Functions and Mechanisms of the Human Ribosome-Translocon Complex

The membrane of the endoplasmic reticulum (ER) in human cells harbors the protein translocon, which facilitates membrane insertion and translocation of almost every newly synthesized polypeptide targeted to organelles of the secretory pathway. The translocon comprises the polypeptide-conducting Sec61 channel and several additional proteins, which are associated with the heterotrimeric Sec61 complex. This ensemble of proteins facilitates ER targeting of precursor polypeptides, Sec61 channel opening and closing, and modification of precursor polypeptides in transit through the Sec61 complex. Recently, cryoelectron tomography of translocons in native ER membranes has given unprecedented insights into the architecture and dynamics of the native, ribosome-associated translocon and the Sec61 channel. These structural data are discussed in light of different Sec61 channel activities including ribosome receptor function, membrane insertion or translocation of newly synthesized polypeptides as well as the possible roles of the Sec61 channel as a passive ER calcium leak channel and regulator of ATP/ADP exchange between cytosol and ER.

Mitochondria Inspire a Lifestyle

Tucked inside our cells, we animals (and plants, and fungi) carry mitochondria, minuscule descendants of bacteria that invaded our common ancestor 2 billion years ago. This unplanned breakthrough endowed our ancestors with a convenient, portable source of energy, enabling them to progress towards more ambitious forms of life. Mitochondria still manufacture most of our energy; we have evolved to invest it to grow and produce offspring, and to last long enough to make it all happen. Yet because the continuous generation of energy is inevitably linked to that of toxic free radicals, mitochondria give us life and give us death. Stripping away clutter and minutiae, here we present a big-picture perspective of how mitochondria work, how they are passed on virtually only by mothers, and how they shape the lifestyles of species and individuals. We discuss why restricting food prolongs lifespan, why reproducing shortens it, and why moving about protects us from free radicals despite increasing their production. We show that our immune cells use special mitochondria to keep control over our gut microbes. And we lay out how the fabrication of energy and free radicals sets the internal clocks that command our everyday rhythms-waking, eating, sleeping. Mitochondria run the show.

Vacuolar-type ATPase: A proton pump to lysosomal trafficking

Vacuolar-type ATPase (V-ATPase), initially identified in yeast and plant vacuoles, pumps protons into the lumen of organelles coupled with ATP hydrolysis. The mammalian counterpart is found ubiquitously in endomembrane organelles and the plasma membrane of specialized cells such as osteoclasts. V-ATPase is also present in unique organelles such as insulin secretory granules, neural synaptic vesicles, and acrosomes of spermatozoa. Consistent with its diverse physiological roles and unique localization, the seven subunits of V-ATPase have 2-4 isoforms that are organelle- or cell-specific. Subunits of the enzyme function in trafficking organelles and vesicles by interacting with small molecule GTPases. During osteoclast differentiation, one of the four isoforms of subunit a, a3, is indispensable for secretory lysosome trafficking to the plasma membrane. Diseases such as osteopetrosis, renal acidosis, and hearing loss are related to V-ATPase isoforms. In addition to its role as an enzyme, V-ATPase has versatile physiological roles in eukaryotic cells.

Application of dehydroalanine as a building block for the synthesis of selenocysteine-containing peptides

Selenocysteine (Sec), the 21^st proteinogenic amino acid, is inserted co-translationally into number of natural proteins. It is coded by a dual function stop codon UGA (opal). It is a redox active amino acid found at the active sites of several enzymes that are involved in oxidation–reduction reactions. These enzymes include the three major mammalian selenoproteins glutathione peroxidase (GPx), thioredoxin reductase (TrxR), and iodothyronine deiodinase (Dio). Although Sec is structurally similar to its sulfur analogue cysteine (Cys), the lower pK_a of the selenol group in Sec as compared to that of Cys and the interesting redox properties of the selenium atom in peptides and proteins play crucial roles in redox catalysis. However, the chemical synthesis of Sec-containing peptides has been a difficult task. In this paper, we report on a new method for the synthesis of Sec and Sec-containing peptides using dehydroalanine (Dha) as a building block.

A new method for the synthesis of Sec and Sec-containing peptides using dehydroalanine (Dha) as a building block is described.

