Background: G-protein coupled receptors (GPCRs) are involved in many different physiological processes and their function can be modulated by small molecules which bind in the transmembrane (TM) domain. Because of their structural and sequence conservation, the TM domains are often used in bioinformatics approaches to first create a multiple sequence alignment (MSA) and subsequently identify ligand binding positions. So far methods have been developed to predict the common ligand binding residue positions for class A GPCRs.Results: Here we present 1) ss-TEA, a method to identify specific ligand binding residue positions for any receptor, predicated on high quality sequence information. 2) The largest MSA of class A non olfactory GPCRs in the public domain consisting of 13324 sequences covering most of the species homologues of the human set of GPCRs. A set of ligand binding residue positions extracted from literature of 10 different receptors shows that our method has the best ligand binding residue prediction for 9 of these 10 receptors compared to another state-of-the-art method.Conclusions: The combination of the large multi species alignment and the newly introduced residue selection method ss-TEA can be used to rapidly identify subfamily specific ligand binding residues. This approach can aid the design of site directed mutagenesis experiments, explain receptor function and improve modelling. The method is also available online via GPCRDB at http://www.gpcr.org/7tm/. © 2011 Sanders et al; licensee BioMed Central Ltd.
Understanding taste is key for optimizing the palatability of seaweeds and other non-animal-based foods rich in protein. The lingual papillae in the mouth hold taste buds with taste receptors for the five gustatory taste qualities. Each taste bud contains three distinct cell types, of which Type II cells carry various G protein-coupled receptors that can detect sweet, bitter, or umami tastants, while type III cells detect sour, and likely salty stimuli. Upon ligand binding, receptor-linked intracellular heterotrimeric G proteins initiate a cascade of downstream events which activate the afferent nerve fibers for taste perception in the brain. The taste of amino acids depends on the hydrophobicity, size, charge, isoelectric point, chirality of the alpha carbon, and the functional groups on their side chains. The principal umami ingredient monosodium l-glutamate, broadly known as MSG, loses umami taste upon acetylation, esterification, or methylation, but is able to form flat configurations that bind well to the umami taste receptor. Ribonucleotides such as guanosine monophosphate and inosine monophosphate strongly enhance umami taste when l-glutamate is present. Ribonucleotides bind to the outer section of the venus flytrap domain of the receptor dimer and stabilize the closed conformation. Concentrations of glutamate, aspartate, arginate, and other compounds in food products may enhance saltiness and overall flavor. Umami ingredients may help to reduce the consumption of salts and fats in the general population and increase food consumption in the elderly.
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Development of novel testing strategies to detect adverse human health effects is of interest to replace in vivo-based drug and chemical safety testing. The aim of the present study was to investigate whether physiologically based kinetic (PBK) modeling-facilitated conversion of in vitro toxicity data is an adequate approach to predict in vivo cardiotoxicity in humans. To enable evaluation of predictions made, methadone was selected as the model compound, being a compound for which data on both kinetics and cardiotoxicity in humans are available. A PBK model for methadone in humans was developed and evaluated against available kinetic data presenting an adequate match. Use of the developed PBK model to convert concentration–response curves for the effect of methadone on human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) in the so-called multi electrode array (MEA) assay resulted in predictions for in vivo dose–response curves for methadone-induced cardiotoxicity that matched the available in vivo data. The results also revealed differences in protein plasma binding of methadone to be a potential factor underlying variation between individuals with respect to sensitivity towards the cardiotoxic effects of methadone. The present study provides a proof-of-principle of using PBK modeling-based reverse dosimetry of in vitro data for the prediction of cardiotoxicity in humans, providing a novel testing strategy in cardiac safety studies.
MULTIFILE
Pre-eclampsia (PE) is a common and severe pregnancy complication and is associated with substantial perinatal morbidity and mortality in mothers and infants. The disease is often characterized by a non-specific presentation which makes it challenging for physician to diagnose PE during regular pregnancy check-ups. To date, there are no diagnostic tests on the market for detection of PE early in pregnancy (first trimester). In this project, we will develop a platform to sensitively analyse calcium-binding proteins (CBPs) which will unlock the full potential of CBPs as predictive PE markers. The technology will also be applicable for other diseases (e.g., dementia and cancer) where CBPs are also known to play a key role in disease pathophysiology. We will develop with phage display antibodies that can recognize calcium binding to specific motifs in proteins. To this end we will synthesize peptide motifs with and without calcium to select antibodies that are specific for calcium bound proteins. These antibodies will be validated for their clinical use. For this goal we will use serum samples from the Improved studie (EU subsidised study) to determine if we can recognize pre-eclampsia in a very early stage. This knowledge can lead to a better treatment of pregnant women suffering from this disease and also will probably increase the well-being for the baby born and the development further in life.
Treatment of crops with insecticides remains essential because globally more than 75 billion dollars is lost through crop destruction by invasive insects. However it is accompanied by severe disadvantages including i. increasing resistance of the target insects against insecticides and ii. the undesired lethality of beneficial insects such as bees and other pollinator species. The significant reduction of insect species during the last years, at least partly caused by the presently available insecticides has also effects on insect-eating species. Last but not least the presence of residual amount of insecticides in the environment (soil and plants), because of poor (bio)degradation, is another distinct disadvantage. Therefore, the overall aim of this proposal is to design and synthesize peptide based biopesticides. This should lead to Nature inspired green alternatives for insect control because "Peptides" are the small equivalents of "proteins", that are biomolecules, which are universally present in all organisms and subject to their natural biodegradation mechanisms, as well as also chemically degraded in the soil (water, heat, UV, oxygen). Design and synthesis of these environmentally benign compounds will eventually take place in a founded company called "INNOVAPEPLINE". Evaluation of candidate peptide based biopesticides can be carried out in collaboration with a recently founded company (spin-out of the University of Glasgow) called "SOLASTA BIO" (founders professors Shireen Davies, Julian Dow and Rob Liskamp) and/or with other (third) parties such as the University of Wageningen. Upon recent identification of promising candidate compounds ("leads"), chemical optimization studies of leads will take place, followed by evaluation in field trials. In this proposal design, synthesis and chemical optimization of the biological activity of new peptides and development of methods to monitor their biodegradation rate will take place. Thereby expanding the repertoire of peptide based biopesticides. (292 words)
