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We offer a selection of recent papers on a variety of topics from the Journal of Biological Chemistry, the Journal of Lipid Research and Â鶹´«Ã½É«ÇéƬ & Cellular Proteomics.

Olive proteins and Parkinson’s disease

Aggregates of alpha synuclein, or alpha SN, are primary components of Lewy bodies, which are linked to the degeneration of dopaminergic neurons in Parkinson’s disease. In the search for therapeutic molecules, researchers have found that phenolic compounds from olive fruit protect against neurodegeneration and exhibit antioxidant properties. Hossein Mohammad–Beigi and an international team screened extracts from 15 olive varieties and found that Koroneiki olives had the most potent effects on alpha SN aggregation. The authors fractionated the extract and identified three compounds that drove alpha SN monomers to form oligomer chains with reduced toxicity. was published in the Journal of Biological Chemistry.

Tregs help fight fatty liver disease

Consumed by people around the world, alcohol is a leading cause of illness and mortality. The liver is the organ primarily responsible for alcohol metabolism and can be damaged by excessive or prolonged consumption. This progressive damage leads to alcohol-induced liver disease, or ALD, which presents as a spectrum of symptoms and severities. Fatty livers are the earliest and most common pathology. Recent studies suggest that fat accumulation makes the liver more vulnerable to inflammation, which is further exacerbated when immune cells called T regulatory cells, or Tregs, are deficient.

published in the Journal of Lipid Research gives insight into the role Tregs play in ALD. and colleagues from Huazhong University of Science and Technology in China used mice to model alcohol-induced fat accumulation in the liver. They found that diseased mice had depleted Tregs as well as aberrant macrophage activation and cytokine production. Treg transfer to the diseased mice relieved inflammation and lipid metabolic disorder and inhibited macrophage activation and cytokine production. They also found that the effects of Tregs are dependent partially on the cytokine IL-10. Their data show a novel role for Tregs in ALD and highlight a potential therapeutic target.

Counting proteins of a single cell

Computer simulations can help scientists understand complex cell signaling pathways, but, to ensure model accuracy, researchers need parameters determined by experiments with live cells. Akira Komatsubra and colleagues in Japan have established a way to measure protein concentration and dissociation constants at the single-cell level. By attaching EGFP and HaloTag genes to the ends of MAPK1 and RSK2 genes, respectively, the authors enabled fluorescence imaging of proteins encoded by the two modified genes and calculated their concentrations and dissociation constants. , published in the Journal of Biological Chemistry, demonstrates an approach to quantifying parameters that could improve the performance of simulation models.

Rethinking a vaccine for malaria

Caused by parasites belonging to the Plasmodium family, malaria is transmitted to humans by female Anopheles mosquitoes. This life-threatening disease is prevalent in developing countries, and the only approved vaccine is largely ineffective, so much recent research has been directed toward developing more potent protection against the parasite. Studies have shown that some attenuated parasite proteins can protect humans, but researchers have been unable to find malaria proteins that confer this protection. Using malaria parasite–infected mice as models, a study by Anthony Siau and colleagues at Nangyang Technological University and Singapore Immunology Network employed immunomic and proteomic techniques to identify a repertoire of parasite proteins associated with protection against Plasmodium yoelii, the parasite used in labs to infect mice. Using such criteria as reproducibility and immunoreactivity, the authors categorized these proteins based on how likely they were to protect against blood-stage malarial infection — the stage when the parasites divide in red blood cells and that is responsible for all clinical malaria symptoms. were published in the journal Â鶹´«Ã½É«ÇéƬ & Cellular Proteomics. When extended to Plasmodium species affecting humans, this extensive data set could be used to help validate and characterize new vaccine formulations for better prevention of malaria.

Staph bacteria’s copper resistance

Many hospital surfaces are copper because the metal has antimicrobial properties that can block the spread of disease, but some strains of Staphylococcus aureus have evolved mechanisms to resist copper’s effect. Zuelay Rosario–Cruz of Rutgers University and a team of researchers identified two genes, copB and copL, that enable S. aureus’ copper resistance. Genetic evidence suggested that the CopB protein plays a role in copper export, while nuclear magnetic resonance identified CopL from Bacillus subtilis, a close relative of S. aureus, as a membrane-bound lipoprotein that could bind extracellular copper. , published in the Journal of Biological Chemistry, suggest mechanisms by which S. aureus thwarts copper and could aid in the development of methods to better limit infections.

