How thick is the layer of thermal volume surrounding the protein?

Investigation on the volume properties of protein hydration layers is reported. Presented results are based on combination of Monte Carlo modeling and available experimental data. Six globular proteins with known data are chosen for analysis. Analyzing the model and the experimental results we found that water molecules bound to proteins by hydrogen bond are preferentially located at the places with local depressions on the protein surface. Consequently, the hydration level is not strictly proportional to the area of charged and polar surfaces, but also depends on the shape of the molecular surface. The thickness of the thermal volume layer as calculated in the framework of the scaled particle theory is 0.6-0.65 A for chosen proteins. The obtained value is significantly lower than that presented for proteins in earlier papers (where proportionality between the hydration level and the area of charged and polar surfaces was assumed), but is close to the value published for small solute molecules. Discussion including the influence of protein size and the thermal motion of the surface is presented.     

Is the fatty acid composition of Daphnia galeata determined by the fatty acid composition of the ingested diet?

1. The fatty acid (FA) composition of Daphnia galeata and their algal food was analysed and showed many similarities, however, some significant differences were also found in the relative abundance of the FA C16 : 4ω3 and docosahexaenoic acid (DHA). Their relative abundances were much lower in daphnids than in their algal diet.
2. When daphnids were fed three distinct emulsion particles with DHA : eicosapentaenoic acid (EPA) ratios of c. 0.7, 2 and 4, the final DHA : EPA ratio in the daphnids always favoured EPA. The increase of the food DHA : EPA ratio resulted in a minor increase of DHA (to c. 2%). Feeding the animals on emulsion particles with increasing ratios of DHA : EPA, caused a minor ( c. 2%) increase of DHA level but EPA levels remained high ( c. 10%).
3. When labelled with [¹⁴C]linoleic acid and [¹⁴C]linolenic acid daphnids showed low conversion of both essential FA into C20 polyunsaturated fatty acids (PUFAs). This low conversion activity might explain the importance of C20 PUFAs as dietary compounds in the food of Daphnia.
4. The results indicate the insignificance of DHA and C16 : 4ω3 for daphnids. As EPA can be derived from C18 : 3ω3 it is not strictly essential, although it might be a significant factor in food quality for Daphnia.     

Is cold the new hot? Elevated ubiquitin-conjugated protein levels in tissues of Antarctic fish as evidence for cold-denaturation of proteins in vivo

Levels of ubiquitin (Ub)-conjugated proteins, as an index of misfolded or damaged proteins, were measured in notothenioid fishes, with both Antarctic (Trematomus bernacchii, T. pennellii, Pagothenia borchgrevinki) and non-Antarctic (Notothenia angustata, Bovichtus variegatus) distributions, as well as non-notothenioid fish from the Antarctic (Lycodichthys dearborni, Family Zoarcidae) and New Zealand (Bellapiscis medius, Family Tripterygiidae), in an effort to better understand the effect that inhabiting a sub-zero environment has on maintaining the integrity of the cellular protein pool. Overall, levels of Ub-conjugated proteins in cold-adapted Antarctic fishes were significantly higher than New Zealand fishes in gill, liver, heart and spleen tissues suggesting that life at sub-zero temperatures impacts protein homeostasis. The highest tissue levels of ubiquitinated proteins were found in the spleen of all fish. Ub conjugate levels in the New Zealand N. angustata, more closely resembled levels measured in other Antarctic fishes than levels measured in other New Zealand species, likely reflecting their recent shared ancestry with Antarctic notothenioids.     

Is location a significant parameter in the layer dependent dissection properties of the aorta?

