Construct, merge, solve and adapt (CMSA) is a recently developed, generic algorithm for combinatorial optimisation. Even though the usefulness of the algorithm has been demonstrated by applications ...to a range of combinatorial optimisation problems, in some applications, it was observed that the algorithm can be sensitive to parameter settings. In this work, we propose a self-adaptive variant of CMSA, called Adapt-CMSA, with the aim of reducing the parameter sensitivity of the original version of CMSA. The advantages of this new CMSA variant are demonstrated in the context of the application to the so-called minimum positive influence dominating set problem. It is shown that, in contrast to CMSA, Adapt-CMSA does not require a computation time intensive parameter tuning process for subsets of the considered set of problem instances. In fact, after tuning Adapt-CMSA only once for the whole set of benchmark instances, the algorithm already obtains state-of-the-art results. Nevertheless, note that the main objective of this paper is not the tackled problem but the improvement of CMSA.
Cholera toxin (CT) and Escherichia coli heat-labile enterotoxin (LT) are structurally similar AB
-type protein toxins. They move from the cell surface to the endoplasmic reticulum where the A1 ...catalytic subunit is separated from its holotoxin by protein disulfide isomerase (PDI), thus allowing the dissociated A1 subunit to enter the cytosol for a toxic effect. Despite similar mechanisms of toxicity, CT is more potent than LT. The difference has been attributed to a more stable domain assembly for CT as compared to LT, but this explanation has not been directly tested and is arguable as toxin disassembly is an indispensable step in the cellular action of these toxins. We show here that PDI disassembles CT more efficiently than LT, which provides a possible explanation for the greater potency of the former toxin. Furthermore, direct examination of CT and LT domain assemblies found no difference in toxin stability. Using novel analytic geometry approaches, we provide a detailed characterization of the positioning of the A subunit with respect to the B pentamer and demonstrate significant differences in the interdomain architecture of CT and LT. Protein docking analysis further suggests that these global structural differences result in distinct modes of PDI-toxin interactions. Our results highlight previously overlooked structural differences between CT and LT that provide a new model for the PDI-assisted disassembly and differential potency of these toxins.
Protein disulfide isomerase (PDI) is mainly located in the endoplasmic reticulum (ER) but is also secreted into the bloodstream where its oxidoreductase activity is involved with thrombus formation. ...Quercetin-3-rutinoside (Q3R) blocks this activity, but its inhibitory mechanism against PDI is not fully understood. Here, we examined the potential inhibitory effect of Q3R on another process that requires PDI: disassembly of the multimeric cholera toxin (CT). In the ER, PDI physically displaces the reduced CTA1 subunit from its non-covalent assembly in the CT holotoxin. This is followed by CTA1 dislocation from the ER to the cytosol where the toxin interacts with its G protein target for a cytopathic effect. Q3R blocked the conformational change in PDI that accompanies its binding to CTA1, which, in turn, prevented PDI from displacing CTA1 from its holotoxin and generated a toxin-resistant phenotype. Other steps of the CT intoxication process were not affected by Q3R, including PDI binding to CTA1 and CT reduction by PDI. Additional experiments with the B chain of ricin toxin found that Q3R could also disrupt PDI function through the loss of substrate binding. Q3R can thus inhibit PDI function through distinct mechanisms in a substrate-dependent manner.
Aggregates of α-synuclein contribute to the etiology of Parkinson’s Disease. Protein disulfide isomerase (PDI), a chaperone and oxidoreductase, blocks the aggregation of α-synuclein. An ...S-nitrosylated form of PDI that cannot function as a chaperone is associated with elevated levels of aggregated α-synuclein and is found in brains afflicted with Parkinson’s Disease. The protective role of PDI in Parkinson’s Disease and other neurodegenerative disorders is linked to its chaperone function, yet the mechanism of neuroprotection remains unclear. Using Thioflavin-T fluorescence and transmission electron microscopy, we show here for the first time that PDI can break down nascent fibrils of α-synuclein. Mature fibrils were not affected by PDI. Another PDI family member, ERp57, could prevent but not reverse α-synuclein aggregation. The disaggregase activity of PDI was effective at a 1:50 molar ratio of PDI:α-synuclein and was blocked by S-nitrosylation. PDI could not reverse the aggregation of malate dehydrogenase, which indicated its disaggregase activity does not operate on all substrates. These findings establish a previously unrecognized disaggregase property of PDI that could underlie its neuroprotective function.
