VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity

Many algorithms that compare protein structures can reveal similarities that suggest related biological functions, even at great evolutionary distances. Proteins with related function often exhibit differences in binding specificity, but few algorithms identify structural variations that effect specificity. To address this problem, we describe the Volumetric Analysis of Surface Properties (VASP), a novel volumetric analysis tool for the comparison of binding sites in aligned protein structures. VASP uses solid volumes to represent protein shape and the shape of surface cavities, clefts and tunnels that are defined with other methods. Our approach, inspired by techniques from constructive solid geometry, enables the isolation of volumetrically conserved and variable regions within three dimensionally superposed volumes. We applied VASP to compute a comparative volumetric analysis of the ligand binding sites formed by members of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains and the serine proteases. Within both families, VASP isolated individual amino acids that create structural differences between ligand binding cavities that are known to influence differences in binding specificity. Also, VASP isolated cavity subregions that differ between ligand binding cavities which are essential for differences in binding specificity. As such, VASP should prove a valuable tool in the study of protein-ligand binding specificity

Cardiopoietic cell therapy for advanced ischemic heart failure: results at 39 weeks of the prospective, randomized, double blind, sham-controlled CHART-1 clinical trial

Cardiopoietic cells, produced through cardiogenic conditioning of patients' mesenchymal stem cells, have shown preliminary efficacy. The Congestive Heart Failure Cardiopoietic Regenerative Therapy (CHART-1) trial aimed to validate cardiopoiesis-based biotherapy in a larger heart failure cohort

Toxic effects of two pesticides, Imazalil and Triadimefon, on the early development of the ascidian Phallusia mamillata (Chordata, Ascidiacea)

Azole compds. are fungicides used in agriculture and in the clin. area and are suspected to produce craniofacial malformations in vertebrates. Toxicity tests on sperm viability, fertilization, and embryogenesis of the solitary ascidian P. mamillata were performed to evaluate the effects of 2 azole derivs., Imazalil and Triadimefon. Ascidian (Chordata, Ascidiacea) embryos and larvae could provide biol. criteria for seawater quality stds. because the larvae are lecitotrophic and have a short pelagic period, allowing to run the larval toxicity tests over a short period of time. Imazalil and Triadimefon proved to have strong consequences on P. mamillata. They could influence the reproductive rate of the animal exerting their effects at different levels: acting as spermiotoxic agents, inhibiting fertilization, and impairing embryol. development. The fertilization rate significantly decreased after 30-min exposure of sperm to 25 mM Imazalil (P < 0.0001) and after exposure of both gametes to 50 mM Imazalil (P < 0.05) and 1 mM Triadimefon (P < 0.0001) as compared to controls. Malformations caused by exposure of embryos to both substances were dose-dependent. Imazalil median teratogenic concn. (TC50 concn., the concn. that resulted in 50% malformed larvae) value was 0.67 mM and median lethal concn. (LC50, the concn. that resulted in 50% embryos dead before completing the development) value was 10.23 mM while for Triadimefon TC50 value was 29.56 and LC50 value was 173.7 mM. Larvae developed from embryos treated with Imazalil and Triadimefon showed alterations of the anterior structures of the trunk: papillary nerves and the anterior central nervous system failed to correctly differentiate, as shown by immunostaining with anti-b-tubulin antibody. Comparing the anomalies caused by retinoic acid, reported in a previous study, it was possible to hypothesize that malformations induced by Imazalil and Triadimefon could be due to a perturbation of the endogenous retinoid content, as it has been proposed for mammals. Ascidians proved to be good models to study the toxic effects of pesticides since they offered both the convenience of working with an invertebrate species and the tissue sensitivity to chem. compd. comparable to vertebrates. [on SciFinder (R)

Toxic effects of two pesticides, Imazalil and Triadimefon, on the early development of the ascidian Phallusia mamillata (Chordata, Ascidiacea)

Azole compds. are fungicides used in agriculture and in the clin. area and are suspected to produce craniofacial malformations in vertebrates. Toxicity tests on sperm viability, fertilization, and embryogenesis of the solitary ascidian P. mamillata were performed to evaluate the effects of 2 azole derivs., Imazalil and Triadimefon. Ascidian (Chordata, Ascidiacea) embryos and larvae could provide biol. criteria for seawater quality stds. because the larvae are lecitotrophic and have a short pelagic period, allowing to run the larval toxicity tests over a short period of time. Imazalil and Triadimefon proved to have strong consequences on P. mamillata. They could influence the reproductive rate of the animal exerting their effects at different levels: acting as spermiotoxic agents, inhibiting fertilization, and impairing embryol. development. The fertilization rate significantly decreased after 30-min exposure of sperm to 25 mM Imazalil (P < 0.0001) and after exposure of both gametes to 50 mM Imazalil (P < 0.05) and 1 mM Triadimefon (P < 0.0001) as compared to controls. Malformations caused by exposure of embryos to both substances were dose-dependent. Imazalil median teratogenic concn. (TC50 concn., the concn. that resulted in 50% malformed larvae) value was 0.67 mM and median lethal concn. (LC50, the concn. that resulted in 50% embryos dead before completing the development) value was 10.23 mM while for Triadimefon TC50 value was 29.56 and LC50 value was 173.7 mM. Larvae developed from embryos treated with Imazalil and Triadimefon showed alterations of the anterior structures of the trunk: papillary nerves and the anterior central nervous system failed to correctly differentiate, as shown by immunostaining with anti-b-tubulin antibody. Comparing the anomalies caused by retinoic acid, reported in a previous study, it was possible to hypothesize that malformations induced by Imazalil and Triadimefon could be due to a perturbation of the endogenous retinoid content, as it has been proposed for mammals. Ascidians proved to be good models to study the toxic effects of pesticides since they offered both the convenience of working with an invertebrate species and the tissue sensitivity to chem. compd. comparable to vertebrates. [on SciFinder (R)

Fluconazole induces teratogenic effects in the tunicate Phallusia mammillata

Fluconazole (FLUCO) is an azole derivative used to treat fungal and yeast infections. Embryotoxicity tests on the ascidian Phallusia mammillata were performed to evaluate the effects of this drug. FLUCO proved to have strong consequences on P. mammillata development. Incidence of malformations and of lethality increased in a dose dependent way. Probit analysis showed that FLUCO had a high TI value (Teratogenic Index, LC50/TC50), thus this substance could be classified as a teratogenic compound for ascidians. Larvae exposed to FLUCO showed a typical phenotype characterized by malformations restricted to the trunk region: the trunk appeared round in shape with flat palps, the sensory vesicle cavity was absent or reduced and the anterior central nervous system failed to correctly differentiate. These anomalies resulted similar to those induced by retinoic acid (RA) treatment. Thus, it could be hypothesized that FLUCO and RA may act with a similar pathogenic mechanism in ascidian larvae, as it has been proposed for mammals

Serotonin in the morphogenesis of ascidian nervous system

The monoamine serotonin (5-HT) exerts key neuromodulatory activities in all animal phyla and it is supposed to play a morphogenetic role during the development. Nevertheless this aspect of serotonin activity is still poorly understood. By immunofluorescence and confocal laser scanning microscopy we studied the serotonergic nervous system of ascidian larvae belonging to the three orders of Aplousobranchia, Phlebobranchia and Stolidobranchia. A basic homology of the serotonergic nervous system was observed in all the species studied as most serotonergic components of nervous system are localized in the brain. However a lot of differences are shown from the fine cellular localization. Our results revealed that divergent developmental strategies exist during terminal differentiation, probably following different adaptation constraint