Current Research Approaches and Challenges in the Obesogen Field

Obesity is a worldwide pandemic that also contributes to the increased incidence of other diseases such as type 2 diabetes. Increased obesity is generally ascribed to positive energy balance. However, recent findings suggest that exposure to endocrine-disrupting chemicals such as obesogens during critical windows of development, may play an important role in the current obesity trends. Several experimental approaches, from in vitro cell cultures to transgenerational in vivo studies, are used to better understand the mechanisms of action of obesogens, each of which contributes to answer different questions. In this review, we discuss current knowledge in the obesogen field and the existing tools developed in research laboratories using tributyltin as a model obesogen. By understanding the advantages and limitations of each of these tools, we will better focus and design experimental approaches that will help expanding the obesogen field with the objective of finding potential therapeutic targets in human populations.

Metabolomics reveals defensive mechanisms adapted by maize on exposure to high molecular weight polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons are an important group of persistent organic pollutants. Using plants to remediate PAHs has been recognized as a cost-effective and environmentally friendly technique. However, the overall impact of PAHs on the regulation of plant metabolism has not yet been explored. In this study, we analyzed the alteration in the maize (Zea mays L.) metabolome on exposure to high molecular weight PAHs such as benzo[a]pyrene (BaP) and pyrene (PYR) in a hydroponic medium, individually and as a mixture (BaP + PYR) using GC-MS. The differences in the metabolites were analyzed using XCMS (an acronym for various forms (X) of chromatography-mass spectrometry), an online-based data analysis tool. A significant variation in metabolites was observed between treatment groups and the unspiked control group. The univariate, multivariate and pathway impact analysis showed there were more significant alterations in metabolic profiles between individual PAHs and the mixture of BaP and PYR. The marked changes in the metabolites of galactose metabolism and aminoacyl tRNA biosynthesis in PAHs treated maize leaves exhibit the adaptive defensive mechanisms for individual and PAHs mixture. Therefore, the metabolomics approach is essential for an understanding of the complex biochemical responses of plants to PAHs contaminants. This knowledge will shed new light in the field of phytoremediation, bio-monitoring, and environmental risk assessment.

The physical basis of fabrication of amyloid-based hydrogels by lysozyme

Schematic of heating- and cooling-induced transitions between HEWL states, and the subsequent formation of the hydrogel.

A recap of RNA recapping

The N7-methylguanosine cap is a hallmark of the 5' end of eukaryotic mRNAs and is required for gene expression. Loss of the cap was believed to lead irreversibly to decay. However, nearly a decade ago, it was discovered that mammalian cells contain enzymes in the cytoplasm that are capable of restoring caps onto uncapped RNAs. In this review, we summarize recent advances in our understanding of cytoplasmic RNA recapping and discuss the biochemistry of this process and its impact on regulating and diversifying the transcriptome. Although most studies focus on mammalian RNA recapping, we also highlight new observations for recapping in disparate eukaryotic organisms, with the trypanosome recapping system appearing to be a fascinating example of convergent evolution. We conclude with emerging insights into the biological significance of RNA recapping and prospects for the future of this evolving area of study. This article is categorized under: RNA Processing > RNA Editing and Modification Translation > Translation Regulation RNA Processing > Capping and 5' End Modifications RNA Turnover and Surveillance > Regulation of RNA Stability.

Regulation of ATG and Autophagy Initiation

ATG is involved in multiple processes of autophagosome formation, including the initial phase of autophagy. The mammalian autophagy complex-ULK1 complex is composed of ULK1, FIP200, ATG13 and ATG101, and the yeast autophagy initiation complex-ATG1 complex is composed of ATG1, ATG13, ATG17, ATG29 and ATG31. After this complex is activated, it binds and phosphorylates ATG9 on the vesicles. Then PI3KC3-C1 (yeast: ATG34: ATG15: ATG6: ATG14 or mammal animal: ATG34: ATG15: BECN1: ATG14L) is recruited to the PAS. Further, ATG12-ATG5-ATG16 complex is localized on PAS (Yeast) or localized on the outer surface of the membrane (mammal) and makes binding of ATG8 (LC3) with PE to form ATG8-PE complex, promoting autophagic membrane elongation, closure and formation autophagosome and autophagosome lysosome.