Reversing mutant accumulation in cancer

The transcription factor p53 functions as a tumor suppressor; in more than half of cancer patients, this protein is mutated and accumulates inside cells. Luciana Rangel and colleagues at the Federal University of Rio de Janeiro report that the small molecule PRIMA-1, which can return mutated p53 to a natural shape, also reverses accumulation of the protein. , published in the Journal of Biological Chemistry, showed that exposing cancer cells to PRIMA-1 reduced aggregates of p53, initiated programmed cell death and inhibited the ability of mutant p53 to trigger aggregation of native p53. The authors suggest these results point toward p53 as a valid drug target.

Digging into the phagosomal proteome

In the process of phagocytosis, immune cells eat up foreign pathogens. The primary phagocytes in the human immune system are dendritic cells, or DCs, which break down pathogens in dynamic compartments called phagosomes and present the resulting antigen to T cells to start an immunogenic response. A phagosome changes its protein composition during its development and in response to various stimuli, but that phagosomal proteome is poorly understood.

In published in Â鶹´«Ã½É«ÇéƬ & Cellular Proteomics, Eik Hoffmann and an international team investigated changes in the phagosomal proteome in DCs derived from resting bone marrow versus those stimulated for immune response by lipopolysaccharide, or LPS. Using label-free mass spectrometric analysis, the authors found that upon LPS stimulation, these phagosomes recruit fewer proteins that help them mature and more proteins that help them present the antigen to T cells, thus changing their proteome. The study also identified other proteins previously not known to participate in phagosome function. This preliminary finding paves the way for better understanding of the phagosomal proteome and its dependence on external stimuli.

Isotope labeling may affect kinetic studies

Kinetic reactions and metabolic pathways can be studied using isotopically labeled substrates. Reactants are labeled by replacing specific atoms with their isotopes and can thus be tracked through time. Serine palmitoyltransferase, or SPT, is the first enzyme in sphingolipid biosynthesis and often is investigated using isotopically labeled L-serine.

In in the Journal of Lipid Research, of the University of Edinburgh and an international team used SPT from humans and the bacteria Sphingomonas paucimobilis to investigate the effect isotope labels may have on catalysis. SPT is conserved among all organisms capable of producing sphingolipids, yet the eukaryotic isoform is membrane-bound whereas the bacterial isoform is soluble and found in the cytoplasm. Campopiano and colleagues monitored SPT-catalyzed reactions using a series of L-serine substrates that differed in the position of an isotopic label. While the human and bacterial forms of SPT showed similar kinetics in many cases, one substrate revealed a kinetic isotope effect in the bacterial SPT that was absent in the human form. This suggests subtle catalytic differences between cytoplasmic and membrane-bound forms of SPT and that the position of isotope labeling should be considered carefully during kinetic experiments.

Â鶹´«Ã½É«ÇéƬ bridges help patch up DNA

Double-strand breaks, or DSBs, in DNA can be lethal to cells, but mechanisms have evolved to correct errors in the genetic code. The protein Ctp1 is key to the initiation of DSB repair, but exactly how it interacts with DNA was until recently unknown. To find out, Sara Andres and colleagues from the National Institute of Environmental Health Sciences and the University of North Carolina performed atomic force microscopy imaging of Ctp1-DNA complexes. in the Journal of Biological Chemistry that they observed polymerized Ctp1 tetramers on dsDNA, forming bridges between strands; when Ctp1 was mutated, cells were sensitized to DNA damage. These images provide valuable mechanistic insights for studying disease-causing DSB repair defects.

Protons and calcium ions shall not pass

Channelrhodopsins, or ChRs, are light-activated ion channels used in neuroscience to induce activity in neurons. But activating ChRs also can allow passage of protons and calcium ions, which may trigger undesirable responses such as glial acidification or intracellular calcium release. To avoid these effects, Yong Ku Cho and colleagues at the Massachusetts Institute of Technology engineered ChRs that permit the passage of only certain ions. By generating and screening hundreds of ChR2 mutants, they found a combination of mutations that produced a ChR variant with tenfold reductions in calcium and proton flux. Their methods offer a means to customize ChRs and could reveal new principles of optogenetic protein engineering. was published in the Journal of Biological Chemistry.