Single Molecular Conductance of Tolanes: Experimental and Theoretical Study on the Junction Evolution Dependent on the Anchoring Group

Employing a scanning tunneling microscopy based beak junction technique and mechanically controlled break junction experiments, we investigated tolane (diphenylacetylene)-type single molecular junctions having four different anchoring groups (SH, pyridyl (PY), NH2, and CN) at a solid/liquid interface. The combination of current–distance and current–voltage measurements and their quantitative statistical analysis revealed the following sequence for junction formation probability and stability: PY > SH > NH2 > CN. For all single molecular junctions investigated, we observed the evolution through multiple junction configurations, with a particularly well-defined binding geometry for PY. The comparison of density functional theory type model calculations and molecular dynamics simulations with the experimental results revealed structure and mechanistic details of the evolution of the different types of (single) molecular junctions upon stretching quantitatively.

Adsorption of biomedical coating molecules, amino acids, and short peptides on magnetite (110)

Superparamagnetic iron oxide nanoparticles for biomedical applications are usually coated with organic molecules to form a steric barrier against agglomeration. The stability of these coatings is well established in the synthesis medium but is more difficult to assess in physiological environment. To obtain a first theoretical estimate of their stability in such an environment, we perform density functional theory calculations of the adsorption of water, polyvinyl alcohol (PVA) and polyethylene glycol (PEG) coating molecules, as well as the monomer and dimer of glycine as a prototype short peptide, on the (110) surface of magnetite (Fe3O4) in vacuo. Our results show that PVA binds significantly stronger to the surface than both PEG and glycine, while the difference between the latter two is quite small. Depending on the coverage, the wateradsorption strength is intermediate between PVA and glycine. Due to its strongly interacting OH side groups, PVA is likely to remain bound to the surface in the presence of short peptides. This stability will have to be further assessed by molecular dynamics in the solvated state for which the present work forms the basis.

Abundances and d13C values of n-alkanes extracted from sediment samples of ODP Hole 116-717C

Siwalik paleosol and Bengal Fan sediment samples were analyzed for the abundance and isotopic composition of n-alkanes in order to test for molecular evidence of the expansion of C4 grasslands on the Indian subcontinent. The carbon isotopic compositions of high-molecular-weight alkanes in both the ancient soils and sediments record a shift from low d13C values (ca. -30 per mil) to higher values (ca. -22 per mil) prior to 6 Ma. This shift is similar in magnitude to that recorded by paleosol carbonate and fossil teeth, and is consistent with a relatively rapid transition from dominantly C3 vegetation to an ecosystem dominated by C4 plants typical of semi-arid grasslands. The n-alkane values from our paleosol samples indicate that the isotopic change began as early as 9 Ma, reflecting either a growing contribution of C4 plants to a dominantly C3 biomass or a decrease in water availability to C3 plants. Molecular and isotopic analyses of other compounds, including n-alcohols and low-molecular weight n-alkanes indicate paleosol organic matter contains contributions from a mixture of sources, including vascular plants, algae and/or cyanobacteria and microorganisms. A range of inputs is likewise reflected in the isotopic composition of the total organic carbon from these samples. In addition, the n-alkanes from two samples show little evidence for pedegenic inputs and we suggest the compounds were derived instead from the paleosol's parent materials. We suggest the record of vegetation in ancient terrestrial ecosystems is better reconstructed using isotopic signatures of molecular markers, rather than bulk organic carbon. This approach provides a means of expanding the spatial and temporal records of C4 plant biomass which will help to resolve possible tectonic, climatic or biological controls on the rise of this important component of the terrestrial biosphere.

