Stimuli-induced folding cascade of a linear oligomeric guest chain programmed through cucurbit[n]uril self-sorting (n = 6, 7, 8)

A six-station linear guest for cucurbit[7]uril and cucurbit[8]uril has been synthesized in order to implement a cascade of transformations driven by external stimuli. The guest chain is sequence-programmed with electron- deficient viologen and electron-rich naphthalene stations linked by either flexible or rigid spacers that affect the chain's folding properties. Together with the orthogonal guest selectivity of the two cucurbiturils, these properties result in self-sorted cucurbituril pseudorotaxane foldamers. Each transformation is controlled by suitable chemical and redox inputs and leads not only to refolding of the guest chain, but also to the liberation of secondary messenger molecules which render the system presented here reminiscent of natural signaling cascades. The steps of the cascade are analyzed by UV/Vis, 1H NMR and electrospray (tandem) mass spectrometry to investigate the different pseudorotaxane structures in detail. With one guest oligomer, three different cucurbiturils, and several different chemical and redox inputs, a chemical system is created which exhibits complex behavior beyond the chemist's paradigm of the pure chemical compound

Supramolecular reactivity in the gas phase: investigating the intrinsic properties of non-covalent complexes

The high vacuum inside a mass spectrometer offers unique conditions to broaden our view on the reactivity of supramolecules. Because dynamic exchange processes between complexes are efficiently suppressed, the intrinsic and intramolecular reactivity of the complexes of interest is observed. Besides this, the significantly higher strength of non-covalent interactions in the absence of competing solvent allows processes to occur that are unable to compete in solution. The present review highlights a series of examples illustrating different aspects of supramolecular gas-phase reactivity ranging from the dissociation and formation of covalent bonds in non-covalent complexes through the reactivity in the restricted inner phase of container molecules and step-by-step mechanistic studies of organocatalytic reaction cycles to cage contraction reactions, processes induced by electron capture, and finally dynamic molecular motion within non-covalent complexes as unravelled by hydrogen–deuterium exchange processes performed in the gas phase

Probing prothrombin structure by limited proteolysis

Prothrombin, or coagulation factor II, is a multidomain zymogen precursor of thrombin that undergoes an allosteric equilibrium between two alternative conformations, open and closed, that react differently with the physiological activator prothrombinase. Specifically, the dominant closed form promotes cleavage at R320 and initiates activation along the meizothrombin pathway, whilst the open form promotes cleavage at R271 and initiates activation along the alternative prethrombin-2 pathway. Here we report how key structural features of prothrombin can be monitored by limited proteolysis with chymotrypsin that attacks W468 in the flexible autolysis loop of the protease domain in the open but not the closed form. Perturbation of prothrombin by selective removal of its constituent Gla domain, kringles and linkers reveals their long-range communication and supports a scenario where stabilization of the open form switches the pathway of activation from meizothrombin to prethrombin-2. We also identify R296 in the A chain of the protease domain as a critical link between the allosteric open-closed equilibrium and exposure of the sites of cleavage at R271 and R320. These findings reveal important new details on the molecular basis of prothrombin functio

THE SANSEVERO CHAPEL, A THREE-DIMENSIONAL POINT OF VIEW

Abstract. In this article, the importance of the three-dimensional survey in architectural spaces will be studied, taking special relevance in the study of the perception of perspective, since three-dimensional space would not be understood from a two-dimensional representation of space. The project aims to develop a comparison between the representation systems based on the automatic acquisition of various data by different 3D survey techniques. In particular, the document reports the results of an analysis based on the Sansevero Chapel in Naples.</p

Assessing changes in epiphytic lichen community after 45 years, a study case in white poplars from northern Iberian Peninsula (Jaca, Aragon)

Epiphytic lichens are used broadly as bioindicators, as they are sessile organisms with slow growth and different species display a wide range of environmental sensitivity. Most studies on epiphytic lichens focus on their use as indicators of the present environmental conditions, but few studies assess the changes that occur over decades. Comparative temporal approaches in lichens are rare, since there are few old datasets and in most cases substrates have disappeared, especially trees. However, in 1973 one of us (X. Llimona) described the lichen community on urban Populus alba in Jaca, and those trees are still alive. Our aim was to study the epiphytic lichen community in 2018 and compare it with the study of 1973. Species richness decreased during these 45 years. While only 36% of species found in 1973 persisted until 2018, these species remaining were observed at a high frequency in the 2018 sampling. Lichens communities from both years were similar on its tolerance to environmental variables, and the locality and their surroundings had the same land use in both years. Thus, the changes in lichen composition between both samplings might be explained by autogenic succession or limitation on dispersion rather than habitat filtering. Our data suggests that, under stable environments, lichen community assembly over decades depends on other traits such as competition rather than lichen sensitivity

Interplay between conformational selection and zymogen activation

Trypsin-like proteases are synthesized as zymogens and activated through a mechanism that folds the active site for efficient binding and catalysis. Ligand binding to the active site is therefore a valuable source of information on the changes that accompany zymogen activation. Using the physiologically relevant transition of the clotting zymogen prothrombin to the mature protease thrombin, we show that the mechanism of ligand recognition follows selection within a pre-existing ensemble of conformations with the active site accessible (E) or inaccessible (E) to binding. Prothrombin exists mainly in the Econformational ensemble and conversion to thrombin produces two dominant changes: a progressive shift toward the E conformational ensemble triggered by removal of the auxiliary domains upon cleavage at R271 and a drastic drop of the rate of ligand dissociation from the active site triggered by cleavage at R320. Together, these effects produce a significant (700-fold) increase in binding affinity. Limited proteolysis reveals how the E-E equilibrium shifts during prothrombin activation and influences exposure of the sites of cleavage at R271 and R320. These new findings on the molecular underpinnings of prothrombin activation are relevant to other zymogens with modular assembly involved in blood coagulation, complement and fibrinolysis

