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Impact of calcium binding and thionylation of S100A1 protein on its NMR derived structure and backbone dynamics
Get PDFS100 proteins play a crucial role in multiple important biological processes in vertebrate organisms acting predominantly as calcium signal transmitters. S100A1 is a typical representative of this family of proteins. Upon binding of four Ca2+ ions it undergoes a dramatic conformational change, resulting in exposure, in each of its two identical subunits, a large hydrophobic cleft that binds to target proteins. It has been shown that abnormal expression of S100A1 is strongly correlated with a number of severe human diseases: cardiomyopathy and neurodegenerative disorders.
A few years ago we have found that thionylation of Cys 85 - the unique cysteine in two identical S100A1 subunits – leads to a drastic increase of the protein affinity for calcium. We postulated that the protein activated by thionylation becomes a more efficient calcium signal transmitter. Therefore, we decided to undertake, using NMR methods, a comparative study of structure and dynamics of native and thionylated human S100A1 in its apo and holo states. In this paper we present the results obtained for the both forms of this protein in its holo state and compare them with the previously published structure of native apo S100.
The main conclusion that we draw from these results is that the increased calcium binding affinity of S100A1 upon thionylation arises, most probably, from rearrangement of the hydrophobic core in its apo form
What we do and do not know about the cellular functions of polyisoprenoids
Get PDFNatural compounds classi fi ed as products of secondary metabolism are widely studied as to their potential biological role. Identi fi cation of possible cellular functions of polyisoprenoids, generally considered as secondary products, has been our focus for some 30 years already. The results of these studies for instance in the context of membrane permeability and protein modification are briefly described and discussed in this chapter
Interspecific somatic hybrids Solanum villosum (+) S. tuberosum, resistant to Phytophthora infestans.
Get PDFThe interspecific somatic hybrids, 4x S. villosum (+) 2x S. tuberosum clone DG 81-68 (VT hybrids), were obtained and characterized molecularly and cytogenetically.
The morphology of fusion-derived plants was intermediate in relation to the parental species. The expected ploidy level of the regenerants was 6x for the VT hybrids, but the real ploidy of the hybrids varied, with some of them being euploids, and others - aneuploids. The hybridity of the regenerants was verified by random amplified polymorphic DNA (RAPD) analysis. Despite the variation in ploidy, the RAPD patterns of the hybrids were mostly uniform, suggesting similarity of the genotypes of the VT clones. Genomic in situ hybridisation (GISH) analysis discriminated between the chromosomes of both parental genomes in VT somatic hybrids and confirmed also their hybridity. The resistance of VT somatic hybrids to Phytophthora infestans was evaluated and all the hybrids were proved to be highly resistant. In search of the mechanisms involved in resistance of the Solanum species to P. infestans, the biochemical reactions occurring early after elicitor treatment were studied. Production of reactive oxygen species (ROS), as one of the earliest reactions induced by pathogens or their elicitors, was examined in the resistant wild species S. villosum, susceptible S. tuberosum clone DG 81-68 and in the VT hybrid, resistant to P. infestans. After treatment of the leaves with elicitor, the relative increase in ROS production was higher in leaves of the susceptible potato clone than in the resistant plants of S. villosum and the somatic hybrid
Proteins contribute insignificantly to the intrinsic buffering capacity of yeast cytoplasm.
Get PDFIntracellular pH is maintained by a combination of the passive buffering of cytoplasmic dissociable compounds and several active systems. Over the years, a large portion of and possibly most of the cell's intrinsic (i.e., passive non-bicarbonate) buffering effect was attributed to proteins, both in higher organisms and in yeast. This attribution was not surprising, given that the concentration of proteins with multiple protonable/deprotonable groups in the cell exceeds the concentration of free protons by a few orders of magnitude. Using data from both high-throughput experiments and in vitro laboratory experiments, we tested this concept. We assessed the buffering capacity of the yeast proteome using protein abundance data and compared it to our own titration of yeast cytoplasm. We showed that the protein contribution is less than 1% of the total intracellular buffering capacity. As confirmed with NMR measurements, inorganic phosphates play a crucial role in the process. These findings also shed a new light on the role of proteomes in maintaining intracellular pH. The contribution of proteins to the intrinsic buffering capacity is negligible, and proteins might act only as a recipient of signals for changes in pH
Plasmid diversity in arctic strains of Psychrobacter spp.
No full textSix strains of Psychrobacter spp. isolated from guano of little auks collected on Spitsbergen island (Arctic) carried nine plasmids that were fully sequenced. These replicons (ranging in size from 2917 to 14924 bp) contained either repA (ColE2-type) or repB (iteron-type) replication systems of a relatively narrow host range, limited to Psychrobacter spp. All but one of the plasmids carried predicted mobilization for conjugal transfer systems, encoding relaxases of the MOBQ, MOBV or MOBP families. The plasmids also contained diverse additional genetic load, including a type II restriction-modification system and a gene encoding a putative subunit C of alkyl hydroperoxide reductase (AhpC)-an antioxidant enzyme and major scavenger of reactive oxygen species. Detailed comparative sequence analyses, extended to all plasmids identified so far in psychrophilic bacteria, distinguished groups of the most ubiquitous replicons, which play a key role in horizontal gene transfer in cold environments
The evolutionary rate of antibacterial drug targets
Get PDFBackground
One of the major issues in the fight against infectious diseases is the notable increase in multiple drug resistance in pathogenic species. For that reason, newly acquired high-throughput data on virulent microbial agents attract the attention of many researchers seeking potential new drug targets. Many approaches have been used to evaluate proteins from infectious pathogens, including, but not limited to, similarity analysis, reverse docking, statistical 3D structure analysis, machine learning, topological properties of interaction networks or a combination of the aforementioned methods. From a biological perspective, most essential proteins (knockout lethal for bacteria) or highly conserved proteins (broad spectrum activity) are potential drug targets. Ribosomal proteins comprise such an example. Many of them are well-known drug targets in bacteria. It is intuitive that we should learn from nature how to design good drugs. Firstly, known antibiotics are mainly originating from natural products of microorganisms targeting other microorganisms. Secondly, paleontological data suggests that antibiotics have been used by microorganisms for million years. Thus, we have hypothesized that good drug targets are evolutionary constrained and are subject of evolutionary selection. This means that mutations in such proteins are deleterious and removed by selection, which makes them less susceptible to random development of resistance. Analysis of the speed of evolution seems to be good approach to test this hypothesis.