Dynamics of halocarbons in coastal surface waters during short term mesocosm experiments

The aim of the present study was to evaluate the influence of different light quality, especially ultraviolet radiation (UVR), on the dynamics of volatile halogenated organic compounds (VHOCs) at the sea surface. Short term experiments were conducted with floating gas-tight mesocosms of different optical qualities. Six halocarbons (CH3I, CHCl3, CH2Br2, CH2ClI, CHBr3 and CH2I2), known to be produced by phytoplankton, together with a variety of biological and environmental variables were measured in the coastal southern Baltic Sea and in the Raunefjord (North Sea). These experiments showed that ambient levels of UVR have no significant influence on VHOC dynamics in the natural systems. We attribute it to the low radiation doses that phytoplankton cells receive in a normal turbulent surface mixed layer. The VHOC concentrations were influenced by their production and removal processes, but they were not correlated with biological or environmental parameters investigated. Diatoms were most likely the dominant biogenic source of VHOCs in the Baltic Sea experiment, whereas in the Raunefjord experiment macroalgae probably contributed strongly to the production of VHOCs. The variable stable carbon isotope signatures (d13C values) of bromoform (CHBr3) also indicate that different autotrophic organisms were responsible for CHBr3 production in the two coastal environments. In the Raunefjord, despite strong daily variations in CHBr3 concentration, the carbon isotopic ratio was fairly stable with a mean value of -26 per mil. During the declining spring phytoplankton bloom in the Baltic Sea, the d13C values of CHBr3 were enriched in 13C and showed noticeable diurnal changes (-12 per mil ± 4). These results show that isotope signature analysis is a useful tool to study both the origin and dynamics of VHOCs in natural systems.

Influence of termal fluctuations in radiation damage cascade production and defect dynamics in tungsten

The detailed study of the deterioration suffered by the materials of the components of a nuclear facility, in particular those forming part of the reactor core, is a topic of great interest which importance derives in large technological and economic implications. Since changes in the atomic-structural properties of relevant components pose a risk to the smooth operation with clear consequences for security and life of the plant, controlling these factors is essential in any development of engineering design and implementation. In recent times, tungsten has been proposed as a structural material based on its good resistance to radiation, but still needs to be done an extensive study on the influence of temperature on the behavior of this material under radiation damage. This work aims to contribute in this regard. Molecular Dynamics (MD) simulations were carried out to determine the influence of temperature fluctuations on radiation damage production and evolution in Tungsten. We have particularly focused our study in the dynamics of defect creation, recombination, and diffusion properties. PKA energies were sampled in a range from 5 to 50 KeV. Three different temperature scenarios were analyzed, from very low temperatures (0-200K), up to high temperature conditions (300-500 K). We studied the creation of defects, vacancies and interstitials, recombination rates, diffusion properties, cluster formation, their size and evolution. Simulations were performed using Lammps and the Zhou EAM potential for W

