Discovering RNA-Protein Interactome by Using Chemical Context Profiling of the RNA-Protein Interface

SummaryRNA-protein (RNP) interactions generally are required for RNA function. At least 5% of human genes code for RNA-binding proteins. Whereas many approaches can identify the RNA partners for a specific protein, finding the protein partners for a specific RNA is difficult. We present a machine-learning method that scores a protein’s binding potential for an RNA structure by utilizing the chemical context profiles of the interface from known RNP structures. Our approach is applicable even when only a single RNP structure is available. We examined 801 mammalian proteins and find that 37 (4.6%) potentially bind transfer RNA (tRNA). Most are enzymes involved in cellular processes unrelated to translation and were not known to interact with RNA. We experimentally tested six positive and three negative predictions for tRNA binding in vivo, and all nine predictions were correct. Our computational approach provides a powerful complement to experiments in discovering new RNPs

Fast synthesis of platinum nanopetals and nanospheres for highly-sensitive non-enzymatic detection of glucose and selective sensing of ions

Novel methods to obtain Pt nanostructured electrodes have raised particular interest due to their high performance in electrochemistry. Several nanostructuration methods proposed in the literature use costly and bulky equipment or are time-consuming due to the numerous steps they involve. Here, Pt nanostructures were produced for the first time by one-step template-free electrodeposition on Pt bare electrodes. The change in size and shape of the nanostructures is proven to be dependent on the deposition parameters and on the ratio between sulphuric acid and chloride-complexes (i.e., hexachloroplatinate or tetrachloroplatinate). To further improve the electrochemical properties of electrodes, depositions of Pt nanostructures on previously synthesised Pt nanostructures are also performed. The electroactive surface areas exhibit a two order of magnitude improvement when Pt nanostructures with the smallest size are used. All the biosensors based on Pt nanostructures and immobilised glucose oxidase display higher sensitivity as compared to bare Pt electrodes. Pt nanostructures retained an excellent electrocatalytic activity towards the direct oxidation of glucose. Finally, the nanodeposits were proven to be an excellent solid contact for ion measurements, significantly improving the time-stability of the potential. The use of these new nanostructured coatings in electrochemical sensors opens new perspectives for multipanel monitoring of human metabolism

Re-visualising international relations:Audio-visual projects and direct encounters with the political in security studies tla

In this paper we discuss how an innovative audio-visual project was adopted to foster active, rather than declarative learning, in critical International Relations (IR). First, we explore the aesthetic turn in IR, to contrast this with forms of representation that have dominated IR scholarship. Second, we describe how students were asked to record short audio or video projects to explore their own insights through aesthetic and non-written formats. Third, we explain how these projects are understood to be deeply embedded in social science methodologies. We cite our inspiration from applying a personal sociological imagination, as a way to counterbalance a ‘marketised’ slant in higher education, in a global economy where students are often encouraged to consume, rather than produce knowledge. Finally, we draw conclusions in terms of deeper forms of student engagement leading to new ways of thinking and presenting new skills and new connections between theory and practice

Rituals of World Politics: On (Visual) Practices Disordering Things

Rituals are customarily muted into predictable and boring routines aimed to stabilise social orders and limit conflict. As a result, their magic lure recedes into the background, and the unexpected, disruptive and disordered elements are downplayed. Our collaborative contribution counters this move by foregrounding rituals of world politics as social practices with notable disordering effects. The collective discussion recovers the disruptive work of a range of rituals designed to sustain the sovereign exercise of violence and war. We do so through engaging a series of ‘world pictures' (Mitchell 2007). We show the worlding enacted in rituals such as colonial treaty-making, state commemoration, military/service dog training, cyber-security podcasts,algorithmically generated maps, the visit of Prince Harry to a joint NATO exercise and border ceremonies in India, respectively. We do so highlighting rituals’ immanent potential for disruption of existing orders, the fissures, failures and unforeseen repercussions. Reappraising the disordering role of ritual practices sheds light on the place of rituals in rearticulating the boundaries of the political. It emphasises the role of rituals in generating dissensus and re-divisions of the sensible rather than in imposing a consensus by policing the boundaries of the political, as Rancière might phrase it. Our images are essential to the account. They help disinterring the fundamentals and ambiguities of the current worldings of security, capturing the affective atmosphere of rituals

Thermal Adaptation of Dihydrofolate Reductase from the Moderate ThermophileGeobacillus stearothermophilus

The thermal melting temperature of dihydrofolate reductase from Geobacillus stearothermophilus (BsDHFR) is 30 °C higher than that of its homologue from the psychrophile Moritella profunda. Additional proline residues in the loop regions of BsDHFR have been proposed to enhance the thermostability of BsDHFR, but site-directed mutagenesis studies reveal that these proline residues contribute only minimally. Instead, the high thermal stability of BsDHFR is partly due to removal of water-accessible thermolabile residues such as glutamine and methionine, which are prone to hydrolysis or oxidation at high temperatures. The extra thermostability of BsDHFR can be obtained by ligand binding, or in the presence of salts or cosolvents such as glycerol and sucrose. The sum of all these incremental factors allows BsDHFR to function efficiently in the natural habitat of G. stearothermophilus, which is characterized by temperatures that can reach 75 °C

Loop Interactions during Catalysis by Dihydrofolate Reductase fromMoritella profunda

Dihydrofolate reductase (DHFR) is often used as a model system to study the relation between protein dynamics and catalysis. We have studied a number of variants of the cold-adapted DHFR from Moritella profunda (MpDHFR), in which the catalytically important M20 and FG loops have been altered, and present a comparison with the corresponding variants of the wellstudied DHFR from Escherichia coli (EcDHFR). Mutations in the M20 loop do not affect the actual chemical step of transfer of hydride from reduced nicotinamide adenine dinucleotide phosphate to the substrate 7,8-dihydrofolate in the catalytic cycle in either enzyme; they affect the steady state turnover rate in EcDHFR but not in MpDHFR. Mutations in the FG loop also have different effects on catalysis by the two DHFRs. Despite the two enzymes most likely sharing a common catalytic cycle at pH 7, motions of these loops, known to be important for progression through the catalytic cycle in EcDHFR, appear not to play a significant role in MpDHFR

Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity

Farnesylation is an important post-translational modification catalyzed by farnesyltransferase (FTase). Until recently it was believed that a C-terminal CaaX motif is required for farnesylation, but recent experiments have revealed larger substrate diversity. In this study, we propose a general structural modeling scheme to account for peptide binding specificity and recapitulate the experimentally derived selectivity profile of FTase in vitro. In addition to highly accurate recovery of known FTase targets, we also identify a range of novel potential targets in the human genome, including a new substrate class with an acidic C-terminal residue (CxxD/E). In vitro experiments verified farnesylation of 26/29 tested peptides, including both novel human targets, as well as peptides predicted to tightly bind FTase. This study extends the putative range of biological farnesylation substrates. Moreover, it suggests that the ability of a peptide to bind FTase is a main determinant for the farnesylation reaction. Finally, simple adaptation of our approach can contribute to more accurate and complete elucidation of peptide-mediated interactions and modifications in the cell