Otubain 1: a non-canonical deubiquitinase with an emerging role in cancer

The ubiquitin system regulates diverse biological processes, many involved in cancer pathogenesis, by altering the ubiquitination state of protein substrates. This is accomplished by ubiquitin ligases and deubiquitinases (DUBs), which respectively add or remove ubiquitin from substrates to alter their stability, activity, localization and interactions. While lack of catalytic activity makes therapeutic targeting of ubiquitin ligases difficult, DUB inhibitors represent an active area of research and the identification of cancer-associated DUBs may lead to the development of novel therapeutics. A growing body of literature demonstrates that the DUB Otubain 1 (OTUB1) regulates many cancer-associated signaling pathways including MAPK, ERa, epithelial-mesenchymal transition (EMT), RHOa, mTORC1, FOXM1 and P53 to promote tumor cell survival, proliferation, invasiveness and therapeutic resistance. In addition, clinical studies have associated elevated OTUB1 expression with high grade, invasiveness and metastasis in several tumor types including lung, breast, ovarian, glioma, colon and gastric. Interestingly, in addition to catalytic DUB activity, OTUB1 displays a catalytic-independent, non-canonical activity where it inhibits the transfer of ubiquitin onto protein substrates by sequestration of E2 ubiquitin-conjugating enzymes. The aim of this review is to describe the canonical and non-canonical activities of OTUB1, summarize roles for OTUB1 in cancer-associated pathways and discuss its potential therapeutic targeting.

Redox Signaling from and to Peroxisomes: Progress, Challenges, and Prospects

SIGNIFICANCE

Peroxisomes are organelles that are best known for their role in cellular lipid and hydrogen peroxide (H₂O₂) metabolism. Emerging evidence suggests that these organelles serve as guardians and modulators of cellular redox balance, and that alterations in their redox metabolism may contribute to aging and the development of chronic diseases such as neurodegeneration, diabetes, and cancer. Recent Advances: H₂O₂ is an important signaling messenger that controls many cellular processes by modulating protein activity through cysteine oxidation. Somewhat surprisingly, the potential involvement of peroxisomes in H₂O₂-mediated signaling processes has been overlooked for a long time. However, recent advances in the development of live-cell approaches to monitor and modulate spatiotemporal fluxes in redox species at the subcellular level have opened up new avenues for research in redox biology and boosted interest in the concept of peroxisomes as redox signaling platforms.

CRITICAL ISSUES

This review first introduces the reader to what is known about the role of peroxisomes in cellular H₂O₂ production and clearance, with a focus on mammalian cells. Next, it briefly describes the benefits and drawbacks of current strategies used to investigate the complex interplay between peroxisome metabolism and cellular redox state. Furthermore, it integrates and critically evaluates literature dealing with the interrelationship between peroxisomal redox metabolism, cell signaling, and human disease.

FUTURE DIRECTIONS

As the precise molecular mechanisms underlying many of these associations are still poorly understood, a key focus for future research should be the identification of primary targets for peroxisome-derived H₂O₂.

Atomic Force Microscopy on Biological Materials Related to Pathological Conditions

Atomic force microscopy (AFM) is an easy-to-use, powerful, high-resolution microscope that allows the user to image any surface and under any aqueous condition. AFM has been used in the investigation of the structural and mechanical properties of a wide range of biological matters including biomolecules, biomaterials, cells, and tissues. It provides the capacity to acquire high-resolution images of biosamples at the nanoscale and allows at readily carrying out mechanical characterization. The capacity of AFM to image and interact with surfaces, under physiologically relevant conditions, is of great importance for realistic and accurate medical and pharmaceutical applications. The aim of this paper is to review recent trends of the use of AFM on biological materials related to health and sickness. First, we present AFM components and its different imaging modes and we continue with combined imaging and coupled AFM systems. Then, we discuss the use of AFM to nanocharacterize collagen, the major fibrous protein of the human body, which has been correlated with many pathological conditions. In the next section, AFM nanolevel surface characterization as a tool to detect possible pathological conditions such as osteoarthritis and cancer is presented. Finally, we demonstrate the use of AFM for studying other pathological conditions, such as Alzheimer's disease and human immunodeficiency virus (HIV), through the investigation of amyloid fibrils and viruses, respectively. Consequently, AFM stands out as the ideal research instrument for exploring the detection of pathological conditions even at very early stages, making it very attractive in the area of bio- and nanomedicine.

Tocopherol polyethylene glycol succinate-modified hollow silver nanoparticles for combating bacteria-resistance

TPGS capped AgNPs could cross the bacterial cell wall and inhibit the activity of efflux pumps, eventually antagonize drug-resistance in the acute peritonitis model mice effectively.

