Prediction of coordination number and relative solvent accessibility in proteins

Knowing the coordination number and relative solvent accessibility of all the residues in a protein is crucial for deriving constraints useful in modeling protein folding and protein structure and in scoring remote homology searches. We develop ensembles of bidirectional recurrent neural network architectures to improve the state of the art in both contact and accessibility prediction, leveraging a large corpus of curated data together with evolutionary information. The ensembles are used to discriminate between two different states of residue contacts or relative solvent accessibility, higher or lower than a threshold determined by the average value of the residue distribution or the accessibility cutoff. For coordination numbers, the ensemble achieves performances ranging within 70.6-73.9% depending on the radius adopted to discriminate contacts (6A-12A). These performances represent gains of 16-20% over the baseline statistical predictor, always assigning an amino acid to the largest class, and are 4-7% better than any previous method. A combination of different radius predictors further improves performance. For accessibility thresholds in the relevant 15-30% range, the ensemble consistently achieves a performance above 77%, which is 10-16% above the baseline prediction and better than other existing predictors, by up to several percentage points. For both problems, we quantify the improvement due to evolutionary information in the form of PSI-BLAST-generated profiles over BLAST profiles. The prediction programs are implemented in the form of two web servers, CONpro and ACCpro, available at http://promoter.ics.uci.edu/BRNN-PRED/.     

Improved typing of human serum transferrin by isoelectric focusing on ultrathin layer polyacrylamide slab gels

Summary An improved method for separating transferrin subtypes through the use of isoelectric focusing on ultrathin layer polyacrylamide gels is described. The most considerable problems encountered in the assessment of the Tf phenotypes after pretreatment with iron donor compounds are pointed out. Useful technical devices for reducing the occurrence of artifactitious extrabands are suggested. Finally, the gene frequencies in three samples from Italian populations are reported.     

Pig heart mitochondrial ATPase : properties of purified and membrane-bound enzyme. Effects of flavonoids.

Soluble ATPase (F1) has been purified from pig heart mitochondria. The purified enzyme had a high specific activity and was homogeneous as checked by ultracentrifugation and electrofocusing. It could be dissociated into subunits by cold-treatment or sodium dodecyl sulfate denaturation. The molecular weights of the two major and three minor subunits could be estimated by sodium dodecyl sulfate gel electrophoresis. The native enzyme had an isoelectric point of 5.2 while the cold-denatured enzyme showed three main bands focusing at pH 5.0, 5.2, and 5.4. Kinetic properties (Vm and Km (atp) have been compared for the soluble and membrane bound ATPase in presence of various anions. Inhibitory effects of Quercetin and other flavonoids have been tested in order to get an insight on the interaction between ATPase and its natural inhibitor.     

Compositional patterns in the nuclear genome of cold-blooded vertebrates

Summary DNA preparations obtained from 122 species of fishes, 5 species of amphibians, and 13 species of reptiles were investigated in their compositional properties by analytical equilibrium centrifugation in CsCl density gradients. These species represented 21 orders of Osteichthyes, 3 orders of Chondrichthyes, 2 orders of amphibians, and 3 orders of reptiles. Modal buoyant densities of fish DNAs ranged from 1.696 to 1.707 g/cm³, the vast majority of values falling, however, between 1.699 and 1.704 g/cm³, which is the range covered by the DNAs of amphibians and reptiles. In all cases, DNA bands in CsCl were only weakly asymmetrical and only very rarely were accompanied by separate satellite bands (mostly on the GC-rich side). Intermolecular compositional heterogeneities were low in the vast majority of cases, and, like CsCl band asymmetries, at least partially due to cryptic or poorly resolved satellites. The present findings indicate, therefore, that DNAs from cold-blooded vertebrates are characterized by a number of common properties, namely a very wide spectrum of modal buoyant densities, low intermolecular compositional heterogeneities, low CsCl band asymmetries, and, in most cases, small amounts of satellite DNAs. In the case of fish DNAs a negative correlation was found between the GC level and the haploid size (c value) of the genome. If polyploidization is neglected, this phenomenon appears to be mainly due to the fact that increases and decreases in GC are associated with contraction and expansion phenomena, respectively, of intergenic noncoding sequences, which are GC poor relative to coding sequences.     

Histone deacetylase and microtubules as targets for the synthesis of releasable conjugate compounds

Design and synthesis of an HDAC inhibitor and its merger with three tubulin binders to create releasable conjugate compounds is described. The biological evaluation includes: (a) in vitro reactivity with glutathione, (b) antiproliferative activity, (c) cell cycle analysis and (d) quantification of protein acetylation. The cellular pharmacology study indicated that the HDAC-inhibitor-drug conjugates retained antimitotic and proapoptotic activity with a reduced potency.     

Contribution of diffusional and non-diffusional limitations to midday depression of photosynthesis in Arbutus unedo L.

It is still unknown whether the midday depression of photosynthesis under severe water stress, frequently observed in plants growing in a Mediterranean-type climate, is primarily a consequence of diffusional or non-diffusional limitations. We carried out combined measurements of gas exchanges and chlorophyll fluorescence in field-grown Arbutus unedo L. trees during late spring and mid summer, and a quantitative limitation analysis was performed to distinguish between the different limitations to photosynthesis, i.e., diffusional [D _L = stomatal (S _L) + mesophyll (MC_L)] and non-diffusional (carboxylation capacity and electron transport, B _L) limitations. Light-saturated assimilation at ambient CO₂ (A _max), stomatal conductance to water vapour (g _sw) and maximum carboxylation rate (V _cmax C _i) showed a marked midday depression during both periods. The total limitations tended to increase during the day and were remarkably similar in June and July (50 and 48%, respectively); on a daily basis, D _L was similar to B _L (about 23%) in June; whereas, in July the former was predominant (38 and 4%, respectively). We concluded that the midday depression in photosynthesis was largely caused by diffusional limitations, with non-diffusional limitations playing a smaller role. Although stomatal closure was the main diffusional limitation, the decline in mesophyll conductance was not negligible during the hottest and driest period.