Proper characterisation of biological tissue is key to understanding the effect of the biomechanical environment in the physiology and pathology of the cardiovascular system. Aortic dissection in particular is a prevalent and sometimes fatal disease that still lacks a complete comprehension of its progression. Its development and outcome, however, depend on the location in the vessel. Dissection properties of arteries are frequently studied via delamination tests, such as the T-peel test and the mixed-mode peel test. So far, a study that performs both tests throughout different locations of the aorta, as well as dissecting several interfaces, is missing. This makes it difficult to extract conclusions in terms of vessel heterogeneity, as a standardised experimental procedure cannot be assured for different studies in literature. Therefore, both dissection tests have been here performed on healthy porcine aortas, dissecting three interfaces of the vessels, i.e., the intima-media, the media-adventitia and the media within itself, considering different locations of the aorta, the ascending thoracic aorta (ATA), the descending thoracic aorta and the infrarenal abdominal aorta (IAA). Significant differences were found for both, layers and location. In particular, dissection forces in the ATA were the highest and the separation of the intima-media interface required significantly the lowest force. Moreover, dissection in the longitudinal direction of the vessel generally required more force than in the circumferential one. These results emphasise the need to characterise aortic tissue considering the specific location and dissected layer of the vessel.

     

Is flight architecture determined by physical constraints or by natural selection?: the case of the midge Chironomus plumosus

Males of the midge Chironomus plumosus fly solely to mate. They maintain station for long periods in moving air. Females patrol in search of males and, after receiving a spermatophore, fly to oviposition sites. The requirements of flight in males and females are therefore fundamentally different. Females are larger than males, on average, so these differences could stem from scaling rules governing the geometry of space. The same explanation might apply to flight differences within the sexes and even to peculiarities of flight architecture in C. plumosus compared to other flying animals. In other words, might flight design be accounted for entirely by mechanical constraints without recourse to natural selection?
To test this hypothesis, the power output of C. plumosu was measured as size-specific muscle mass. Contrary to expectation, little evidence was found of scaling effects in this measure of power. Despite its being among the smallest of animals to fly, C. plumosus turns out to have the largest mass of flight muscle, relative to body size, yet found among animals. Differences both between C. plumosus and other species and within C. plumosus are, in general, more readily accounted for by the requirements of the mating system within the viscous universe encountered by small flying animals. We conclude that it is natural selection rather than mechanical constraint that is the primary influence determining the architecture of flight in this small animal.     

Are synthetic proteins relevant to the problem of protein folding?

The possibility to derive the analogs of native proteins by the chemical synthesis is considered to be a serious argument for the concept of posttranslational protein folding. The present paper analyzes for the first time chemically synthesized proteins to reveal whether they are relevant to the problem of protein folding. The results enable the following conclusions to be drawn. The acquisition of the peculiar conformations by the chemically synthesized proteins to exhibit the specific functions is conditioned by the highly marked features of the secondary and tertiary structures of the corresponding native proteins. These features will make themselves evident only if favorable conditions are carefully chosen during the experiments for each individual protein. Thus, in our opinion, the possibility to derive a synthetic protein is hardly evidence for the posttranslational folding of proteins.     

Is the post-disturbance composition of a plant population determined by selection for outcrossed seedlings or by the composition of the seedbank?

Seedbanks are expected to buffer populations against disturbances, such as fire, thatcould alter the genetic composition of smaller, ephemeral adult populations. However,seedling genotypes may be influenced by the spatially heterogeneous nature of both theseedbank and the disturbance (for example, germination may vary with local disturbance)and also by selection acting on germination and post-germination performance. We usedmicrosatellite-DNA surveys of seedlings emerging from the soil-stored seedbanks ofGrevillea macleayana after wildfire to compare diversity and spatial structurein seedlings and adults, and through resampling of the seedling data set, to determinewhether the resultant adult population reflected the effects of selection or randomseedling mortality. The large post-fire seedling cohorts captured the full allelicdiversity of the pre-fire adult population. However, we found a mismatch in the genotypicstructure of adults and seedlings. Seedlings displayed larger heterozygous deficits thanadults; however, over the ensuing 11 years, seedling heterozygosity eventually matchedvalues for the pre-fire adults. Increasing heterozygosity among adults has generally beenattributed to heterosis and/or reduction in Wahlund effects via self-thinning.Resampling of early post-fire seedlings to generate samples of equivalent size tosurvivors at 11 years showed that increases in heterozygosity must be driven by selectionfavouring outcrossed seed. This finding is important in an evolutionary context but alsohas implications for the restoration of natural or managed populations where a seedbank isa viable source of recruits.     

