Peptide Array X-Linking (PAX): A New Peptide-Protein Identification Approach

Many protein interaction domains bind short peptides based on canonical sequence consensus motifs. Here we report the development of a peptide array-based proteomics tool to identify proteins directly interacting with ligand peptides from cell lysates. Array-formatted bait peptides containing an amino acid-derived cross-linker are photo-induced to crosslink with interacting proteins from lysates of interest. Indirect associations are removed by high stringency washes under denaturing conditions. Covalently trapped proteins are subsequently identified by LC-MS/MS and screened by cluster analysis and domain scanning. We apply this methodology to peptides with different proline-containing consensus sequences and show successful identifications from brain lysates of known and novel proteins containing polyproline motif-binding domains such as EH, EVH1, SH3, WW domains. These results suggest the capacity of arrayed peptide ligands to capture and subsequently identify proteins by mass spectrometry is relatively broad and robust. Additionally, the approach is rapid and applicable to cell or tissue fractions from any source, making the approach a flexible tool for initial protein-protein interaction discovery.National Institutes of Health (U.S.) (Grant R21-CA-140030-01

THE CONCISE GUIDE TO PHARMACOLOGY 2021/22: G protein-coupled receptors

The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes over 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/bph.15538. G protein-coupled receptors are one of the six major pharmacological targets into which the Guide is divided, with the others being: ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2021, and supersedes data presented in the 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate

The Concise Guide to PHARMACOLOGY 2023/24: G protein-coupled receptors.

The Concise Guide to PHARMACOLOGY 2023/24 is the sixth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of approximately 1800 drug targets, and about 6000 interactions with about 3900 ligands. There is an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (https://www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes almost 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/bph.16177. G protein-coupled receptors are one of the six major pharmacological targets into which the Guide is divided, with the others being: ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2023, and supersedes data presented in the 2021/22, 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate

A molecular analysis of desiccation tolerance mechanisms in the anhydrobiotic nematode Panagrolaimus superbus using expressed sequenced tags

<p>Abstract</p> <p>Background</p> <p>Some organisms can survive extreme desiccation by entering into a state of suspended animation known as anhydrobiosis. <it>Panagrolaimus superbus </it>is a free-living anhydrobiotic nematode that can survive rapid environmental desiccation. The mechanisms that <it>P. superbus </it>uses to combat the potentially lethal effects of cellular dehydration may include the constitutive and inducible expression of protective molecules, along with behavioural and/or morphological adaptations that slow the rate of cellular water loss. In addition, inducible repair and revival programmes may also be required for successful rehydration and recovery from anhydrobiosis.</p> <p>Results</p> <p>To identify constitutively expressed candidate anhydrobiotic genes we obtained 9,216 ESTs from an unstressed mixed stage population of <it>P. superbus</it>. We derived 4,009 unigenes from these ESTs. These unigene annotations and sequences can be accessed at <url>http://www.nematodes.org/nembase4/species_info.php?species=PSC</url>. We manually annotated a set of 187 constitutively expressed candidate anhydrobiotic genes from <it>P. superbus</it>. Notable among those is a putative lineage expansion of the <it>lea </it>(late embryogenesis abundant) gene family. The most abundantly expressed sequence was a member of the nematode specific <it>sxp/ral-2 </it>family that is highly expressed in parasitic nematodes and secreted onto the surface of the nematodes' cuticles. There were 2,059 novel unigenes (51.7% of the total), 149 of which are predicted to encode intrinsically disordered proteins lacking a fixed tertiary structure. One unigene may encode an exo-β-1,3-glucanase (GHF5 family), most similar to a sequence from <it>Phytophthora infestans</it>. GHF5 enzymes have been reported from several species of plant parasitic nematodes, with horizontal gene transfer (HGT) from bacteria proposed to explain their evolutionary origin. This <it>P. superbus </it>sequence represents another possible HGT event within the Nematoda. The expression of five of the 19 putative stress response genes tested was upregulated in response to desiccation. These were the antioxidants <it>glutathione peroxidase, dj-1 </it>and <it>1-Cys peroxiredoxin</it>, an <it>shsp </it>sequence and an <it>lea </it>gene.</p> <p>Conclusions</p> <p><it>P. superbus </it>appears to utilise a strategy of combined constitutive and inducible gene expression in preparation for entry into anhydrobiosis. The apparent lineage expansion of <it>lea </it>genes, together with their constitutive and inducible expression, suggests that LEA3 proteins are important components of the anhydrobiotic protection repertoire of <it>P. superbus</it>.</p

