Electrostatic steering and ionic tethering in enzyme–ligand binding: Insights from simulations

To bind at an enzyme’s active site, a ligand must diffuse or be transported to the enzyme’s surface, and, if the binding site is buried, the ligand must diffuse through the protein to reach it. Although the driving force for ligand binding is often ascribed to the hydrophobic effect, electrostatic interactions also influence the binding process of both charged and nonpolar ligands. First, electrostatic steering of charged substrates into enzyme active sites is discussed. This is of particular relevance for diffusion-influenced enzymes. By comparing the results of Brownian dynamics simulations and electrostatic potential similarity analysis for triose-phosphate isomerases, superoxide dismutases, and β-lactamases from different species, we identify the conserved features responsible for the electrostatic substrate-steering fields. The conserved potentials are localized at the active sites and are the primary determinants of the bimolecular association rates. Then we focus on a more subtle effect, which we will refer to as “ionic tethering.” We explore, by means of molecular and Brownian dynamics simulations and electrostatic continuum calculations, how salt links can act as tethers between structural elements of an enzyme that undergo conformational change upon substrate binding, and thereby regulate or modulate substrate binding. This is illustrated for the lipase and cytochrome P450 enzymes. Ionic tethering can provide a control mechanism for substrate binding that is sensitive to the electrostatic properties of the enzyme’s surroundings even when the substrate is nonpolar.

Activation of αvβ3-Vitronectin Binding Is a Multistage Process in which Increases in Bond Strength Are Dependent on Y747 and Y759 in the Cytoplasmic Domain of β3

Integrin receptors serve as mechanical links between the cell and its structural environment. Using αvβ3 integrin expressed in K562 cells as a model system, the process by which the mechanical connection between αvβ3 and vitronectin develops was analyzed by measuring the resistance of these bonds to mechanical separation. Three distinct stages of activation, as defined by increases in the αvβ3-vitronectin binding strength, were defined by mutational, biochemical, and biomechanical analyses. Activation to the low binding strength stage 1 occurs through interaction with the vitronectin ligand and leads to the phosphorylation of Y747 in the β3 subunit. Stage 2 is characterized by a 4-fold increase in binding strength and is dependent on stage1 and the phosphorylation of Y747. Stage 3 is characterized by a further 2.5-fold increase in binding strength and is dependent on stage 2 events and the availability of Y759 for interaction with cellular proteins. The Y747F mutant blocked the transition from stage 1 to stage 2, and the Y759F blocked the transition from stage 2 to stage 3. The data suggest a model for tension-induced activation of αvβ3 integrin.

Modelling and testing volatility spillovers in oil and financial markets for USA, UK and China

The primary purpose of the paper is to analyze the conditional correlations, conditional covariances, and co-volatility spillovers between international crude oil and associated financial markets. The paper investigates co-volatility spillovers (namely, the delayed effect of a returns shock in one physical or financial asset on the subsequent volatility or co-volatility in another physical or financial asset) between the oil and financial markets. The oil industry has four major regions, namely North Sea, USA, Middle East, and South-East Asia. Associated with these regions are two major financial centers, namely UK and USA. For these reasons, the data to be used are the returns on alternative crude oil markets, returns on crude oil derivatives, specifically futures, and stock index returns in UK and USA. The paper will also analyze the Chinese financial markets, where the data are more recent. The empirical analysis will be based on the diagonal BEKK model, from which the conditional covariances will be used for testing co-volatility spillovers, and policy recommendations. Based on these results, dynamic hedging strategies will be suggested to analyze market fluctuations in crude oil prices and associated financial markets.

Lonnie Holley exploration and analysis of his artworks in two settings : the yard and the museum

The contemporary artist, Lonnie Holley, creates assemblage sculptures using found objects that he then places in his multi-layered yard art environment. With the rise in prestige of folk art, many art galleries and museums have displayed the works of Holley, removing them from the yard art environment and placing them in the gallery setting. This paper addresses how meaning changes when the context of Holley’s artworks changes.

