Statistics for the analysis of molecular dynamics simulations : providing P values for agonist-dependent GPCR activation

Molecular dynamics (MD) is the common computational technique for assessing efficacy of GPCR-bound ligands. Agonist efficacy measures the capability of the ligand-bound receptor of reaching the active state in comparison with the free receptor. In this respect, agonists, neutral antagonists and inverse agonists can be considered. A collection of MD simulations of both the ligand-bound and the free receptor are needed to provide reliable conclusions. Variability in the trajectories needs quantification and proper statistical tools for meaningful and non-subjective conclusions. Multiple-factor (time, ligand, lipid) ANOVA with repeated measurements on the time factor is proposed as a suitable statistical method for the analysis of agonist-dependent GPCR activation MD simulations. Inclusion of time factor in the ANOVA model is consistent with the time-dependent nature of MD. Ligand and lipid factors measure agonist and lipid influence on receptor activation. Previously reported MD simulations of adenosine A2a receptor (A2aR) are reanalyzed with this statistical method. TM6-TM3 and TM7-TM3 distances are selected as dependent variables in the ANOVA model. The ligand factor includes the presence or absence of adenosine whereas the lipid factor considers DOPC or DOPG lipids. Statistical analysis of MD simulations shows the efficacy of adenosine and the effect of the membrane lipid composition. Subsequent application of the statistical methodology to NECA A2aR agonist, with resulting P values in consistency with its pharmacological profile, suggests that the method is useful for ligand comparison and potentially for dynamic structure-based virtual screening

Quantifying conformational changes in GPCRs : glimpse of a common functional mechanism

Background: G-protein-coupled receptors (GPCRs) are important drug targets and a better understanding of their molecular mechanisms would be desirable. The crystallization rate of GPCRs has accelerated in recent years as techniques have become more sophisticated, particularly with respect to Class A GPCRs interacting with G-proteins. These developments have made it possible for a quantitative analysis of GPCR geometrical features and binding-site conformations, including a statistical comparison between Class A GPCRs in active (agonist-bound) and inactive (antagonist-bound) states. Results: Here we implement algorithms for the analysis of interhelical angles, distances, interactions and binding-site volumes in the transmembrane domains of 25 Class A GPCRs (7 active and 18 inactive). Two interhelical angles change in a statistically significant way between average inactive and active states: TM3-TM6 (by -9°) and TM6-TM7 (by +12°). A third interhelical angle: TM5-TM6 shows a trend, changing by -9°. In the transition from inactive to active states, average van der Waals interactions between TM3 and TM7 significantly increase as the average distance between them decreases by >2 Å. Average H-bonding between TM3 and TM6 decreases but is seemingly compensated by an increase in H-bonding between TM5 and TM6. In five Class A GPCRs, crystallized in both active and inactive states, increased H-bonding of agonists to TM6 and TM7, relative to antagonists, is observed. These protein-agonist interactions likely favour a change in the TM6-TM7 angle, which creates a narrowing in the binding pocket of activated receptors and an average ~200 Å3 reduction in volume. Conclusions: In terms of similar conformational changes and agonist binding pattern, Class A GPCRs appear to share a common mechanism of activation, which can be exploited in future drug development

Sex Cord-Gonadal Stromal Tumor of the Rete Testis

A 34-year-old tetraplegic patient with suppurative epididymitis was found on follow-up examination and ultrasonography to have a testicular mass. The radical orchiectomy specimen contained an undifferentiated spindled sex cord-stromal tumor arising in the rete testis. Testicular sex cord-stromal tumors are far less common than germ cell neoplasms and are usually benign. The close relationship between sex cords and ductules of the rete testis during development provides the opportunity for these uncommon tumors to arise anatomically within the rete tesis. This undifferentiated sex cord-stromal tumor, occurring in a previously unreported location, is an example of an unusual lesion mimicking an intratesticular malignant neoplasm

The Relationship Between Minority Business Enterprises and Corporate Purchasing Personnel: Perceptions from Both Sides of the Table

This paper addresses the nature of the difficulties MBEs face when conducting business with large companies through MBE purchasing programs. Data collected from MBEs and purchasing personnel were analyzed with logistic regression to demonstrate that MBEs and their corporate purchasing counterparts have different perceptions across human, environmental, and organizational dimensions of transaction cost economics. These differences help to explain the problems: (1) that MBEs have in selling to large companies and the problems that MBEs and purchasing personnel have in implementing MBE purchasing programs; (2) of reaching agreement in the marketplace; and, (3) of collectively pursuing the economic development of the minority business community. We offer recommendations for improving the relationship between these parties

Recapitulating Parkinson's disease pathology in a three-dimensional human neural cell culture model.