Aplicación de la física estadística a los medios granulares

Esta tesis se centra en el estudio de medios granulares blandos y atascados mediante la aplicación de la física estadística. Esta aproximación se sitúa entre los tradicionales enfoques macro y micromecánicos: trata de establecer cuáles son las propiedades macroscópicas esperables de un sistema granular en base a un análisis de las propiedades de las partículas y las interacciones que se producen entre ellas y a una consideración de las restricciones macroscópicas del sistema. Para ello se utiliza la teoría estadística junto con algunos principios, conceptos y definiciones de la teoría de los medios continuos (campo de tensiones y deformaciones, energía potencial elástica, etc) y algunas técnicas de homogeneización. La interacción entre las partículas es analizada mediante las aportaciones de la teoría del contacto y de las fuerzas capilares (producidas por eventuales meniscos de líquido cuando el medio está húmedo). La idea básica de la mecánica estadística es que entre todas soluciones de un problema físico (como puede ser el ensamblaje en equilibrio estático de partículas de un medio granular) existe un conjunto que es compatible con el conocimiento macroscópico que tenemos del sistema (por ejemplo, su volumen, la tensión a la que está sometido, la energía potencial elástica que almacena, etc.). Este conjunto todavía contiene un número enorme de soluciones. Pues bien, si no hay ninguna información adicional es razonable pensar que no existe ningún motivo para que alguna de estas soluciones sea más probable que las demás. Entonces parece natural asignarles a todas ellas el mismo peso estadístico y construir una función matemática compatible. Actuando de este modo se obtiene cuál es la función de distribución más probable de algunas cantidades asociadas a las soluciones, para lo cual es muy importante asegurarse de que todas ellas son igualmente accesibles por el procedimiento de ensamblaje o protocolo. Este enfoque se desarrolló en sus orígenes para el estudio de los gases ideales pero se puede extender para sistemas no térmicos como los analizados en esta tesis. En este sentido el primer intento se produjo hace poco más de veinte años y es la colectividad de volumen. Desde entonces esta ha sido empleada y mejorada por muchos investigadores en todo el mundo, mientras que han surgido otras, como la de la energía o la del fuerza-momento (tensión multiplicada por volumen). Cada colectividad describe, en definitiva, conjuntos de soluciones caracterizados por diferentes restricciones macroscópicas, pero de todos ellos resultan distribuciones estadísticas de tipo Maxwell-Boltzmann y controladas por dichas restricciones. En base a estos trabajos previos, en esta tesis se ha adaptado el enfoque clásico de la física estadística para el caso de medios granulares blandos. Se ha propuesto un marco general para estudiar estas colectividades que se basa en la comparación de todas las posibles soluciones en un espacio matemático definido por las componentes del fuerza-momento y en unas funciones de densidad de estados. Este desarrollo teórico se complementa con resultados obtenidos mediante simulación de la compresión cíclica de sistemas granulares bidimensionales. Se utilizó para ello un método de dinámica molecular, MD (o DEM). Las simulaciones consideran una interacción mecánica elástica, lineal y amortiguada a la que se ha añadido, en algunos casos, la fuerza cohesiva producida por meniscos de agua. Se realizaron cálculos en serie y en paralelo. Los resultados no solo prueban que las funciones de distribución de las componentes de fuerza-momento del sistema sometido a un protocolo específico parecen ser universales, sino que también revelan que existen muchos aspectos computacionales que pueden determinar cuáles son las soluciones accesibles. This thesis focuses on the application of statistical mechanics for the study of static and jammed packings of soft granular media. Such approach lies between micro and macromechanics: it tries to establish what the expected macroscopic properties of a granular system are, by starting from a micromechanical analysis of the features of the particles, and the interactions between them, and by considering the macroscopic constraints of the system. To do that, statistics together with some principles, concepts and definitions of continuum mechanics (e.g. stress and strain fields, elastic potential energy, etc.) as well as some homogenization techniques are used. The interaction between the particles of a granular system is examined too and theories on contact and capillary forces (when the media are wet) are revisited. The basic idea of statistical mechanics is that among the solutions of a physical problem (e.g. the static arrangement of particles in mechanical equilibrium) there is a class that is compatible with our macroscopic knowledge of the system (volume, stress, elastic potential energy,...). This class still contains an enormous number of solutions. In the absence of further information there is not any a priori reason for favoring one of these more than any other. Hence we shall naturally construct the equilibrium function by assigning equal statistical weights to all the functions compatible with our requirements. This procedure leads to the most probable statistical distribution of some quantities, but it is necessary to guarantee that all the solutions are likely accessed. This approach was originally set up for the study of ideal gases, but it can be extended to non-thermal systems too. In this connection, the first attempt for granular systems was the volume ensemble, developed about 20 years ago. Since then, this model has been followed and improved upon by many researchers around the world, while other two approaches have also been set up: energy and force-moment (i.e. stress multiplied by volume) ensembles. Each ensemble is described by different macroscopic constraints but all of them result on a Maxwell-Boltzmann statistical distribution, which is precisely controlled by the respective constraints. According to this previous work, in this thesis the classical statistical mechanics approach is introduced and adapted to the case of soft granular media. A general framework, which includes these three ensembles and uses a force-moment phase space and a density of states function, is proposed. This theoretical development is complemented by molecular dynamics (or DEM) simulations of the cyclic compression of 2D granular systems. Simulations were carried out by considering spring-dashpot mechanical interactions and attractive capillary forces in some cases. They were run on single and parallel processors. Results not only prove that the statistical distributions of the force-moment components obtained with a specific protocol seem to be universal, but also that there are many computational issues that can determine what the attained packings or solutions are.

