AMH-RII : visió molecular de problemes hormonals en la diferenciació sexual

En l'esser humà, la sisena setmana del desenvolupament embrionari marca l'inici de la diferenciació dels conductes genitals. A l'embrió mascle, es genera una hormona que produeix la degeneració dels conductes de Müller (l'hormona anti-mülleriana AMH), sense l'acció repressora de la qual, aquests conductes portarien a la generació de les trompes i la matriu. Una part important de la repressió d'aquesta hormona es basa en processos de fixació a les membranes cel·lulars, gràcies a un receptor específic (l'AMH-RII). Qualsevol error en aquests processos que involucren tant a l'hormona com al seu receptor, pot donar lloc a un singular fenomen d'hermafroditisme. Un equip d'investigadors de la UAB ha pogut elaborar una modelització tridimensional del receptor de l'hormona, que facilita l'estudi de les diferents mutacions que pot patir i, per tant, la comprensió d'aquesta estranya malaltia genètica.En el ser humano, la sexta semana del desarrollo embrionario marca el inicio de la diferenciación de los conductos genitales. En el embrión masculino, se genera una hormona que produce la degeneració de los conductos de Müller (la hormona anti-mülleriana AMH), sin la acción represora de la cual, estos conductos llevarían a la generación de las trompes y la matriz. Una parte importante de la represión de esta hormona se basa en procesos de fijación en las membranas celulares, gracias a un receptor específico (el AMH-RII). Cualquier error en estos procesos que involucran tanto a la hormona como a su receptor, puede dar lugar a un singular fenómeno de hermafroditismo. Un equipo de investigadores de la UAB ha podido elaborar una modelización tridimensional del receptor de la hormona que facilitará el estudio de las diferentes mutaciones que puede sufrir y, por lo tanto, la comprensión de esta extraña enfermedad genética

Determinació teòrica de constants de velocitat : el radical hidroxil com a iniciador de processos d'oxidació atmosfèrica /

Consultable des del TDXTítol obtingut de la portada digitalitzadaAquest és un treball de Química Teòrica aplicada a l'estudi de la Química Atmosfèrica, en particular, de quatre reaccions que transcorren principalment a la troposfera terrestre. La troposfera actua com a depuradora de l'atmosfera: en ella es degraden la majoria de substàncies emeses a l'atmosfera, i el principal agent oxidant que fa de depurador és el radical hidroxil. En aquesta tesi es calculen les constants de velocitat i es determinen els mecanismes de les següents reaccions del radical hidroxil (algunes també amb substitució isotòpica): OH + H2O à H2O + OH (R1), OH + CH4 à H2O + CH3 (R2), OH + CH3COCH3 à P (R3) y OH + CH3SH à P (R4). La metodologia emprada per calcular les constants de velocitat ha estat la Teoria Variacional de l'Estat de Transició (VTST) amb correcció multidimensional per a l'efecte túnel (MT) en els casos en què s'ha considerat necessari. La informació de la superfície d'energia potencial necessària per als càlculs s'ha obtingut amb mètodes ab initio de la Mecànica Quàntica. Alguna d'aquestes reaccions presenten mecanismes competitius i/o varis màxims d'energia lliure al llarg del camí de reacció. Per a aquests casos s'ha aplicat el Model Estadístic Unificat. L'estudi de les reaccions R i R2, a part del seu interès químic, s'ha utilitzat per analitzar alguns aspectes que cal tenir en compte en el càlcul de les constants de velocitat: el nivell de càlcul electrònic, l'efecte de la formació de complexos al llarg del camí de reacció,...Amb l'estudi aquests estudis s'han marcat unes pautes (un protocol) que ha servit per a l'estudi de R3 i R4. Aquestes dues últimes reaccions tenen mecanismes més complexos, que encara no estaven ben establerts, i els resultats d'aquesta tesi proporcionen informació que permet entendre millor aquests processos.This is a work of Theoretical Chemistry applied to Atmospheric Chemistry. Four tropospheric reactions have been studied. In the troposphere, the hidroxil radical initiates the degradation of most of the species emitted to the atmosphere, thus, it cleans our atmosphere. The rate constants and the reaction mechanisms of the following reactions have been established (some of them also with isotopic substitution): OH + H2O à H2O + OH (R1), OH + CH4 à H2O + CH3 (R2), OH + CH3COCH3 à P (R3) y OH + CH3SH à P (R4). The rate constant calculations have been carried out by means of Variational Transition State Theory (VTST) plus multidimensional tunneling (MT) corrections when necessary. The information required from the potential energy surface has been obtained by ab initio Quantum Mechanics calculations. Some of these reactions present competitive channels, and/or several dynamical bottlenecks along the reaction path. In this situation, the Canonical Unified Statistical Model has been applied. With the work carried out on reactions R1 and R2, apart from the chemical results, we have analyzed several aspects that affect the calculation of the rate constants: electronic structure level of calculation, the effect of the existence of these complexes along the reaction path, … This information has been used to establish a protocol, which has been used to study reactions R3 and R4. These last two reactions have competitive channels and the reaction mechanisms were not well understood. The results from this thesis bring new information about these two reactions and allow a better knowing of this processes