Monotopic Membrane Proteins Join the Fold

Monotopic membrane proteins, classified by topology, are proteins that embed into a single face of the membrane. These proteins are generally underrepresented in the Protein Data Bank (PDB), but the past decade of research has revealed new examples that allow the description of generalizable features. This Opinion article summarizes shared characteristics including oligomerization states, modes of membrane association, mechanisms of interaction with hydrophobic or amphiphilic substrates, and homology to soluble folds. We also discuss how associations of monotopic enzymes in pathways can be used to promote substrate specificity and product composition. These examples highlight the challenges in structure determination specific to this class of proteins, but also the promise of new understanding from future study of these proteins that reside at the interface.

Inhibition of proliferation and migration of tumor cells through lipoic acid-modified oligoethylenimine-mediated p53 gene delivery

Inhibition of proliferation and migration of tumor cells through lipoic acid-modified oligoethylenimine-mediated p53 gene delivery.

α-Conotoxin GI triazole-peptidomimetics: potent and stable blockers of a human acetylcholine receptor

A conotoxin peptidomimetic was developed as a potential muscle relaxant that is highly potent and blood plasma stable.

Novel styrylpyrazole-glucosides and their dioxolo-bridged doppelgangers: synthesis and cytotoxicity

Novel styrylpyrazole-glucoside conjugates4and5are reported, with5c, aN-glucosyldioxolo derivative being very active against stomach cancer (AGS) cells.

The Possible Role of PD-1 Protein in Ganoderma lucidum-Mediated Immunomodulation and Cancer Treatment

Background:Ganoderma lucidum has been used in Chinese medicine for thousands years to improve health and to promote longevity. One important function of G lucidum is to modulate the immune system. However, the underlying mechanism is not well understood. Programmed cell death protein 1 (PD-1) is a cell surface protein present in certain immune cells (eg, B- and Tcells) and plays an important role in modulating the immune response. The role of PD-1 protein in G lucidum-mediated immunomodulation is unknown. Methods: Cultured human Blymphocytes and extract prepared from G lucidum spores (GLE) were used to determine PD-1 protein in G lucidum-mediated immunomodulation. Both western blotting and immunofluorescence (IF) microscopy assays were used to determine the effect of GLE treatment on PD-1 protein expression. A reverse transcription-based quantitative polymerase chain reaction (real-time PCR) assay was used to determine the effect of GLE on transcription of pdcd-1 gene. Results: Both our western blotting and IF staining results demonstrated great reduction in PD-1 protein and in proportion of PD-1+ cells in these B-lymphocytes. Our real-time PCR results indicated that this PD-1 protein reduction was not caused by a transcriptional inhibition of the gene. In addition, our western blotting study further revealed that the GLE treatment caused an increase in expression of CCL5 chemokine in the cultured B-lymphocytes. Conclusions: PD-1 protein is an important target of G lucidum-mediated immunomodulation. G lucidum and its bioactive compounds can be developed into novel immunomodulators for prevention and treatment of cancer and many other diseases.

Cell Apoptosis and Autophagy in Renal Fibrosis

Renal fibrosis is the final common pathway of all chronic kidney diseases progressing to end-stage renal diseases. Autophagy, a highly conserved lysosomal degradation pathway, plays important roles in maintaining cellular homeostasis in all major types of kidney cells including renal tubular cells as well as podocytes, mesangial cells and endothelial cells in glomeruli. Autophagy dysfunction is implicated in the pathogenesis of various renal pathologies. Here, we analyze the pathological role and regulation of autophagy in renal fibrosis and related kidney diseases in both glomeruli and tubulointerstitial compartments. Further research is expected to gain significant mechanistic insights and discover pathway-specific and kidney-selective therapies targeting autophagy to prevent renal fibrosis and related kidney diseases.

A highly specific fluorescent probe for rapid detection of hypochlorous acidin vivoand in water samples

We report the development of a new chromogenic and fluorogenic probe for the detection of HOCl in zebrafish, mice with arthritis and environmental water samples.

In vivo biosynthesis of tyrosine analogs and their concurrent incorporation into a residue-specific manner for enzyme engineering

A cellular system for the in vivo biosynthesis of Tyr-analogs and their concurrent incorporation into target proteins is reported.