URBAN DESIGN STRATEGIES FOR THE UPCYCLING OF URBAN INFRASTRUCTURE RESIDUAL POCKETS: 3D CITY MODELLING FROM OPEN DATA AND LOW-COST RAPID MAPPING TOOLS

This paper deals with the 3D City Modelling specific procedure developed as a tool to support strategies for urban regeneration, within the framework of the B-ROAD research project.The B-ROAD research project, whose acronym stands for Below the Road, is developing urban design strategies for upcycling urban infrastructure residual pockets.The B-ROAD’s methodology is conceived as research by design as it is carried out by creating pilot scenarios, disclosing the latent and still unexpressed potential of these wasted areas and displaying their potential transformations, to turn them into precious resources for the contemporary city.The 3D City Modelling of the study area has proved to be essential and strategic yet often complex and critical as most of the spatial and architectural features of B-ROAD spaces, as well as their potential, cannot be detected nor represented through the traditional means of representation of urbanised land, as aerial survey-based representations, or GIS. Likewise, traditional, or even cutting-edge, survey techniques that can be used to acquire missing data are often costly and time-consuming, thus making it hardly impossible to achieve the purpose of extensive and deep knowledge of such a vast area. Thus, 3D City Modelling aimed at examining spaces and providing a final representation of pilot scenarios has been a crucial stage requiring a specific in-depth study.</p

Cryo-EM structure of the prothrombin-prothrombinase complex

The intrinsic and extrinsic pathways of the coagulation cascade converge to a common step where the prothrombinase complex, comprising the enzyme factor Xa (fXa), the cofactor fVa, Ca2+ and phospholipids, activates the zymogen prothrombin to the protease thrombin. The reaction entails cleavage at 2 sites, R271 and R320, generating the intermediates prethrombin 2 and meizothrombin, respectively. The molecular basis of these interactions that are central to hemostasis remains elusive. We solved 2 cryogenic electron microscopy (cryo-EM) structures of the fVa-fXa complex, 1 free on nanodiscs at 5.3-Å resolution and the other bound to prothrombin at near atomic 4.1-Å resolution. In the prothrombin-fVa-fXa complex, the Gla domains of fXa and prothrombin align on a plane with the C1 and C2 domains of fVa for interaction with membranes. Prothrombin and fXa emerge from this plane in curved conformations that bring their protease domains in contact with each other against the A2 domain of fVa. The 672ESTVMATRKMHDRLEPEDEE691 segment of the A2 domain closes on the protease domain of fXa like a lid to fix orientation of the active site. The 696YDYQNRL702 segment binds to prothrombin and establishes the pathway of activation by sequestering R271 against D697 and directing R320 toward the active site of fXa. The cryo-EM structure provides a molecular view of prothrombin activation along the meizothrombin pathway and suggests a mechanism for cleavage at the alternative R271 site. The findings advance our basic knowledge of a key step of coagulation and bear broad relevance to other interactions in the blood

Eye-tracking while reading passives: An event structure account of difficulty

Among existing accounts of passivisation difficulty, some argue it depends on the predicate semantics (i.e. passives are more difficult with subject-experiencer than agent-patient verbs). Inconsistent with the accounts that predict passive difficulty, Paolazzi et al. (2019) found that passives were read faster than actives at the verb and object by-phrase in a series of self-paced reading experiments, with no modulation of verb type. However, self-paced reading provides limited direct measurement of late revision/interpretive processing. We used modified stimuli from Paolazzi et al. (2019) to re-examine this issue in two eye-tracking while reading experiments. We found that in late measures, passives with subject-experiencer verbs had longer fixation durations than actives at the verb and two subsequent regions but no difference was observed across agent-patient verbs. Subject-experiencer verbs provide a state, but the passive structure requires an event. Thus, the required eventive interpretation is coerced with subject-experiencers (if possible) and induces difficulty

Age-Related Differences in Plasma Proteins: How Plasma Proteins Change from Neonates to Adults

The incidence of major diseases such as cardiovascular disease, thrombosis and cancer increases with age and is the major cause of mortality world-wide, with neonates and children somehow protected from such diseases of ageing. We hypothesized that there are major developmental differences in plasma proteins and that these contribute to age-related changes in the incidence of major diseases. We evaluated the human plasma proteome in healthy neonates, children and adults using the 2D-DIGE approach. We demonstrate significant changes in number and abundance of up to 100 protein spots that have marked differences in during the transition of the plasma proteome from neonate and child through to adult. These proteins are known to be involved in numerous physiological processes such as iron transport and homeostasis, immune response, haemostasis and apoptosis, amongst others. Importantly, we determined that the proteins that are differentially expressed with age are not the same proteins that are differentially expressed with gender and that the degree of phosphorylation of plasma proteins also changes with age. Given the multi-functionality of these proteins in human physiology, understanding the differences in the plasma proteome in neonates and children compared to adults will make a major contribution to our understanding of developmental biology in humans.GE Healthcare Life Sciences Australia funded Sherif Tawfilis' time in the initial laboratory aspects of this project, some aspects of data analysis and preparation of the manuscript. This study was funded by internal Haematology Research Team funds. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript