A model of threshold behavior reveals rescue mechanisms of bystander proteins in conformational diseases

Transcription factors and chaperone proteins play a role in launching a faster response to heat stress and aggregation

Proteins, under conditions of cellular stress, typically tend to unfold and form lethal aggregates leading to neurological diseases like Parkinson's and Alzheimer's. A clear understanding of the conditions that favor dis-aggregation and restore the cell to its healthy state after they have been stressed is therefore important in dealing with these diseases. The heat shock response (HSR) mechanism is a signaling network that deals with these undue protein aggregates and aids in the maintenance of homeostasis within a cell. This framework, on its own, is a mathematically well studied mechanism. However, not much is known about how the various intermediate mis-folded protein states of the aggregation process interact with some of the key components of the HSR pathway such as the Heat Shock Protein (HSP), the Heat Shock Transcription Factor (HSF) and the HSP-HSF complex. In this article, using kinetic parameters from the literature, we propose and analyze two mathematical models for HSR that also include explicit reactions for the formation of protein aggregates. Deterministic analysis and stochastic simulations of these models show that the folded proteins and the misfolded aggregates exhibit bistability in a certain region of the parameter space. Further, the models also highlight the role of HSF and the HSF-HSP complex in reducing the time lag of response to stress and in re-folding all the mis-folded proteins back to their native state. These models, therefore, call attention to the significance of studying related pathways such as the HSR and the protein aggregation and re-folding process in conjunction with each other.

Development, growth and maintenance of β-cell mass: models are also part of the story

Pancreatic β-cells in the islets of Langerhans play a crucial role in regulating glucose homeostasis in the circulation. Loss of β-cell mass or function due to environmental, genetic and immunological factors leads to the manifestation of diabetes mellitus. The mechanisms regulating the dynamics of pancreatic β-cell mass during normal development and diabetes progression are complex. To fully unravel such complexity, experimental and clinical approaches need to be combined with mathematical and computational models. In the natural sciences, mathematical and computational models have aided the identification of key mechanisms underlying the behavior of systems comprising multiple interacting components. A number of mathematical and computational models have been proposed to explain the development, growth and death of pancreatic β-cells. In this review, we discuss some of these models and how their predictions provide novel insight into the mechanisms controlling β-cell mass during normal development and diabetes progression. Lastly, we discuss a handful of the major open questions in the field.

Surveying the floodgates: estimating protein flux into the endoplasmic reticulum lumen in Saccharomyces cerevisiae

Endoplasmic reticulum resident proteins, along with all proteins traveling through the secretory pathway must enter endoplasmic reticulum lumen through membrane-embedded translocons. In Saccharomyces cerevisiae the heterotrimeric endoplasmic reticulum translocon is composed of the Sec61p, Sss1p, and Sbh1p core subunits. While the involvement of various molecules associated with the Sec61 complex has been thoroughly characterized, little attention has been given to the overall flux through these channels. In this work we carried out a meta-analysis to estimate the average and absolute flux of proteins into the endoplasmic reticulum lumen. We estimate an average of 460 proteins enter the endoplasmic reticulum every second, with an absolute minimum and maximum flux of 78 and 3700 molecules per second, respectively. With current technologies limiting the ability to obtain accurate measurements of these events, our estimates shed light on the flow of protein entering the endoplasmic reticulum lumen.

Inferring the Effects of Honokiol on the Notch Signaling Pathway in SW480 Colon Cancer Cells

In a tumor cell, the development of acquired therapeutic resistance and the ability to survive in extracellular environments that differ from the primary site are the result of molecular adaptations in potentially highly plastic molecular networks. The accurate prediction of intracellular networks in a tumor remains a difficult problem in cancer informatics. In order to make truly rational patient-driven therapeutic decisions, it will be critical to develop methodologies that can accurately infer the molecular circuitry in the cells of a specific tumor. Despite enormous heterogeneity, cellular networks elicit deterministic digital-like responses. We discuss the use and limitations of methodologies that model molecular networks in cancer cells as a digital circuit. We also develop a network model of Notch signaling in colon cancer using a novel reverse engineering logic-based method and published western blot data to elucidate the interactions likely present in the circuits of the SW480 colon cancer cell line. Within this framework, we make predictions related to the role that honokiol may be playing as an anti-cancer drug.

