SciCombinator

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Concept: Protein subunit

160

‘Omics analysis (transcriptomics, proteomics) quantifies changes in gene/protein expression, providing a snapshot of changes in biochemical pathways over time. Although tools such as modelling that are needed to investigate the relationships between genes/proteins already exist, they are rarely utilised. We consider the potential for using Structural Equation Modelling to investigate protein-protein interactions in a proposed Rubisco protein degradation pathway using previously published data from 2D electrophoresis and mass spectrometry proteome analysis. These informed the development of a prior model that hypothesised a pathway of Rubisco Large Subunit and Small Subunit degradation, producing both primary and secondary degradation products. While some of the putative pathways were confirmed by the modelling approach, the model also demonstrated features that had not been originally hypothesised. We used Bayesian analysis based on Markov Chain Monte Carlo simulation to generate output statistics suggesting that the model had replicated the variation in the observed data due to protein-protein interactions. This study represents an early step in the development of approaches that seek to enable the full utilisation of information regarding the dynamics of biochemical pathways contained within proteomics data. As these approaches gain attention, they will guide the design and conduct of experiments that enable 'Omics modelling to become a common place practice within molecular biology.

Concepts: Protein, Molecular biology, Proteomics, Proteome, Monte Carlo method, Protein subunit, Markov chain Monte Carlo, Bayesian inference

30

Neurotransmitter-gated ion channels adopt different gating modes to fine-tune signaling at central synapses. At glutamatergic synapses, high and low activity of AMPA receptors (AMPARs) is observed when pore-forming subunits coassemble with or without auxiliary subunits, respectively. Whether a common structural pathway accounts for these different gating modes is unclear. Here, we identify two structural motifs that determine the time course of AMPAR channel activation. A network of electrostatic interactions at the apex of the AMPAR ligand-binding domain (LBD) is essential for gating by pore-forming subunits, whereas a conserved motif on the lower, D2 lobe of the LBD prolongs channel activity when auxiliary subunits are present. Accordingly, channel activity is almost entirely abolished by elimination of the electrostatic network but restored via auxiliary protein interactions at the D2 lobe. In summary, we propose that activation of native AMPAR complexes is coordinated by distinct structural pathways, favored by the association/dissociation of auxiliary subunits.

Concepts: Protein, Receptor, Action potential, Protein subunit, Subunit, Channel, AMPA receptor, Motif

28

The quality of wheat (Triticum aestivum L.) for making bread is largely due to the strength and extensibility of wheat dough, which in turn is due to the properties of polymeric glutenin. Polymeric glutenin consists of high- and low-molecular-weight glutenin protein subunits linked by disulphide bonds between cysteine residues. Glutenin subunits differ in their effects on dough mixing properties. The research presented here investigated the effect of a specific, recently discovered, glutenin subunit on dough mixing properties. This subunit, Bx7.1, is unusual in that it has a cysteine in its repetitive domain. With site-directed mutagenesis of the gene encoding Bx7.1, a guanine in the repetitive domain was replaced by an adenine, to provide a mutant gene encoding a subunit (MutBx7.1) in which the repetitive-domain cysteine was replaced by a tyrosine residue. Bx7.1, MutBx7.1 and other Bx-type glutenin subunits were heterologously expressed in Escherichia coli and purified. This made it possible to incorporate each individual subunit into wheat flour and evaluate the effect of the cysteine residue on dough properties. The Bx7.1 subunit affected dough mixing properties differently from the other subunits. These differences are due to the extra cysteine residue, which may interfere with glutenin polymerisation through cross-linkage within the Bx7.1 subunit, causing this subunit to act as a chain terminator.

Concepts: Protein, Protein structure, Amino acid, Escherichia coli, Wheat, Protein subunit, Bread, Flour

28

The avian Herbst corpuscles are the equivalent of the Pacinian corpuscles in mammals, and detect vibration and the movement of joints and feathers. Therefore, they can be regarded as rapidly adapting low-threshold mechanoreceptors. In recent years, it has been establish that some ion channels are involved in mechanosensation and are present in both mechanosensory neurons and mechanoreceptors. Here we have used immunohistochemistry to localize some putative mechanoproteins in the Herbst corpuscles from the rictus of Columba livia. The proteins investigated were the subunits of the epithelial Na(+) channel (ENaC), the transient-receptor potential vanilloid 4 (TRPV4), and the acid-sensing ion channel 2 (ASIC2). Immunoreactivity for ENaC subunits was never found in Herbst corpuscles, while the axon expressed ASIC2 and TRPV4 immunoreactivity. Moreover, TRPV4 was also detected in the cell forming the inner core. The present results demonstrate for the first time the occurrence of mechanoproteins in avian low-threshold mechanoreceptors and provide further evidence for a possible role of the ion channels in mechanosensation. Anat Rec, 2012. © 2012 Wiley Periodicals, Inc.

