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Doctora en Ciencias de la Ingeniería, Mención Química / Las nuevas industrias han incorporado el uso de enzimas psicrófilas dentro de sus procesos de producción, lo que les ha permitido reducir tanto el consumo de sustratos como la producción de compuestos tóxicos, además de ahorrar energía, permitiendo una disminución de costos e impacto ambiental y por ello un aumento en la rentabilidad del proceso. Estas enzimas tienen un alto potencial a nivel industrial biotecnológico, y dentro de éstas, las lipasas son foco de atención dada su alta capacidad de sintetizar e hidrolizar enlaces ésteres y su exquisita selectividad de sustratos. Sus aplicaciones involucran la producción de alimentos, detergentes, fármacos, cosméticos, síntesis de compuestos químicos como biopolímeros y agroquímicos y su uso como biosensores, entre otras. En este trabajo, se determinó el modelo tridimensional de una lipasa activa a bajas temperaturas mediante modelamiento por homología. Este modelo presentó una evaluación positiva lo que permitió trabajar con él para caracterizar a esta enzima. Con este modelo se logró identificar y estudiar la participación de tres aminoácidos en la triada catalítica: Ser 239, His 391 y Asp 361, los cuales presentaban una acertada distribución espacial. Mediante docking molecular se estudió la unión y acoplamiento de estos tres aminoácidos con 4 tipos de sustratos diferentes, presentando preferencia por sustratos con cadenas aciladas de 6 carbonos. Se generaron mutaciones para cada uno de los aminoácidos candidatos, se realizaron modelos de su estructura tridimensional y se analizaron las distribuciones de cargas y energías. Así mismo, las mutaciones fueron sometidas a docking molecular para conocer la interacción de la triada mutada con estos cuatro sustratos. En todos los casos, las energías de interacción fueron drásticamente menores a la energía presentada por la lipasa nativa, demostrando la importancia de esta triada específica. Para validar estos resultados, cada uno de los residuos fue reemplazado utilizando mutagénesis sitio dirigida y se estudio su efecto en la actividad enzimática. Todas las mutaciones presentaron perdidas de la actividad, probando que ser239-asp361-his391 corresponde a la triada catalítica. Finalmente, se estudió el fenómeno de activación interfacial que acompaña a la actividad catalítica en gran parte del grupo de lipasas y esterasas. La comparación con modelos de enzimas que presentaron estructuras secundarias tipo tapas, reveló dos posibles estructuras α8 y G2 en la lipasa estudiada, que podrían estar participando en este fenómeno. Se concluye entonces, que la estructura de esta lipasa que fue predicha en base al alineamiento con otras lipasas de estructuras tridimensionales conocidas, corresponde al tipo α/β hidrolasa. Además, este trabajo logró predecir correctamente que los aminoácidos que forman la triada catalítica son Ser239, Asp361, e His391 lo cual fue validado mediante mutagénesis sitio-dirigida, reflejando la falta de actividad de mutantes con la triada modificada. Finalmente, los análisis del modelo tridimensional creado mostraron dos posibles estructuras que podrían mediar la activación interfacial.

Riboswitches are cis-acting gene regulatory RNAs, which function without involvement of proteins. They have been implicated as drug targets and are attractive systems for the study of RNA-ligand binding and RNA folding. The purine riboswitch was used as a model system for RNA-ligand docking. Published binding data was successfully reproduced in silico and compounds predicted to bind the riboswitch in a virtual screening were tested experimentally. Structural data confirming the predicted binding mode for several cases was obtained. The problems encountered were not specific to RNA-ligand docking but known from the far more explored field of protein-ligand docking.The SAM-I riboswitch was also subjected to virtual ligand screening. This receptor is a system of greater complexity than the purine riboswitch and consequently posed a harder challenge to the docking protocol. After initial validation of the docking setup based on previously published data, a set of compounds selected from the in-house database of commercially available compounds was screened. One compound identfied in silico was cofirmed to bind experimentally.The k-turn motif found in the SAM-I riboswitch was investigated with respect to its folding. The k-turn motif was found to be foldable in context of the SAMI riboswitch as well as in isolation as was expected. Furthermore, mutations disrupting key interactions within the k-turn motif were found to be prohibitive of k-turn folding in isolation as well as in context of the riboswitch, leading to a loss of ligand binding. Interestingly, two sequences were identfied which fold in context of the riboswitch but do not fold in isolation. This confirms the contribution of tertiary interactions to k-turn folding. This conclusion was backed up with structural data is a system of greater complexity than the purine riboswitch and consequently posed a harder challenge to the docking protocol. After initial validation of the to its folding. The k-turn motif was found to be foldable in context of the SAMI riboswitch as well as in isolation as was expected. Furthermore, mutations disrupting key interactions within the k-turn motif were found to be prohibitive of k-turn folding in isolation as well as in context of the riboswitch, leading to a loss of ligand binding. Interestingly, two sequences were identi ed which fold in context of the riboswitch but do not fold in isolation. This con rms the contribution of tertiary interactions to k-turn folding. This conclusion was backed

