock to the benefit of the environment. Field plots of stay-green and wild-type Lolium perenne were defoliated at intervals to simulate grazing. There were variations in foliar protein content and proteolysis throughout the year, but no significant differences between genotypes when material was analysed fresh or after it was cut and dried to simulate hay-making, which possibly induced senescence. In a subsequent experiment with stay-green and wild-type L temulentum, increased protein retention and decreased protein degradability were observed in stay-green leaves that were allowed to senescence naturally and extensively on the plant. That there is no difference between the two L. perenne genotypes suggests that as a field crop in grazed pastures the stay-green genotype would not confer a nutritional advantage in terms of protein degradability. It is possible that grazing promotes a high proportion of non-senescent to senescent leaf material within the sward and thus any advantage conferred by the stay-green phenotype would be effectively masked by an abundance of mature foliage. It is suggested that the stay-green trait would be of benefit in areas where agricultural practice permits extensive natural senescence to occur.

Regulation of apoptosis in African swine fever virus-infected macrophages

A number of viruses have evolved antiapoptotic mechanisms to promote infected-cell survival, either to ensure efficient productive viral replication or to promote long-term survival of virus-infected cells. Recent studies identified critical African swine fever virus genes involved in the complex regulation of ASFV-host interactions. Here we review the present knowledge of the recently identified ASFV genes with special attention to those which affect viral virulence, host range, and pathogenesis by regulating viral-induced apoptotic mechanisms.

Stability and interactions of the amino-terminal domain of ClpB from Escherichia coli

ClpB is a member of a multichaperone system in Escherichia coli (with DnaK, DnaJ, and GrpE) that reactivates aggregated proteins. The sequence of ClpB contains two ATP-binding regions that are enclosed between the N- and C-terminal extensions. Whereas it has been found that the N-terminal region of ClpB is essential for the chaperone activity, the structure of this region is not known, and its biochemical properties have not been studied. We expressed and purified the N-terminal fragment of ClpB (residues 1-147). Circular dichroism of the isolated N-terminal region showed a high content of alpha-helical structure. Differential scanning calorimetry showed that the N-terminal region of ClpB is thermodynamically stable and contains a single folding domain. The N-terminal domain is monomeric, as determined by gel-filtration chromatography, and the elution profile of the N-terminal domain does not change in the presence of the N-terminally truncated ClpB (ClpBDeltaN). This indicates that the N-terminal domain does not form strong contacts with ClpBDeltaN. Consistently, addition of the separated N-terminal domain does not reverse an inhibition of ATPase activity of ClpBDeltaN in the presence of casein. As shown by ELISA measurements, full-length ClpB and ClpBDeltaN bind protein substrates (casein, inactivated luciferase) with similar affinity. We also found that the isolated N-terminal domain of ClpB interacts with heat-inactivated luciferase. Taken together, our results indicate that the N-terminal fragment of ClpB forms a distinct domain that is not strongly associated with the ClpB core and is not required for ClpB interactions with other proteins, but may be involved in recognition of protein substrates.

Thermodynamic analysis of the binding of component enzymes in the assembly of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus

The peripheral subunit-binding domain (PSBD) of the dihydrolipoyl acetyltransferase (E2, EC 2.3.1.12) binds tightly but mutually exclusively to dihydrolipoyl dehydrogenase (E3, EC 1.8.1.4) and pyruvate decarboxylase (E1, EC 1.2.4.1) in the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. Isothermal titration calorimetry (ITC) experiments demonstrated that the enthalpies of binding (DeltaH degrees ) of both E3 and E1 with the PSBD varied with salt concentration, temperature, pH, and buffer composition. There is little significant difference in the free energies of binding (DeltaG degrees = -12.6 kcal/mol for E3 and = -12.9 kcal/mol for E1 at pH 7.4 and 25 degrees C). However, the association with E3 was characterized by a small, unfavorable enthalpy change (DeltaH degrees = +2.2 kcal/mol) and a large, positive entropy change (TDeltaS degrees = +14.8 kcal/mol), whereas that with E1 was accompanied by a favorable enthalpy change (DeltaH degrees = -8.4 kcal/mol) and a less positive entropy change (TDeltaS degrees = +4.5 kcal/mol). Values of DeltaC(p) of -316 cal/molK and -470 cal/molK were obtained for the binding of E3 and E1, respectively. The value for E3 was not compatible with the DeltaC(p) calculated from the nonpolar surface area buried in the crystal structure of the E3-PSBD complex. In this instance, a large negative DeltaC(p) is not indicative of a classical hydrophobic interaction. In differential scanning calorimetry experiments, the midpoint melting temperature (T(m)) of E3 increased from 91 degrees C to 97.1 degrees C when it was bound to PSBD, and that of E1 increased from 65.2 degrees C to 70.0 degrees C. These high T(m) values eliminate unfolding as a major source of the anomalous DeltaC(p) effects at the temperatures (10-37 degrees C) used for the ITC experiments.

