Oxidative protein folding in the mitochondrial intermembrane space

Disulfide bond formation is a crucial step for oxidative folding and necessary for the acquisition of a protein's native conformation. Introduction of disulfide bonds is catalyzed in specialized subcellular compartments and requires the coordinated action of specific enzymes. The intermembrane space of mitochondria has recently been found to harbor a dedicated machinery that promotes the oxidative folding of substrate proteins by shuttling disulfide bonds. The newly identified oxidative pathway consists of the redox-regulated receptor Mia40 and the sulfhydryl oxidase Erv1. Proteins destined to the intermembrane space are trapped by a disulfide relay mechanism that involves an electron cascade from the incoming substrate to Mia40, then on to Erv1, and finally to molecular oxygen via cytochrome c. This thiol–disulfide exchange mechanism is essential for the import and for maintaining the structural stability of the incoming precursors. In this review we describe the mechanistic parameters that define the interaction and oxidation of the substrate proteins in light of the recent publications in the mitochondrial oxidative folding field

Bipartite quantum states and random complex networks

We introduce a mapping between graphs and pure quantum bipartite states and show that the associated entanglement entropy conveys non-trivial information about the structure of the graph. Our primary goal is to investigate the family of random graphs known as complex networks. In the case of classical random graphs we derive an analytic expression for the averaged entanglement entropy $\bar S$ while for general complex networks we rely on numerics. For large number of nodes $n$ we find a scaling $\bar{S} \sim c \log n +g_e$ where both the prefactor $c$ and the sub-leading O(1) term $g_e$ are a characteristic of the different classes of complex networks. In particular, $g_e$ encodes topological features of the graphs and is named network topological entropy. Our results suggest that quantum entanglement may provide a powerful tool in the analysis of large complex networks with non-trivial topological properties.Comment: 4 pages, 3 figure

Ground-State Entanglement in Interacting Bosonic Graphs

We consider a collection of bosonic modes corresponding to the vertices of a graph $\Gamma.$ Quantum tunneling can occur only along the edges of $\Gamma$ and a local self-interaction term is present. Quantum entanglement of one vertex with respect the rest of the graph is analyzed in the ground-state of the system as a function of the tunneling amplitude $\tau.$ The topology of $\Gamma$ plays a major role in determining the tunneling amplitude $\tau^*$ which leads to the maximum ground-state entanglement. Whereas in most of the cases one finds the intuitively expected result $\tau^*=\infty$ we show that it there exists a family of graphs for which the optimal value of$\tau$ is pushed down to a finite value. We also show that, for complete graphs, our bi-partite entanglement provides useful insights in the analysis of the cross-over between insulating and superfluid ground statesComment: 5 pages (LaTeX) 5 eps figures include

Topology and energy transport in networks of interacting photosynthetic complexes

We address the role of topology in the energy transport process that occurs in networks of photosynthetic complexes. We take inspiration from light harvesting networks present in purple bacteria and simulate an incoherent dissipative energy transport process on more general and abstract networks, considering both regular structures (Cayley trees and hyperbranched fractals) and randomly-generated ones. We focus on the the two primary light harvesting complexes of purple bacteria, i.e., the LH1 and LH2, and we use network-theoretical centrality measures in order to select different LH1 arrangements. We show that different choices cause significant differences in the transport efficiencies, and that for regular networks centrality measures allow to identify arrangements that ensure transport efficiencies which are better than those obtained with a random disposition of the complexes. The optimal arrangements strongly depend on the dissipative nature of the dynamics and on the topological properties of the networks considered, and depending on the latter they are achieved by using global vs. local centrality measures. For randomly-generated networks a random arrangement of the complexes already provides efficient transport, and this suggests the process is strong with respect to limited amount of control in the structure design and to the disorder inherent in the construction of randomly-assembled structures. Finally, we compare the networks considered with the real biological networks and find that the latter have in general better performances, due to their higher connectivity, but the former with optimal arrangements can mimic the real networks' behaviour for a specific range of transport parameters. These results show that the use of network-theoretical concepts can be crucial for the characterization and design of efficient artificial energy transport networks.Comment: 14 pages, 16 figures, revised versio

Transitions between bursting modes in the integrated oscillator model for pancreatic β-cells

Insulin-secreting $\beta$-cells of pancreatic islets of Langerhans produce bursts of electrical impulses, resulting in intracellular Ca$^{2+}$ oscillations and pulsatile insulin secretion. The mechanism for this bursting activity has been the focus of mathematical modeling for more than three decades, and as new data are acquired old models are modified and new models are developed. Comprehensive models must now account for the various modes of bursting observed in islet $\beta$-cells, which include fast bursting, slow bursting, and compound bursting. One such model is the Integrated Oscillator Model (IOM), in which $\beta$-cell electrical activity, intracellular Ca$^{2+}$ , and glucose metabolism interact via numerous feedforward and feedback pathways. These interactions can produce metabolic oscillations with a sawtooth time course or a pulsatile time course, reflecting very different oscillation mechanisms. In this report, we determine conditions favorable to one form of oscillations or the other, and examine the transitions between modes of bursting and the relationship of the transitions to the patterns of metabolic oscillations. Importantly, this work clarifies what can be expected in experimental measurements of $\beta$-cell oscillatory activity, and suggests pathways through which oscillations of one type can be converted to oscillations of another type.R. Bertram was supported by grant number DMS-1612193 from the National Science Foundatio

From early stress to 12-month development in very preterm infants: Preliminary findings on epigenetic mechanisms and brain growth

Very preterm (VPT) infants admitted to Neonatal Intensive Care Unit (NICU) are at risk for altered brain growth and less-than-optimal socio-emotional development. Recent research suggests that early NICU-related stress contributes to socio-emotional impairments in VPT infants at 3 months through epigenetic regulation (i.e., DNA methylation) of the serotonin transporter gene (SLC6A4). In the present longitudinal study we assessed: (a) the effects of NICU-related stress and SLC6A4 methylation variations from birth to discharge on brain development at term equivalent age (TEA); (b) the association between brain volume at TEA and socio-emotional development (i.e., Personal-Social scale of Griffith Mental Development Scales, GMDS) at 12 months corrected age (CA). Twenty-four infants had complete data at 12-month-age. SLC6A4 methylation was measured at a specific CpG previously associated with NICU-related stress and socio-emotional stress. Findings confirmed that higher NICU-related stress associated with greater increase of SLC6A4 methylation at NICU discharge. Moreover, higher SLC6A4 discharge methylation was associated with reduced anterior temporal lobe (ATL) volume at TEA, which in turn was significantly associated with less-than-optimal GMDS Personal-Social scale score at 12 months CA. The reduced ATL volume at TEA mediated the pathway linking stress-related increase in SLC6A4 methylation at NICU discharge and socio-emotional development at 12 months CA. These findings suggest that early adversity-related epigenetic changes might contribute to the long-lasting programming of socio-emotional development in VPT infants through epigenetic regulation and structural modifications of the developing brain

Experimental estimation of entanglement at the quantum limit

Entanglement is the central resource of quantum information processing and the precise characterization of entangled states is a crucial issue for the development of quantum technologies. This leads to the necessity of a precise, experimental feasible measure of entanglement. Nevertheless, such measurements are limited both from experimental uncertainties and intrinsic quantum bounds. Here we present an experiment where the amount of entanglement of a family of two-qubit mixed photon states is estimated with the ultimate precision allowed by quantum mechanics.Comment: 4 pages, 3 figure