Evolutionary conservation of domain-domain interactions

Background

Recently, there has been much interest in relating domain-domain interactions (DDIs) to protein-protein interactions (PPIs) and vice versa, in an attempt to understand the molecular basis of PPIs.

Results

Here we map structurally derived DDIs onto the cellular PPI networks of different organisms and demonstrate that there is a catalog of domain pairs that is used to mediate various interactions in the cell. We show that these DDIs occur frequently in protein complexes and that homotypic interactions (of a domain with itself) are abundant. A comparison of the repertoires of DDIs in the networks of Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens shows that many DDIs are evolutionarily conserved.

Conclusion

Our results indicate that different organisms use the same 'building blocks' for PPIs, suggesting that the functionality of many domain pairs in mediating protein interactions is maintained in evolution.     

Alanine-scanning mutagenesis of alpha-helix D segment of interleukin-13 reveals new functionally important residues of the cytokine

We documented that alpha-helices A, C, and D in human interleukin-13 (IL13) participate in interaction with its respective receptors. We hypothesized that alpha-helix D is the site II of the cytokine that binds IL13Ralpha1, a component of the normal tissue heterodimeric signaling IL13/4 receptor (IL13/4R), and that alpha-helix D independently binds a monomeric IL13Ralpha2 receptor, which is a non-signaling glioma-restricted receptor for IL13. Therefore, we alanine-scanned mutagenized helix D of IL13 to identify the residues involved in the respective receptors interaction. Recombinant muteins of IL13 were produced in Escherichia coli, and their structural integrity and identity were verified. The alanine mutants were tested in functional cellular assays, in which IL13 interaction with IL13Ralpha2 (glioma cells) or an ability to functionally stimulate IL13/4R (TF-1 cells) were examined, and also in binding assays. We found that residues 105, 106, and 109 of the d-helix of IL13 are responsible for interacting with the glioma-associated receptor. Moreover, glutamic acids at positions 92 and 110, and leucine at position 104 was found to be important for IL13/4R stimulation. Thus, alpha-helix D of IL13 is the primary site responsible for interaction with the IL13 binding proteins. We propose a model that illustrates the binding mode of IL13 with cancer-related IL13Ralpha2 and physiological IL13/4R.     

Radiosynthesis and evaluation of IGF1R PET ligand [11C]GSK1838705A

Radiosynthesis and evaluation of [¹¹C]GSK1838705A in mice using microPET and determination of specificity in human GBM UG87MR cells are described herein. The radioligand was synthesized by reacting desmethyl-GSK1838705A with [¹¹C]CH₃I using GE FX2MeI module in ～5% yield (EOS), >95% radiochemical purity and a specific activity of 2.5 ± 0.5 Ci/μmol. MicroPET imaging in mice indicated that [¹¹C]GSK1838705A penetrated blood brain barrier (BBB) and showed retention of radiotracer in brain. The radioligand exhibited high uptake in U87MG cells with >70% specific binding to IGF1R. Our experiments suggest that [¹¹C]GSK-1838705A can be a potential PET radiotracer for the in vivo quantification of IGF1R expression in GBM and other brain tumors.     

Substrate binding in the multidrug transporter MdfA in detergent solution and in lipid nanodiscs

MdfA from Escherichia coli is a prototypical secondary multi-drug (Mdr) transporter that exchanges drugs for protons. MdfA-mediated drug efflux is driven by the proton gradient and enabled by conformational changes that accompany the recruitment of drugs and their release. In this work, we applied distance measurements by W-band double electron-electron resonance (DEER) spectroscopy to explore the binding of mito-TEMPO, a nitroxide-labeled substrate analog, to Gd(III)-labeled MdfA. The choice of Gd(III)-nitroxide DEER enabled measurements in the presence of excess of mito-TEMPO, which has a relatively low affinity to MdfA. Distance measurements between mito-TEMPO and MdfA labeled at the periplasmic edges of either of three selected transmembrane helices (TM3¹⁰¹, TM5¹⁶⁸, and TM9³¹⁰) revealed rather similar distance distributions in detergent micelles (n-dodecyl-β-d-maltopyranoside, DDM)) and in lipid nanodiscs (ND). By grafting the predicted positions of the Gd(III) tag on the inward-facing (I_f) crystal structure, we looked for binding positions that reproduced the maxima of the distance distributions. The results show that the location of the mito-TEMPO nitroxide in DDM-solubilized or ND-reconstituted MdfA is similar (only 0.4 nm apart). In both cases, we located the nitroxide moiety near the ligand binding pocket in the I_f structure. However, according to the DEER-derived position, the substrate clashes with TM11, suggesting that for mito-TEMPO-bound MdfA, TM11 should move relative to the I_f structure. Additional DEER studies with MdfA labeled with Gd(III) at two sites revealed that TM9 also dislocates upon substrate binding. Together with our previous reports, this study demonstrates the utility of Gd(III)-Gd(III) and Gd(III)-nitroxide DEER measurements for studying the conformational behavior of transporters.     

