Computer simulation of protein systems

Ligand binding to dihydrofolate reductase (DHFR) is discussed. This is an extremely important enzyme, as it is the target of several drugs (inhibitors) which are used clinically as antibacterials, antiprotozoals and in cancer chemotherapy. DHFR catalyzes the NADPH (reduced nicotinamide adenine dinucleotide phosphate) dependent reduction of dihydrofolate to tetrahydrofolate, which is used in several pathways of purine and pyrimidine iosynthesis, including that of thymidylate. Since DNA synthesis is dependent on a continuing supply of thymidylate, a blockade of DHFR resulting in a depletion of thymidylate can lead to the cessation of growth of a rapidly proliferating cell line. DHFR exhibits a significant species to species variability in its sensitivity to various inhibitors. For example, trimethoprim, an inhibitor of DHFR, binds to bacterial DHFR's 5 orders of magnitude greater than to vertebrate DHFR's. The structural mechanics, dynamics and energetics of a family of dihydrofolate reductases are studied to rationalize the basis for the inhibitor of these enyzmes and to understand the molecular basis of the difference in the binding constants between the species. This involves investigating the conformational changes induced in the protein on binding the ligand, the internal strain imposed by the enzyme on the ligand, the restriction of fluctuations in atom positions due to binding and the consequent change in entropy

A robust nanoscale experimental quantification of fracture energy in a bilayer material system

Accurate measurement of interfacial properties is critical any time two materials are bonded—in composites, tooth crowns, or when biomaterials are attached to the human body. Yet, in spite of this importance, reliable methods to measure interfacial properties between dissimilar materials remain elusive. Here we present an experimental approach to quantify the interfacial fracture energy Γ[subscript i] that also provides unique mechanistic insight into the interfacial debonding mechanism at the nanoscale. This approach involves deposition of an additional chromium layer (superlayer) onto a bonded system, where interface debonding is initiated by the residual tensile stress in the superlayer, and where the interface can be separated in a controlled manner and captured in situ. Contrary to earlier methods, our approach allows the entire bonded system to remain in an elastic range during the debonding process, such that Γ[subscript i] can be measured accurately. We validate the method by showing that moisture has a degrading effect on the bonding between epoxy and silica, a technologically important interface. Combining in situ through scanning electron microscope images with molecular simulation, we find that the interfacial debonding mechanism is hierarchical in nature, which is initiated by the detachment of polymer chains, and that the three-dimensional covalent network of the epoxy-based polymer may directly influence water accumulation, leading to the reduction of Γ[subscript i] under presence of moisture. The results may enable us to design more durable concrete composites that could be used to innovate transportation systems, create more durable buildings and bridges, and build resilient infrastructure.National Science Foundation (U.S.) (Grant CMS-0856325

Use of quercetin in animal feed : effects on the P-gp expression and pharmacokinetics of orally administrated enrofloxacin in chicken

Modulation of P-glycoprotein (P-gp, encoded by Mdr1) by xenobiotics plays central role in pharmacokinetics of various drugs. Quercetin has a potential to modulate P-gp in rodents, however, its effects on P-gp modulation in chicken are still unclear. Herein, study reports role of quercetin in modulation of P-gp expression and subsequent effects on the pharmacokinetics of enrofloxacin in broilers. Results show that P-gp expression was increased in a dose-dependent manner following exposure to quercetin in Caco-2 cells and tissues of chicken. Absorption rate constant and apparent permeability coefficient of rhodamine 123 were decreased, reflecting efflux function of P-gp in chicken intestine increased by quercetin. Quercetin altered pharmacokinetic of enrofloxacin by decreasing area under curve, peak concentration, and time to reach peak concentration and by increasing clearance rate. Molecular docking shows quercetin can form favorable interactions with binding pocket of chicken xenobiotic receptor (CXR). Results provide convincing evidence that quercetin induced P-gp expression in tissues by possible interaction with CXR, and consequently reducing bioavailability of orally administered enrofloxacin through restricting its intestinal absorption and liver/kidney clearance in broilers. The results can be further extended to guide reasonable use of quercetin to avoid drug-feed interaction occurred with co-administered enrofloxacin or other similar antimicrobials.Peer reviewedFinal Published versio

NMR Structures of Apo L. casei Dihydrofolate Reductase and Its Complexes with Trimethoprim and NADPH: Contributions to Positive Cooperative Binding from Ligand-Induced Refolding, Conformational Changes, and Interligand Hydrophobic Interactions

bS Supporting Information The enzyme dihydrofolate reductase (DHFR; 5,6,7,8-tetra-hydrofolate:NADPH oxidoreductase, EC 1.5.1.3) catalyzes the reduction of 7,8-dihydrofolate (DHF) to 5,6,7,8-tetrahydro-folate (THF) using NADPH as coenzyme.1 Since THF and its metabolites are precursors of purine and pyrimidine bases, the normal functioning of this enzyme is essential for proliferating cells. This makes DHFR an excellent target for antifolate drugs such as methotrexate (anticancer), pyrimethamine (antimalarial), and trimethoprim (antibacterial). Such agents act by inhibiting the enzyme in parasitic or malignant cells.1,2 The cooperative binding of ligands to DHFR plays an important role not only in the enzyme catalytic cycle (negative cooperativity in THF/ NADPH binding)3 but also in enzyme inhibition (positive cooperativity in antifolate/NADPH binding).4 The effects of positive cooperative binding in controlling enzyme inhibition ar