Influence of free radicals signal from dental resins on the radio-induced signal in teeth in EPR retrospective dosimetry

In case of radiological accident, retrospective dosimetry is needed to reconstruct the absorbed dose of overexposed individuals not wearing personal dosimeters at the onset of the incident. In such a situation, emergency mass triage will be required. In this context, it has been shown that Electron Paramagnetic Resonance (EPR) spectroscopy would be a rapid and sensitive method, on the field deployable system, allowing dose evaluation of a great number of people in a short time period. This methodology uses tooth enamel as a natural dosimeter. Ionising radiations create stable free radicals in the enamel, in a dose dependent manner, which can be detected by EPR directly in the mouth with an appropriate resonator. Teeth are often subject to restorations, currently made of synthetic dimethacrylate-based photopolymerizable composites. It is known that some dental composites give an EPR signal which is likely to interfere with the dosimetric signal from the enamel. So far, no information was available about the occurrence of this signal in the various composites available on the market, the magnitude of the signal compared to the dosimetric signal, nor its evolution with time. In this study, we conducted a systematic characterization of the signal (intensity, kinetics, interference with dosimetric signal) on 19 most widely used composites for tooth restoration, and on 14 experimental resins made with the most characteristic monomers found in commercial composites. Although a strong EPR signal was observed in every material, a rapid decay of the signal was noted. Six months after the polymerization, the signal was negligible in most composites compared to a 3 Gy dosimetric signal in a tooth. In some cases, a stable atypical signal was observed, which was still interfering with the dosimetric signal

Antithrombotic therapy after bioprosthetic aortic valve replacement: ACTION Registry survey results

AIMS: A variety of antithrombotic regimens have been described for the early postoperative period after bioprosthetic aortic valve replacement (AVR). This study reviews antithrombotic practice for patients undergoing bioprosthetic AVR with or without coronary artery bypass graft (CABG) amongst the centers participating in the ACTION (Anticoagulation Treatment Influence on Postoperative Patients) Registry. METHODS AND RESULTS: An antithrombotic therapy questionnaire was answered by the 49 centers participating in the ACTION Registry located in Europe, Middle East, Canada and Asia. The 43% of centers prescribe vitamin K antagonist (VKA), 20% prescribe VKA and acetyl salicylic acid (ASA), 33% prescribe only ASA and 4% do not prescribe any therapy after bioprosthetic AVR. For patients undergoing bioprosthetic AVR and CABG 39% of the centers prescribe VKA and ASA, 37% prescribe VKA and 24% prescribe ASA. After the first three postoperative months following bioprosthetic AVR, 61% of the centers prescribe only ASA, while 39% do not prescribe any therapy. Patients with bioprosthetic AVR and CABG receive ASA in 90% centers, in 2% centers VKA and ASA, and 8% centers do not prescribe any antithrombotic. CONCLUSION: This study demonstrates that, despite guidelines published by several professional societies, medical practice for the prevention of thrombotic events early after bioprosthetic AVR varies widely among cardiac surgical center

Galectin-9 binds IgM-BCR to regulate B cell signaling

The galectin family of secreted lectins are important regulators of immune cell function; however, their role in B cell responses is poorly understood. Here, the authors identify IgM-BCR as a ligand for galectin-9. In resting naive cells, they show that galectin-9 mediates a close association between IgM and CD22