Bacterial Hsp70 resolves misfolded states and accelerates productive folding of a multi-domain protein

The ATP-dependent Hsp70 chaperones (DnaK in E. coli) mediate protein folding in cooperation with J proteins and nucleotide exchange factors (E. coli DnaJ and GrpE, respectively). The Hsp70 system prevents protein aggregation and increases folding yields. Whether it also enhances the rate of folding remains unclear. Here we show that DnaK/DnaJ/GrpE accelerate the folding of the multi-domain protein firefly luciferase (FLuc) 20-fold over the rate of spontaneous folding measured in the absence of aggregation. Analysis by single-pair FRET and hydrogen/deuterium exchange identified inter-domain misfolding as the cause of slow folding. DnaK binding expands the misfolded region and thereby resolves the kinetically-trapped intermediates, with folding occurring upon GrpE-mediated release. In each round of release DnaK commits a fraction of FLuc to fast folding, circumventing misfolding. We suggest that by resolving misfolding and accelerating productive folding, the bacterial Hsp70 system can maintain proteins in their native states under otherwise denaturing stress conditions. The Hsp70 system prevents protein aggregation and increases folding yields, but it is unknown whether it also enhances the rate of folding. Here the authors combine refolding assays, FRET and hydrogen/deuterium exchange-mass spectrometry measurements to study the folding of firefly luciferase and find that the bacterial Hsp70 actively promotes the folding of this multi-domain protein

The proteostasis network and its decline in ageing

Ageing is a major risk factor for the development of many diseases, prominently including neurodegenerative disorders such as Alzheimer disease and Parkinson disease. A hallmark of many age-related diseases is the dysfunction in protein homeostasis (proteostasis), leading to the accumulation of protein aggregates. In healthy cells, a complex proteostasis network, comprising molecular chaperones and proteolytic machineries and their regulators, operates to ensure the maintenance of proteostasis. These factors coordinate protein synthesis with polypeptide folding, the conservation of protein conformation and protein degradation. However, sustaining proteome balance is a challenging task in the face of various external and endogenous stresses that accumulate during ageing. These stresses lead to the decline of proteostasis network capacity and proteome integrity. The resulting accumulation of misfolded and aggregated proteins affects, in particular, postmitotic cell types such as neurons, manifesting in disease. Recent analyses of proteome-wide changes that occur during ageing inform strategies to improve proteostasis. The possibilities of pharmacological augmentation of the capacity of proteostasis networks hold great promise for delaying the onset of age-related pathologies associated with proteome deterioration and for extending healthspan

Workload Equity in Vehicle Routing Problems: A Survey and Analysis

Over the past two decades, equity aspects have been considered in a growing number of models and methods for vehicle routing problems (VRPs). Equity concerns most often relate to fairly allocating workloads and to balancing the utilization of resources, and many practical applications have been reported in the literature. However, there has been only limited discussion about how workload equity should be modeled in VRPs, and various measures for optimizing such objectives have been proposed and implemented without a critical evaluation of their respective merits and consequences. This article addresses this gap with an analysis of classical and alternative equity functions for biobjective VRP models. In our survey, we review and categorize the existing literature on equitable VRPs. In the analysis, we identify a set of axiomatic properties that an ideal equity measure should satisfy, collect six common measures, and point out important connections between their properties and those of the resulting Pareto-optimal solutions. To gauge the extent of these implications, we also conduct a numerical study on small biobjective VRP instances solvable to optimality. Our study reveals two undesirable consequences when optimizing equity with nonmonotonic functions: Pareto-optimal solutions can consist of non-TSP-optimal tours, and even if all tours are TSP optimal, Pareto-optimal solutions can be workload inconsistent, i.e. composed of tours whose workloads are all equal to or longer than those of other Pareto-optimal solutions. We show that the extent of these phenomena should not be underestimated. The results of our biobjective analysis are valid also for weighted sum, constraint-based, or single-objective models. Based on this analysis, we conclude that monotonic equity functions are more appropriate for certain types of VRP models, and suggest promising avenues for further research.Comment: Accepted Manuscrip

A large neighbourhood based heuristic for two-echelon routing problems

In this paper, we address two optimisation problems arising in the context of city logistics and two-level transportation systems. The two-echelon vehicle routing problem and the two-echelon location routing problem seek to produce vehicle itineraries to deliver goods to customers, with transits through intermediate facilities. To efficiently solve these problems, we propose a hybrid metaheuristic which combines enumerative local searches with destroy-and-repair principles, as well as some tailored operators to optimise the selections of intermediate facilities. We conduct extensive computational experiments to investigate the contribution of these operators to the search performance, and measure the performance of the method on both problem classes. The proposed algorithm finds the current best known solutions, or better ones, for 95% of the two-echelon vehicle routing problem benchmark instances. Overall, for both problems, it achieves high-quality solutions within short computing times. Finally, for future reference, we resolve inconsistencies between different versions of benchmark instances, document their differences, and provide them all online in a unified format

Genotype and environment interaction on yield and quality parameters of organically grown winter wheat – Triticum aestivum L. genotypes

The interaction of genotype and environment upon yield and quality parameters of eight winter wheat (Triticum aestivum L.) genotypes was studied under organic conditions in Austria over two growing periods, 2001/2002 and 2002/2003, respectively. Two sites that have significantly different climatic conditions, Innviertel and Marchfeld, were chosen for the field experiment. Study site weather and soil conditions are important yield-affecting factors. Although the yield of Marchfeld-grown genotypes were lower, they had shown higher quality parameter values. Soil moisture conditions increase the grain yield but decrease its quality. To obtain seed with higher quality, a production site with favourable climate conditions should be chosen

Review

Molecular chaperones are highly conserved proteins that promote proper folding of other proteinsin vivo. Diverse chaperone systems assistde novoprotein folding and trafficking, the assembly of oligomeric complexes, and recovery from stress-induced unfolding. A fundamental function of molecular chaperones is to inhibit unproductive protein interactions by recognizing and protecting hydrophobic surfaces that are exposed during folding or following proteotoxic stress. Beyond this basic principle, it is now clear that chaperones can also actively and specifically accelerate folding reactions in an ATP-dependent manner. We focus on the bacterial Hsp70 and chaperonin systems as paradigms, and review recent work that has advanced our understanding of how these chaperones act as catalysts of protein folding