Pelizaeus-Merzbacher Disease: Molecular and Cellular Pathologies and Associated Phenotypes

Pelizaeus-Merzbacher disease (PMD) represents a group of disorders known as hypomyelinating leukodystrophies, which are characterized by abnormal development and maintenance of myelin in the central nervous system. PMD is caused by different types of mutations in the proteolipid protein 1 (PLP1) gene, which encodes a major myelin membrane lipoprotein. These mutations in the PLP1 gene result in distinct cellular and molecular pathologies and a spectrum of clinical phenotypes. In this chapter, I discuss the historical aspects and current understanding of the mechanisms underlying how different PLP1 mutations disrupt the normal process of myelination and result in PMD and other disorders.

Differential Scanning Fluorimetry and Hydrogen Deuterium Exchange Mass Spectrometry to Monitor the Conformational Dynamics of NBD1 in Cystic Fibrosis

Cystic fibrosis (CF) is one of the most common, lethal autosomal recessive diseases in Caucasians with a life expectancy of 37-47 years. The CF transmembrane conductance regulator (CFTR) is a plasma membrane ion channel, confined to apical membrane of epithelia, and ensures transepithelial water and solute movement across secretory epithelia in several organs. Numerous CF mutations, including the most prevalent deletion of F508 (ΔF508) in the nucleotide binding domain 1 (NBD1) leads to CFTR global misfolding and premature intracellular degradation at the endoplasmic reticulum (ER). To better understand the misfolding mechanism caused by CF-causing point mutations in the NBD1, which is poorly understood, differential scanning fluorimetry (DSF) and hydrogen deuterium exchange coupled with mass spectrometry (HDX-MS) are the choice of techniques. These established methods can measure the conformational dynamics of the NBD1 globally and at peptide resolution level by monitoring backbone amide HDX, respectively, and will be instrumental to evaluate the mechanism of action of CF mutations and folding correctors that rescue CFTR folding defects via stabilizing the mutant NBD1.

The impact of species, respiration type, growth phase and genetic inventory on absolute metal content of intact bacterial cells

Absolute metal ion content was determined from whole cells of different microbial species and changes were related to growth conditions and change of encoded genes.

Dimers of glutaredoxin 2 as mitochondrial redox sensors in selenite-induced oxidative stress

Grx2 coordinates an iron–sulfur cluster, forming inactive dimers. In mitochondria, Grx2 monomerization, after oxidative stress, determines iron release triggering apoptosis.

Supramolecular assembly of functional peptide–polymer conjugates

The following review gives an overview about synthetic peptide–polymer conjugates as macromolecular building blocks and their self-assembly into a variety of supramolecular architectures, from supramolecular polymer chains, to anisotropic 1D arrays, 2D layers, and more complex 3D networks.

Non-equilibrium thermodynamics as a tool to compute temperature at the catalyst surface

The NET theory predicts the coupling between reaction rates and thermal driving forces and gives new insights into why Arrhenius plots may turn out to be non-linear.

Synthesis and evaluation of photo-activatable β-diarylsydnone-l-alanines for fluorogenic photo-click cyclization of peptides

β-Diarylsydnone-l-alanines were designed and introduced into peptides allowing photo-cyclization only in phosphate containing buffer with concomitant fluorescence generation in live cells.

Plant selenium toxicity: Proteome in the crosshairs

The metalloid element, selenium (Se) is in many ways special and perhaps because of this its research in human and plant systems is of great interest. Despite its non-essentiality, higher plants take it up and metabolize it via sulfur pathways, but higher amounts of Se cause toxic symptoms in plants. However, the molecular mechanisms of selenium phytotoxicity have been only partly revealed; the data obtained so far point out that Se toxicity targets the plant proteome. Besides seleno- and oxyproteins, nitroproteins are also formed due to Se stress. In order to minimize proteomic damages induced by Se, certain plants are able to redirect selenocysteine away from protein synthesis thus preventing Se-protein formation. Additionally, the damaged or malformed selenoproteins, oxyproteins and nitroproteins may be removed by proteasomes. Based on the literature this review sets Se toxicity mechanisms into a new concept and it draws attention to the importance of Se-induced protein-level changes.

Chemical and mechanistic analysis of photodynamic inhibition of Alzheimer's β-amyloid aggregation

Inhibition of Aβ₄₂ aggregation by photoexcited thioflavin T that generates singlet oxygen to oxidize monomeric Aβ₄₂.