Results
In this study we show that pN/pS ratio of genes coding for known drug targets is significantly lower than the genome average and also lower than that for essential genes identified by experimental methods. Similar results are observed in the case of dN/dS analysis. Both analyzes suggest that drug targets tend to evolve slowly and that the rate of evolution is a better predictor of drugability than essentiality.
Conclusions
Evolutionary rate can be used to score and find potential drug targets. The results presented here may become a useful addition to a repertoire of drug target prediction methods. As a proof of concept, we analyzed GO enrichment among the slowest evolving genes. These may become the starting point in the search for antibiotics with a novel mechanism
Cu(II) complex formation by ACES buffer.
Get PDFACES (N-(2-Acetamido)-2-aminoethanesulfonic acid), a popular Good's buffer, binds Cu(II) ions with a moderate affinity. Although this interaction was the subject of previous studies, no consensus in the literature was found. We used potentiometry to establish binding constants, and controlled the potentiometric model selection and binding constant calculations by UV-vis spectroscopy. As a result, we obtained a consistent set of complex stoichiometries and binding constants in this system, which contains Cu(2+), CuL(+), CuL2, CuH-1L2(-1) and CuH(-)2L2(-2) complexes. The negative indexes at H atoms in these formulae denote the Cu(II) assisted deprotonation of the amide nitrogen present in the ACES molecule. The affinity of ACES for Cu(II) strongly depends on the concentration and ACES:Cu(II) ratio, reaching submicromolar apparent affinities at ratios higher than 100. These results will enable more accurate determinations of biologically relevant stability constants of Cu(II) complexes using ACES buffer
Luminescence of colloidal ZnO nanoparticles synthesized in alcohols and biological application of ZnO passivated by MgO.
Get PDFThis report presents the results of spectroscopic measurements of colloidal ZnO nanoparticles synthesized in various alcohols. Luminescence of colloidal ZnO was monitored, under different reaction condition, to elucidate the mechanism of the visible emission. We perform the process in different alcohols, temperatures and reaction time for two different reactants: water and NaOH. Based on the presented and previously published results it is apparent that the luminescence of the nanoparticles is influenced by several competing phenomena: the formation of new nucleation centers, the growth of the nanoparticles and surface passivation. Superimposed on the above effects is a size dependent luminescence alterations resulted from the quantum confinement. The study contributes to understanding the origin of ZnO nanoparticles green emission which is important in a rational design of fluorescent probes for nontoxic biological applications. Thus produced nanoparticles are coated with a magnesium oxide layer, and introduced into the HeLa cancer cell
Genetic diversity in a moulting colony of southern elephant seals in comparison with breeding colonies
Get PDFABSTRACT: Southern elephant seals Mirounga leonina migrate seasonally between pelagic foraging
areas in the Southern Ocean and breeding and moulting sites on subantarctic islands. Here
we characterized genetic diversity of the elephant seal moulting colony from King George Island
(KGI), South Shetlands Archipelago, in comparison with breeding colonies described in earlier
studies. Although KGI serves as a breeding site, the numbers of elephant seals are up to 3 times
higher during the moulting season, suggesting post-breeding immigration from other sites, or that
large numbers of individuals skip the breeding season every year. High haplotype diversity and a
high percentage of shared haplotypes is consistent with the hypothesis of immigration from other
South Atlantic colonies, which is also supported by satellite tracking data from earlier studies.
Estimates of effective population size at both mtDNA and microsatellite loci were unexpectedly
high compared with the census size of the KGI colony, suggesting that they were elevated due to
the presence of immigrants. However, we detected few immigrants and no genetic structure in the
KGI colony, which could result from the genetic similarity between KGI and other breeding
colonies from the South Atlantic, but could also be an effect of an insufficient sampling scheme.
These results show the need for genetic monitoring of southern elephant seal colonies throughout
their annual cycle to better understand the range of their seasonal movements and patterns of
gene flow. The southern elephant seal serves as a model to study links between spatio-temporal
environmental variability, population dynamics, and individual movements, physiology and
reproductive behavior. Understanding the patterns of dispersal and gene flow in this species is
essential to adequately address these general questions
Presja gatunków obcych na lądowe ekosystemy Morskiej Antarktyki.
Get PDFDue to geographic and historical isolation of
the Antarctic continent, there are currently very few
alien species introduced to the terrestrial ecosystems.
However, due to increased man-made pressure
and amelioration of climate in this region, the threat
of the establishment of non-native species will grow
markedly. Many diasporas can be quite easily, unintentionally
transported in good condition to the
Antarctic with research stations supplies. Flexible
species are characterized by a very wide ecological
amplitude, high adaptation capabilities and diverse
ways of reproduction. They may thrive under harsh
environmental conditions and colonize recipient
ecosystems. The impact of those organisms will be
unpredictable