Interactions of Metal Cations in Bioorganic Environment Computational Study Using Quantum Mechanics and Molecular Mechanics Tools Zdeněk Futera Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied by QM/MM computational technique. The whole re- action mechanism is divided into three phases - hydration of [RuII (η6 - benzene)(en)Cl]+ , consequent binding DNA and final intra-strand cross-link formation between two adjacent guanines. Free energy profiles of all reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex is described by DFT. For that purpose, special QM/MM software was developed to couple Gaussian and Amber programs. Calculated free energy barriers of Ru(II) hydration as well as DNA binding process are in good agreement with experimentally determined rate constants. Reaction pathway for cross-link formation was predicted that is feasible from both thermodynamical and kinetical point of view.

Made available in DSpace on 2015-03-26T13:42:37Z (GMT). No. of bitstreams: 1 texto completo.pdf: 1636951 bytes, checksum: 5c4c3aea8b56b9b0913479b27b012cea (MD5) Previous issue date: 2007-08-01 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Proteins of the family of LRR-RLKs (receptor-like-kinases with leucine-rich repeats) have a conceptual relevance in signaling events but in plants information regarding function is limited to a few members of this family. The receptors NIK1, NIK2 and NIK3 of Arabidopsis thaliana belong to the sub-family LRRII-RLK and were initially identified by their capacity to interact with the geminivirus NSP protein. In response to an unknown stimulus, NSP-interacting kinases (NIKs) are activated after the formation of dimmers and intermolecular autophosphorylation. The inhibition of autophosphorylation of NIK by NSP and the activation of NIK genes increase the susceptibility to viral infection, suggesting that this protein is involved in a defense pathway against geminivirus infection. The downstream components of this pathway, mediated by the protein NIK, have yet to be identified. In the present study, the biochemical and functional characterization of two ribosomal proteins, L10 and L18 were described, these being capable of interacting with the protein NIK via the yeast two-hybrid system. In vitro studies demonstrated that the protein NIK is capable of phosphorylating the protein L10, but not L18. Of the members of the LRRIIRLK family, the protein NIK2 phosphorylates L10, while NIK3 presents a low capacity for phosphorylation of the substrate. However, the development protein SERK1 does not use L10 as a substrate. Assays of transient expression in tobacco plants, revealed that the L18 protein is located in the cytoplasm, as well as around the nucleus and the nucleoli of some cells. In turn, in 97% of the cells, L10 was localized only in the cytoplasm, although it was also found in the nucleus, in approximately 3% of the observed cells. The transient expression of NIK1 and NIK2 redirects the L10 protein to the nucleus in approximately 30% of the cells. In contrast, NIK3 does not relocalize the L10 protein to the nucleus, and L18 does not change its localization in the presence of the NIKs. In plants infected with TGMV, a change only in the cytoplasmic localization of L10 was observed, accumulating in points of the cytoplasm when not co-localized with NIK. To prove genetically the interactions of L10-NIK and L18-NIK, null alleles for the genes L10 and L18 de Arabidopsis, containing T-DNA insertion, were obtained and inoculated with CaLCuV. The inactivation of the genes L10 and L18 restored the elevated susceptibility phenotype of nik1 and the knockout plants, principally l10, presented severe symptoms and high rates of infection when compared with the wild columbia plants. The results of this work are consistent with a model that places the ribosomal proteins L10 and L18 as functional components of the defense signaling pathway mediated by the protein NIK, L10 being a component immediately downstream of the transmembrane receptor. / As proteínas da família das LRR-RLKs (receptor-like-quinases com repetições ricas em leucina) possuem uma relevância conceitual em eventos de sinalização mas, em plantas, a informação funcional ainda é restrita a alguns membros desta família. Os receptores NIK1, NIK2 e NIK3 de Arabidopsis thaliana pertecem à sub-familia LRRII-RLK e foram inicialmente identificados pela sua capacidade de interagir com a proteína NSP de geminivírus. Em resposta a um estímulo desconhecido, NSP-interacting kinases (NIKs) são ativadas após a formação de dímeros e autofosforilação intermolecular. A inibição da autofosforilação de NIK por NSP e a inativação de genes NIKs aumenta a suscetibilidade à infecção viral, sugerindo que esta proteína estaria envolvida em uma via de defesa contra a infecção por geminivírus. Os componentes downstream dessa via de sinalização, mediada pela proteína NIK, ainda não foram identificados. No presente estudo foi descrita a caracterização bioquímica e funcional de duas proteínas ribossomais, L10 e L18, as quais foram capazes de interagir com a proteína NIK através do sistema de duplo híbrido de leveduras. Estudos in vitro demonstraram que a proteína NIK é capaz de fosforilar a proteína L10, mas não L18. Entre os membros da família LRRII-RLK, a proteína NIK2 fosforila L10, enquanto NIK3 apresenta uma baixa capacidade de fosforilação do substrato. No entanto, a proteína de desenvolvimento SERK1 não utiliza L10 como substrato. Ensaios de expressão transiente, em plantas de tabaco, revelaram que a proteína L18 está localizada no citoplasma, bem como ao redor do núcleo e no nucléolo de algumas células. Por sua vez, em 97% das células, L10 foi localizada apenas no citoplasma, embora tenha sido encontrada no núcleo, em aproximadamente 3% das células observadas. A expressão transiente de NIK1 e NIK2 redireciona a proteína L10 para o núcleo em aproximadamente 30% das células. Em contraste, NIK3 não relocaliza a proteína L10 para o núcleo, e L18 não muda sua localização na presença das NIKs. Em plantas infectadas com TGMV, observou-se mudança apenas na localização citoplasmática de L10, acumulando-se em pontos do citoplasma quando não colocalizada com NIK. Para se comprovar geneticamente as interações de L10-NIK e L18- NIK, alelos nulos para os genes L10 e L18 de Arabidopsis, contendo inserção de T-DNA, foram obtidos e inoculados com o CaLCuV. A inativação dos genes L10 e L18 recapitulou o fenótipo de suscetibilidade aumentada de nik1 e as plantas knockout, principalmente l10, apresentaram sintomas severos e taxa de infecção alta quanto comparados com as plantas selvagens columbia. Os resultados deste trabalho são consistentes com um modelo que posiciona as proteínas ribossomais L10 e L18 como componentes funcionais da via de sinalização de defesa mediada pela proteína NIK, sendo L10 um componente imediatamente downstream ao receptor transmembrana.

Les structures cristallographiques de macromolécules comme les protéines, obtenues par la biologie structurale sont des modèles statiques. Or, c'est la flexibilité et la dynamique de ces macromolécules qui sont généralement responsables de leurs fonctions. La simulation permet d'explorer cette flexibilité lors de différents phénomènes qui ont lieu dans ces systèmes : une réaction chimique, des interactions avec une petite molécule… Simuler de tels phénomènes est un défi car la dynamique moléculaire classique ne permet pas de les observer. Des algorithmes permettent d'accélérer l'échantillonnage des dynamiques pour lever cette limitation et de calculer les barrières d'activation pour de tels phénomènes. Simultanément, le choix du niveau de calcul est crucial car il faut concilier la taille importante des systèmes, la nature des interactions et les phénomènes électroniques impliqués. Dans ce travail, différentes méthodes, dont principalement la métadynamique soit au niveau classique ou quantique, ou encore en combinant les deux niveaux quantique/classique, seront utilisées pour modéliser quatre processus complexes : des changements de conformations d'une protéine, des interactions entre métalloprotéine et inhibiteur, des réactions en solution et dans une enzyme. / Crystallographic structures of macromolecules, such as proteins, obtained by structural biology are static models. However, flexibility and dynamics of macromolecules are generally responsible for their functions. Modeling allows us to explore this flexibility in different phenomena that take place in these systems: a chemical reaction, interaction with a small molecule... Modeling such phenomena is a challenge because they cannot be observed by classical molecular dynamics. Algorithms can accelerate sampling of dynamics to simulate these events and calculate their activation barriers. Simultaneously, the choice of the level of calculation is crucial because it must merge with the size of the systems, the nature of interactions and the electronic phenomena involved.In this thesis, some methods, mainly metadynamics at classical level, quantum or the hybrid quantum/classical level, will be used to model four complex processes: conformational changes of proteins, metalloprotein/inhibitor interactions, reactivity in solution and enzymatic reactivity.

