Disruption of Intrinsic Motions as a Mechanism for Enzyme Inhibition

AbstractClostridium difficile (C. diff) is one of the most common and most severe hospital-acquired infections; its consequences range from lengthened hospital stay to outright lethality. C. diff causes cellular damage through the action of two large toxins TcdA and TcdB. Recently, there has been increased effort toward developing antitoxin therapies, rather than antibacterial treatments, in hopes of mitigating the acquisition of drug resistance. To date, no analysis of the recognition mechanism of TcdA or TcdB has been attempted. Here, we use small molecule flexible docking followed by unbiased molecular dynamics to obtain a more detailed perspective on how inhibitory peptides, exemplified by two species HQSPWHH and EGWHAHT function. Using principal component analysis and generalized masked Delaunay analysis, an examination of the conformational space of TcdB in its apo form as well as forms bound to the peptides and UDP-Glucose was performed. Although both species inhibit by binding in the active site, they do so in two very different ways. The simulations show that the conformational space occupied by TcdB bound to the two peptides are quite different and provide valuable insight for the future design of toxin inhibitors and other enzymes that interact with their substrates through conformational capture mechanisms and thus work by the disruption of the protein’s intrinsic motions

Governing the Land-Sea Interface to Achieve Sustainable Coastal Development

Coastal regions are essential to achieving the Sustainable Development Goals (SDGs) given their importance for human habitation, resource provisioning, employment, and cultural practice. They are also regions where different ecological, disciplinary, and jurisdictional boundaries both overlap and are obscured. We thus propose the land-sea interface as areas where governance systems are most in need of frameworks for systems analysis to meet the SDGs—which are inherently interconnected— and integrate complex interdependencies between human livelihoods, energy, transport, food production, and nutrient flows (among others). We propose a strategic land-sea governance framework built on the sustainable transitions literature to plan for governance to achieve sustainable development across the land-sea interface. To illustrate our proposal, we compare governance planning processes across four case-based scenarios: an industrialized coastal country, a least developed coastal country, a developing coastal country with local dependencies on ocean resources, and a small island developing state primarily dependent on tourism. Through the lens of aligning governance actors and actions vertically (subnational to national), horizontally (across sectors), and programmatically (from goals to implementation), we propose scales at which governance systems may be misaligned, such as where different agencies that affect marine systems have conflicting visions and goals, leading to stalled progress or counterproductive actions. Where possible, we also highlight strategies to align across scales of high level strategic policy, tactical scale institutional mandates and cooperation, and on the ground activities and operations, such as aligning actors based on an analysis of interdependencies of goals

Reproductive system of V assobia brevifl ora (Solanaceae) in Aguas Chiquitas, Tucumán

Vassobia brevifl ora (Sendtn.) Hunz. es un arbusto o árbol pequeño, nativo de Sudamérica, distribuido en Brasil, Paraguay, Bolivia,Argentina. Aunque es una especie común de ambientes secundarios de ecotonos (Chaco-Yungas, Chaco-Campos), su sistema reproductivo es poco conocido. El objetivo de este trabajo es describir el sistema reproductivo de V. breviflora, a partir de observaciones y experimentos de campo realizados en la Reserva Natural de Aguas Chiquitas, Tucumán, Argentina. V. breviflora es polinizada por insectos. El sistema reproductivo fue determinado mediante experimentos de polinización controlada, consistentes de seis tratamientos con flores embolsadas (autogamia espontánea (aee), autogamia manual (ame), geitonogamia manual, xenogamia manual, emasculación, emasculación con xenogamia manual (exme)) y tres tratamientos con flores libres (polinización espontánea, emasculación, suplementación manual). Cada tratamiento fue aplicado a 23 flores por planta (mediana). El éxito promedio de polinización fue mayor en los tratamientos de entrecruzamiento (cercano a 1) mientras que en los de autogamia y geitonogamia varió entre 0.57 y 0.75. El índice de autogamia (éxito de ame / éxito de aee) fue 0.98, y el índice de autocompatibilidad (promedio de ame / promedio de exme) fue 0.81. La producción de semillas varió significativamente entre tratamientos (rango de promedios = 13-29 semillas por fruto). La suplementación manual de flores libres produjo menos semillas que lo esperado. Vassobia breviflora es autocompatible y probablemente apomíctica. Sin embargo, la producción de semillas es mayor como producto del entrecruzamiento. En conjunto los resultados muestran que el sistema reproductivo es autocompatible en el límite del apareamiento mixto.Fil: Cisneros, Claudia. Universidad Nacional de Tucumán. Facultad de Ciencias Naturales e Instituto Miguel Lillo; ArgentinaFil: Valoy, Mariana Eugenia. Fundación Miguel Lillo; ArgentinaFil: Bernacki, Facundo G.. Fundación Miguel Lillo; ArgentinaFil: Varela, Omar. Fundación Miguel Lillo; Argentina. Universidad Nacional de Chilecito; ArgentinaFil: Ordano, Mariano Andrés. Universidad Nacional de Tucumán. Instituto de Ecología Regional. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Ecología Regional; Argentina. Fundación Miguel Lillo; ArgentinaXXXVII Jornadas Argentinas de BotánicaSan Miguel de TucumánArgentinaSociedad Argentina de BotánicaFundación Miguel Lill