Methods in molecular cardiology: protein analysis

Several protein analysis techniques are described in this review to give insight into the potential applications for research. Protein analysis can be performed in several ways. All techniques are derived from the same general principle, the migration of charged particles in an electrical field. Electrophoresis of biomolecules, like proteins, provides the possibility to identify and characterise the molecules based upon different chemical properties. Immobilisation of the proteins after electrophoresis on paper is necessary to allow easy handling of the materials (blotting). These techniques also provide information on the state of a protein, whether it is activated or inactivated. To show the use of the described techniques in cardiology, two applications are provided in this review.

Soft protein-protein docking in internal coordinates

The association of two biological macromolecules is a fundamental biological phenomenon and an unsolved theoretical problem. Docking methods for ab initio prediction of association of two independently determined protein structures usually fail when they are applied to a large set of complexes, mostly because of inaccuracies in the scoring function and/or difficulties on simulating the rearrangement of the interface residues on binding. In this work we present an efficient pseudo-Brownian rigid-body docking procedure followed by Biased Probability Monte Carlo Minimization of the ligand interacting side-chains. The use of a soft interaction energy function precalculated on a grid, instead of the explicit energy, drastically increased the speed of the procedure. The method was tested on a benchmark of 24 protein-protein complexes in which the three-dimensional structures of their subunits (bound and free) were available. The rank of the near-native conformation in a list of candidate docking solutions was <20 in 85% of complexes with no major backbone motion on binding. Among them, as many as 7 out of 11 (64%) protease-inhibitor complexes can be successfully predicted as the highest rank conformations. The presented method can be further refined to include the binding site predictions and applied to the structures generated by the structural proteomics projects. All scripts are available on the Web.

Hepatitis E antibody profiles in serum and urine

The aim of this study was to evaluate anti-HEV antibody profiles in urine specimens in comparison to corresponding serum samples to assess the utility of urine as a clinical specimen. Paired serum and urine specimens from 71 hepatitis E patients, 33 non-E hepatitis patients, 63 patients with nonhepatic diseases, and 26 healthy individuals were tested by recombinant HEV protein (55 kD)-based indirect enzyme-linked immunosorbent assay (ELISA). Uronegativity for anti-HEV IgM was noted in 71 (100%) serologically confirmed patients with hepatitis E. Hepatitis E patients (10/10) showed urinary absence or very low levels of total IgM by capture ELISA, suggesting absence or low levels of filtration, and/or local synthesis, and/or transudation of IgM in urine during infection. When these patients were tested for total IgG and IgA, microquantities of immunoglobulins were noted in all urine samples (10/10 for each). However, the proportions of uropositivity for anti-HEV IgG and IgA in hepatitis E patients were low and indicated only 21.42% and 49.33% concordance with seropositivity, respectively. Control groups also showed low and variable uropositivity for anti-HEV IgG and IgA. Overall, HEV-specific antibodies exhibited by serum in recent and past infections were not found in urine. The study demonstrated the inadequacy of urine specimens for detection of hepatitis E antibodies.

