Do parallel beta-helix proteins have a unique fourier transform infrared spectrum?

Several polypeptides have been found to adopt an unusual domain structure known as the parallel beta-helix. These domains are characterized by parallel beta-strands, three of which form a single parallel beta-helix coil, and lead to long, extended beta-sheets. We have used ATR-FTIR (attenuated total reflectance-fourier transform infrared spectroscopy) to analyze the secondary structure of representative examples of this class of protein. Because the three-dimensional structures of parallel beta-helix proteins are unique, we initiated this study to determine if there was a corresponding unique FTIR signal associated with the parallel beta-helix conformation. Analysis of the amide I region, emanating from the carbonyl stretch vibration, reveals a strong absorbance band at 1638 cm(-1) in each of the parallel beta-helix proteins. This band is assigned to the parallel beta-sheet structure. However, components at this frequency are also commonly observed for beta-sheets in many classes of globular proteins. Thus we conclude that there is no unique infrared signature for parallel beta-helix structure. Additional contributions in the 1638 cm(-1) region, and at lower frequencies, were ascribed to hydrogen bonding between the coils in the loop/turn regions and amide side-chain interactions, respectively. A 13-residue peptide that forms fibrils and has been proposed to form beta-helical structure was also examined, and its FTIR spectrum was compared to that of the parallel beta-helix proteins.     

A biological cosmos of parallel universes: Does protein structural plasticity facilitate evolution?

While Darwin pictured organismal evolution as "descent with modification" more than 150 years ago, a detailed reconstruction of the basic evolutionary transitions at the molecular level is only emerging now. In particular, the evolution of today's protein structures and their concurrent functions has remained largely mysterious, as the destruction of these structures by mutation seems far easier than their construction. While the accumulation of genomic and structural data has indicated that proteins are related via common ancestors, naturally occurring protein structures are often considered to be evolutionarily robust, thus leaving open the question of how protein structures can be remodelled while selective pressure forces them to function. New information on the proteome, however, increasingly explains the nature of local and global conformational diversity in protein evolution, which allows the acquisition of novel functions via molecular transition forms containing ancestral and novel structures in dynamic equilibrium. Such structural plasticity may permit the evolution of new protein folds and help account for both the origins of new biological functions and the nature of molecular defects.     

Sulfation pattern in glycosaminoglycan: Does it have a code?

Heparan sulfate chains (HS) are initially synthesized on core proteins as linear polysaccharides composed of glucuronic acid--N-acetylglucosamine repeating units and subjected to marked structural modification by sulfation (N-, 2-O-, 6-O-, 3-O-sulfotransferases) and epimerization (C5-epimerase) at the Golgi lumen and further by desulfation (6-O- endosulfatase) at the cell surface, after which divergent fine structures are generated. The expression patterns and specificity of the modifying enzymes are, at least partly, responsible for the elaboration of these fine structures of heparan sulfate. HS interacts with many proteins including growth factors (GF) and morphogens through specific fine structures. Recent biochemical and genetic studies have presented evidence that HS plays important roles in cell behavior and organogenesis. In knock-down experiments of heparan sulfate 6-O-sulfotransferase, 6-O-sulfated units in HS have been shown to act as a stimulator or suppressor according to individual GF/morphogen signaling systems.     

Did the last common ancestor have a biological membrane?

All theories about the origin and evolution of membrane bound cells necessarily have to cope with the nature of the last common ancestor of cellular life. One of the most important aspect of this ancestor, whether it had a closed biological membrane or not, has recently been intensely debated. Having a consensus about it would be an important step towards an eventual (though probably still remote) synthesis of the best elements of the current multitude of cell evolution models. Here I analyse the structural and functional conservation of the few universally distributed proteins that were undoubtedly present in the last common ancestor and that carry out membrane-associated functions. These include the SecY subunit of the protein-conducting channel, the signal recognition particle, the signal recognition particle receptor, the signal peptidase, and the proton ATPase. The conserved structural and functional aspects of these proteins indicate that the last common ancestor was associated with a hydrophobic layer with two hydrophilic sides (an inside and an outside) that had a full-fledged and asymmetric protein insertion and translocation machinery and served as a permeability barrier for protons and other small molecules. It is difficult to escape the conclusion that the last common ancestor had a closed biological membrane from which all cellular membranes evolved.     

Does the tsetse parturition rhythm have a circadian basis?

Abstract. Under an LD 12:12h photoregime at constant temperature, parturition in Glossina morsitans centralis is a gated event occurring late in the afternoon. When flies are switched to continuous light the rhythm quickly dampens, but its persistence for at least two 24-h cycles beyond the final scotophase suggests the rhythm has a circadian basis. A weak rhythm appears after 7 days of continuous light, perhaps in response to the daily disturbance caused by feeding. Return of the flies to LD 12:12h restores the rhythm after exposure to a single scotophase.     

