Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion

The tethered particle motion (TPM) allows the direct detection of activity of a variety of biomolecules at the single molecule level. First pioneered for RNA polymerase, it has recently been applied also to other enzymes. In this work we employ TPM for a systematic investigation of the kinetics of DNA looping by wild-type Lac repressor (wt-LacI) and by hinge mutants Q60G and Q60 + 1. We implement a novel method for TPM data analysis to reliably measure the kinetics of loop formation and disruption and to quantify the effects of the protein hinge flexibility and of DNA loop strain on such kinetics. We demonstrate that the flexibility of the protein hinge has a profound effect on the lifetime of the looped state. Our measurements also show that the DNA bending energy plays a minor role on loop disruption kinetics, while a strong effect is seen on the kinetics of loop formation. These observations substantiate the growing number of theoretical studies aimed at characterizing the effects of DNA flexibility, tension and torsion on the kinetics of protein binding and dissociation, strengthening the idea that these mechanical factors in vivo may play an important role in the modulation of gene expression regulation.     

Selectivity in the mechanism of action of antimicrobial mastoparan peptide Polybia-MP1

Many potent antimicrobial peptides also present hemolytic activity, an undesired collateral effect for the therapeutic application. Unlike other mastoparan peptides, Polybia-MP1 (IDWKKLLDAAKQIL), obtained from the venom of the social wasp Polybia paulista, is highly selective of bacterial cells. The study of its mechanism of action demonstrated that it permeates vesicles at a greater rate of leakage on the anionic over the zwitterionic, impaired by the presence of cholesterol or cardiolipin; its lytic activity is characterized by a threshold peptide to lipid molar ratio that depends on the phospholipid composition of the vesicles. At these particular threshold concentrations, the apparent average pore number is distinctive between anionic and zwitterionic vesicles, suggesting that pores are similarly formed depending on the ionic character of the bilayer. To prospect the molecular reasons for the strengthened selectivity in Polybia-MP1 and its absence in Mastoparan-X, MD simulations were carried out. Both peptides presented amphipathic alpha-helical structures, as previously observed in Circular Dichroism spectra, with important differences in the extension and stability of the helix; their backbone solvation analysis also indicate a different profile, suggesting that the selectivity of Polybia-MP1 is a consequence of the distribution of the charged and polar residues along the peptide helix, and on how the solvent molecules orient themselves according to these electrostatic interactions. We suggest that the lack of hemolytic activity of Polybia-MP1 is due to the presence and position of Asp residues that enable the equilibrium of electrostatic interactions and favor the preference for the more hydrophilic environment.     

Study of the mechanism of action of anoplin, a helical antimicrobial decapeptide with ion channel-like activity, and the role of the amidated C-terminus.

Anoplin, an antimicrobial, helical decapeptide from wasp venom, looses its biological activities by mere deamidation of its C-terminus. Secondary structure determination, by circular dichroism spectroscopy in amphipathic environments, and lytic activity in zwitterionic and anionic vesicles showed quite similar results for the amidated and the carboxylated forms of the peptide. The deamidation of the C-terminus introduced a negative charge at an all-positive charged peptide, causing a loss of amphipathicity, as indicated by molecular dynamics simulations in TFE/water mixtures and this subtle modification in a peptide's primary structure disturbed the interaction with bilayers and biological membranes. Although being poorly lytic, the amidated form, but not the carboxylated, presented ion channel-like activity on anionic bilayers with a well-defined conductance step; at approximately the same concentration it showed antimicrobial activity. The pores remain open at trans-negative potentials, preferentially conducting cations, and this situation is equivalent to the interaction of the peptide with bacterial membranes that also maintain a high negative potential inside.     

Relevance of RAPD Analysis for Revealing Phylogenetic Relationships between Cultivars of Durum Wheat Triticum durum Desf.

A comparison of similarity indices between 64 durum wheat cultivars calculated using pedigree analysis and RAPD method showed a correspondence between these two approaches to estimation of genetic diversity. The associations between the results of RAPD clustering and coefficients of parentage (² test) and the coefficient of correlation between similarity matrices were statistically significant. However, the correlation was rather weak while pedigree analysis and RAPD method did not yield completely identical estimates of genetic diversity in the set of cultivars studied.     

Evaluation of Polymorphism at Microsatellite Loci of Spring Durum Wheat (Triticum durum Desf.) Varieties and the Use of SSR-Based Analysis in Phylogenetic Studies

Polymorphism at 28 SSR loci was analyzed and described in 45 cultivars of spring durum wheat created in the former USSR and Russia during the last 80 years. Each cultivar was shown to have a unique allele combination. This allows SSR markers to be used to identify durum wheat varieties. Meanwhile, these markers can hardly be used to detect phylogenetic relationships among varieties and to specify their pedigrees, because genetic distances calculated on the basis of these markers do not correlate with the distance calculated by coefficient of parentage.     

Evaluation of polymorphism at microsatellite loci of spring durum wheat (Triticum durum Desf.) varieties and the use of SSR-based analysis in phylogenetic studies

Polymorphism at 28 SSR loci was analyzed and described in 45 cultivars of spring durum wheat created in the former USSR and Russia during the last 80 years. Each cultivar was shown to have a unique allele combination. This allows SSR markers to be used to identify durum wheat varieties. Meanwhile, these markers can hardly be used to detect phylogenetic relationships among varieties and to specify their pedigrees, because genetic distances calculated on the basis of these markers do not correlate with the distance calculated by coefficient of parentage.     

Involvement of exon 6-mediated calpastatin intracellular movements in the modulation of calpain activation

Background

To establish the physiological role of calpain, it is necessary to define how the protease can escape from the effect of its natural inhibitor calpastatin, since both proteins co-localize into the cell cytosol.

Methods

To answer this question, we have overexpressed four fluorescent calpastatin constructs, differing in the composition of their XL- and L-domains, and the intracellular trafficking of this protein inhibitor has been followed by single cell fluorescence imaging.

Results and conclusions

By the use of these calpastatin forms differing in the type of exon-derived sequences contained in the XL- and L-domains, we have demonstrated that the sequence coded by exon 6, containing multiple phosphorylation sites, is directly involved in determining the cell localization of calpastatin. In fact, exposure to cAMP promotes the recruitment into aggregates of those calpastatin forms containing the exon 6 sequence. These protein movements are directly related to the level of cytosolic inhibitory capacity and thereby to the extent of intracellular calpain activation.

General significance

The recruitment of calpastatin into aggregates allows the translocation and activation of the protease to the membranes; on the contrary, the presence of large amounts of calpastatin in the cytosol prevents both processes, protecting the cell from undesired proteolysis.     

In vitro Analysis of Defence Mechanism in the System Solanum tuberosum-Alternaria alternata

In a preliminary study on the interaction between an Alternaria alternata pathotype and Solanum tuberosum a series of parameters, indicative of active and passive defence processes, was investigated in vitro using tolerant (Chiquita) and susceptible (Superior) cultivars. Ion leakage experiments along with growth of suspension cultures and plating efficiencies in the presence of fungal culture filtrates suggest that toxin tolerance is a valuable character in distinguishing between resistant and susceptible genotypes. As far as active defence was concerned, although TLC patterns suggested the synthesis of different fluorescent compounds, probably phenolic acid, when fungal elicitors were applied to Chiquita or susceptible tissue,cultures, no consistent pattern suggesting a relationship with defence could be observed. On the other hand, peroxidase isozyme analysis after different dual culture periods showed the activation of ionically and covalently bound peroxidases in the prese,nce of the pathogen only in cv. Chiquita.