Development-dependent disappearance of caspase-3 in skeletal muscle is post-transcriptionally regulated

Caspase-3, a major player in apoptosis, engages apoptosis-activated cells into an irreversible pathway leading to cell death. In this article, we report that caspase-3 protein is absent from rat and mouse adult skeletal muscles, despite the abundant presence of its mRNA. During skeletal muscle development, caspase-3 protein is present in neonatal animals, but its expression gradually decreases, and disappears completely by 1 month of age, when there is still abundant caspase-3 mRNA. This discordance between caspase-3 message and protein expression is unique to skeletal muscle, as in all other analyzed tissues the protein presence correlates with the presence of the mRNA. The only circumstance in which caspase-3 protein appears in adults is in regenerating muscles; once regeneration is complete, however, it again becomes undetectable in repaired muscles. We conclude that caspase-3 protein in skeletal muscle is uniquely regulated at the post-transcriptional level, unseen in other tissues such as brain, heart, lung, kidney, thymus, spleen, liver, or testis. The post-transcriptional regulation of caspase-3 might serve as a fail-safe mechanism to avoid accidental cell death.

Nitrogen fertilizer factory effects on the amino acid and nitrogen content in the needles of Scots pine

The aim of the research was to evaluate the content of amino acids in the needles of Pinus sylvestris growing in the area affected by a nitrogen fertilizer factory and to compare them with other parameters of needles, trees, and sites. Three young-age stands of Scots pine were selected at a distance of 0.5 km, 5 km, and 17 km from the factory. Examination of the current-year needles in winter of the year 2000 revealed significant (p < 0.05) differences between the site at a 0.5-km distance from the factory and the site at a 17-km distance from the factory--with the site closest to the factory showing the highest concentrations of protein (119%), total arginine (166%), total other amino acids (depending on amino acid, the effect ranged between 119 and 149%), free arginine (771%), other free amino acids (glutamic acid, threonine, serine, lysine--depending on amino acid, the effect ranged between 162 and 234%), also the longest needles, widest diameter, largest surface area, and heaviest dry weight (respectively, 133, 110, 136, and 169%). The gradient of nitrogen concentration in the needles was assessed on the selected plots over the period of 1995-2000, with the highest concentration (depending on year, 119 to 153%) documented in the site located 0.5 km from the factory. Significant correlations were determined between the total amino acid contents (r = 0.448 -0.939, p < 0.05), some free amino acid (arginine, aspartic acid, glutamic acid, lysine, threonine, and serine) contents (r = 0.418 - 0.975, p < 0.05), and air pollutant concentration at the sites, the distance between the sites and the factory, and characteristics of the needles. No correlation was found between free or total arginine content and defoliation or retention of the needles. In conclusion, it was revealed that elevated mean monthly concentration of ammonia (26 microg m(-3)) near the nitrogen fertilizer factory caused changes in nitrogen metabolism, especially increasing (nearly eight times) concentration of free arginine in the needles of Scots pine.

Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis

The methods of continuum electrostatics are used to calculate the binding free energies of a set of protein-protein complexes including experimentally determined structures as well as other orientations generated by a fast docking algorithm. In the native structures, charged groups that are deeply buried were often found to favor complex formation (relative to isosteric nonpolar groups), whereas in nonnative complexes generated by a geometric docking algorithm, they were equally likely to be stabilizing as destabilizing. These observations were used to design a new filter for screening docked conformations that was applied, in conjunction with a number of geometric filters that assess shape complementarity, to 15 antibody-antigen complexes and 14 enzyme-inhibitor complexes. For the bound docking problem, which is the major focus of this paper, native and near-native solutions were ranked first or second in all but two enzyme-inhibitor complexes. Less success was encountered for antibody-antigen complexes, but in all cases studied, the more complete free energy evaluation was able to identify native and near-native structures. A filter based on the enrichment of tyrosines and tryptophans in antibody binding sites was applied to the antibody-antigen complexes and resulted in a native and near-native solution being ranked first and second in all cases. A clear improvement over previously reported results was obtained for the unbound antibody-antigen examples as well. The algorithm and various filters used in this work are quite efficient and are able to reduce the number of plausible docking orientations to a size small enough so that a final more complete free energy evaluation on the reduced set becomes computationally feasible.