Catalytic mechanism of human DNA polymerase λ with Mg2+ and Mn2+ from ab initio quantum mechanical/molecular mechanical studies

DNA polymerases play a crucial role in the cell cycle due to their involvement in genome replication and repair. Understanding the reaction mechanism by which these polymerases carry out their function can provide insights into these processes. Recently, the crystal structures of human DNA polymerase λ (Polλ) have been reported both for pre- and post- catalytic complexes (García-Díaz et al., DNA Repair, 3, 1333, 2007). Here we employ the pre-catalytic complex as a starting structure for the determination of the catalytic mechanism of Polλ using ab initio quantum mechanical/molecular mechanical methods. The reaction path has been calculated using Mg2+ and Mn2+ as the catalytic metals. In both cases the reaction proceeds through a two step mechanism where the 3′-OH of the primer sugar ring is deprotonated by one of the conserved Asp residues (D490) in the active site before the incorporation of the nucleotide to the nascent DNA chain. A significant charge transfer is observed between both metals and some residues in the active site as the reaction proceeds. The optimized reactant and product structures agree with the reported crystal structures. In addition, the calculated reaction barriers for both metals are close to experimentally estimated barriers. Energy decomposition analysis to explain individual residue contributions suggests that several amino acids surrounding the active site are important for catalysis. Some of these residues, including R420, R488 and E529, have been implicated in catalysis by previous mutagenesis experiments on the homologous residues on Polβ. Furthermore, Polλ residues R420 and E529 found to be important from the energy decomposition analysis, are homologous to residues R183 and E295 in Polβ, both of which are linked to cancer. In addition, residues R386, E391, K422 and K472 appear to have an important role in catalysis and could be a potential target for mutagenesis experiments. There is partial conservation of these residues across the Pol X family of DNA polymerases

The use of influential power in ocean governance

Ensuring inclusivity, especially the meaningful participation of diverse actors, is a key component of good governance. However, existing ocean governance frameworks have not yet achieved an equitable and fair playing field and are indeed often characterized by inequitable practices. In this perspective piece, we argue that one of the reasons for this lack of inclusion are the existing power frameworks and ways in which power is exercised within fora nominally intended to foster inclusion and cooperation. By focusing on four case studies of basic ocean governance processes, we explore how influential and interactive power is exercised in intergovernmental meetings, international conferences, and regional negotiations. These case studies demonstrate how specific exercises of power that undermine procedural inclusivity influence decision-making and the setting of agendas, and exclude important voices from ocean governance fora. This perspective piece contributes to the existing literature on power by highlighting how power is exercised within fundamental aspects of ocean governance. This paper merely scratches the surface, and more actions and research are needed to uncover and, more importantly, reverse deeply-rooted and self-perpetuating power structures in ocean governance

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Polarizable MD and QM/MM Investigation of Acrylamide-based Leads to Target the Main Protease of SARS-CoV-2

The main protease (Mpro) of SARS-CoV-2 is an essential enzyme for the replication of the virus causing the COVID-19 pandemic. Because there is no known homologue in humans, it has been proposed as a primary target for antiviral drug development. Here, we explore the potential of five acrylamide warhead molecules as possible leads to target MPro by polarizable MD and QM/MM calculations. All calculations involving a classical potential were calculated with the AMOEBA polarizable force field, while electronic structure calculations were performed within the framework of density functional theory. Our MD simulations show that at least one of the analyzed compounds may show promise as a lead for further development as a non-covalent inhibitor. The QM/MM calculations suggest that the compound could be considered as a non-covalent inhibitor, since the formation of a covalent bond with Cys145 has an unfavorable kinetic barrier for that compound

Investigation of the Stability of D5SIC-DNAM-Incorporated DNA duplex in Taq Polymerase Binary system: A Systematic Classical MD Approach

DNA polymerases are fundamental enzymes that play a crucial role in processing DNA with high fidelity and accuracy ensuring the faithful transmission of genetic information. The recognition of unnatural base pairs (UBPs) by polymerases, enabling their replication, represents a significant and groundbreaking discovery with profound implications for genetic expansion. Romesberg et al. examined the impact of DNA containing 2,6-dimethyl-2H-isoquiniline-1-thione: D5SIC (DS) and 2-methoxy-3-methylnaphthalene: DNAM (DN) UBPs bound to T. aquaticus DNA polymerase (Taq) through crystal structure analysis. Here, we have used polarizable and nonpolarizable classical molecular dynamics (MD) simulations to investigate the structural aspects and stability of Taq in complex with a DNA duplex including a DS-DN pair in the terminal templating and priming positions. Our results suggest that the flexibility of UBP-incorporated DNA in the terminal position is arrested by the polymerase, thus preventing fraying and mispairing. Our investigation also reveals that the UBP remains in an intercalated conformation inside the active site, exhibiting two distinct orientations in agreement with experimental findings. Our analysis pinpoints particular residues responsible for favorable interactions with the UBP, with some relying on van der Waals interactions while others on Coulombic forces