Statistical distributions obtained from the compression of monodisperse, soft and frictionless particles

The cyclic compression of several granular systems has been simulated with a molecular dynamics code. All the samples consisted of bidimensional, soft, frictionless and equal-sized particles that were initially arranged according to a squared lattice and were compressed by randomly generated irregular walls. The compression protocols can be described by some control variables (volume or external force acting on the walls) and by some dimensionless factors, that relate stiffness, density, diameter, damping ratio and water surface tension to the external forces, displacements and periods. Each protocol, that is associated to a dynamic process, results in an arrangement with its own macroscopic features: volume (or packing ratio), coordination number, and stress; and the differences between packings can be highly significant. The statistical distribution of the force-moment state of the particles (i.e. the equivalent average stress multiplied by the volume) is analyzed. In spite of the lack of a theoretical framework based on statistical mechanics specific for these protocols, it is shown how the obtained distributions of mean and relative deviatoric force-moment are. Then it is discussed on the nature of these distributions and on their relation to specific protocols.

Multiscale modeling of the plastic behaviour in single crystal tungsten: from atomistic to crystal plasticity simulations

En una planta de fusión, los materiales en contacto con el plasma así como los materiales de primera pared experimentan condiciones particularmente hostiles al estar expuestos a altos flujos de partículas, neutrones y grandes cargas térmicas. Como consecuencia de estas diferentes y complejas condiciones de trabajo, el estudio, desarrollo y diseño de estos materiales es uno de los más importantes retos que ha surgido en los últimos años para la comunidad científica en el campo de los materiales y la energía. Debido a su baja tasa de erosión, alta resistencia al sputtering, alta conductividad térmica, muy alto punto de fusión y baja retención de tritio, el tungsteno (wolframio) es un importante candidato como material de primera pared y como posible material estructural avanzado en fusión por confinamiento magnético e inercial. Sin embargo, el tiempo de vida del tungsteno viene controlado por diversos factores como son su respuesta termo-mecánica en la superficie, la posibilidad de fusión y el fallo por acumulación de helio. Es por ello que el tiempo de vida limitado por la respuesta mecánica del tungsteno (W), y en particular su fragilidad, sean dos importantes aspectos que tienes que ser investigados. El comportamiento plástico en materiales refractarios con estructura cristalina cúbica centrada en las caras (bcc) como el tungsteno está gobernado por las dislocaciones de tipo tornillo a escala atómica y por conjuntos e interacciones de dislocaciones a escalas más grandes. El modelado de este complejo comportamiento requiere la aplicación de métodos capaces de resolver de forma rigurosa cada una de las escalas. El trabajo que se presenta en esta tesis propone un modelado multiescala que es capaz de dar respuestas ingenieriles a las solicitudes técnicas del tungsteno, y que a su vez está apoyado por la rigurosa física subyacente a extensas simulaciones atomísticas. En primer lugar, las propiedades estáticas y dinámicas de las dislocaciones de tipo tornillo en cinco potenciales interatómicos de tungsteno son comparadas, determinando cuáles de ellos garantizan una mayor fidelidad física y eficiencia computacional. Las grandes tasas de deformación asociadas a las técnicas de dinámica molecular hacen que las funciones de movilidad de las dislocaciones obtenidas no puedan ser utilizadas en los siguientes pasos del modelado multiescala. En este trabajo, proponemos dos métodos alternativos para obtener las funciones de movilidad de las dislocaciones: un modelo Monte Cario cinético y expresiones analíticas. El conjunto de parámetros necesarios para formular el modelo de Monte Cario cinético y la ley de movilidad analítica son calculados atomísticamente. Estos parámetros incluyen, pero no se limitan a: la determinación de las entalpias y energías de formación de las parejas de escalones que forman las dislocaciones, la parametrización de los efectos de no Schmid característicos en materiales bcc,etc. Conociendo la ley de movilidad de las dislocaciones en función del esfuerzo aplicado y la temperatura, se introduce esta relación como ecuación de flujo dentro de un modelo de plasticidad cristalina. La predicción del modelo sobre la dependencia del límite de fluencia con la temperatura es validada experimentalmente con ensayos uniaxiales en tungsteno monocristalino. A continuación, se calcula el límite de fluencia al aplicar ensayos uniaxiales de tensión para un conjunto de orientaciones cristalográticas dentro del triángulo estándar variando la tasa de deformación y la temperatura de los ensayos. Finalmente, y con el objetivo de ser capaces de predecir una respuesta más dúctil del tungsteno para una variedad de estados de carga, se realizan ensayos biaxiales de tensión sobre algunas de las orientaciones cristalográficas ya estudiadas en función de la temperatura.-------------------------------------------------------------------------ABSTRACT ----------------------------------------------------------Tungsten and tungsten alloys are being considered as leading candidates for structural and functional materials in future fusion energy devices. The most attractive properties of tungsten for the design of magnetic and inertial fusion energy reactors are its high melting point, high thermal conductivity, low sputtering yield and low longterm disposal radioactive footprint. However, tungsten also presents a very low fracture toughness, mostly associated with inter-granular failure and bulk plasticity, that limits its applications. As a result of these various and complex conditions of work, the study, development and design of these materials is one of the most important challenges that have emerged in recent years to the scientific community in the field of materials for energy applications. The plastic behavior of body-centered cubic (bcc) refractory metals like tungsten is governed by the kink-pair mediated thermally activated motion of h¿ (\1 11)i screw dislocations on the atomistic scale and by ensembles and interactions of dislocations at larger scales. Modeling this complex behavior requires the application of methods capable of resolving rigorously each relevant scale. The work presented in this thesis proposes a multiscale model approach that gives engineering-level responses to the technical specifications required for the use of tungsten in fusion energy reactors, and it is also supported by the rigorous underlying physics of extensive atomistic simulations. First, the static and dynamic properties of screw dislocations in five interatomic potentials for tungsten are compared, determining which of these ensure greater physical fidelity and computational efficiency. The large strain rates associated with molecular dynamics techniques make the dislocation mobility functions obtained not suitable to be used in the next steps of the multiscale model. Therefore, it is necessary to employ mobility laws obtained from a different method. In this work, we suggest two alternative methods to get the dislocation mobility functions: a kinetic Monte Carlo model and analytical expressions. The set of parameters needed to formulate the kinetic Monte Carlo model and the analytical mobility law are calculated atomistically. These parameters include, but are not limited to: enthalpy and energy barriers of kink-pairs as a function of the stress, width of the kink-pairs, non-Schmid effects ( both twinning-antitwinning asymmetry and non-glide stresses), etc. The function relating dislocation velocity with applied stress and temperature is used as the main source of constitutive information into a dislocation-based crystal plasticity framework. We validate the dependence of the yield strength with the temperature predicted by the model against existing experimental data of tensile tests in singlecrystal tungsten, with excellent agreement between the simulations and the measured data. We then extend the model to a number of crystallographic orientations uniformly distributed in the standard triangle and study the effects of temperature and strain rate. Finally, we perform biaxial tensile tests and provide the yield surface as a function of the temperature for some of the crystallographic orientations explored in the uniaxial tensile tests.

