Visualization of Protein Folding Funnels in Lattice Models

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estudo da interação não-nativa no enovelamento de proteínas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo da dinâmica de solvatação de peptídeos por QM/MM

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Coarse-grained peptide models: conformational sampling, peptide association and dynamical properties for peptides

In dieser Arbeit wird ein vergröbertes (engl. coarse-grained, CG) Simulationsmodell für Peptide in wässriger Lösung entwickelt. In einem CG Verfahren reduziert man die Anzahl der Freiheitsgrade des Systems, so dass manrngrössere Systeme auf längeren Zeitskalen untersuchen kann. Die Wechselwirkungspotentiale des CG Modells sind so aufgebaut, dass die Peptid Konformationen eines höher aufgelösten (atomistischen) Modells reproduziert werden.rnIn dieser Arbeit wird der Einfluss unterschiedlicher bindender Wechsel-rnwirkungspotentiale in der CG Simulation untersucht, insbesondere daraufhin,rnin wie weit das Konformationsgleichgewicht der atomistischen Simulation reproduziert werden kann. Im CG Verfahren verliert man per Konstruktionrnmikroskopische strukturelle Details des Peptids, zum Beispiel, Korrelationen zwischen Freiheitsgraden entlang der Peptidkette. In der Dissertationrnwird gezeigt, dass diese “verlorenen” Eigenschaften in einem Rückabbildungsverfahren wiederhergestellt werden können, in dem die atomistischen Freiheitsgrade wieder in die CG-Strukturen eingefügt werden. Dies gelingt, solange die Konformationen des CG Modells grundsätzlich gut mit der atomistischen Ebene übereinstimmen. Die erwähnten Korrelationen spielen einerngrosse Rolle bei der Bildung von Sekundärstrukturen und sind somit vonrnentscheidender Bedeutung für ein realistisches Ensemble von Peptidkonformationen. Es wird gezeigt, dass für eine gute Übereinstimmung zwischen CG und atomistischen Kettenkonformationen spezielle bindende Wechselwirkungen wie zum Beispiel 1-5 Bindungs- und 1,3,5-Winkelpotentiale erforderlich sind. Die intramolekularen Parameter (d.h. Bindungen, Winkel, Torsionen), die für kurze Oligopeptide parametrisiert wurden, sind übertragbarrnauf längere Peptidsequenzen. Allerdings können diese gebundenen Wechselwirkungen nur in Kombination mit solchen nichtbindenden Wechselwirkungspotentialen kombiniert werden, die bei der Parametrisierung verwendet werden, sind also zum Beispiel nicht ohne weiteres mit einem andere Wasser-Modell kombinierbar. Da die Energielandschaft in CG-Simulationen glatter ist als im atomistischen Modell, gibt es eine Beschleunigung in der Dynamik. Diese Beschleunigung ist unterschiedlich für verschiedene dynamische Prozesse, zum Beispiel für verschiedene Arten von Bewegungen (Rotation und Translation). Dies ist ein wichtiger Aspekt bei der Untersuchung der Kinetik von Strukturbildungsprozessen, zum Beispiel Peptid Aggregation.rn