Getting Deeper into the Molecular Events of Heme Binding Mechanisms : A Comparative Multi-level Computational Study of HasAsm and HasAyp Hemophores

Altres ajuts: acord transformatiu CRUE-CSICMany biological systems obtain their activity by the inclusion of metalloporphyrins into one or several binding pockets. However, decoding the molecular mechanism under which these compounds bind to their receptors is something that has not been widely explored and is a field with open questions. In the present work, we apply computational techniques to unravel and compare the mechanisms of two heme-binding systems, concretely the HasA hemophores from Gram negative bacteria Serratia marcescens (HasAsm) and Yersinia pestis (HasAyp). Despite the high sequence identity between both systems, the comparison between the X-ray structures of their apo and holo forms suggests different heme-binding mechanisms. HasAyp has extremely similar structures for heme-free and heme-bound forms, while HasAsm presents a very large displacement of a loop that ultimately leads to an additional coordination to the metal with respect to HasAyp. We combined Gaussian accelerated molecular dynamics simulations (GaMDs) in explicit solvent and protein-ligand docking optimized for metalloligands. GaMDs were first carried out on heme-free forms of both hemophores. Then, protein-ligand dockings of the heme were performed on cluster representatives of these simulations and the best poses were then subjected to a new series of GaMDs. A series of analyses reveal the following: (1) HasAyp has a conformational landscape extremely similar between heme-bound and unbound states with no to limited impact on the binding of the cofactor, (2) HasAsm presents as a slightly broader conformational landscape in its apo state but can only visit conformations similar to the X-ray of the holo form when the heme has been bound. Such behavior results from a complex cascade of changes in interactions that spread from the heme-binding pocket to the flexible loop previously mentioned. This study sheds light on the diversity of molecular mechanisms of heme-binding and discusses the weight between the pre-organization of the receptor as well as the induced motions resulting in association. Heme-containing enzymes and proteins are important for many biological and biotechnological processes. However, very little is known about heme-binding mechanisms. To shed light on this, we report a multi-level approach combining Gaussian accelerated molecular dynamics and protein−ligand dockings optimized for metallic moieties. The protocol unveils the difference in heme recruitment between HasAsm and HasAyp hemophores and shows its possible applicability to other heme-binding proteins

Comparing hydrolysis and transglycosylation reactions catalyzed by Thermus thermophilus β-glycosidase. A combined MD and QM/MM study

The synthesis of oligosaccharides and other carbohydrate derivatives is of relevance for the advancement of glycosciences both at the fundamental and applied level. For many years, glycosyl hydrolases (GHs) have been explored to catalyze the synthesis of glycosidic bonds. In particular, retaining GHs can catalyze a transglycosylation (T) reaction that competes with hydrolysis (H). This has been done either employing controlled conditions in wild type GHs or by engineering new mutants. The goal, which is to increase the T/H ratio, has been achieved with moderate success in several cases despite the fact that the molecular basis for T/H modulation are unclear. Here we have used QM(DFT)/MM calculations to compare the glycosylation, hydrolysis and transglycosylation steps catalyzed by wild type Thermus thermophilus β-glycosidase (family GH1), a retaining glycosyl hydrolase for which a transglycosylation yield of 36% has been determined experimentally. The three transition states have a strong oxocarbenium character and ring conformations between H and E. The atomic charges at the transition states for hydrolysis and transglycosylation are very similar, except for the more negative charge of the oxygen atom of water when compared to that of the acceptor Glc. The glycosylation transition state has a stronger S character than the deglycosylation ones and the proton transfer is less advanced. At the QM(PBE0/TZVP)/MM level, the TS for transglycosylation has shorter O4GLC-C1FUC (forming bond) distance and longer OE2 -C1 (breaking) distance than the hydrolysis one, although the HACC proton is closer to the Glu164 base in the hydrolysis TS. The QM(SCC-DFTB)/MM free energy maxima show the inverted situation, although the hydrolysis TS presents significant structural fluctuations. The 3-OHGLC group of the acceptor Glc (transglycosylation) and WAT432 (neighbor water in hydrolysis) are identified to stabilize the oxocarbenium transition states through interaction with O5 and O4 . The analysis of interaction suggests that perturbing the Glu392-Fuc interaction could increase the T/H ratio, either by direct mutation of this residue or indirectly as reported experimentally in the Asn390I and Phe401S cases. The molecular understanding of similarities and differences between hydrolysis and transglycosylation steps may be of help in the design of new biocatalysts for glycan synthesi

