Browsing by Author "Schüller, Andreas"
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- ItemAndrographolide activates the canonical Wnt signalling pathway by a mechanism that implicates the non-ATP competitive inhibition of GSK-3 beta: autoregulation of GSK-3 beta in vivo(2015) Tapia Rojas, C.; Schüller, Andreas; Lindsay, C. B.; Ureta, R. C.; Mejias Reyes, C.; Hancke, J.; Melo Ledermann, Francisco Javier; Inestrosa Cantín, NibaldoWnt/β-catenin signalling is an important pathway that regulates multiple biological processes, including cell adhesion and determination of cell fate during animal development; in the adult nervous system it regulates the structure and function of synapses. Wnt-signalling dysfunction is associated with several neurodegenerative diseases such as schizophrenia and Alzheimer's disease. The use of natural compounds is an interesting strategy in the search for drugs with the therapeutic potential to activate this signalling pathway. In the present study, we report that andrographolide (ANDRO), a component of Andrographis paniculata, is a potent activator of Wnt signalling. Our results indicate that ANDRO activates this pathway, inducing the transcription of Wnt target genes by a mechanism that bypasses Wnt ligand binding to its receptor. In vitro kinase assays demonstrate that ANDRO inhibits glycogen synthase kinase (GSK)-3β by a non-ATP-competitive, substrate-competitive mode of action. In silico analyses suggest that ANDRO interacts with the substrate-binding site of GSK-3β. Finally, we demonstrated that the increase seen in the levels of GSK-3β phosphorylated at Ser9 is the result of an autoregulatory mechanism of the kinase in vivo, although not through activation of protein phosphatase type 1. Our results suggest that ANDRO could be used as a potential therapeutic drug for disorders caused by Wnt-signalling dysfunction such as neurodegenerative diseases.
- ItemCalculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions(2019) Ribeiro, J.; Ríos Vera, C.; Melo Ledermann, Francisco Javier; Schüller, AndreasSummary Intra- and intermolecular contact surfaces are routinely calculated for a large array of applications in bioinformatics but are typically approximated from differential solvent accessible surface area calculations and not calculated directly. These approximations do not properly take the effects of neighboring atoms into account and tend to deviate considerably from the true contact surface. We implemented an extension of the original Shrake-Rupley algorithm to accurately estimate interatomic contact surface areas of molecular structures and complexes. Our extended algorithm is able to calculate the contact area of an atom to all nearby atoms by directly calculating overlapping surface patches, taking into account the possible shielding effects of neighboring atoms. Here, we present a versatile software tool and web server for the calculation of contact surface areas, as well as buried surface areas and solvent accessible surface areas (SASA) for different types of biomolecules, such as proteins, nucleic acids and small organic molecules. Detailed results are provided in tab-separated values format for analysis and Protein Databank files for visualization. Direct contact surface area calculation resulted in improved accuracy in a benchmark with a non-redundant set of 245 protein–DNA complexes. SASA-based approximations underestimated protein–DNA contact surfaces on average by 40%. This software tool may be useful for surface-based intra- and intermolecular interaction analyses and scoring function development. Availability and implementation A web server, stand-alone binaries for Linux, MacOS and Windows and C++ source code are freely available from http://schuellerlab.org/dr_sasa/. Supplementary information Supplementary data are available at Bioinformatics online.
- ItemComputer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function(2012) Schüller, Andreas; Slater, A. W.; Norambuena, T.; Cifuentes, J. J.; Almonacid, L. I.; Melo Ledermann, Francisco JavierCurrently, about 20 crystal structures per day are released and deposited in the Protein Data Bank. A significant fraction of these structures is produced by research groups associated with the structural genomics consortium. The biological function of many of these proteins is generally unknown or not validated by experiment. Therefore, a growing need for functional prediction of protein structures has emerged. Here we present an integrated bioinformatics method that combines sequence-based relationships and three-dimensional (3D) structural similarity of transcriptional regulators with computer prediction of their cognate DNA binding sequences. We applied this method to the AraC/XylS family of transcription factors, which is a large family of transcriptional regulators found in many bacteria controlling the expression of genes involved in diverse biological functions. Three putative new members of this family with known 3D structure but unknown function were identified for which a probable functional classification is provided. Our bioinformatics analyses suggest that they could be involved in plant cell wall degradation (Lin2118 protein from Listeria innocua, PDB code 3oou), symbiotic nitrogen fixation (protein from Chromobacterium violaceum, PDB code 3oio), and either metabolism of plant-derived biomass or nitrogen fixation (protein from Rhodopseudomonas palustris, PDB code 3mn2).