Charge-transport simulations in organic semiconductors

In this thesis we have extended the methods for microscopic charge-transport simulations for organic semiconductors. In these materials the weak intermolecular interactions lead to spatially localized charge carriers, and the charge transport occurs as an activated hopping process between diabatic states. In addition to weak electronic couplings between these states, different electrostatic environments in the organic material lead to a broadening of the density of states for the charge energies which limits carrier mobilities.rnThe contributions to the method development includern(i) the derivation of a bimolecular charge-transfer rate,rn(ii) the efficient evaluation of intermolecular (outer-sphere) reorganization energies,rn(iii) the investigation of effects of conformational disorder on intramolecular reorganization energies or internal site energiesrnand (iv) the inclusion of self-consistent polarization interactions for calculation of charge energies.These methods were applied to study charge transport in amorphous phases of small molecules used in the emission layer of organic light emitting diodes (OLED).rnWhen bulky substituents are attached to an aromatic core in order to adjust energy levels or prevent crystallization, a small amount of delocalization of the frontier orbital to the substituents can increase electronic couplings between neighboring molecules. This leads to improved charge-transfer rates and, hence, larger charge-mobility. We therefore suggest using the mesomeric effect (as opposed to the inductive effect) when attaching substituents to aromatic cores, which is necessary for example in deep blue OLEDs, where the energy levels of a host molecule have to be adjusted to those of the emitter.rnFurthermore, the energy landscape for charges in an amorphous phase cannot be predicted by mesoscopic models because they approximate the realistic morphology by a lattice and represent molecular charge distributions in a multipole expansion. The microscopic approach shows that a polarization-induced stabilization of a molecule in its charged and neutral states can lead to large shifts, broadening, and traps in the distribution of charge energies. These results are especially important for multi-component systems (the emission layer of an OLED or the donor-acceptor interface of an organic solar cell), if the change in polarizability upon charging (or excitation in case of energy transport) is different for the components. Thus, the polarizability change upon charging or excitation should be added to the set of molecular parameters essential for understanding charge and energy transport in organic semiconductors.rnWe also studied charge transport in self-assembled systems, where intermolecular packing motives induced by side chains can increase electronic couplings between molecules. This leads to larger charge mobility, which is essential to improve devices such as organic field effect transistors, where low carrier mobilities limit the switching frequency.rnHowever, it is not sufficient to match the average local molecular order induced by the sidernchains (such as the pitch angle between consecutive molecules in a discotic mesophase) with maxima of the electronic couplings.rnIt is also important to make the corresponding distributions as narrow as possible compared to the window determined by the closest minima of thernelectronic couplings. This is especially important in one-dimensional systems, where charge transport is limited by the smallest electronic couplings.rnThe immediate implication for compound design is that the side chains should assist the self-assemblingrnprocess not only via soft entropic interactions, but also via stronger specific interactions, such as hydrogen bonding.rnrnrnrn

Proteins in silico-modeling and sampling

Proteins are linear chain molecules made out of amino acids. Only when they fold to their native states, they become functional. This dissertation aims to model the solvent (environment) effect and to develop & implement enhanced sampling methods that enable a reliable study of the protein folding problem in silico. We have developed an enhanced solvation model based on the solution to the Poisson-Boltzmann equation in order to describe the solvent effect. Following the quantum mechanical Polarizable Continuum Model (PCM), we decomposed net solvation free energy into three physical terms– Polarization, Dispersion and Cavitation. All the terms were implemented, analyzed and parametrized individually to obtain a high level of accuracy. In order to describe the thermodynamics of proteins, their conformational space needs to be sampled thoroughly. Simulations of proteins are hampered by slow relaxation due to their rugged free-energy landscape, with the barriers between minima being higher than the thermal energy at physiological temperatures. In order to overcome this problem a number of approaches have been proposed of which replica exchange method (REM) is the most popular. In this dissertation we describe a new variant of canonical replica exchange method in the context of molecular dynamic simulation. The advantage of this new method is the easily tunable high acceptance rate for the replica exchange. We call our method Microcanonical Replica Exchange Molecular Dynamic (MREMD). We have described the theoretical frame work, comment on its actual implementation, and its application to Trp-cage mini-protein in implicit solvent. We have been able to correctly predict the folding thermodynamics of this protein using our approach.

Tracking individual membrane proteins and their biochemistry: The power of direct observation

The advent of single molecule fluorescence microscopy has allowed experimental molecular biophysics and biochemistry to transcend traditional ensemble measurements, where the behavior of individual proteins could not be precisely sampled. The recent explosion in popularity of new super-resolution and super-localization techniques coupled with technical advances in optical designs and fast highly sensitive cameras with single photon sensitivity and millisecond time resolution have made it possible to track key motions, reactions, and interactions of individual proteins with high temporal resolution and spatial resolution well beyond the diffraction limit. Within the purview of membrane proteins and ligand gated ion channels (LGICs), these outstanding advances in single molecule microscopy allow for the direct observation of discrete biochemical states and their fluctuation dynamics. Such observations are fundamentally important for understanding molecular-level mechanisms governing these systems. Examples reviewed here include the effects of allostery on the stoichiometry of ligand binding in the presence of fluorescent ligands; the observation of subdomain partitioning of membrane proteins due to microenvironment effects; and the use of single particle tracking experiments to elucidate characteristics of membrane protein diffusion and the direct measurement of thermodynamic properties, which govern the free energy landscape of protein dimerization. The review of such characteristic topics represents a snapshot of efforts to push the boundaries of fluorescence microscopy of membrane proteins to the absolute limit.