Comparison of Wildlife Impacts Associated with Uranium In-Situ Recovery and Wind Farms in Wyoming

Wyoming has multiple resources including non-renewable sources, renewable sources, as well as its wildlife. Two of these resources are uranium and wind. Currently wind farms in Wyoming are generating approximately 5 million MW of power, with less of an impact on wildlife than in-situ facilities. In-situ facilities in 2007 produced an estimated 32 million MW of power from uranium, with a greater impact to wildlife than wind farms. Both resources have a great potential in Wyoming and both will have an impact on wildlife. Currently wind farms show less of an impact on wildlife but they are also producing fewer megawatts. The potential for wind-generated energy over the next century shows wildlife impacts will be greater than impacts from ISR facilities.

Enrichment of the Phenotypic and Genotypic Data Warehouse analysis using Question Answering systems to facilitate the decision making process in cereal breeding programs

Currently there are an overwhelming number of scientific publications in Life Sciences, especially in Genetics and Biotechnology. This huge amount of information is structured in corporate Data Warehouses (DW) or in Biological Databases (e.g. UniProt, RCSB Protein Data Bank, CEREALAB or GenBank), whose main drawback is its cost of updating that makes it obsolete easily. However, these Databases are the main tool for enterprises when they want to update their internal information, for example when a plant breeder enterprise needs to enrich its genetic information (internal structured Database) with recently discovered genes related to specific phenotypic traits (external unstructured data) in order to choose the desired parentals for breeding programs. In this paper, we propose to complement the internal information with external data from the Web using Question Answering (QA) techniques. We go a step further by providing a complete framework for integrating unstructured and structured information by combining traditional Databases and DW architectures with QA systems. The great advantage of our framework is that decision makers can compare instantaneously internal data with external data from competitors, thereby allowing taking quick strategic decisions based on richer data.

The nurses´ experience on nursing students and their clinical learning process in hospital

Nursing studies program, and relationships between University academic program and Hospitals, all influence bedsides nurses´ experience on nursing clinical learning process.

Postcolonial healing landscapes and mental health in a remote Indigenous community in subarctic Ontario, Canada

The concept of therapeutic landscape is concerned with a holistic, socio-ecological model of health, but most studies have attempted to explore land-health links from a Western perspective. On an Indigenous reserve in Northern Ontario, part of the Canadian subarctic, we explore the importance of spaces and places in creating postcolonial therapeutic landscapes to treat the wounds inflicted by colonialism. The aim of this research is to gain insight from views and experiences of First Nations residents living on reservations that are undergoing a process of regaining traditional spiritual beliefs and teachings to construct therapeutic spaces to face mental health problems caused by legal opioid analgesic abuse. This qualitative study used semi-structured interviews with Cree and Ojibwe participants to understand how they are reconnecting with earth, spirituality and traditional animist beliefs on their way to recovery. We find that practices such as taking part in ceremonies and ritual spaces, and seeking knowledge and advice from Elders assist with personal healing and enable Indigenous people to be physically and mentally healthy. Our research findings provide important insights into the relationship between space, healing and culture as determinants of health and well-being and document some key factors that contribute to substance abuse recovery.

An Exploration of Sociometric Status and Peer Relations in Youth Sport

More than 10 years ago, it was suggested that sociometry and systematic observation were two potentially useful but under-utilized methods for the study of peers in youth sport (Smith, 2003). Despite this call, the methods used to study peers in sport remain largely focused on athletes' perceptions through questionnaires and interviews. Thus, the purpose of this descriptive study was to investigate the utility of sociometry in relation to sport competence and observed athlete behavior in youth sport. Three adolescent female volleyball teams were videotaped during three practice sessions, and sport competence and sociometric status were assessed using questionnaires. An observational coding system was developed and used to code athlete behaviors and data were compared across sociometric status groups. Results revealed significant differences between sociometric status groups on peer ratings of sport competence, but not on athlete behavior. However, interesting findings emerged with respect to how status groups interacted with teammates and coaches. Thus, sport competence seems to be an important factor in gaining acceptance among youth peer groups. Further, sociometry and behavioral observation appear to be useful techniques that should continue to be employed in the study of peer relations in youth sport.

Microbial translocation and immune activation in HIV infection

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014