Ionophores and receptors using cation-π interactions: Collarenes

Cation-π interactions are important forces in molecular recognition by biological receptors, enzyme catalysis, and crystal engineering. We have harnessed these interactions in designing molecular systems with circular arrangement of benzene units that are capable of acting as ionophores and models for biological receptors. [n]Collarenes are promising candidates with high selectivity for a specific cation, depending on n, because of their structural rigidity and well-defined cavity size. The interaction energies of [n]collarenes with cations have been evaluated by using ab initio calculations. The selectivity of these [n]collarenes in aqueous solution was revealed by using statistical perturbation theory in conjunction with Monte Carlo and molecular dynamics simulations. It has been observed that in [n]collarenes the ratio of the interaction energies of a cation with it and the cation with the basic building unit (benzene) can be correlated to its ion selectivity. We find that collarenes are excellent and efficient ionophores that bind cations through cation-π interactions. [6]Collarene is found to be a selective host for Li+ and Mg2+, [8]collarene for K+ and Sr2+, and [10]collarene for Cs+ and Ba2+. This finding indicates that [10]collarene and [8]collarene could be used for effective separation of highly radioactive isotopes, 137Cs and 90Sr, which are major constituents of nuclear wastes. More interestingly, collarenes of larger cavity size can be useful in capturing organic cations. [12]Collarene exhibits a pronounced affinity for tetramethylammonium cation and acetylcholine, which implies that it could serve as a model for acetylcholinestrase. Thus, collarenes can prove to be novel and effective ionophores/model-receptors capable of heralding a new direction in molecular recognition and host-guest chemistry.