DNA triplex-based fluorescence turn-on sensors for adenosine using a fluorescent molecular rotor 5-(3-methylbenzofuran-2-yl) deoxyuridine

Fluorescence turn-on detection of adenosine based on microenvironmental and conformational changes of a fluorescent molecular rotor in the DNA triplex is reported.

Synthetic strategies for fluorination of carbohydrates

Different synthetic strategies for accomplishing regio- and stereoselective fluorinations of carbohydrate scaffolds are discussed in light of the biological implications arising from such substitutions.

Site-specific post-imprinting modification of molecularly imprinted polymer nanocavities with a modifiable functional monomer for prostate cancer biomarker recognition

Recognition of glycans of glycoproteins using biotic materials such as antibodies is challenging due to lack of antigenicity. Polymeric materials suitable for the molecular recognition of glycoproteins have attracted considerable attention. In this study, we aimed to develop abiotic molecular materials for the recognition of prostate-specific antigen (PSA), a known biomarker for prostate cancer. We used a non-covalent bonding-based molecular imprinting technique to introduce post-imprinting poly(ethylene glycol)-based capping agent into a low-affinity recognition cavity. Details of the binding properties of these groups were investigated to optimize their affinity and selectivity for PSA. Molecularly imprinted polymers (MIPs) were prepared using a bottom-up approach based on surface-initiated atom transfer radical polymerization from a PSA-conjugated sensor chip with a functional monomer-bearing carboxy and secondary amine groups as interaction and post-imprinting modification (PIM) sites, respectively. PSA was orientationally conjugated on the sensor chip through diesters between the immobilized 3-fluorophenyl boronic acid and the cis-diol groups of PSA glucans. Treatment with the capping agent selectively inactivated low-affinity recognition cavities while protecting high-affinity cavities with the addition of a low concentration of PSA as a dynamic protection agent. The MIP thickness is critical in the present molecular imprinting, as a value of less than 5 nm can enable high selectivity. We believe that the proposed strategy based on a non-covalent molecular imprinting approach combined with a PIM-based capping treatment provides a novel method for the development of highly sensitive and selective glycoprotein recognition materials for use in biomarker sensing.

Identification of cancer prognosis-associated lncRNAs based on the miRNA-TF co-regulatory motifs and dosage sensitivity

By integrating dosage sensitivity and motif regulation data, we established a framework and identified a total of 33 cancer prognosis-associated lncRNAs.

Synchrotron-based infrared microspectroscopy study on the radiosensitization effects of Gd nanoparticles at megavoltage radiation energies

Synchrotron-based infrared microspectroscopy is a powerful technique for disentangling biochemical effects in nanoparticle-based radiotherapy approaches.

Supramolecular micellar drug delivery system based on multi-arm block copolymer for highly effective encapsulation and sustained-release chemotherapy

A novel multi-arm polyphosphoester-based nanomaterial provides high drug loading efficiency and sustained-release drug delivery for effective chemotherapy.

Epigenetic regulation of progesterone receptors and the onset of labour

Progesterone plays a crucial role in maintaining pregnancy by promoting myometrial quiescence. The withdrawal of progesterone action signals the end of pregnancy and, in most mammalian species, this is achieved by a rapid fall in progesterone concentrations. However, in humans circulating progesterone concentrations remain high up to and during labour. Efforts to understand this phenomenon led to the ‘functional progesterone withdrawal’ hypothesis, whereby the pro-gestation actions of progesterone are withdrawn, despite circulating concentrations remaining elevated. The exact mechanism of functional progesterone withdrawal is still unclear and in recent years has been the focus of intense research. Emerging evidence now indicates that epigenetic regulation of progesterone receptor isoform expression may be the crucial mechanism by which functional progesterone withdrawal is achieved, effectively precipitating human labour despite high concentrations of circulating progesterone. This review examines current evidence that epigenetic mechanisms play a role in determining whether the pro-gestation or pro-contractile isoform of the progesterone receptor is expressed in the pregnant human uterus. We explore the mechanism by which these epigenetic modifications are achieved and, importantly, how these underlying epigenetic mechanisms are influenced by known regulators of uterine physiology, such as prostaglandins and oestrogens, in order to phenotypically transform the pregnant uterus and initiate labour.