Role of uppermost superficial surface layer of articular cartilage in the lubrication mechanism of joints

The uppermost superficial surface layer of articular cartilage, the 'lamina splendens' which provides a very low friction lubrication surface in articular joints, was investigated using atomic force microscopy (AFM). Complementary specimens were also observed under SEM at -10 degrees C without dehydration or sputter ion coating. Fresh adult pig osteochondral specimens were prepared from the patellas of pig knee joints and digested with the enzymes, hyaluronidase, chondroitinase ABC and alkaline protease. Friction coefficients between a pyrex glass plate and the osteochondral specimens digested by enzymes as well as natural (undigested) specimens were measured, using a thrust collar apparatus. Normal saline, hyaluronic acid (HA) and a mixture of albumin, globulin, HA (AGH) were used as lubrication media. The surface irregularities usually observed in SEM studies were not apparent under AFM. The articular cartilage surface was resistant to hyaluronidase and also to chondroitinase ABC, but a fibrous structure was exhibited in alkaline protease enzymes-digested specimens. AFM analysis revealed that the thickness of the uppermost superficial surface layer of articular cartilage was between 800 nm and 2 microm in adult pig articular cartilage. The coefficient of friction (c.f.) was significantly higher in chondroitinase ABC and alkaline protease enzymes digested specimens. Generally, in normal saline lubrication medium, c.f. was higher in comparison to HA and AGH lubrication media. The role of the uppermost, superficial surface layer of articular cartilage in the lubrication mechanism of joints is discussed.

Dietary fat, cholesterol and colorectal cancer in a prospective study

The relationships between consumption of total fat, major dietary fatty acids, cholesterol, consumption of meat and eggs, and the incidence of colorectal cancers were studied in a cohort based on the Finnish Mobile Clinic Health Examination Survey. Baseline (1967-1972) information on habitual food consumption over the preceding year was collected from 9959 men and women free of diagnosed cancer. A total of 109 new colorectal cancer cases were ascertained late 1999. High cholesterol intake was associated with increased risk for colorectal cancers. The relative risk between the highest and lowest quartiles of dietary cholesterol was 3.26 (95% confidence interval 1.54-6.88) after adjusting for age, sex, body mass index, occupation, smoking, geographic region, energy intake and consumption of vegetables, fruits and cereals. Consumption of total fat and intake of saturated, monounsaturated, or polyunsaturated fatty acids were not significantly associated with colorectal cancer risk. Nonsignificant associations were found between consumption of meat and eggs and colorectal cancer risk. The results of the present study indicate that high cholesterol intake may increase colorectal cancer risk, but do not suggest the presence of significant effects of dietary fat intake on colorectal cancer incidence.

Application of an improved biuret method to the determination of total protein in urine and cerebrospinal fluid without concentration step by use of Hitachi 7170 auto-analyzer

A biuret automated colorimetric assay for total protein in urine and cerebrospinal fluids was established. The procedures were as follows. Acidify all urine sample before analysis. Add precipitant Na(2)WO(4) to urine samples. After 10 min, centrifuge, decant the supernatant fluid, drain the inverted tubes on absorbent tissue, dissolve the precipitation with 0.1 mol/L NaOH, and finally adapt the reconstituted urine to the Hitachi 7170 analyzer. A cell-free cerebrospinal fluid sample produced by centrifugation can be inserted in an auto-analyzer for protein measurement directly. The program: mix 35 microl sample (CSF or reconstituted urine) and standard with 0.2 mol/L NaOH; incurable at 37 degrees C for 5 min, and real A1. Add concentrated biuret reagent, and 10 min later measure absorbance A2 at 546 nm vs. reagent blank. Secondary wavelength was 700 nm. The test results were calculated against a one-point standard. This biuret colorimetric method was relatively simple, fast, and accurate for the determination of protein in urine and cerebrospinal fluid, with a wide linearity extending from 0.125 g/L up to 6 g/L, had a good correlation with Benzethonium chloride turbidimetry technique, and was a practical routine method.