Extensive loss of dopaminergic neurons, and aggregation of the protein α-synuclein into ubiquitin-positive Lewy bodies represents a major neuropathological hallmark of Parkinson's disease. At present the generation of large nuclear-associated Lewy bodies from endogenous wild-type α-synuclein, translationally regulated under its own promoter in human cell culture models requires costly and time-consuming protocols. Here, we demonstrate that fully differentiated human SH-SY5Y neuroblastoma cells grown in three-dimensional cell culture develop Lewy body-like pathology upon exposure to exogenous α-synuclein species. In contrast to most cell- and rodent-based models that exhibit multiple diffuse α-synuclein aggregates throughout the cytoplasm, a single large nuclear inclusion immuno-positive for α-synuclein and ubiquitin is rapidly obtained in our model. This was achieved, without the need for over-expression of α-synuclein or genetic modification of the cell line. However, phosphorylation of α-synuclein within these inclusions was not observed. The system described here provides an ideal tool to screen compounds to therapeutically intervene in Lewy body formation and to investigate the mechanisms involved in disease progression in synucleinopathies

Descrit el possible mecanisme d'activació del receptor cannabinoide 1

Un estudi, publicat a la revista Journal of Medicinal Chemistry pels investigadors Óscar Díaz, James Dalton i Jesús Giraldo de l'Institut de Neurociències, descriu el possible mecanisme d'activació del receptor cannabinoide 1 (CB1). Aquest receptor és activat pel principal component psicoactiu del cànnabis; així doncs, conèixer i comprendre el seu mecanisme d'activació afavorirà el desenvolupament de fàrmacs que modulen el seu funcionament de manera més econòmica i eficient.Un estudio, publicado en la revista Journal of Medicinal Chemistry por los investigadores Óscar Díaz, James Dalton y Jesús Giraldo del Instituto de Neurociencias, describe el posible mecanismo de activación del receptor cannabinoide 1 (CB1). Este receptor es activado por el principal componente psicoactivo del cannabis; así pues, conocer y comprender su mecanismo de activación favorecerá el desarrollo de fármacos que modulen su funcionamiento, de manera más económica y eficiente.A study published in the Journal of Medicinal Chemistry by the Neuroscience Institute researchers Óscar Díaz, James Dalton and Jesús Giraldo, describes the potential activation mechanism of cannabinoid receptor 1 (CB1). This receptor is activated by the main psychoactive component of cannabis; thus, knowing and understanding its mechanism of activation will favor the development of drugs that modulate their functioning, in a more economic and efficacious way

Structural insights into positive and negative allosteric regulation of a G protein-coupled receptor through protein-lipid interactions

Lipids are becoming known as essential allosteric modulators of G protein-coupled receptor (GPCRs). However, how they exert their efects on GPCR conformation at the atomic level is still unclear. In light of recent experimental data, we have performed several long-timescale molecular dynamics (MD) simulations, totalling 24 μs, to rigorously map allosteric modulation and conformational changes in the β2 adrenergic receptor (β2AR) that occur as a result of interactions with three diferent phospholipids. In particular, we identify diferent sequential mechanisms behind receptor activation and deactivation, respectively, mediated by specifc lipid interactions with key receptor regions. We show that net negatively charged lipids stabilize an active-like state of β2AR that is able to dock Gsα protein. Clustering of anionic lipids around the receptor with local distortion of membrane thickness is also apparent. On the other hand, net-neutral zwitterionic lipids inactivate the receptor, generating either fully inactive or intermediate states, with kinetics depending on lipid headgroup charge distribution and hydrophobicity. These chemical diferences alter membrane thickness and density, which diferentially destabilize the β2AR active state through lateral compression efects