Neste trabalho estudamos o espectro de absorção da clorofila d, incluindo os efeitos do solvente metanol, utilizando a Teoria do Funcional da Densidade Dependente do Tempo em combinação com o método s-QM/MM. Diferentes abordagens para a descrição do meio solvente, que vão desde o modelo contínuo polarizável até a inclusão de moléculas explícitas do solvente, são utilizadas. Observamos que a inclusão do solvente desloca o espectro, em relação ao calculado em vácuo, para o vermelho. A inclusão de 20 moléculas explícitas de metanol e 880 representadas como as cargas pontuais do seus átomos para a descrição do meio solvente foi a que melhor concordou com os valores experimentais. Mediante cálculos de mecânica quântica obtivemos para o complexo composto por a molécula de clorofila d e apenas uma de metanol explícita um deslocamento do átomo de magnésio da clorofila d em relação ao anel de 0,31 Å. Mediante a analise da função de distribuição radial de pares obtida da simulação clássica comprovamos que esse átomo de magnésio é penta-coordenado. Além disso, é usada uma estrutura simplificada da clorofila d baseado na localização dos orbitais moleculares participantes das transições eletrônicas com o objetivo de diminuir o custo computacional dos cálculos de mecânica quântica. Os espectros calculados para a clorofila d não apresentaram diferenças significativas com os calculados para a simplificação proposta. Como complementação o espectro Raman da clorofila d isolada é calculado mediante DFT e alguns dos modos normais são caracterizados. / In this work we study the absorption spectrum of chlorophyll d, including the effects of the solvent methanol, using the Time Dependent Density Functional Theory in combination with the method s-QM/MM. Different approaches for the description of the solvent medium, ranging from the polarizable continuum model to the inclusion of explicit solvent molecules, are used. We note that the inclusion of solvent shifts the spectrum, relative to that calculated in vacuum, to the red side of the spectrum. The inclusion of 20 explicit molecules of methanol and 880 represented as point charges of their atoms for the description of the solvent medium was the one that best agreed with the experimental values. By quantum mechanics calculations we obtained for the complex composed of the molecule of chlorophyll d and only one explicit methanol molecule a displacement of the magnesium atom of chlorophyll d in relation to the ring of 0,31 Å. By means of the analysis of the radial distribution function obtained from the classic simulation we can see that this atom of magnesium is penta-coordinated. In addition, a simplified structure of chlorophyll d is used based on the location of the molecular orbitals involved in the electronic transitions in order to reduce the computational cost of quantum mechanics calculations. The spectra calculated for chlorophyll d did not show significant differences with those calculated for the proposed simplification. As a complement the Raman spectrum of isolated chlorophyll d is calculated by DFT and some of the normal modes are characterized.

As transições eletrônicas que apresenta as energias mais baixas no retinal e em quatro retinais sintéticos foram analisadas em dois diferentes ambientes: no vácuo e ligados à proteína bacterioopsina por uma base de Schiff protonada, utilizando diversos métodos de química teórica. Os resultados aqui apresentados fornecem indicativos de que três estados eletrônicos estão envolvidos na formação da primeira banda de absorção dos aldeídos, enquanto que, no caso dos compostos ligados à proteína apenas dois estados estariam envolvidos. As análises discutidas neste trabalho também sugerem uma possível explicação para o envolvimento de dois estados eletrônicos excitados no processo de fotoisomerização do retinal ligado à bacterioopsina. / Low-lying electronic transitions of retinal and of four synthetic retinals were analyzed in two different environments: in vacuum and linked to bacterioopsin through a protonated Schiff base, employing several methods of theoretical chemistry. The results here reported suggest that the first absorption band of the aldehydes involves three electronic states, while for the case of protein linked compounds, two states would be embraced. Our discussions also provided a possible explanation about the involvement of two electronic excited states in the photoisomerization process of retinal linked to bacterioopsin.

Absorção e Emissão de radiação eletromagnética por moléculas na região do UV-Vis fornece informações sobre os estados eletrônicos excitados, sendo propriedades de grande interesse devido a sua relação com processos biológicos, bem como suas possíveis aplicações em diagnósticos e tecnologia. Essas propriedades são sensíveis ao meio em que as moléculas se encontram, tornando-se assim natural a busca por métodos teóricos que possibilitam descrever essas interações. Neste trabalho, nós usamos a metodologia Sequential-Quantum Mechanics/Molecular Mechanics para estudar o espectro de absorção e de emissão de moléculas de relevância biológica, quando em solução. Simulações clássicas Monte Carlo foram usadas pra construir uma configuração eletrostática média do líquido para posterior cálculo das propriedades, feito através dos métodos multiconfiguracionais CASSCF e CASPT2. Cuidados especiais foram tomados para incluir a polarização eletrônica que o soluto sofre devido à presença do solvente. Nossa contribuição é a adaptação do método do Gradiente de Energia Livre para permitir a obtenção de geometrias de estados excitados do soluto em solução. A técnica foi implementada em um programa e aplicada com sucesso nos sistemas estudados. As perspectivas agora se abrem para a obtenção de intersecções cônicas em meio solvente, permitindo assim o estudo de decaimentos não-radiativos em sistemas solvatados. / Absorption and emission of electromagnetic radiation by molecules in the UV-Vis region yields information about the electronic excited states, being properties of great interest due its relation with biological process, as well as its possible applications in diagnostics and technology. These properties are sensible to the environment in which the molecules are, making natural the search for theoretical methods that describe these interactions. In this work, we have used the Sequential-Quantum Mechanics/Molecular Mechanics methodology to study the spectrum of absorption and emission of molecules of biological relevance, when in solution. Classical Monte Carlo simulations were carried out to construct an average solvent electrostatic configuration and used to represent the liquid in posterior quantum mechanics calculation of the properties, performed by using the multiconfigurational methods CASSCF and CASPT2. Special cares were taken to include the electronic polarization of the solute due the solvent. Our contribution is the adaptation of the Free Energy Gradient method to allow the determination of the solute excited states geometries in solution. The method was implemented in a computer program and successfully applied in the systems studied. The perspectives are now open to the calculation of conical intersection in solvent environment, enabling the study of nonradioactive decays in solvated systems.