Dominant protein interactions that influence the pathogenesis of conformational diseases

Misfolding of exportable proteins can trigger endocrinopathies. For example, misfolding of insulin can result in autosomal dominant mutant INS gene-induced diabetes of youth, and misfolding of thyroglobulin can result in autosomal recessive congenital hypothyroidism with deficient thyroglobulin. Both proinsulin and thyroglobulin normally form homodimers; the mutant versions of both proteins misfold in the ER, triggering ER stress, and, in both cases, heterozygosity creates potential for cross-dimerization between mutant and WT gene products. Here, we investigated these two ER-retained mutant secretory proteins and the selectivity of their interactions with their respective WT counterparts. In both cases and in animal models of these diseases, we found that conditions favoring an increased stoichiometry of mutant gene product dominantly inhibited export of the WT partner, while increased relative level of the WT gene product helped to rescue secretion of the mutant partner. Surprisingly, the bidirectional consequences of secretory blockade and rescue occur simultaneously in the same cells. Thus, in the context of heterozygosity, expression level and stability of WT subunits may be a critical factor influencing the effect of protein misfolding on clinical phenotype. These results offer new insight into dominant as well as recessive inheritance of conformational diseases and offer opportunities for the development of new therapies.

Insulin therapy for pre-hyperglycemic beta-cell endoplasmic reticulum crowding

Insulin therapy improves β-cell function in early stages of diabetes by mechanisms that may exceed alleviation of glucotoxicity. In advance type 2 diabetes, hyperglycemia causes β-cell damage and ultimately β-cell loss. At such an advanced stage, therapeutic modalities are often inadequate. Growing evidence indicates that in early stages of type-2 diabetes and some types of monogenic diabetes linked with malfunctioning endoplasmic-reticulum (ER), the β-cell ER fails to process sufficient proinsulin once it becomes overloaded. These changes manifest with ER distention (ER-crowding) and deficiency of secretory granules. We hypothesize that insulin therapy may improves β-cell function by alleviating ER-crowding. To support this hypothesis, we investigated pre-diabetic β-cell changes in hProC(A7)Y-CpepGFP transgenic mice that develop prolonged pre-diabetes due to proinsulin dysmaturation and ER-crowding. We attenuated the β-cell ER proinsulin synthesis with a treat-to-target insulin therapy while avoiding hypoglycemia and weight gain. Alleviation of ER-crowding resulted in temporary improvement in proinsulin maturation, insulin secretion and glucose tolerance. Our observations suggest that alleviation of pre-diabetic ER-crowding using a treat-to-target insulin therapy may improve β-cell function and may prevent further metabolic deterioration.

Cellular strategies for regulating functional and nonfunctional protein aggregation

Growing evidence suggests that aggregation-prone proteins are both harmful and functional for a cell. How do cellular systems balance the detrimental and beneficial effect of protein aggregation? We reveal that aggregation-prone proteins are subject to differential transcriptional, translational, and degradation control compared to nonaggregation-prone proteins, which leads to their decreased synthesis, low abundance, and high turnover. Genetic modulators that enhance the aggregation phenotype are enriched in genes that influence expression homeostasis. Moreover, genes encoding aggregation-prone proteins are more likely to be harmful when overexpressed. The trends are evolutionarily conserved and suggest a strategy whereby cellular mechanisms specifically modulate the availability of aggregation-prone proteins to (1) keep concentrations below the critical ones required for aggregation and (2) shift the equilibrium between the monomeric and oligomeric/aggregate form, as explained by Le Chatelier’s principle. This strategy may prevent formation of undesirable aggregates and keep functional assemblies/aggregates under control.