Molecular basis of membrane stability and dynamics

Dit proefschrift is onderverdeeld in vier verschillende delen, die overeenkomen met de vier verschillende onderwerpen die ik heb gewerkt . In hoofdstukken 2-4, bestudeerden we het werkingsmechanisme van antimicrobiële peptiden. We concentreerden ons op twee korte peptiden, de cyclische BPC194 en zijn lineaire analoge BPC193. Hoewel beide bezitten dezelfde aminozuursequentie, maar het cyclische peptide kan microbiële cellen te doden. Met behulp van een combinatie van fluorescentie-gebaseerde technieken met moleculaire dynamica simulaties, kwamen we erachter dat het cyclisch peptide plooien in de juiste conformatie op membraanbindende, inserts diep, vormt poriën en fuseren de membranen . In hoofdstuk 5, wij ontwerpen en gesynthetiseerd een DNA - peptide hybride te moduleren de oligomerisatie van een membraan kanaal met behulp van complementaire DNA-strengen of een G-quadruplex motief. In beide gevallen heeft de daaruit zender heeft voorkeur voor een specifieke oligomere toestand van een vaste grootte . In hoofdstuk 6 hebben we de effecten van koolhydraten op het membraan organisatie. We combineerden fluorescentie microscopie met moleculaire dynamische simulaties en ontdekte dat alleen de niet-reducerende koolhydraten, sucrose en trehalose, hebben een effect op de lipid raft organisatie. Die twee disachariden worden meestal gesynthetiseerd door verschillende organismen, om te overleven in extreme uitdroging omstandigheden. In hoofdstuk 7 bestudeerden we de lokalisatie, oligomerisatie en dynamiek van verschillende plasmamembraan aminozuur transporters van S. cerevisiae. De verdeling van deze eiwitten in het membraan niet homogeen. We kwamen erachter dat de reden dat de extreem trage verspreiding die we gemeten voor die eiwitten samen met hun lage bedragen zou kunnen zijn

Structural basis for the enhanced activity of cyclic antimicrobial peptides:The case of BPC194

AbstractWe report the molecular basis for the differences in activity of cyclic and linear antimicrobial peptides. We iteratively performed atomistic molecular dynamics simulations and biophysical measurements to probe the interaction of a cyclic antimicrobial peptide and its inactive linear analogue with model membranes. We establish that, relative to the linear peptide, the cyclic one binds stronger to negatively charged membranes. We show that only the cyclic peptide folds at the membrane interface and adopts a β-sheet structure characterised by two turns. Subsequently, the cyclic peptide penetrates deeper into the bilayer while the linear peptide remains essentially at the surface. Finally, based on our comparative study, we propose a model characterising the mode of action of cyclic antimicrobial peptides. The results provide a chemical rationale for enhanced activity in certain cyclic antimicrobial peptides and can be used as a guideline for design of novel antimicrobial peptides

Composition dependence of lithium diffusion in lithium silicide: a density functional theory study

The lithiation process of silicon was investigated by using ab initio molecular dynamics. Diffusion coefficients of Li in Li–Si alloys were calculated to be in the range between 2.08×10−9 and 3.53×10−7 cm2 s−1 at room temperature. The results showed that the Li mobility is strongly dependent on the composition of the LixSi alloys. The Li diffusivity in a LixSi alloy can be enhanced by two orders of magnitude when x is increased from 1.0 to 3.75, which can be explained by the instability of the Si network, owing to charge transfer from Li to Si

Anàlisi i creació d'un sistema híbrid recomanador de vins per al sector vitivinícola

El sector del vino, uno de los más antiguos y tradicionales del mundo, está lentamente modernizándose. Debido a esto, hay muchas oportunidades para implementar conceptos que ya han sido demostrados que funcionan en otros campos como por ejemplo los sistemas recomendadores. Durante las últimas dos décadas se han hecho grandes avances tanto en eficiencia como en precisión y gracias a esto, estos sistemas se encuentran integrados en la mayoría de proveedores de entretenimiento, información y productos del mundo como YouTube, Amazon, Netflix e incluso foros como Quora. Este proyecto de final de carrera está hecho en HappyCustomerBox, con colaboración de Upwine, un software de catas online. El objetivo principal es la creación de un sistema recomendador que mejore la calidad de los vinos que reciben los usuarios y aumente las ventas de vinos por parte de las bodegas.The wine industry, one of the world's oldest and most traditional is slowly modernizing. There are many opportunities to implement concepts such as recommender systems that have been proven to work in other fields. During the last two decades, many improvements have been made in both precision and efficiency of such systems, this fact has prompted them to be integrated in many providers of entertainment, information and even products worldwide. Some examples of them are YouTube, Amazon, Netflix and even internet forums such as Quora. This bachelor thesis is developed in HappyCustomerBox, in collaboration with Upwine, an online tasting software. The project's main objective is the creation of a recommender system with the goal of improving the quality of users' purchases and to increase the amount of wine sold by cellars

Vascular endothelial growth factor and placenta growth factor concentrations in Down's syndrome and control pregnancies.

Vascular endothelial growth factor (VEGF) and placenta growth factor (PLGF) are considered to play important roles in angiogenesis and vascular permeability during placental development. Since trisomy 21 placentae show trophoblastic hypoplasia and hypovascularity, we investigated PLGF and VEGF synthesis in Down's syndrome pregnancies. Maternal serum was collected from 102 euploid and 24 trisomy 21 pregnancies between 15 and 20 weeks gestation and tested for these two factors by enzyme-linked immunosorbent assays. Protein extracts from 15 normal and six trisomy 21 placentae were also tested. VEGF was not detected in maternal serum, while PLGF increased significantly with gestational age. Serum PLGF, transformed as a multiple of the gestational age median (MoM), in Down's syndrome pregnancies was significantly lower than in euploid controls (mean 0.67 +/- 0.043 MoM versus 1.00 +/- 0.047 MoM, analysis of variance F = 11.605, P < 0.001 ). Both VEGF and PLGF were detected in placental protein extracts without variation according to gestational age. Down's syndrome placentae had significantly less PLGF compared to normal placentae (Mann-Whitney, P < 0.05 ) but no difference was observed in placental VEGF content (Mann-Whitney, P = 0.94 ). Considering the biological properties of PLGF, this decrease may provide new insights into the mechanism(s) leading to the structural and functional anomalies described in trisomy 21 placentae

Single liposome analysis of peptide translocation by the ABC transporter TAPL

ATP-binding cassette (ABC) transporters use ATP to drive solute transport across biological membranes. Members of this superfamily have crucial roles in cell physiology, and some of the transporters are linked to severe diseases. However, understanding of the transport mechanism, especially of human ABC exporters, is scarce. We reconstituted the human lysosomal polypeptide ABC transporter TAPL, expressed in Pichia pastoris, into lipid vesicles (liposomes) and performed explicit transport measurements. We analyzed solute transport at the single liposome level by monitoring the coincident fluorescence of solutes and proteoliposomes in the focal volume of a confocal microscope. We determined a turnover number of eight peptides per minute, which is two orders of magnitude higher than previously estimated from macroscopic measurements. Moreover, we show that TAPL translocates peptides against a large concentration gradient. Maximal filling is not limited by an electrochemical gradient but by trans-inhibition. Countertransport and reversibility studies demonstrate that peptide translocation is a strictly unidirectional process. Altogether, these data are included in a refined model of solute transport by ABC exporters