Number of natively unfolded proteins scales with genome size

Natively unfolded proteins exist as an ensemble of flexible conformations lacking a well defined tertiary structure along a large portion of their polypeptide chain. Despite the absence of a stable configuration, they are involved in important cellular processes. In this work we used from three indicators of folding status, derived from the analysis of mean packing and mean contact energy of a protein sequence as well as from VSL2, a disorder predictor, and we combined them into a consensus score to identify natively unfolded proteins in several genomes from Archaea, Bacteria and Eukarya. We found a high correlation among the number of predicted natively unfolded proteins and the number of proteins in the genomes. More specifically, the number of natively unfolded proteins scaled with the number of proteins in the genomes, with exponent 1.81 +- 0.10. This scaling law may be important to understand the relation between the number of natively unfolded proteins and their roles in cellular processes.Comment: Submitted to Biophysics and Bioengineering Letters http://padis2.uniroma1.it:81/ojs/index.php/CISB-BB

Transfer of metal ions in the soil-root interface: influence of copper(II) on the stability of the fibrils

A network of Ca-polygalacturonate arranged in fibrils similar to those of plant roots (Gessa C. and Deiana S., (1990); C.Gessa and Deiana S., (1990)) constitutes a very useful model far the study of the ionic transfer both in the soil-root interface and in the apoplast. Due to the fact that important properties of the network, such as the hydration degree and the absorption phenomena, vary dramatically with the reticulating ion (Gessa C. and Deiana S., (1989)), this note reports on the influence of the metal ions on the fibrillar structure of the network and gives further information about the transfer of the metal ions to the roots

GLOBAL 3D/4D APPLICATIONS: BEYOND ALL BARRIERS

Le soluzioni SkylineGlobe by Skyline Software Systems, Inc. si propongono come un ambiente utile all’integrazione di dati e sistemi provenienti da diverse piattaforme di ambito territoriale per l’acquisizione, la creazione, l’annotazione, la pubblicazione, l’erogazione, la visualizzazione, l’interrogazione e l’analisi di geodatasets in un ambiente 3D/4D di facile utilizzo, distribuzione e condivisione.SkylineGlobe by Skyline Software Systems, Inc. stands as a fair solution for data and system integration from territorial platforms in order to acquire, create, authoring, publish, network, visualize, query and analyze geodatasets in a easy to use, to deliver and to share, 3D/4D environment

Codon Bias Patterns of E.coliE.coli's Interacting Proteins

Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon bias index, $CompAI$, that is based on the competition between cognate and near-cognate tRNAs during translation, without being tuned to the usage bias of highly expressed genes. We perform a genome-wide evaluation of codon bias for $E.coli$, comparing $CompAI$ with other widely used indices: $tAI$, $CAI$, and $Nc$. We show that $CompAI$ and $tAI$ capture similar information by being positively correlated with gene conservation, measured by ERI, and essentiality, whereas, $CAI$ and $Nc$ appear to be less sensitive to evolutionary-functional parameters. Notably, the rate of variation of $tAI$ and $CompAI$ with ERI allows to obtain sets of genes that consistently belong to specific clusters of orthologous genes (COGs). We also investigate the correlation of codon bias at the genomic level with the network features of protein-protein interactions in $E.coli$. We find that the most densely connected communities of the network share a similar level of codon bias (as measured by $CompAI$ and $tAI$). Conversely, a small difference in codon bias between two genes is, statistically, a prerequisite for the corresponding proteins to interact. Importantly, among all codon bias indices, $CompAI$ turns out to have the most coherent distribution over the communities of the interactome, pointing to the significance of competition among cognate and near-cognate tRNAs for explaining codon usage adaptation

Effects of Al substitution on goethite formation

Goethites containing up to 32.7 mole % Al were synthesized and characterized through diffractometry, spectrometry, DSC and chemical techniques. Results indicate that crystal growth was favoured or hindered depending on the percentage of aluminum incorporated into the structure. Goethites to which 5-10 mole % Al were initially added crystallized best, as shown by the highest crystallite dimensions calculated from X-ray and Mössbauer analyses, and by the lowest surface areas values. Over such substitution degree goethite crystallization was hindered and for sample synthesized in presence of 40 mole % Al the separation of a discrete amount of gibbsite and bayerite occurred. Both crystallinity and Al-substitution degree influenced the goethite dehydroxylation endothermic peak temperature playing a competitive action in the peak shift. In fact, the increase in the thermal stability induced by the presence of Al3+ ions into the structure was counteracted by the decrease due to the particle size reduction. The stabilizing effect of aluminum was confirmed by the oxalate treatment which removed from the Al-free sample a Fe amount higher than that from the sample containing about 20 mole % Al, although both had similar crystallinity

Transfer of metal ions at the soil-root interface: role of VO²⁺ on Fe³⁺ mobilization from a Fe(III)-network

This note reports the role of VO(IV) on Fe(III) mobilization from a Fe(III)-polygalacturonate network. The effect of the reaction on the physical properties of the system is also considered

Role of the polygalacturonate network on the iron (III) reduction by caffeic acid

This communication reports the role of polygalacturonate network on the Fe(III) reduction by caffeic acid. The effect of phosphate ions on the redox reaction is also considered