Is heat shock protein re-induction during tolerance related to the stressor-specific induction of heat shock proteins?

The existence of stressor-specific induction programs of heat shock proteins (hsps) leads us to analyze the possible occurrence of a stressor-specific tolerance induced by either heat shock, arsenite, or cadmium. As a measure of this tolerance re-induction of hsps was studied. In this paper, we tested whether the refractory state is either valid for each specific hsp (implying independent regulation of every member of the heat shock protein family) or extends from small subsets of the hsp-family to even larger groups of proteins (indicating a more common denominator in their regulation). (Re-)induction of hsps does not seem to be regulated at the level of each individual hsp since differences in induced synthesis of hsps between two stressor conditions are not supplemented systematically upon the sequential application of the two stressors. The most notable example in this respect is hsp60. A pretreatment with cadmium, which hardly induces synthesis of this hsp, does induce a tolerance to (re)-induction by heat shock, which normally induces hsp60. This suggests the existence of a more common denominator regulating the coordinate expression of at least some hsps. From our data we conclude that the degree, but not the pattern, of hsp re-induction is influenced by the type of stressor used in the pretreatment. The pattern of hsps induced by a secondary applied stressor still shows most of its stressor-specificity and seems to be independent of any pretreatment. The possible implications of stressor-specificity are discussed. © 1996 Wiley-Liss, Inc.     

Pressure-dependent changes in the structure of the melittin α-helix determined by NMR

A novel method is described, which uses changes in NMR chemical shifts to characterise the structural change in a protein with pressure. Melittin in methanol is a small -helical protein, and its chemical shifts change linearly and reversibly with pressure between 1 and 2000 bar. An improved relationship between structure and HN shift has been calculated, and used to drive a molecular dynamics-based calculation of the change in structure. With pressure, the helix is compressed, with the H—O distance of the NH—O=C hydrogen bonds decreased by 0.021 ± 0.039 Å, leading to an overall compression along the entire helix of about 0.4 Å, corresponding to a static compressibility of 6 ×10^–6 bar^–1. The backbone dihedral angles and are altered by no more than ± 3° for most residues with a negative correlation coefficient of –0.85 between _i and _i–1, indicating that the local conformation alters to maintain hydrogen bonds in good geometries. The method is shown to be capable of calculating structural change with high precision, and the results agree with structural changes determined using other methodologies.     

Is population structure in the European white stork determined by flyway permeability rather than translocation history?

European white stork are long considered to diverge to eastern and western migration pools as a result of independent overwintering flyways. In relatively recent times, the western and northern distribution has been subject to dramatic population declines and country‐specific extirpations. A number of independent reintroduction programs were started in the mid 1950s to bring storks back to historical ranges. Founder individuals were sourced opportunistically from the Eastern and Western European distributions and Algeria, leading to significant artificial mixing between eastern and western flyways. Here we use mitochondrial and microsatellite DNA to test the contention that prior to translocation, eastern and western flyways were genetically distinct. The data show a surprising lack of structure at any spatial or temporal scale suggesting that even though birds were moved between flyways, there is evidence of natural mixing prior to the onset of translocation activities. Overall a high retention of genetic diversity, high N_ef, and an apparent absence of recent genetic bottleneck associated with early 20th century declines suggest that the species is well equipped to respond to future environmental pressures.     

Is the hydrophobic core a universal structural element in proteins?

The hydrophobic core, when subjected to analysis based on the fuzzy oil drop model, appears to be a universal structural component of proteins irrespective of their secondary, supersecondary, and tertiary conformations. A study has been performed on a set of nonhomologous proteins representing a variety of CATH categories. The presence of a well-ordered hydrophobic core has been confirmed in each case, regardless of the protein’s biological function, chain length or source organism. In light of fuzzy oil drop (FOD) analysis, various supersecondary forms seem to share a common structural factor in the form of a hydrophobic core, emerging either as part of the whole protein or a specific domain. The variable status of individual folds with respect to the FOD model reflects their propensity for conformational changes, frequently associated with biological function. Such flexibility is expressed as variable stability of the hydrophobic core, along with specific encoding of potential conformational changes which depend on the properties of helices and β-folds.     

