Contribution of a putative salt bridge and backbone dynamics in the structural instability of human prion protein upon R208H mutation

Molecular dynamics simulation method is used to assess the contribution of a disease-associated salt bridge in the early stages of the conformational rearrangement of human prion protein upon Arg²⁰⁸→His mutation, which causes Creutzfeldt-Jakob disease. Previous investigations have suggested that the breakage of this putative salt bridge (D¹⁴⁴/E¹⁴⁶ ↔ Arg²⁰⁸) between helix 1 and helix 3 is responsible for such a mutation-driven process. So far, no experimental data has been reported in order to distinguish the contribution of this single salt bridge in the initial steps of amyloid formation. Consequently, we decided to investigate the role of this salt bridge in early conformational rearrangements. To remove the salt bridge without perturbations in the backbone structure, the neutralized states of the involved residues were used. Three 10-ns molecular dynamics simulations on three initial structures have been performed. The results revealed that the early stages of the conformational rearrangements, against common belief, are mainly associated with the mutation-induced global changes in the backbone dynamics but not with the breaking of the salt bridge.     

The Relationship Between Selenium Levels and Breast Cancer: A Systematic Review and Meta-Analysis

Breast cancer is the most common cancer type. In several studies, hints have been provided that there is a correlation between selenium deficiency and the incidence of breast cancer. Findings of these published reports are, however, inconsistent. This study serves as a pioneering study aiming at combining the results of studies using a meta-analytic method. A total of 16 articles published between 1980 and 2012 worldwide were selected through searching PubMed, Scopus, and Google scholar databases, and the information were analyzed using a meta-analytic method [random effects model]. I ² statistics were used to examine heterogeneity. The information was then analyzed by STATA version 12. In this study, due to the non-uniform methods used to measure selenium concentrations, selenium levels were measured in the various subgroups in both case and control groups. There were significant correlations between selenium concentration and breast cancer [P?<?0.05]. Hence, the mean risk differentiating criteria were estimated to be 0.63 [95 % confidence interval [95% CI] 0.93 to 0.32] in serum and toenails. Subgroup analysis showed that the value in toenails was ?0.07 [95% CI ?0.16 to 0.03] and in serum ?1.04 [95% CI 1.71 to ?0.38]. In studies in which selenium concentrations were measured in serum, a significant correlation was observed between selenium concentration and breast cancer. In contrast, in studies in which selenium concentration was measured in toenails, the correlation was not significant. Therefore, the selenium concentration can be used as one predictor for breast cancer.     

Statistical analysis of the processes controlling choline and ethanolamine glycerophospholipid molecular species composition

The regulation and maintenance of the cellular lipidome through biosynthetic, remodeling, and catabolic mechanisms are critical for biological homeostasis during development, health and disease. These complex mechanisms control the architectures of lipid molecular species, which have diverse yet highly regulated fatty acid chains at both the sn1 and sn2 positions. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) serve as the predominant biophysical scaffolds in membranes, acting as reservoirs for potent lipid signals and regulating numerous enzymatic processes. Here we report the first rigorous computational dissection of the mechanisms influencing PC and PE molecular architectures from high-throughput shotgun lipidomic data. Using novel statistical approaches, we have analyzed multidimensional mass spectrometry-based shotgun lipidomic data from developmental mouse heart and mature mouse heart, lung, brain, and liver tissues. We show that in PC and PE, sn1 and sn2 positions are largely independent, though for low abundance species regulatory processes may interact with both the sn1 and sn2 chain simultaneously, leading to cooperative effects. Chains with similar biochemical properties appear to be remodeled similarly. We also see that sn2 positions are more regulated than sn1, and that PC exhibits stronger cooperative effects than PE. A key aspect of our work is a novel statistically rigorous approach to determine cooperativity based on a modified Fisher's exact test using Markov Chain Monte Carlo sampling. This computational approach provides a novel tool for developing mechanistic insight into lipidomic regulation.     

D224V and S128Y mutation in FSHRED influence thumb movement differentially: An intricate insight gained by short-term molecular dynamics simulation

Follicle-stimulating hormone-follicle-stimulating hormone receptor (FSH-FSHR) interaction is one of the most thoroughly studied signaling pathways primarily because of being implicated in sexual reproduction in mammals by way of maintaining gonadal function and sexual fertility. Despite material advances in understanding the role of point mutations, their mechanistic basis in FSH-FSHR signaling is still confined to mystically altered behavior of sTYS335 (sulfated tyrosine) yet lacking a substantial theory. To understand the structural basis of receptor modulation, we choose two behaviorally contradicting mutations, namely S128Y (activating) and D224Y (inactivating), found in FSH receptor responsible for ovarian hyperstimulation syndrome and ovarian dysgenesis, respectively. Using short-term molecular dynamics simulations, the atomic scale investigations reveal that the binding pattern of sTYS with FSH and movement of the thumb region of FSHR show distinct contrasting patterns in the two mutants, which supposedly could be a critical factor for differential FSHR behavior in activating and inactivating mutations.