Computational insight into the catalytic implication of head/tail-first orientation of arachidonic acid in human 5-lipoxygenase : consequences for the positional specificity of oxygenation

In the present work we have combined homology modeling, protein-ligand dockings, quantum mechanics/molecular mechanics calculations and molecular dynamics simulations to generate human 5-lipoxygenase (5-LOX):arachidonic acid (AA) complexes consistent with the 5-lipoxygenating activity (which implies hydrogen abstraction at the C position). Our results suggest that both the holo and the apo forms of human Stable 5-LOX could accommodate AA in a productive form for 5-lipoxygenation. The former, in a tail-first orientation, with the AA carboxylate end interacting with Lys409, gives the desired structures with C close to the Fe-OH cofactor and suitable barrier heights for H abstraction. Only when using the apo form structure, a head-first orientation with the AA carboxylate close to His600 (a residue recently proposed as essential for AA positioning) is obtained in the docking calculations. However, the calculated barrier heights for this head-first orientation are in principle consistent with 5-LOX specificity, but also with 12/8 regioselectivity. Finally, long MD simulations give support to the recent hypothesis that the Phe177 + Tyr181 pair needs to close the active site access during the chemical reaction, and suggest that in the case of a head-first orientation Phe177 may be the residue interacting with the AA carboxylate

Accounting for the instantaneous disorder in the enzyme-substrate Michaelis complex to calculate the Gibbs free energy barrier of an enzyme reaction

Many enzyme reactions present instantaneous disorder. These dynamic fluctuations in the enzyme-substrate Michaelis complexes generate a wide range of energy barriers that cannot be experimentally observed, but that determine the measured kinetics of the reaction. These individual energy barriers can be calculated using QM/MM methods, but then the problem is how to deal with this dispersion of energy barriers to provide kinetic information. So far, the most usual procedure has implied the so-called exponential average of the energy barriers. In this paper, we discuss the foundations of this method, and we use the free energy perturbation theory to derive an alternative equation to get the Gibbs free energy barrier of the enzyme reaction. In addition, we propose a practical way to implement it. We have chosen four enzyme reactions as examples. In particular, we have studied the hydrolysis of a glycosidic bond catalyzed by the enzymeThermus thermophilusβ-glycosidase, and the mutant Y284P Ttb-gly, and the hydrogen abstraction reactions from C 13and C 7of arachidonic acid catalyzed by the enzyme rabbit 15-lipoxygenase-1

Comparing Hydrolysis and Transglycosylation Reactions Catalyzed by Thermus thermophilus β-Glycosidase. A Combined MD and QM/MM Study

The synthesis of oligosaccharides and other carbohydrate derivatives is of relevance for the advancement of glycosciences both at the fundamental and applied level. For many years, glycosyl hydrolases (GHs) have been explored to catalyze the synthesis of glycosidic bonds. In particular, retaining GHs can catalyze a transglycosylation (T) reaction that competes with hydrolysis (H). This has been done either employing controlled conditions in wild type GHs or by engineering new mutants. The goal, which is to increase the T/H ratio, has been achieved with moderate success in several cases despite the fact that the molecular basis for T/H modulation are unclear. Here we have used QM(DFT)/MM calculations to compare the glycosylation, hydrolysis and transglycosylation steps catalyzed by wild type Thermus thermophilus β-glycosidase (family GH1), a retaining glycosyl hydrolase for which a transglycosylation yield of 36% has been determined experimentally. The three transition states have a strong oxocarbenium character and ring conformations between 4H3 and 4E. The atomic charges at the transition states for hydrolysis and transglycosylation are very similar, except for the more negative charge of the oxygen atom of water when compared to that of the acceptor Glc. The glycosylation transition state has a stronger SN2 character than the deglycosylation ones and the proton transfer is less advanced. At the QM(PBE0/TZVP)/MM level, the TS for transglycosylation has shorter O4GLC-C1FUC (forming bond) distance and longer OE2GLU338-C1FUC (breaking) distance than the hydrolysis one, although the HACC proton is closer to the Glu164 base in the hydrolysis TS. The QM(SCC-DFTB)/MM free energy maxima show the inverted situation, although the hydrolysis TS presents significant structural fluctuations. The 3-OHGLC group of the acceptor Glc (transglycosylation) and WAT432 (neighbor water in hydrolysis) are identified to stabilize the oxocarbenium transition states through interaction with O5FUC and O4FUC. The analysis of interaction suggests that perturbing the Glu392-Fuc interaction could increase the T/H ratio, either by direct mutation of this residue or indirectly as reported experimentally in the Asn390I and Phe401S cases. The molecular understanding of similarities and differences between hydrolysis and transglycosylation steps may be of help in the design of new biocatalysts for glycan synthesis

