A functional and structural comparative analysis of large tumor antigens reveals evolution of different importin α-dependent nuclear localization signals.

Nucleocytoplasmic transport regulates the passage of proteins between the nucleus and cytoplasm. In the best characterized pathway, importin (IMP) α bridges cargoes bearing basic, classical nuclear localization signals (cNLSs) to IMPß1, which mediates transport through the nuclear pore complex. IMPα recognizes three types of cNLSs via two binding sites: the major binding site accommodates monopartite cNLSs, the minor binding site recognizes atypical cNLSs, while bipartite cNLSs simultaneously interact with both major and minor sites. Despite the growing knowledge regarding IMPα-cNLS interactions, our understanding of the evolution of cNLSs is limited. We combined bioinformatic, biochemical, functional, and structural approaches to study this phenomenon, using polyomaviruses (PyVs) large tumor antigens (LTAs) as a model. We characterized functional cNLSs from all human (H)PyV LTAs, located between the LXCXE motif and origin binding domain. Surprisingly, the prototypical SV40 monopartite NLS is not well conserved; HPyV LTA NLSs are extremely heterogenous in terms of structural organization, IMPα isoform binding, and nuclear targeting abilities, thus influencing the nuclear accumulation properties of full-length proteins. While several LTAs possess bipartite cNLSs, merkel cell PyV contains a hybrid bipartite cNLS whose upstream stretch of basic amino acids can function as an atypical cNLS, specifically binding to the IMPα minor site upon deletion of the downstream amino acids after viral integration in the host genome. Therefore, duplication of a monopartite cNLS and subsequent accumulation of point mutations, optimizing interaction with distinct IMPα binding sites, led to the evolution of bipartite and atypical NLSs binding at the minor site.

Importin α/ß-dependent nuclear transport of human parvovirus B19 nonstructural protein 1 is essential for viral replication.

Human parvovirus B19 (B19V) is a major human pathogen causing a variety of diseases, characterized by a selective tropism to human progenitor cells in bone marrow. In similar fashion to all Parvoviridae members, the B19V ssDNA genome is replicated within the nucleus of infected cells through a process which involves both cellular and viral proteins. Among the latter, a crucial role is played by non-structural protein (NS)1, a multifunctional protein involved in genome replication and transcription, as well as modulation of host gene expression and function. Despite the localization of NS1 within the host cell nucleus during infection, little is known regarding the mechanism of its nuclear transport pathway. In this study we undertake structural, biophysical, and cellular approaches to characterize this process. Quantitative confocal laser scanning microscopy (CLSM), gel mobility shift, fluorescence polarization and crystallographic analysis identified a short sequence of amino acids (GACHAKKPRIT-182) as the classical nuclear localization signal (cNLS) responsible for nuclear import, mediated in an energy and importin (IMP) α/ß-dependent fashion. Structure-guided mutagenesis of key residue K177 strongly impaired IMPα binding, nuclear import, and viral gene expression in a minigenome system. Further, treatment with ivermectin, an antiparasitic drug interfering with the IMPα/ß dependent nuclear import pathway, inhibited NS1 nuclear accumulation and viral replication in infected UT7/Epo-S1 cells. Thus, NS1 nuclear transport is a potential target of therapeutic intervention against B19V induced disease.

Selenium and L-carnitine protects from valproic acid-Induced oxidative stress and mitochondrial damages in rat cortical neurons.

Oxidative stress and mitochondrial dysfunction have been associated with valproic acid (VPA) induced neurotoxicity. Mitochondria are vulnerable to oxidative damage and are also a major source of superoxide free radicals. Therefore, the need for mitochondrial protective and antioxidant agents for reducing valporic acid toxicity in central nerve system (CNS) is essential. In the present study, we investigated the potential beneficial effects of sodium selenite (SS) and L-carnitine (LC) against valproic acid -induced oxidative stress and mitochondrial dysfunction in isolated rat cortical neurons. Valproic acid (50, 100 and 200 µM) treatment caused a significant decrease in cellular viability, which was accompanied by increases in reactive oxygen species (ROS) generation, GSSG and GSH content, lipid peroxidation and lysosomal and mitochondrial damages. Sodium selenite (1 µM) and L-carnitine (1 mM) pretreatment attenuated valproic acid-induced decrease in cell viability. In addition, sodium selenite (1 µM) and L-carnitine (1 mM) pretreatment significantly protected against valproic acid-induced raise in oxidative stress, mitochondrial and lysosomal dysfunction, lipid peroxidation levels and depletion of GSH content. Our results in the current study provided insights into the protective mechanism by L-carnitine and sodium selenite, which is liked, to neuronal ROS generation and mitochondrial and lysosomal damages.