Tryptophan End-Tagging Confers Antifungal Activity on a Tick-Derived Peptide by Triggering Reactive Oxygen Species Production

WHO has identified several Candida species including Candida albicans as critical priority fungal pathogens due to greater infection prevalence and formation of recalcitrant biofilms. Novel antifungal agents are urgently needed, and antimicrobial peptides (AMPs) are being considered as potential alternatives, but inactivity in physiological salt environments, serum, and plasma often limits further therapeutic development. Tryptophan end-tagging is a strategy to overcome these limitations and is thought to selectively enhance membrane permeabilization in both fungal and bacterial plasma membranes. Here, we show that C-terminal tryptophan end-tagging of the tick-derived peptide Os-C transforms an inactive peptide into Os-C(W5), an antifungal peptide capable of preventing the formation of C. albicans biofilms. Mechanistic insight is provided by circular dichroism spectroscopy and molecular dynamics simulations, which demonstrate that tryptophan end-tagging alters the secondary structure of Os-C, while the latter reveals that end-tagging reduces interactions with, and insertion into, a model C. albicans membrane but promotes peptide aggregation on its surface. Interestingly, this leads to the induction of reactive oxygen species production rather than membrane permeabilization, and consequently, oxidative stress leads to cell wall damage. Os-C(W5) does not induce the hemolysis of human erythrocytes. Reduced cell adhesion and viability contribute to decreased biofilm extracellular matrix formation which, although reduced, is retained in the serum-containing medium. In this study, tryptophan end-tagging was identified as a promising strategy for enhancing the antifungal activity, including the biofilm inhibitory activity of Os-C against C. albicans in physiological salt environments.</p

Research Progress Reports, 1962. Fruit and Vegetable Processing and Technology Division, Department of Horticulture.

Tomato variety evaluation for processing, 1962 / W. A. Gould, J. R. Geisman and Wade Schulte -- Evaluation of snap bean varieties for processing, 1962 / Wilbur A. Gould -- Handling and holding studies of mechanically harvested tomatoes. 1. Processed product quality / W. A. Gould, W. D. Bash, J. R. Geisman, D. E. Yingst, G. A. Marlowe and W. N. Brown -- Handling and holding studies of mechanically harvested tomatoes. 2. Spore counts / Winston D. Bash and W. A. Gould -- Handling and holding studies of mechanically harvested tomatoes. 3. pH / Winston D. Bash and W. A. Gould -- Handling and holding studies of mechanically harvested tomatoes. 4. Chlorine residuals / Donald E. Yingst and W. A. Gould -- Removal of insects and residues from sweet corn by washing techniques / J. R. Geisman and W. A. Gould -- Removal of pesticides and radioactive fallout from fruits and vegetables / J. R. Geisman, R. P. Blackmore, R. W. Hirzel and W. S. Stinson -- The effect of apple variety and browning prevention treatments during preparation on the quality of frozen apple pies / D. Robert Davis and James F. Gallander -- Effect of three tomato peeling methods on efficiency and product quality / Wade A. Schulte and W. A. Gould -- Effects of cooling rates on vacuum of canned pumpkin / Winston D. Bash -- New flavors for sauerkraut / J. R. Geisman and Robert Reyda -- Flavor of tomato juice / Wilbur A. Gould, Natholyn Dalton and John Hal Johnson -- Fruit juice blends offer a promising new field for apple cider / D. Robert Davi

Evaluation Research and Institutional Pressures: Challenges in Public-Nonprofit Contracting

This article examines the connection between program evaluation research and decision-making by public managers. Drawing on neo-institutional theory, a framework is presented for diagnosing the pressures and conditions that lead alternatively toward or away the rational use of evaluation research. Three cases of public-nonprofit contracting for the delivery of major programs are presented to clarify the way coercive, mimetic, and normative pressures interfere with a sound connection being made between research and implementation. The article concludes by considering how public managers can respond to the isomorphic pressures in their environment that make it hard to act on data relating to program performance.This publication is Hauser Center Working Paper No. 23. The Hauser Center Working Paper Series was launched during the summer of 2000. The Series enables the Hauser Center to share with a broad audience important works-in-progress written by Hauser Center scholars and researchers