A molecular level picture of the stabilization of A-DNA in mixed ethanol–water solutions

Advances in computer power, methodology, and empirical force fields now allow routine “stable” nanosecond-length molecular dynamics simulations of DNA in water. The accurate representation of environmental influences on structure remains a major, unresolved issue. In contrast to simulations of A-DNA in water (where an A-DNA to B-DNA transition is observed) and in pure ethanol (where disruption of the structure is observed), A-DNA in ≈85% ethanol solution remains in a canonical A-DNA geometry as expected. The stabilization of A-DNA by ethanol is likely due to disruption of the spine of hydration in the minor groove and the presence of ion-mediated interhelical bonds and extensive hydration across the major groove.

Molecular switch in signal transduction: Reaction paths of the conformational changes in ras p21

Conformational changes in ras p21 triggered by the hydrolysis of GTP play an essential role in the signal transduction pathway. The path for the conformational change is determined by molecular dynamics simulation with a holonomic constraint directing the system from the known GTP-bound structure (with the γ-phosphate removed) to the GDP-bound structure. The simulation is done with a shell of water molecules surrounding the protein. In the switch I region, the side chain of Tyr-32, which undergoes a large displacement, moves through the space between loop 2 and the rest of the protein, rather than on the outside of the protein. As a result, the charged residues Glu-31 and Asp-33, which interact with Raf in the homologous RafRBD–Raps complex, remain exposed during the transition. In the switch II region, the conformational changes of α2 and loop 4 are strongly coupled. A transient hydrogen bonding complex between Arg-68 and Tyr-71 in the switch II region and Glu-37 in switch I region stabilizes the intermediate conformation of α2 and facilitates the unwinding of a helical turn of α2 (residues 66–69), which in turn permits the larger scale motion of loop 4. Hydrogen bond exchange between the protein and solvent molecules is found to be important in the transition. Possible functional implications of the results are discussed.

Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor

The prevailing paradigm for G protein-coupled receptors is that each receptor is narrowly tuned to its ligand and closely related agonists. An outstanding problem is whether this paradigm applies to olfactory receptor (ORs), which is the largest gene family in the genome, in which each of 1,000 different G protein-coupled receptors is believed to interact with a range of different odor molecules from the many thousands that comprise “odor space.” Insights into how these interactions occur are essential for understanding the sense of smell. Key questions are: (i) Is there a binding pocket? (ii) Which amino acid residues in the binding pocket contribute to peak affinities? (iii) How do affinities change with changes in agonist structure? To approach these questions, we have combined single-cell PCR results [Malnic, B., Hirono, J., Sato, T. & Buck, L. B. (1999) Cell 96, 713–723] and well-established molecular dynamics methods to model the structure of a specific OR (OR S25) and its interactions with 24 odor compounds. This receptor structure not only points to a likely odor-binding site but also independently predicts the two compounds that experimentally best activate OR S25. The results provide a mechanistic model for olfactory transduction at the molecular level and show how the basic G protein-coupled receptor template is adapted for encoding the enormous odor space. This combined approach can significantly enhance the identification of ligands for the many members of the OR family and also may shed light on other protein families that exhibit broad specificities, such as chemokine receptors and P450 oxidases.

The importance of reactant positioning in enzyme catalysis: A hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase

Hybrid quantum mechanics/molecular mechanics calculations using Austin Model 1 system-specific parameters were performed to study the SN2 displacement reaction of chloride from 1,2-dichloroethane (DCE) by nucleophilic attack of the carboxylate of acetate in the gas phase and by Asp-124 in the active site of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. The activation barrier for nucleophilic attack of acetate on DCE depends greatly on the reactants having a geometry resembling that in the enzyme or an optimized gas-phase structure. It was found in the gas-phase calculations that the activation barrier is 9 kcal/mol lower when dihedral constraints are used to restrict the carboxylate nucleophile geometry to that in the enzyme relative to the geometries for the reactants without dihedral constraints. The calculated quantum mechanics/molecular mechanics activation barriers for the enzymatic reaction are 16.2 and 19.4 kcal/mol when the geometry of the reactants is in a near attack conformer from molecular dynamics and in a conformer similar to the crystal structure (DCE is gauche), respectively. This haloalkane dehalogenase lowers the activation barrier for dehalogenation of DCE by 2–4 kcal/mol relative to the single point energies of the enzyme's quantum mechanics atoms in the gas phase. SN2 displacements of this sort in water are infinitely slower than in the gas phase. The modest lowering of the activation barrier by the enzyme relative to the reaction in the gas phase is consistent with mutation experiments.