Análisis del sector y mercado gasista nacional e internacional. : el Hub ibérico y su adaptación al sistema español

Actualmente existe un gran interés orientado hacia el mercado del gas natural. Son muchas las razones por las que este combustible se posiciona como uno de los más importantes dentro del panorama energético mundial. Además de que salvaría el hueco dejado por el carbón y el petróleo, supone una alternativa mucho más limpia que se podría desarrollar aún más tanto a nivel doméstico, industrial como en el mundo de los transportes. La industria del gas natural está cambiando rápidamente fundamentalmente por la aparición del gas no convencional y sus técnicas de extracción. Por lo que se está produciendo un cambio en la economía de la producción de gas así como en la dinámica y los movimientos del GNL a lo largo de todo el planeta. El propósito de este estudio es enfocar el estado del sector y mercado del gas natural en todo el mundo y de esta forma subrayar las principales regiones que marcan la tendencia general de los precios de todo el planeta. Además, este trabajo reflejará los pronósticos esperados para los próximos años así como un resumen de las tendencias que se han seguido hasta el momento. Particularmente, se centrará la atención en el movimiento hacia los sistemas basados en forma de hub que comenzaron en EE.UU. y que llegaron a Reino Unido y al continente Europeo a principios del S.XX. Esta tendencia es la que se pretende implantar en España con el fin de conseguir una mayor competitividad, flexibilidad y liquidez en los precios y en el sistema gasista. De esta forma, poco a poco se irá construyendo la estructura hacia un Mercado Único Europeo que es el objetivo final que plantean los organismos de los estados miembros. Sin embargo, para la puesta en marcha de este nuevo modelo es necesario realizar una serie de cambios en el sistema como la modificación de la Ley de Hidrocarburos, la designación de un Operador de Mercado, elaboración de una serie de reglas para regular el mercado así como fomentar la liquidez del mercado. Cuando tenga lugar el cambio regulatorio, la liquidez del sistema español incrementará y se dará la oportunidad de crear nuevas formas para balancear las carteras de gas y establecer nuevas estrategias para gestionar el riesgo. No obstante, antes de que se hagan efectivos los cambios en la legislación, se implantaría uno de los modelos planteados en el “Gas Target Model”, el denominado “Modelo de Asignación de Capacidad Implícita”. La introducción de este modelo sería un primer paso para la integración de un mercado de gas sin la necesidad de afrontar un cambio legislativo, lo que serviría de VIII impulso para alcanzar el “Modelo de Área de Mercado” que sería el mejor para el sistema gasista español y se conectaría ampliamente con el resto de mercados europeos. Las conclusiones del estudio en relación a la formación del nuevo modelo en forma de hub plantean la necesidad de aprovechar al máximo la nueva situación y conseguir implantar el hub lo antes posible para poder dotar al sistema de mayor competencia y liquidez. Además, el sistema español debe aprovechar su gran capacidad y moderna infraestructura para convertir al país en la entrada de gas del suroeste de Europa ampliando así la seguridad de suministro de los países miembros. Otra conclusión que se puede extraer del informe es la necesidad de ampliar el índice de penetración del gas en España e incentivar el consumo frente a otros combustibles fósiles como el carbón y el petróleo. Esto situaría al gas natural como la principal energía de respaldo con respecto a las renovables y permitiría disminuir los precios del kilovatio hora del gas natural. El estudio y análisis de la dinámica que se viene dando en la industria del gas en el mundo es fundamental para poder anticiparse y planear las mejores estrategias frente a los cambios que poco a poco irán modificando el sector y el mercado gasista. ABSTRACT There is a great deal of focus on the natural gas market at the moment. Whether you view natural gas as bridging the gap between coal/oil and an altogether cleaner solution yet to be determined, or as a destination fuel which will be used not only for heating and gas fired generation but also as transportation fuel, there is no doubt that natural gas will have an increasingly important role to play in the global energy landscape. The natural gas industry is changing rapidly, as shale gas exploration changes the economics of gas production and LNG connects regions across the globe. The purpose of this study is to outline the present state of the global gas industry highlighting the differing models around the world. This study will pay particular attention to the move towards hub based pricing that has taken hold first in the US and over the past decade across the UK and Continental Europe. In the coming years the Spanish model will move towards hub based pricing. As gas market regulatory change takes hold, liquidity in the Spanish gas market will increase, bringing with it new ways to balance gas portfolios and placing an increasing focus on managing price risk. This study will in turn establish the links between the changes that have taken place in other markets as a way to better understanding how the Spanish market will evolve in the coming years.