Concepts: Protein, Cell, Action potential, Ion channel, Ion channels, Protein subunit, Membrane potential, Pacinian corpuscle

27

Catharanthus roseus is the sole source of two most important monoterpene indole alkaloid (MIA) anti-cancer agents, vinblastine and vincristine. MIAs possess a terpene and an indole moiety derived from terpenoid and shikimate pathways, respectively. Geranyl diphosphate (GPP), the entry point to the formation of terpene moiety, is a product of the condensation of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) by GPP synthase (GPPS). Here, we report three genes encoding proteins with sequence similarity to large subunit (CrGPPS.LSU) and small subunit (CrGPPS.SSU) of heteromeric GPPSs, and a homomeric GPPSs. CrGPPS.LSU is a bifunctional enzyme producing both GPP and geranyl geranyl diphosphate (GGPP), CrGPPS.SSU is inactive, whereas CrGPPS is a homomeric enzyme forming GPP. Co-expression of both subunits in Escherichia coli resulted in heteromeric enzyme with enhanced activity producing only GPP. While CrGPPS.LSU and CrGPPS showed higher expression in older and younger leaves, respectively, CrGPPS.SSU showed an increasing trend and decreased gradually. Methyl jasmonate (MeJA) treatment of leaves significantly induced the expression of only CrGPPS.SSU. GFP localization indicated that CrGPPS.SSU is plastidial whereas CrGPPS is mitochondrial. Transient overexpression of AmGPPS.SSU in C. roseus leaves resulted in increased vindoline, immediate monomeric precursor of vinblastine and vincristine. Although C. roseus has both heteromeric and homomeric GPPS enzymes, our results implicate the involvement of only heteromeric GPPS with CrGPPS.SSU regulating the GPP flux for MIA biosynthesis.

Concepts: Protein, Metabolism, Protein subunit, Terpene, Terpenoid, Isopentenyl pyrophosphate, Terpenes and terpenoids, Dimethylallyl pyrophosphate

24

To improve the therapeutic/diagnostic potentials of drugs and/or imaging contrast agents, various targeted delivery systems are actively being developed. Especially protein nanocages, hollow and highly symmetrical nanometer-sized cage structures that are self-assembled from multiple protein subunits, are emerging as powerful targeted delivery tools. Their natural abundance, biocompatibility, low toxicity, well defined size and high symmetry are a few of the favorable characteristics which render protein nanocages as near ideal carriers for pharmaceuticals and/or imaging probes. This review aims to highlight current progress in the development and application of protein nanocages in targeted drug delivery approaches with an emphasis on the use of antibodies as targeting motifs to achieve high selectivity toward specific targets.

Concepts: Protein, Pharmacology, Drug, Drugs, Group, Pharmaceutical drug, Protein subunit, Targeted drug delivery

18

Dynamic assembly/disassembly of signaling complexes are crucial for cellular functions. Specialized latency and activation chaperones control the biogenesis of protein phosphatase 2A (PP2A) holoenzymes that contain a common scaffold and catalytic subunits and a variable regulatory subunit. Here we show that the butterfly-shaped TIPRL (TOR signaling pathway regulator) makes highly integrative multibranching contacts with the PP2A catalytic subunit, selective for the unmethylated tail and perturbing/inactivating the phosphatase active site. TIPRL also makes unusual wobble contacts with the scaffold subunit, allowing TIPRL, but not the overlapping regulatory subunits, to tolerate disease-associated PP2A mutations, resulting in reduced holoenzyme assembly and enhanced inactivation of mutant PP2A. Strikingly, TIPRL and the latency chaperone, α4, coordinate to disassemble active holoenzymes into latent PP2A, strictly controlled by methylation. Our study reveals a mechanism for methylation-responsive inactivation and holoenzyme disassembly, illustrating the complexity of regulation/signaling, dynamic complex disassembly, and disease mutations in cancer and intellectual disability.

Concepts: Protein, Signal transduction, Enzyme, Catalysis, Protein folding, Kinase, Protein subunit, Phosphatase

15

Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted F0 region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the F0 region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the F0 region support a Brownian ratchet mechanism for proton-translocation driven rotation in ATP synthases.

Concepts: DNA, Photosynthesis, Cell, Adenosine triphosphate, Mitochondrion, Cellular respiration, Protein subunit, ATP synthase

12

Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal antibodies (mAbs) and identified a previously unknown epitope, the envelope dimer epitope (EDE), that bridges two envelope protein subunits that make up the 90 repeating dimers on the mature virion. The mAbs to EDE were broadly reactive across the dengue serocomplex and fully neutralized virus produced in either insect cells or primary human cells, with 50% neutralization in the low picomolar range. Our results provide a path to a subunit vaccine against dengue virus and have implications for the design and monitoring of future vaccine trials in which the induction of antibody to the EDE should be prioritized.

Concepts: Immune system, Antibody, Protein, Bacteria, Infection, Monoclonal antibodies, Immunology, Protein subunit

10

Mutations in the polycystin genes,PKD1orPKD2,results in Autosomal Dominant Polycystic Kidney Disease (ADPKD). Although a genetic basis of ADPKD is established, we lack a clear understanding of polycystin proteins' functions as ion channels. This question remains unsolved largely because polycystins localize to the primary cilium - a tiny, antenna-like organelle. Using a new ADPKD mouse model, we observe primary cilia that are abnormally long in cells associated with cysts after conditional ablation ofPkd1orPkd2. Using primary cultures of collecting duct cells, we show that polycystin-2, but not polycystin-1, is a required subunit for the ion channel in the primary cilium. The polycystin-2 channel preferentially conducts K+and Na+; intraciliary Ca2+, enhances its open probability. We introduce a novel method for measuring heterologous polycystin-2 channels in cilia, which will have utility in characterizingPKD2variants that cause ADPKD.

Concepts: Protein, Kidney, Cell, Eukaryote, Organelle, Protein subunit, Polycystic kidney disease, Cilium