Computational modeling approaches have lately been earning their place as viable tools in drug discovery. Research efforts more often include computational component and the usage of the scientific software is commonplace at more stages of the drug discovery pipeline. However, as software takes on more responsibility and the computational methods grow more involved, the gap grows between research entities that have the means to maintain the necessary computational infrastructure and those that lack the technical expertise or financial means to obtain and include computational component in their scientific efforts. To fill this gap and to meet the need of many, mainly academic, labs numerous community contributions collectively known as open source projects play an increasingly important role. This work describes design, implementation and application of a set of drug discovery workflows based on the CHARMMing (CHARMM interface and graphics) web-server. The protocols described herein include docking, virtual target screening, de novo drug design, SAR/QSAR modeling as well as chemical education. The performance of the newly developed workflows is evaluated by applying them to a number of scientific problems that include reproducibility of crystal poses of small molecules in protein-ligand systems, identification of potential targets of a library of natural compounds as well as elucidating molecular targets of a vitamin. The results of these inquiries show that protocols developed as part of this effort perform comparably to commercial products, are able to produce results consistent with the experimental data and can substantially enrich the research efforts of labs with otherwise little or no computational component.

Automated spacecraft docking is a concept of operations with several important potential applications. One application that has received a great deal of attention recently is that of an automated docking capable unmanned re-supply spacecraft. In addition to being useful for re-supplying orbiting space stations, automated shuttles would also greatly facilitate the manned exploration of nearby space objects, including the Moon, near-Earth asteroids, or Mars. These vehicles would allow for longer duration human missions than otherwise possible and could even accelerate human colonization of other worlds. This thesis develops an optimal docking controller for an automated docking capable spacecraft. An innovative vision-based relative navigation system called VisNav is used to provide real-time relative position and orientation estimates, while a Kalman post-filter generates relative velocity and angular rate estimates from the VisNav output. The controller's performance robustness is evaluated in a closed-loop automated spacecraft docking simulation of a scenario in circular lunar orbit. The simulation uses realistic dynamical models of the two vehicles, both based on the European Automated Transfer Vehicle. A high-fidelity model of the VisNav sensor adds realism to the simulated relative navigation measurements. The docking controller's performance is evaluated in the presence of measurement noise, with the cases of sensor noise only, vehicle mass errors plus sensor noise, errors in vehicle moments of inertia plus sensor noise, initial starting position errors plus sensor noise, and initial relative attitude errors plus sensor noise each being considered. It was found that for the chosen cases and docking scenario, the final controller was robust to both types of mass property modeling errors, as well as both types of initial condition modeling errors, even in the presence of sensor noise. The VisNav system was found to perform satisfactorily in all test cases, with excellent estimate error convergence characteristics for the scenario considered. These results demonstrate preliminary feasibility of the presented docking system, including VisNav, for space-based automated docking applications.

It is a vitally important task to achieve control of the weight and center of gravity of lightship during building a new ship. If the lightship weight is slightly out of control, the deadweight inadequacy and a deviation from the initial design target will be caused. The basic performance and function of a ship at sea are also resulted. Furthermore, if the lightship weight is incompletely under control, it will bring about an unsafe vessel, ship-delivery difficulty and a severe loss for shipbuilder. Docking arrangement is optimized to allocate by using the state-of-the-art finite element method to analyze the lightweight distribution as the load and the ship girder as a beam; in addition, the dock is recognized as a spring-liked elastic foundation subjected to compression only. It is verified by comparison between measurement of the lightship weight by means of the weight control system on land and the traditional inclining experiment. Based on the results, it can be shown that the whole system is reliable, available and efficient. The load cell is utilized as a component of the weight control system to measure the compressive force (i.e., ship weight) at a specified dock. The main function of the system is to determine the lightweight and its C.G. on-land construction instead of the time-consuming and labor-wasting traditional way. The presented methodology will be beneficial for weight control of a new-ship building in the future.

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Vykdytas tyrimas, kurio tikslas - atlikti junginių - α-GalCer analogų – paiešką. Analogai turėtų pasižymėti α-GalCer agonistiniu poveikiu NKT ląstelėms, tačiau, skirtingai nei α-GalCer, neturėtų būti toksiški. Ieškomi junginiai – potencialios vaistinės medžiagos, skirtos opinio kolito ir kitų uždegiminių žarnyno ligų gydymui. Atlikus atitinkamos mokslinės literatūros analizę, išnagrinėjus α-GalCer bei baltymo CD1d struktūrą, jų jungimosi ypatumus ir reikalavimus junginio, kuris galėtų pakeisti α-GalCer, struktūrai, sumodeliuoti junginiai, kurie ištirti kompleksacijos būdu. Kompleksacijos proceso metu atrinkti šeši junginiai, kurie panašiausiai į α-GalCer jungiasi su baltymu CD1d bei turėtų pasižymėti pageidaujamomis savybėmis. Šių junginių struktūros pasiūlytos sintezei. / The aim of investigation performed is to propose possible analogues of α-GalCer. The analogues must have same beneficial properties as α-GalCer except the toxicity. The compounds we are looking for is a potential therapeutic agents to treat ulcerative colitis and other inflamatory bowel diseases. After studying scietific literature, the structure of α-GalCer and protein CD1d, their binding properties, and the requirements for the structure of possible analogue of α-GalCer, we accomplished molecular modeling of several compounds and performed docking. Docking revealed six compounds that are the most believable to have same binding properties with CD1d as α-GalCer does and same therapeutic properties. The structures of those compounds were proposed for a synthesis and other examination will be performed later.