Does one subgenome become dominant in the formation and evolution of a polyploid?

BackgroundPolyploids are common in flowering plants and they tend to have more expanded ranges of distributions than their diploid progenitors. Possible mechanisms underlying polyploid success have been intensively investigated. Previous studies showed that polyploidy generates novel changes and that subgenomes in allopolyploid species often differ in gene number, gene expression levels and levels of epigenetic alteration. It is widely believed that such differences are the results of conflicts among the subgenomes. These differences have been treated by some as subgenome dominance, and it is claimed that the magnitude of subgenome dominance increases in polyploid evolution.ScopeIn addition to changes which occurred during evolution, differences between subgenomes of a polyploid species may also be affected by differences between the diploid donors and changes which occurred during polyploidization. The variable genome components in many plant species are extensive, which would result in exaggerated differences between a subgenome and its progenitor when a single genotype or a small number of genotypes are used to represent a polyploid or its donors. When artificially resynthesized polyploids are used as surrogates for newly formed genotypes which have not been exposed to evolutionary selection, differences between diploid genotypes available today and those involved in the formation of the natural polyploid genotypes must also be considered.ConclusionsContrary to the now widely held views that subgenome biases in polyploids are the results of conflicts among the subgenomes and that one of the parental subgenomes generally retains more genes which are more highly expressed, available results show that subgenome biases mainly reflect legacy from the progenitors and that they can be detected before the completion of polyploidization events. Further, there is no convincing evidence that the magnitudes of subgenome biases have significantly changed during evolution for any of the allopolyploid species assessed.     

Does a biological clock reside in the eye of quail?

The site (intra- vs. extraocular) of the circadian clock driving an ocular melatonin rhythm in Japanese quail was investigated by alternately covering the left and right eyes of individual quail, otherwise held in constant light (LL), for 12-hr periods. This procedure exposed each eye to a light-dark (LD) 12:12 light cycle 180 degrees (12 hr) out of phase with the LD 12:12 light cycle experienced by the other eye. This protocol entrained the melatonin rhythm in the left eye of quail 180 degrees out of phase with the rhythm expressed in the right eye. These results are compatible with the hypothesis that an independent light-entrainable circadian pacemaker resides in each eye; they are incompatible with the hypothesis that a single (or functionally single) extraocular pacemaker drives the ocular melatonin rhythm in both eyes. However, the results are also compatible with a model in which two independent extraocular circadian pacemakers, each with an exclusive photic input from one eye, drive the ocular melatonin rhythm.     

Does FSH signaling have a gender?

FSH is the main endocrine control of mammalian reproduction. FSH triggers somatic cells of the gonads which support germ cells metabolically, i.e. Sertoli cells of the seminiferous tubules, and granulosa cells harboring the oocyte, within the ovarian follicle. FSH leads to similar biological responses in both cell types since it stimulates proliferation and differentiation, according to the developmental stage. However, FSH receptor knock-out female mice are infertile, unlike male mice. Hence, FSH is not equally important in both sexes. Nevertheless, does FSH induce distinct signalling mechanisms in its target cells ? Here, we compare the signalling mechanisms induced by FSH in ovarian and testicular physiology.     

Does zoo herpetology have a future?

Fifty-two North American zoo reptile and amphibian departments were surveyed to determine their contributions to recognized American Zoo and Aquarium Association (AZA)-sponsored programs and formalized research projects over the past 10 years. Surveys also requested information concerning the allocation of resources for conservation and research programs, staff educational background, and entry level salaries. Twenty-two institutions responded to the survey, collectively indicating a total of 164 technical papers, 16 field studies, and 101 non-technical articles completed between 1987 and 1997. Of the 164 technical papers published, 130 (79%) were contributed by three institutions. Of the 16 field studies, seven were outside the United States, whereas nine focused on native species and ecosystems. Six of the reported field studies involved only financial or logistical support. Of the 101 non-technical articles, 42 (42%) were contributed by a single institution. Twenty-one formalized in-house research projects were reported. However, only four appeared to have a clearly defined objective. Survey respondents also reported nine species of reptiles and one amphibian taxon are managed by Species Survival Plans (SSPs). There are currently 12 Taxon Advisory Group (TAG) coordinators, with four of the current coordinators having served on multiple TAG committees. There are 41 AZA-approved studbooks for reptiles and two for amphibians, with 29 having actually been published to date. The average starting salary reported in our survey for entry level keeper positions was $19,500 (range, $13,500–30,000). The average level of education reported was high school graduate. There was no correlation between productivity and higher wages, or level of education. Only one institution received funding specifically for research. We conclude that zoo herpetology departments are not realizing their potential for formalized research and conservation projects and propose recommendations for future involvement. Zoo Biol 17:453–462, 1998. © 1998 Wiley-Liss, Inc.     