Mapping the early steps in the pH-induced conformational conversion of the prion protein

Under certain conditions, the prion protein (PrP) undergoes a conformational change from the normal cellular isoform, PrPC, to PrPSc, an infectious isoform capable of causing neurodegenerative diseases in many mammals. Conversion can be triggered by low pH, and in vivo this appears to take place in an endocytic pathway and/or caveolae-like domains. It has thus far been impossible to characterize the conformational change at high resolution by experimental methods. Therefore, to investigate the effect of acidic pH on PrP conformation, we have performed 10-ns molecular dynamics simulations of PrPC in water at neutral and low pH. The core of the protein is well maintained at neutral pH. At low pH, however, the protein is more dynamic, and the sheet-like structure increases both by lengthening of the native β-sheet and by addition of a portion of the N terminus to widen the sheet by another two strands. The side chain of Met-129, a polymorphic codon in humans associated with variant Creutzfeldt–Jakob disease, pulls the N terminus into the sheet. Neutralization of Asp-178 at low pH removes interactions that inhibit conversion, which is consistent with the Asp-178–Asn mutation causing human prion diseases.

QSAR e dinâmica molecular no estudo de sistemas biomoleculares: predição da atividade biológica de antagonistas do receptor sigma-1 e simulações de bicamadas lipídicas

Diferentes abordagens teóricas têm sido utilizadas em estudos de sistemas biomoleculares com o objetivo de contribuir com o tratamento de diversas doenças. Para a dor neuropática, por exemplo, o estudo de compostos que interagem com o receptor sigma-1 (Sig-1R) pode elucidar os principais fatores associados à atividade biológica dos mesmos. Nesse propósito, estudos de Relações Quantitativas Estrutura-Atividade (QSAR) utilizando os métodos de regressão por Mínimos Quadrados Parciais (PLS) e Rede Neural Artificial (ANN) foram aplicados a 64 antagonistas do Sig-1R pertencentes à classe de 1-arilpirazóis. Modelos PLS e ANN foram utilizados com o objetivo de descrever comportamentos lineares e não lineares, respectivamente, entre um conjunto de descritores e a atividade biológica dos compostos selecionados. O modelo PLS foi obtido com 51 compostos no conjunto treinamento e 13 compostos no conjunto teste (r² = 0,768, q² = 0,684 e r²teste = 0,785). Testes de leave-N-out, randomização da atividade biológica e detecção de outliers confirmaram a robustez e estabilidade dos modelos e mostraram que os mesmos não foram obtidos por correlações ao acaso. Modelos também foram gerados a partir da Rede Neural Artificial Perceptron de Multicamadas (MLP-ANN), sendo que a arquitetura 6-12-1, treinada com as funções de transferência tansig-tansig, apresentou a melhor resposta para a predição da atividade biológica dos compostos (r²treinamento = 0,891, r²validação = 0,852 e r²teste = 0,793). Outra abordagem foi utilizada para simular o ambiente de membranas sinápticas utilizando bicamadas lipídicas compostas por POPC, DOPE, POPS e colesterol. Os estudos de dinâmica molecular desenvolvidos mostraram que altas concentrações de colesterol induzem redução da área por lipídeo e difusão lateral e aumento na espessura da membrana e nos valores de parâmetro de ordem causados pelo ordenamento das cadeias acil dos fosfolipídeos. As bicamadas lipídicas obtidas podem ser usadas para simular interações entre lipídeos e pequenas moléculas ou proteínas contribuindo para as pesquisas associadas a doenças como Alzheimer e Parkinson. As abordagens usadas nessa tese são essenciais para o desenvolvimento de novas pesquisas em Química Medicinal Computacional.