Los Paisajes del Petróleo en la Península de Abşheron, Azerbaiyán. De la Utopía Estalinista al Colapso y Futuro Incierto de la Ciudad Petrolera de Neft Daşhları.

RESUMEN. Estudio sobre el modelo de planificación-producción de las ciudades extractivas y productivas de la antigua Unión Soviética –resultado de la materialización del régimen económico centralizado- y de sus consecuencias actuales derivadas de una falta de política medioambiental. Se centra en la ciudad extractiva de Neft Daşhları, de su colapso y de todo el paisaje energético petrolífero que constituye la península de Abşheron. ABSTRACT. Study about production-planning model of extraction and production cities of the former Soviet Union –resulted of the economic centralized system- and their present consequences resulting of a lack of environmental policy. It focuses on the extractive city: Neft Daşhları, its collapse and the entire energy landscape constitutes The Abşheron Peninsula.

La arquitectura en la construcción del paisaje: herramientas y principios de los proyectos del Duero Internacional (1953-1964) en su relación con la Escuela de Oporto

El examen a la singular aportación de João Archer, Nunes de Almeida y Rogério Ramos a la construcción del paisaje energético a través de la arquitectura se revela hoy de gran oportunidad para el avance de nuestra disciplina. Este colectivo de arquitectos que estudian en la Escuela de Oporto en el periodo en que el maestro Carlos Ramos realiza la reforma de la enseñanza de la Arquitectura en Portugal, proyecta y construye desde el interior del oficio de proyectos de la Hidroeléctica do Douro, las tres infraestructuras hidroeléctricas y las respectivas estructuras urbanas de Picote, Miranda y Bemposta, ubicadas en el Duero Internacional. El proceso cuyos parámetros de proyecto se exponen, está comprendido entre 1953 y 1964, y representa uno de los momentos más significativos y hercúleos en términos de infraestructura, industrialización y modernización de un Portugal entonces extremamente retrasado por la política de aislamiento de la dictadura de Salazar. Esto parece ser también el primer proyecto arquitectónico de infraestructuras a la escala del territorio en el cual se reconocen trazos específicos de la Escuela de Oporto y en donde se efectúa la revisión y transición de una modernidad enmarcada por el rigor de Loos y por un racionalismo de linaje gropiano, para un regionalismo crítico apropiado a la cultura del lugar, muy vinculado a Lúcio Costa, Wright y Aalto. Así, más que los logros espaciales, técnicos o constructivos conseguidos en los edificios, se expone el proceso utilizado por sus autores, su forma de entender y hacer un paisaje industrial de dimensión social y humanista a través de una arquitectura poética y minimalista sustentada en la cultura y en el carácter del lugar, valorando los argumentos, herramientas, principios y mecanismos que pueden constituirse referencia para nuestro oficio y aportar conocimiento que oriente la arquitectura hacia la construcción del paisaje contemporáneo. ABSTRACT Examining the singular contribution of João Archer, Nunes de Almeida and Rogério Ramos to the construction of the energy landscape through architecture, presents today a great opportunity for the advancement of our discipline. This collective of architects studying at the Porto School during the period in which master Carlos Ramos reformed the education of architecture in Portugal, designed and built from the Hidroeléctrica do Douro project office itself, the three hydropower infrastructures and the respective urban structures of Picote), Miranda and Bemposta, located in the International Douro. The project parameters are set between 1953 and 1964, representing one of the most significant moments of infrastructure, industrialization and modernization in a country at the time extremely delayed by the isolation resulting from the Salazar dictatorship. This is also the first architectural project of infrastructures within the scale of territory in which specific traits of the Porto School are recognized and wherein it came into effect the revision and transition from a modernity marked by the Loos rigor and Gropius rationalism lineage to a critical regionalism appropriate to the culture of the place, connected to Lúcio Costa, Wright and Aalto. Thus, rather than space, technical or constructive achievements of the buildings, it is exposed the process used by the authors, their way of understanding and projecting an industrial landscape with a social and humanistic dimension through a poetic and minimal architecture sustained in culture and character of the place, valuing arguments, tools, principles and mechanisms that can become a reference for our profession and provide knowledge to guide architecture towards the construction of the contemporary landscape.

Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability

The anomalous temperature dependence of protein folding has received considerable attention. Here we show that the temperature dependence of the folding of protein L becomes extremely simple when the effects of temperature on protein stability are corrected for; the logarithm of the folding rate is a linear function of 1/T on constant stability contours in the temperature–denaturant plane. This convincingly demonstrates that the anomalous temperature dependence of folding derives from the temperature dependence of the interactions that stabilize proteins, rather than from the super Arrhenius temperature dependence predicted for the configurational diffusion constant on a rough energy landscape. However, because of the limited temperature range accessible to experiment, the results do not rule out models with higher order temperature dependences. The significance of the slope of the stability-corrected Arrhenius plots is discussed.

Characteristic temperatures of folding of a small peptide

We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the folding of a small peptide is a multistage process associated with two characteristic temperatures, the collapse temperature Tθ and the folding temperature Tƒ. Our results give supporting evidence for the energy landscape picture and funnel concept. These ideas were previously developed in the context of studies of simplified protein models, and here are checked in an all-atom Monte Carlo simulation.

Stretching single-domain proteins: Phase diagram and kinetics of force-induced unfolding

Single-molecule force spectroscopy reveals unfolding of domains in titin on stretching. We provide a theoretical framework for these experiments by computing the phase diagrams for force-induced unfolding of single-domain proteins using lattice models. The results show that two-state folders (at zero force) unravel cooperatively, whereas stretching of non-two-state folders occurs through intermediates. The stretching rates of individual molecules show great variations reflecting the heterogeneity of force-induced unfolding pathways. The approach to the stretched state occurs in a stepwise “quantized” manner. Unfolding dynamics and forces required to stretch proteins depend sensitively on topology. The unfolding rates increase exponentially with force f till an optimum value, which is determined by the barrier to unfolding when f = 0. A mapping of these results to proteins shows qualitative agreement with force-induced unfolding of Ig-like domains in titin. We show that single-molecule force spectroscopy can be used to map the folding free energy landscape of proteins in the absence of denaturants.

Protein fluctuations are sensed by stimulated infrared echoes of the vibrations of carbon monoxide and azide probes

The correlation functions of the fluctuations of vibrational frequencies of azide ions and carbon monoxide in proteins are determined directly from stimulated photon echoes generated with femtosecond infrared pulses. The asymmetric stretching vibration of azide bound to carbonic anhydrase II exhibits a pronounced evolution of its vibrational frequency distribution on the time scale of a few picoseconds, which is attributed to modifications of the ligand structure through interactions with the nearby Thr-199. When azide is bound in hemoglobin, a more complex evolution of the protein structure is required to interchange the different ligand configurations, as evidenced by the much slower relaxation of the frequency distribution in this case. The time evolution of the distribution of frequencies of carbon monoxide bound in hemoglobin occurs on the ≈10-ps time scale and is very nonexponential. The correlation functions of the frequency fluctuations determine the evolution of the protein structure local to the probe and the extent to which the probe can navigate those parts of the energy landscape where the structural configurations are able to modify the local potential energy function of the probe.