Is loss of function of the prion protein the cause of prion disorders?

Transmissible spongiform encephalopathies are fatal neurodegenerative diseases that involve misfolding of the prion protein. Recent studies have provided evidence that normal prion protein might have a physiological function in neuroprotective signaling, suggesting that loss of prion protein activity might contribute to the pathogenesis of prion disease. However, studies using knockout animals do not support the loss-of-function hypothesis and argue that prion neurodegeneration might be associated with a gain of a toxic activity by the misfolded prion protein. Thus, the mechanism of neurodegeneration in spongiform encephalopathies remains enigmatic.     

Is the glycolytic flux in Lactococcus lactis primarily controlled by the redox charge? Kinetics of NAD(+) and NADH pools determined in vivo by 13C NMR

The involvement of nicotinamide adenine nucleotides (NAD(+), NADH) in the regulation of glycolysis in Lactococcus lactis was investigated by using (13)C and (31)P NMR to monitor in vivo the kinetics of the pools of NAD(+), NADH, ATP, inorganic phosphate (P(i)), glycolytic intermediates, and end products derived from a pulse of glucose. Nicotinic acid specifically labeled on carbon 5 was synthesized and used in the growth medium as a precursor of pyridine nucleotides to allow for in vivo detection of (13)C-labeled NAD(+) and NADH. The capacity of L. lactis MG1363 to regenerate NAD(+) was manipulated either by turning on NADH oxidase activity or by knocking out the gene encoding lactate dehydrogenase (LDH). An LDH(-) deficient strain was constructed by double crossover. Upon supply of glucose, NAD(+) was constant and maximal (approximately 5 mm) in the parent strain (MG1363) but decreased abruptly in the LDH(-) strain both under aerobic and anaerobic conditions. NADH in MG1363 was always below the detection limit as long as glucose was available. The rate of glucose consumption under anaerobic conditions was 7-fold lower in the LDH(-) strain and NADH reached high levels (2.5 mm), reflecting severe limitation in regenerating NAD(+). However, under aerobic conditions the glycolytic flux was nearly as high as in MG1363 despite the accumulation of NADH up to 1.5 mm. Glyceraldehyde-3-phosphate dehydrogenase was able to support a high flux even in the presence of NADH concentrations much higher than those of the parent strain. We interpret the data as showing that the glycolytic flux in wild type L. lactis is not primarily controlled at the level of glyceraldehyde-3-phosphate dehydrogenase by NADH. The ATP/ADP/P(i) content could play an important role.     

Separation of the molecular forms of the insulin-like growth factor (IGF)—Binding proteins by affinity chromatography

Association of IGFBP-1, IGFBP-2 and IGFBP-3 with other proteins in human serum and placental cell membranes was investigated using affinity chromatography matrix with immobilized antibodies. Circulating IGFBP-1 was found to be predominantly bound to α₂-macroglobulin and not in the binary complex with its ligand, IGFBP-2 complexes and/or polymers were detected, which was not acknowledged before, and IGFBP-3 molecular forms were differentiated into those that form binary/ternary complexes and those that form stable associations with other serum proteins. As for placental membranes, both IGFBP-1 dimers and high molecular mass IGFBP-1 associations, most probably with α₂-macroglobulin, were recognized and resolved.     

Is the relation between nutrient supply and biodiversity co‐determined by the type of nutrient limitation?