Synthesis of organic compounds from carbon monoxide and water by UV photolysis

The photolysis of water vapor with carbon monoxide at 1849 Å yields alcohols, aldehydes and organic acids, with an overall quantum yield of 3.3×10^–2. This rather high quantum yield could have led to a contribution of 10¹¹ organic molecules cm^–2 sec^–1 to the pool of organic material on the primitive Earth. The reactions are initiated by the photolysis of water molecules and the resulting hydrogen atoms reduce the carbon monoxide to a variety of one and two carbon compounds. The organic molecules are dissolved in water and thus escape destruction by photolysis. Photolysis of water vapor with carbon dioxide did not yield organic compounds under these conditions.     

Glioma Pericytes Promote Angiogenesis by Producing Periostin

Glioma is the prevalent aggressive primary brain tumor, with a very poor prognosis. The absence of advanced understanding of the roles played by the cells within the glioma microenvironment limits the development of effective drugs. A recent study indicates that periostin expressed by pericytes is crucial for glioma angiogenesis. Here, we describe succinctly the results and implications of this discovery in what we know about pericytes within the glioma microenvironment. The emerging knowledge from this work will benefit the development of therapies for gliomas.

     

The fruit fly PUB: a phagostimulation unit bioassay system to quantitatively measure ingestion of baits by individual flies

Abstract:  A bioassay to investigate quantitative phagostimulation and ingestion physiology of baits on individual fruit flies is presented. The study was undertaken using two fruit fly species: the Mediterranean fruit fly ( Ceratitis capitata ), a cosmopolitan insect pest, and the Ethiopian fruit fly ( Dacus ciliatus ), a quarantine insect in Israel. Our model bait suspension included spinosad as the toxic agent, and 1% yeast hydrolysate with 10% sucrose as phagostimulant. A preliminary toxicology study showed that the two fruit flies are highly sensitive to low concentrations of spinosad baited with this phagostimulant. The maximum concentration needed to kill 90% of the female flies was 4.2 and 8.5 p.p.m. for C. capitata and D. ciliatus , respectively. The bioassay was able to detect the ingestion of low volumes (e.g. 1  μ l) of tested solutions. The bioassay was also able to detect differences in intake of different concentrations of spinosad solutions and relate ingestion to fruit fly mortality. Additionally, the bioassay was sensitive enough to highlight differences in intake related to the physiological status of the fruit fly and fly species. The bioassay can also be used to follow ingestion kinetics of baits. We expect that this bioassay will contribute in the exploration of more efficient bait systems for fruit flies.     

Ethylene formation in plant mitochondria. Dependence on the transport of 1-aminocyclopropane-1-carboxylic acid across the membrane

The mitochondrial fraction isolated from plumular hooks of etiolated pea seedlings ( Pisum sativum L. cv. Kelvedon Wonder) displayed a ten-fold higher rate of ethylene formation from 1-aminocyclopropane-1-carboxylic acid [ACC; 3.2 nmol C₂H₄ (mg protein ⁻¹)h⁻¹], than the tissue from which it was isolated. When the ionophores valinomycin or nigericin were added, a 60- to 70-fold increase in activity in intact mitochondria over the activity in plumular hooks was obtained for ethylene formation under the same conditions, and a 20-fold increase was obtained upon addition of gramicidin. The addition of ionophores did not affect the rate of ethylene formation in submitochondrial particles (55% inside-out as determined by cytochrome oxidase latency) which already exhibited a 2–3-fold higher specific activity than intact mitochondria. Low concentrations of the detergents cholate and deoxycholate increased mitochondrial ethylene formation activity and had no effect on the rate of the reaction in submitochondrial particles. These results support the suggestion that ACC conversion to ethylene is associated with the inner side of the inner mitochondrial membrane and that transport across the intact mitochondrial membrane is rate-limiting in the reaction.     

Effect of Inhibitors and Stimulators of Ethylene Production on Gall Development in Meloidogyne javanica-Infected Tomato Roots

Excised tomato roots infected with Meloidogyne javanica produced ethylene at 3-6 times the rate of noninfected roots. This increase in ethylene production started 5 days after inoculation. Gall growth and ethylene production in infected roots were accelerated by 1-aminocyclopropane-1-carboxylic acid (ACC), indole acetic acid (IAA), and ethrel known as ethylene production stimulators. When inhibitors of ethylene production, like aminoethoxyvinylglycine (AVG) or aminoxyacetic acid (AOA), or inhibitors of ethylene action like silver thiosulfate (STS), were applied, gall growth and ethylene production were inhibited. Enhanced expansion of parenchymatous cells was observed in sections from nematode-induced galls and ethylene-treated roots. Lignification of xylem elements and fibers in the vascular cylinder was markedly inhibited in the gall, compared with noninfected root tissue. Because ethylene is known to induce cell expansion and to inhibit lignification, it is suggested that this plant hormone plays a major role in the development of M. javanica-induced galls. Ethylene affects gall size by enhancing parenchymatous tissue development and allows expansion of giant cells and the nematode body by reducing tissue lignification.