Anàlisi ambiental de La Pleta : oficina tècnica del Parc del Garraf

En aquest projecte s'ha analitzat la viabilitat de l'autosuficiència de la Pleta, l'oficina tècnica del Parc del Garraf, a partir de diferents recursos renovables. S'ha realitzat un estudi del consum hídric i energètic i de la generació de residus per tal d'avaluar les deficiències de cada sistema, per poder-hi aplicar les mesures pertinents. Els resultats obtinguts mostren que un 40% de l'aigua que es consumeix a l'edifici prové dels camions cisterna que la subministren. Per tant, la principal proposta de millora va encaminada a reduir aquest volum d'aigua i per aconseguir-ho, es proposa augmentar la superfície de recollida d'aigua de pluja aprofitant la zona pavimentada del pati de magatzems. Les altres propostes intentaran reduir el volum total d'aigua consumida, com per exemple canviar el filtre actual de les aixetes per airejadors que permeten estalviar fins a un 50% d'aigua, instal·larEn este proyecto se ha analizado la viabilidad de la autosuficiencia de la Pleta, la oficina técnica del Parc del Garraf, a partir de diferentes recursos renovables. Se ha realizado un estudio del consumo hídrico y energético y de la generación de residuos para evaluar lasThis project analyzes whether or not the self-sufficiency is viable in Pleta using different renewable resources. We carried out a study of water and energy consumption and waste generation to study the weaknesses of each system, thus being able to implement appropriate corrective measures. It has been seen that 40% of the water consumed in the building comes from tankers. For this reason the main improvement is related to reducing the volume of this water. Other proposals seek to reduce the total volume of water consumed. Talking about energy, it must be said that the sources used are diesel and FV panels. As for the diesel, it is important to make a difference between the consumption of the generator which produces electricity and the consumption of the boiler for heating. Once this system has been analyzed, it has been shown that FV solar panels produce 73% of Pleta's electricity, all other electricity is supplied by the generator. But the main problem is the large consumption of diese

El codisseny com a nova perspectiva d’innovació docent universitària: Una aplicació centrada en la construcció de coneixement a partir d’experiències d’aprenentatge servei

El codisseny és una metodologia per la qual estudiants i professorat treballen conjuntament en la transformació dels processos educatius comuns. Aquesta comunicació presenta dues experiències de codisseny, a la Universitat de Barcelona i a la Universitat de Girona, amb l'objectiu de millorar els instruments d'aprenentatge i reflexió a les assignatures que plantegen projectes d'aprenentatge servei als estudiants, i ajudar-los a traçar ponts entre situacions d'experiència i coneixements teòrics

Understanding the Molecular Mechanism of the Ala-versus-Gly Concept Controlling the Product Specificity in Reactions Catalyzed by Lipoxygenases:A Combined Molecular Dynamics and QM/MM Study of Coral 8R-Lipoxygenase

Lipoxygenases (LOXs) are a family of enzymes that catalyze the highly specific hydroperoxidation of polyunsaturated fatty acids, such as arachidonic acid. Different stereo- or/and regioisomer hydroperoxidation products lead later to different metabolites that exert opposite physiological effects in the animal body and play a central role in inflammatory processes. The Gly-Ala switch of a single residue is crucial for the stereo- and regiocontrol in many lipoxygenases. Herein, we have combined molecular dynamics simulations with quantum mechanics/molecular mechanics calculations to study the hydrogen abstraction step and the molecular oxygen addition step of the hydroperoxidation reaction of arachidonic acid catalyzed by both wild-type Coral 8<i>R</i>-LOX and its Gly427Ala mutant. We have obtained a detailed molecular understanding of this Ala-versus-Gly concept. In wild type, molecular oxygen adds to C₈ of arachidonic acid with an <i>R</i> stereochemistry. In the mutant, Ala427 pushes Leu385, blocks the region over C₈, and opens an oxygen access channel now directed to C₁₂, where molecular oxygen is added with an <i>S</i> stereochemistry. Thus, the specificity turns out to be dramatically inverted. Since Leu385 is highly conserved among many lipoxygenase isoforms, this mechanism can be general, and we propose that the presence of such type of bulky and hydrophobic residues can be key in controlling the extreme regio- and stereospecificity of lipoxygenases and, as a consequence, their physiological effects