InterGEO: a digital platform for university education on geomorphological heritage

The project InterGEO was carried out with the objective to disseminate knowledge on geomorphological heritage by developing a digital learning platform. It aims at improving students' autonomy by the reduction of face-to-face teaching and increasing autonomous learning as well as promoting international interactions between students interested in geomorphological heritage. A completely free-access virtual course on geomorphosites was developed with the Learning Management System Moodle. The course is divided into 24 thematic chapters, each of them containing a short description, a list of references and selected publications, as well as other educational material (videos, virtual fieldtrips, etc.). In particular, several videos allow presenting in a dynamic way concepts and examples. The paper presents the tool and its use in academic programmes in six European universities, where it was tested, in various contexts (Bachelors' and Masters' programmes; students in geography or geology; general courses in geomorphology and specific courses on geoheritage and geoconservation), before discussing the advantages and challenges the tool is facing. The InterGEO platform is an easy-to-use and friendly educational tool, which allows developing blended learning activities; it is flexible and adaptable in various learning contexts.The coordination tasks (appointment of an assistant) and two workshops in Lausanne were financed by the University of Lausanne (Teaching Innovation Fund and Investment Fund of the Faculty of Geosciences and Environment, FGSE). The videos were designed and created with support of the universities of Lausanne (TIF) and Savoie Mont Blanc (IDEFI Promising and ReflexPro; LabEx ITEM)

Rhinitis in the geriatric population

The current geriatric population in the United States accounts for approximately 12% of the total population and is projected to reach nearly 20% (71.5 million people) by 2030[1]. With this expansion of the number of older adults, physicians will face the common complaint of rhinitis with increasing frequency. Nasal symptoms pose a significant burden on the health of older people and require attention to improve quality of life. Several mechanisms likely underlie the pathogenesis of rhinitis in these patients, including inflammatory conditions and the influence of aging on nasal physiology, with the potential for interaction between the two. Various treatments have been proposed to manage this condition; however, more work is needed to enhance our understanding of the pathophysiology of the various forms of geriatric rhinitis and to develop more effective therapies for this important patient population

Technology-enhanced learning in higher education : How to enhance student engagement through blended learning

Blended learning has risen in popularity in the last two decades as it has been shown to be an effective approach for accommodating an increasingly diverse student population in higher education and enriching the learning environment by incorporating online teaching resources. Blending significant elements of the learning environment such as face-to-face, online and self-paced learning leads to better student experiences and outcomes and more efficient teaching and course management practices if combined appropriately. Hence, an appropriate systematic and dynamic approach of blended learning design is crucial for a positive outcome, starting with planning for integrating blended elements into a course and creating blended activities and implementing them. Evaluating their effectiveness and knowing in which environments they work better and improving the blended activities designed from both the student’s and instructor’s perspective are critical for the next delivery of the course. This article aims to increase awareness of higher education educators about how traditional face-to-face learning can be transformed into blended courses so as to develop student engagement with both in-class and online approaches, whilst being time effective for the instructor

Structural Basis for Broad Neutralization of Hepatitis C Virus Quasispecies

Monoclonal antibodies directed against hepatitis C virus (HCV) E2 protein can neutralize cell-cultured HCV and pseudoparticles expressing envelopes derived from multiple HCV subtypes. For example, based on antibody blocking experiments and alanine scanning mutagenesis, it was proposed that the AR3B monoclonal antibody recognized a discontinuous conformational epitope comprised of amino acid residues 396–424, 436–447, and 523–540 of HCV E2 envelope protein. Intriguingly, one of these segments (436–447) overlapped with hypervariable region 3 (HVR3), a domain that exhibited significant intrahost and interhost genetic diversity. To reconcile these observations, amino-acid sequence variability was examined and homology-based structural modelling of E2 based on tick-borne encephalitis virus (TBEV) E protein was performed based on 413 HCV sequences derived from 18 subjects with chronic hepatitis C. Here we report that despite a high degree of amino-acid sequence variability, the three-dimensional structure of E2 is remarkably conserved, suggesting broad recognition of structural determinants rather than specific residues. Regions 396–424 and 523–540 were largely exposed and in close spatial proximity at the surface of E2. In contrast, region 436–447, which overlaps with HVR3, was >35 Å away, and estimates of buried surface were inconsistent with HVR3 being part of the AR3B binding interface. High-throughput structural analysis of HCV quasispecies could facilitate the development of novel vaccines that target conserved structural features of HCV envelope and elicit neutralizing antibody responses that are less vulnerable to viral escape