- ItemExploring DNA dynamics within oligonucleosomes with coarse-grained simulations : SIRAH force field extension for protein-DNA complexes(2018) Brandner, Astrid; Schüller, Andreas; Melo Ledermann, Francisco Javier; Pantano, Sergio
- ItemIngeniería racional de la enzima resveratrol O-metiltransferasa para la síntesis biológica de pinoestilbeno(2022) Herrera Toro, Daniela Paula; Parra, Loreto; Schüller, Andreas; Pontificia Universidad Católica de Chile. Escuela de IngenieríaLos estilbenos son compuestos fenólicos derivados del metabolismo secundario de las plantas y cumplen un rol fundamental en su respuesta defensiva. El resveratrol es uno de los estilbenos más estudiados debido a sus propiedades benéficas para la salud humana. Sin embargo, al ser consumido, es metabolizado rápidamente mostrando una baja biodisponibilidad. Se ha reportado que derivados metilados de resveratrol, tienen una mayor estabilidad y biodisponibilidad, y por tanto un mayor valor agregado y atractivo industrial. El avance en la biocatálisis y la ingeniería metabólica ha permitido que la biosíntesis de resveratrol y derivados, mediante microorganismos optimizados, sea una alternativa sustentable a la síntesis química y a su extracción desde fuentes naturales. Existen escasos estudios que aborden la biosíntesis de pinoestilbeno, resveratrol mono-metilado, de elevado valor comercial. Principalmente porque las enzimas caracterizadas con actividad Ometiltransferasa (OMT), presentan una baja eficiencia en catalizar la mono-metilación de resveratrol, favoreciendo la di-metilación de este compuesto en una reacción secuencial de dos pasos, obteniendo pteroestilbeno como principal producto. Para generar una ruta alternativa de biosíntesis de pinoestilbeno, en esta investigación aplicamos una estrategia de ingeniería racional de proteínas en la enzima resveratrol OMT de Vitis vinifera (VvROMT), la que presenta la mayor eficiencia catalítica descrita en di-metilar resveratrol y obtener pteroestilbeno. En ausencia de la estructura cristalográfica de VvROMT, construimos un modelo tridimensional por homología en una conformación cerrada y catalíticamente competente, en complejo con resveratrol y S-adenosil-metionina. Caracterizamos el sitio de unión a sustrato de VvROMT a través de diferentes herramientas in silico, lo que nos permitió identificar cuatro residuos críticos. Construimos las variantes W20A, F24A, F311A, y F318A mediante mutagénesis sitio dirigida y observamos una disminución considerable de su actividad enzimática a partir de resveratrol, validando nuestro modelo estructural. Luego, mediante un diseño racional, aplicando una estrategia basada en estructura y un análisis comparativo de los residuos del sitio activo entre VvROMT y otras estilbeno OMTs, generamos ocho variantes. La variante F311W/L117F generó hasta un 67% de conversión a pinoestilbeno después de 24 h de reacción mientras que con la enzima nativa no se detectó pinoestilbeno y se obtuvo un 44,2% de conversión a pteroestilbeno. Por otro lado, la variante L117F presentó una mejora global en su actividad específica. Logramos modificar exitosamente la preferencia de sustrato de VvROMT, pasando desde una di-metilación secuencial a mono-metilar resveratrol y obtener pinoestilbeno como principal producto. Estas variantes pueden ser incluidas en rutas sintéticas existentes para la biosíntesis sustentable de pinoestilbeno en sistemas recombinantes. Nuestros resultados sugieren que el sitio activo de VvROMT puede ser ingenierizado para diversificar la producción de estilbenos y otros compuestos fenólicos industrialmente competitivos y beneficiosos para la salud y nutrición humana.
- ItemPDIviz: analysis and visualization of protein-DNA binding interfaces(2015) Ribeiro J.; Melo Ledermann, Francisco Javier; Schüller, AndreasSummary: Specific recognition of DNA by proteins is a crucial step of many biological processes. PDIviz is a plugin for the PyMOL molecular visualization system that analyzes protein–DNA binding interfaces by comparing the solvent accessible surface area of the complex against the free protein and free DNA. The plugin provides three distinct three-dimensional visualization modes to highlight interactions with DNA bases and backbone, major and minor groove, and with atoms of different pharmacophoric type (hydrogen bond donors/acceptors, hydrophobic and thymine methyl). Each mode comes in three styles to focus the visual analysis on the protein or DNA side of the interface, or on the nucleotide sequence. PDIviz allows for the generation of publication quality images, all calculated data can be written to disk, and a command line interface is provided for automating tasks. The plugin may be helpful for the detailed identification of regions involved in DNA base and shape readout, and can be particularly useful in rapidly pinpointing the overall mode of interaction. Availability and implementation: Freely available at http://melolab.org/pdiviz/ as a PyMOL plugin. Tested with incentive, educational, and open source versions of PyMOL on Windows, Mac and Linux systems.
- ItemTripeptide inhibitors of dengue and West Nile virus NS2B-NS3 protease(2011) Schüller, Andreas; Yin, Z.; Chia, C. S. B.; Doan, D. N. P.; Kim, H.; Shang, L.; Loh, T. P.; Hill, J.; Vasudevan, S. G.A series of tripeptide aldehyde inhibitors were synthesized and their inhibitory effect against dengue virus type 2 (DENV2) and West Nile virus (WNV) NS3 protease was evaluated side by side with the aim to discover potent flaviviral protease inhibitors and to examine differences in specificity of the two proteases. The synthesized inhibitors feature a varied N-terminal cap group and side chain modifications of a P2-lysine residue. In general a much stronger inhibitory effect of the tripeptide inhibitors was observed toward WNV protease. The inhibitory concentrations against DENV2 protease were in the micromolar range while they were submicromolar against WNV. The data suggest that a P2-arginine shifts the specificity toward DENV2 protease while WNV protease favors a lysine in the P2 position. Peptides with an extended P2-lysine failed to inhibit DENV2 protease suggesting a size-constrained S2 pocket. Our results generally encourage the investigation of di- and tripeptide aldehydes as inhibitors of DENV and WNV protease.