Correlative studies have shown a ‘hump‐backed’ relation between the vegetation N:P ratio and plant species diversity with the highest diversity at balanced N:P ratios (between 10 and 14). We tested the hypothesis that adding growth‐limiting nutrients to mesotrophic grasslands that were in shortage of either N (N:P ratio<10) or P (N:P ratio>14) would lead to an increase of plant diversity. Thereto, we studied the effects of long‐term (11 yr) experimentally increased N and/or P supply on soil nutrient pools, vegetation nutrient dynamics and biodiversity in a riverine grassland in the Netherlands with a low soil N:P ratio (N shortage) and a peat grassland with a high soil N:P ratio (P shortage), respectively. Eleven years of nutrient addition hardly had any effects on the total stocks of C, N and P in the soils of both sites, due to the large size of the soil nutrient pools already present and to the management at both sites (annual hay‐making and ‐removal). However, in the riverine grassland the treatments increased the cycling of the small pool of labile N and P compounds resulting in large increases in annual fluxes of especially N. In the unfertilised controls, species establishments balanced more or less species losses during an 11 year period, thus leading to a dynamic equilibrium of the species pool. However, contrary to our hypothesis, addition of the growth‐limiting nutrient led at both sites to a reduction of species diversity even when total biomass remained below critical levels. Species diversity and species evenness were strongly determined by N mineralisation and to a lesser extent by total soil N and extractable P, respectively. Total aboveground biomass of the vegetation was determined by total soil N. Our study shows that patterns found in correlative studies of the relation between plant diversity and soil and vegetation N:P ratio can not be translated into successful experimental manipulations to enhance biodiversity. The most likely explanation is that colonization limitation occurred in the fertilized plots and that not sufficient diaspores of potentially new species could reach and/or colonize the plots to compensate for the species extinctions as a result of increased nutrient supply.     

Multiple molecular forms of β-amylase in seeds and vegetative tissues of barley

The molecular forms of -amylase present in developing, mature, germinating and malted grains of barley (Hordeum vulgare L.), and in vegetative tissues, have been studied using Western-blot analyses and isoelectric focusing of isoenzymes. Five isoforms with different relative molecular masses (M_rs) could be recognised. The major isoform present in the mature grain, called isoform B, had an M_r of about 60 000. This was converted on malting or germination to two lower-M_r forms called C and D. Previous work (R. Lundgard and B. Svensson, 1986, Carlsberg Res. Commun. 51, 487–491) has shown that these result from partial proteolysis of isoform B. Isoenzyme analyses showed complex patterns of bands, with pIs between about 5.0 and 6.0. Two allelic types were present in the eight lines. A number of new bands with a range of pIs appeared during germination and malting.An isoform with the same M_r as D and a minor low-M_r isoform (E) were present in young developing whole caryopses (8–12 d after anthesis), but not in older developing endosperms (14–21 d after anthesis). Isoenzyme analyses also showed different patterns of bands in these two tissues, while hybrid-dot analyses indicated the presence of separate populations of mRNAs. It is suggested that the early endosperm isoforms (D and E) are green -amylases present in the pericarp and-or testa of the young caryopses.Roots but not shoots or leaves also contained an isoform with the same M_r as D, although the pattern of isoenzymes differed from that present in the seed tissues.The fifth isoform, A, was a diffuse high-M_r form present in small amounts in all seed and vegetative tissues, and may correspond to a constitutively expressed form.These multiple molecular forms of -amylase are discussed in relation to the recent report that -amylase is encoded by two structural loci, with a total copy number of two to three per haploid genome (Kreis et al, 1988, Genet. Res. Camb. 51, 13–16).Abbreviations M_r relative molecular mass - SDS-PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis     

Application of the pCloDF13 bacteriocin release protein in the release of heterologous proteins by Escherichia coli : Production of plant α-galactosidase

Summary The bacteriocin release protein (BRP) mediated release of several eukaryotic proteins was studied in Escherichia coli. The genes for the plant proteins -galactosidase and thaumatin, and for the mammalian proteins prochymosine and prophospholipase A₂, were cloned behind the OmpA signal peptide. The -galactosidase was expressed and secreted into the periplasm. Prochymosine and thaumatin were poorly expressed. Release experiments showed that about 5 mg/l of -galactosidase was excreted into the extracellular medium upon induction of the BRP.