Streptococcus mutans yidC1 and yidC2 Impact Cell Envelope Biogenesis, the Biofilm Matrix, and Biofilm Biophysical Properties

YidC proteins are membrane-localized chaperone insertases that are universally conserved in all bacteria and are traditionally studied in the context of membrane protein insertion and assembly. Both YidC paralogs of the cariogenic pathogen Streptococcus mutans are required for proper envelope biogenesis and full virulence, indicating that these proteins may also contribute to optimal biofilm formation in streptococci. Here, we show that the deletion of either yidC results in changes to the structure and physical properties of the EPS matrix produced by S. mutans , ultimately impairing optimal biofilm development, diminishing its mechanical stability, and facilitating its removal. Importantly, the universal conservation of bacterial yidC orthologs, combined with our findings, provide a rationale for YidC as a possible drug target for antibiofilm therapies.

Real-Time Fluorescence Detection of Calcium Efflux During Vacuolar Membrane Fusion

During in vitro homotypic yeast vacuole fusion Ca²⁺ is transported into and out of the organelle lumen. In vitro, Ca²⁺ is taken up from the medium by vacuoles upon the addition of ATP. During the docking stage of vacuole fusion Ca²⁺ is effluxed from the lumen upon the formation of trans-SNARE complexes between vesicles. Here we describe a real-time fluorescence-based assay to monitor the transport of this cation using purified organelles. Extraluminal Ca²⁺ is detected when the cation binds the low-affinity fluorescent dye Fluo-4 dextran. This allows for the use of a 96-well microtiter plate to be read in a fluorescence plate reader. Thus, in addition to a curve of calibrated Ca²⁺ standards, up to 91 experimental conditions can be monitored in a single microplate using this method.

Predicting the Effect of Mutations on Protein Folding and Protein-Protein Interactions

The function of a protein is largely determined by its three-dimensional structure and its interactions with other proteins. Changes to a protein's amino acid sequence can alter its function by perturbing the energy landscapes of protein folding and binding. Many tools have been developed to predict the energetic effect of amino acid changes, utilizing features describing the sequence of a protein, the structure of a protein, or both. Those tools can have many applications, such as distinguishing between deleterious and benign mutations and designing proteins and peptides with attractive properties. In this chapter, we describe how to use one of such tools, ELASPIC, to predict the effect of mutations on the stability of proteins and the affinity between proteins, in the context of a human protein-protein interaction network. ELASPIC uses a wide range of sequential and structural features to predict the change in the Gibbs free energy for protein folding and protein-protein interactions. It can be used both through a web server and as a stand-alone application. Since ELASPIC was trained using homology models and not crystal structures, it can be applied to a much broader range of proteins than traditional methods. It can leverage precalculated sequence alignments, homology models, and other features, in order to drastically lower the amount of time required to evaluate individual mutations and make tractable the analysis of millions of mutations affecting the majority of proteins in a genome.

Allosteric Regulation of Protein Kinases Downstream of PI3-Kinase Signalling

Allostery is a basic principle that enables proteins to process and transmit cellular information. Protein kinases evolved allosteric mechanisms to transduce cellular signals to downstream signalling components or effector molecules. Protein kinases catalyse the transfer of the terminal phosphate from ATP to protein substrates upon specific stimuli. Protein kinases are targets for the development of small molecule inhibitors for the treatment of human diseases. Drug development has focussed on ATP-binding site, while there is increase interest in the development of drugs targeting alternative sites, i.e. allosteric sites. Here, we review the mechanism of regulation of protein kinases, which often involve the allosteric modulation of the ATP-binding site, enhancing or inhibiting activity. We exemplify the molecular mechanism of allostery in protein kinases downstream of PI3-kinase signalling with a focus on phosphoinositide-dependent protein kinase 1 (PDK1), a model kinase where small compounds can allosterically modulate the conformation of the kinase bidirectionally.

A Binding Potency Assay for Pritumumab and Ecto-Domain Vimentin

Pritumumab, a natural human IgG1kappa mAb, was isolated from the regional lymph node of a patient with cervical cancer. This antibody has been reported to bind the cytoskeletal protein vimentin, and to cell surface expressed vimentin referred to as ecto-domain vimentin (EDV). Here, we report details of the development of a potency of binding assay for pritumumab as a prerequisite before pursuing clinical trials. The enzyme linked immunosorbent assay (ELISA) to detect antibody-binding antigen can serve as a potency assay for release of manufactured samples to be used in clinical studies. Several layers of controls for this assay along with suitability testing for reagents and components of the assay must be developed before the assay can be incorporated for stability testing and release of manufatured samples.