The Target Set Selection (TSS) problem is an NP-hard combinatorial optimization problem with origins in the field of social networks. There are various problem variants, all dealing with finding a ...smallest subset of vertices of a graph such that their influence is propagated to all nodes of the graph under a specific diffusion model. Despite the practical relevance of the problem, most existing research efforts have focused on theoretical properties restricted to certain classes of graphs. The richness in terms of theoretical results is in contrast to the scarceness of research aiming at efficiently solving the TSS problem. In this work we propose a Biased Random Key Genetic Algorithm (BRKGA) for solving the TSS problem in large-scale social networks. We consider the problem in combination with the Linear Threshold diffusion model. The obtained results show that our approach outperforms a recent heuristic from the literature.
Many AB toxins contain an enzymatic A moiety that is anchored to a cell-binding B moiety by a disulfide bridge. After receptor-mediated endocytosis, some AB toxins undergo retrograde transport to the ...endoplasmic reticulum (ER) where reduction of the disulfide bond occurs. The reduced A subunit then dissociates from the holotoxin and enters the cytosol to alter its cellular target. Intoxication requires A chain separation from the holotoxin, but, for many toxins, it is unclear if reduction alone is sufficient for toxin disassembly. Here, we examined the link between reduction and disassembly for several ER-translocating toxins. We found disassembly of the reduced
heat-labile enterotoxin (Ltx) required an interaction with one specific ER-localized oxidoreductase: protein disulfide isomerase (PDI). In contrast, the reduction and disassembly of ricin toxin (Rtx) and Shiga toxin 1 (Stx1) were coupled events that did not require PDI and could be triggered by reductant alone. PDI-deficient cells accordingly exhibited high resistance to Ltx with continued sensitivity to Rtx and Stx1. The distinct structural organization of each AB toxin thus appears to determine whether holotoxin disassembly occurs spontaneously upon disulfide reduction or requires the additional input of PDI.
Protein disulfide isomerase (PDI) is a ubiquitously expressed member of the thioredoxin family with related but independent oxidoreductase and chaperone properties. As a chaperone, PDI plays a ...crucial role in preventing the aggregation of misfolded proteins. Notably, PDI is known to inhibit alpha‐synuclein (SYN) fibrillization, a pathological hallmark of Parkinson's disease, but the mechanism by which PDI blocks the formation of SYN fibrils is unknown. Here, we report for the first time that PDI not only prevents SYN aggregation but is able to reverse aggregation both in vitro and in cultured cells. Assays using Thioflavin‐T fluorescence and transmission electron microscopy revealed that PDI is able to break down nascent but not mature fibrils. Furthermore, PDI was able to inhibit and reverse cellular fibrillization in HEK293T cells as assessed by protein‐fragment complementation and non‐reducing SDS‐PAGE. These data suggest a novel disaggregase function for PDI that disrupts the SYN fibrils most commonly found in Parkinson's disease. Current treatments for PD are limited to palliative care, but strategies focused on targeted therapeutic intervention are becoming popular. Thus, our work suggests the disaggregase property of PDI may lend itself to therapeutic development for Parkinson's disease.
Support or Funding Information
This work was supported, in part, by a LIFE at UCF Richard Tucker Gerontology Applied Research Award and a UCF College of Medicine competitive research grant.
This is from the Experimental Biology 2019 Meeting. There is no full text article associated with this published in The FASEB Journal.
Abstract only
Neurotoxic amyloid fibrils of α‐synuclein contribute to the etiology of Parkinson's disease. Protein disulfide isomerase (PDI) provides a protective effect against neurodegeneration ...that is linked to its chaperone function and its ability to disrupt protein aggregation. Here, we report PDI can both prevent and reverse the aggregation of α‐synuclein. Assays using Thioflavin T fluorescence or transmission electron microscopy demonstrated PDI can inhibit the formation of α‐synuclein fibrils when added at the onset of aggregation and can reverse fibrillization when added to intermediate fibrils 30 h after the initiation of aggregation. The chaperone but not oxidoreductase activity of PDI was required to disrupt α‐synuclein fibrillization. Biophysical studies found that substrate binding leads to the partial unfolding of PDI, which provides a possible molecular basis for the dissolution of α‐synuclein fibrils: the structural expansion of unfolded PDI could push against two or more proteins in the fibril, thus acting as a wedge to displace individual proteins from the aggregate. These data establish a new functional property for the chaperone activity of PDI that may explain how it protects against neurodegeneration.
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