Does experimental evolution produce better biological control agents? A critical review of the evidence

Biological control of crop pests is considered a good alternative or complement to the use of pesticides. However, legislation restricts the importation of natural enemies of pests. A potential way to circumvent this limitation is by using experimental evolution and/or artificial selection to improve native biological control agents. Here, we review studies that have used these methodologies and evaluate their success. Experimental evolution or artificial selection has been used on a wide range of traits, with most focusing on improving the performance of natural enemies in ecologically relevant environments, such as in the presence of pesticides or at different temperatures. Although most studies were poorly replicated, the selected traits generally improved following the selection process. However, correlated responses (often in the form of trade‐offs) with other traits of interest were common. We suggest that the selection procedure can be improved by increasing replication and performing experimental evolution under more semi‐natural environments, to ensure that the most useful traits are being selected.     

Does nitrogen fertilization have an impact on the trade-off between willow growth and defensive secondary metabolism?

The effect of nitrogen fertilization on the phytomass production, shoot length and leaf secondary phenolics in nine Salix myrsinifolia clones was investigated. Cuttings taken from 1-year-old and 2-year-old shoot parts of field cultivated clones were grown at three concentrations of nitrogen (7, 150 and 300 ppm) in a greenhouse for one growing season. The willow clones differed significantly in phytomass yield and secondary phenolics content. Nitrogen fertilization affected significantly the growth and secondary metabolism of willow clones. In most clones, the addition of nitrogen from a sub-optimum concentration (7 ppm) to an optimum concentration (150 ppm) appeared to reduce the amounts of salicortin, chlorogenic acid and unknown salicylate and increased shoot phytomass, but a supraoptimum nitrogen concentration (300 ppm) resulted in highly variable growth and secondary phenolic responses. A significantly negative correlation between leaf phytomass and amount of total phenolics at sub-optimum and optimum N-treatments indicates trade-off between growth and secondary metabolism in willow clones at these treatments. However, the leaf phytomass:total amount of phenolics ratio varied significantly among clones, and in all clones it was not significantly lower at sub-optimum N-treatment than at optimum N-treatment.     

What is the relationship between the global structures of apo and holo proteins?

It is well known that ligand binding and release may induce a wide range of structural changes in a receptor protein, varying from small movements of loops or side chains in the binding pocket to large‐scale domain hinge‐bending and shear motions or even partial unfolding that facilitates the capture and release of a ligand. An interesting question is what in general are the conformational changes triggered by ligand binding? The aim of this work is analyze the magnitude of structural changes in a protein resulting from ligand binding to assess if the state of ligand binding needs to be included in template‐based protein structure prediction algorithms. To address this issue, a nonredundant dataset of 521 paired protein structures in the ligand‐free and ligand‐bound form was created and used to estimate the degree of both local and global structure similarity between the apo and holo forms. In most cases, the proteins undergo relatively small conformational rearrangements of their tertiary structure upon ligand binding/release (most root‐mean‐square‐deviations from native, RMSD, are <1 Å). However, a clear difference was observed between single‐ and multiple‐domain proteins. For the latter, RMSD changes greater than 1 Å and sometimes larger were found for almost 1/3 of the cases; these are mainly associated with large‐scale hinge‐bending movements of entire domains. The changes in the mutual orientation of individual domains in multiple‐domain proteins upon ligand binding were investigated using a mechanistic model based on mass‐weighted principal axes as well as interface buried surface calculations. Some preferences toward the anticipated mechanism of protein domain movements are predictable based on the examination of just the ligand‐free structural form. These results have applications to protein structure prediction, particularly in the context of protein domain assembly, if additional information concerning ligand binding is exploited. Proteins 2008. © 2007 Wiley‐Liss, Inc.     

Does a relationship exist between ioduria,magnesiuria and calciuria?

We investigated the mutual relations between ioduria in the one hand, and calciuria, magnesiuria, and creatininuria, on the other hand in a randomly selected group of the population of the Czech Republic. The individual parameters were always determined in the sample of monitoring urine after night fasting, concentration according to the WHO/ICCIDD, we observed a parallel increase of calciuria, magnesiuria and creatininuria. The values of calciuria, magnesiuria and creatininuria correlated positively with ioduria both in children and in adults aged 6-93 years without any statistical effect of sex.     

Does glucagon have a positive inotropic effect in the human heart?

Glucagon is considered to exert cardiostimulant effects, most notably the enhancement of heart rate and contractility, due to the stimulation of glucagon receptors associated with Gs protein stimulation which causes adenylyl cyclase activation and the consequent increase in 3′,5′-cyclic adenosine monophosphate production in the myocardium. These effects have been extensively demonstrated in experimental studies in different animal species. However, efforts to extrapolate the experimental data to patients with low cardiac output states, such as acute heart failure or cardiogenic shock, have been disappointing. The experimental and clinical data on the cardiac effects of glucagon are described here.