Revisiting the flocculation kinetics of destabilized asphaltenes.

A comprehensive review of the recently published work on asphaltene destabilization and flocculation kinetics is presented. Four different experimental techniques were used to study asphaltenes undergoing flocculation process in crude oils and model oils. The asphaltenes were destabilized by different n-alkanes and a geometric population balance with the Smoluchowski collision kernel was used to model the asphaltene aggregation process. Additionally, by postulating a relation between the aggregation collision efficiency and the solubility parameter of asphaltenes and the solution, a unified model of asphaltene aggregation model was developed. When the aggregation model is applied to the experimental data obtained from several different crude oil and model oils, the detection time curves collapsed onto a universal single line, indicating that the model successfully captures the underlying physics of the observed process.

Dimer covering and percolation frustration.

Covering a graph or a lattice with nonoverlapping dimers is a problem that has received considerable interest in areas, such as discrete mathematics, statistical physics, chemistry, and materials science. Yet, the problem of percolation on dimer-covered lattices has received little attention. In particular, percolation on lattices that are fully covered by nonoverlapping dimers has not evidently been considered. Here, we propose a procedure for generating random dimer coverings of a given lattice. We then compute the bond percolation threshold on random and ordered coverings of the square and the triangular lattices on the remaining bonds connecting the dimers. We obtain p_{c}=0.367713(2) and p_{c}=0.235340(1) for random coverings of the square and the triangular lattices, respectively. We observe that the percolation frustration induced as a result of dimer covering is larger in the low-coordination-number square lattice. There is also no relationship between the existence of long-range order in a covering of the square lattice and its percolation threshold. In particular, an ordered covering of the square lattice, denoted by shifted covering in this paper, has an unusually low percolation threshold and is topologically identical to the triangular lattice. This is in contrast to the other ordered dimer coverings considered in this paper, which have higher percolation thresholds than the random covering. In the case of the triangular lattice, the percolation thresholds of the ordered and random coverings are very close, suggesting the lack of sensitivity of the percolation threshold to microscopic details of the covering in highly coordinated networks.

The fractal aggregation of asphaltenes.

This paper discusses time-resolved small-angle neutron scattering results that were used to investigate asphaltene structure and stability with and without a precipitant added in both crude oil and model oil. A novel approach was used to isolate the scattering from asphaltenes that are insoluble and in the process of aggregating from those that are soluble. It was found that both soluble and insoluble asphaltenes form fractal clusters in crude oil and the fractal dimension of the insoluble asphaltene clusters is higher than that of the soluble clusters. Adding heptane also increases the size of soluble asphaltene clusters without modifying the fractal dimension. Understanding the process of insoluble asphaltenes forming fractals with higher fractal dimensions will potentially reveal the microscopic asphaltene destabilization mechanism (i.e., how a precipitant modifies asphaltene-asphaltene interactions). It was concluded that because of the polydisperse nature of asphaltenes, no well-defined asphaltene phase stability envelope exists and small amounts of asphaltenes precipitated even at dilute precipitant concentrations. Asphaltenes that are stable in a crude oil-precipitant mixture are dispersed on the nanometer length scale. An asphaltene precipitation mechanism is proposed that is consistent with the experimental findings. Additionally, it was found that the heptane-insoluble asphaltene fraction is the dominant source of small-angle scattering in crude oil and the previously unobtainable asphaltene solubility at low heptane concentrations was measured.