La bioluminescence est un processus complexe dans lequel la réaction chimique d'un substrat, catalysée par une protéine, entraîne l'apparition d'une émission de lumière dans le spectre visible. Dans le cas des lucioles, un insecte émettant dans le domaine du jaune-vert, le substrat se nomme luciférine et la protéine luciférase. Cependant, la taille et la complexité de ce système chimique limite sa compréhension, notamment celle du mécanisme réactionnel.L'apport de la chimie théorique dans ce domaine est essentiel et a prouvé son utilité dans de nombreux cas. L'utilisation de la méthode QM/MM, méthode hybride couplant la mécanique quantique et la mécanique moléculaire permet de modéliser et d'étudier ces systèmes biologiques.Cette thèse se focalise sur deux approches différentes de l'étude de la bioluminescence chez les lucioles. La première consiste à étudier l'effet de certaines modifications chimiques sur la couleur de la bioluminescence. On s'intéresse plus particulièrement à un analogue de la luciférine et à certaines luciférases issues d'autres systèmes bioluminescents. Par cette étude on cherche à rationaliser et à prédire l'effet ainsi que l’impact de ces changements sur l’émission. Le deuxième sujet explore deux étapes du mécanisme réactionnel de la bioluminescence: d'une part, la coordination du dioxygène sur un intermédiaire de la réaction, une étape encore non étudiée et d'autre part la réaction de tautomérisation dans l'état excité et au sein de la protéine entre deux formes émissives possibles de la luciférine / The bioluminescence is a complex process that involves the reaction of a substrate, catalysed by an enzyme that sheds light in the visible spectra. In fireflies, the light emitted has a yellow-green tone thanks to the interaction between the substrate luciferin and the protein luciferase. However the size and the complexity of the system prevent its comprehension especially when dealing with the reaction mechanism.The use of computational chemistry is key to understand and improve the comprehension of the bioluminescence. The hybrid QM/MM method that combines quantum mechanics with molecular mechanics is a great tool to model and study bioluminescent systems.This thesis deals with two different approaches of the bioluminescence in fireflies. The first one is related to the study of chemical modifications that tune the emission colour. We will discuss about one analogue of the luciferin and on new luciferases from others bioluminescent species. The goals of this study are to rationalise and predict both the effect and the impact of these modifications on the emission. The second subject deals with two different steps of the bioluminescent mechanism. The first one discusses the binding of the dioxygen to the bioluminescent intermediate, which was so far unstudied and the second one about the tautomerization in the excited state and in the protein of two possible emissive forms of the luciferin

This thesis contains three main sections. In the first section, we examine methodologies to discriminate Type II protein kinase inhibitors from the Type I inhibitors. We have studied the structure of 55 Type II kinase inhibitors and have notice specific descriptive geometric features. Using this information we have developed a pharmacophore and a shape based screening approach. We have found that these methods did not effectively discriminate between the two inhibitor types used independently, but when combined in a consecutive way – pharmacophore search first, then shape based screening, we have found a method that successfully filtered out all Type I molecules. The effect of protonation states and using different conformer generators were studied as well. This method was then tested on a freely available database of decoy molecules and again shown to be discriminative. In the second section of the thesis, we implement and assess swarm-based docking methods. We implement a repulsive particle swarm optimization (RPSO) based conformational search approach into Autodock 3.05. The performance of this approach with different parameters was then tested on a set of 51 protein ligand complexes. The effect of using different factoring for the cognitive, social and repulsive terms and the importance of the inertia weight were explored. We found that the RPSO method gives similar performance to the particle swarm optimization method. Compared to the genetic algorithm approach used in Autodock 3.05, our RPSO method gives better results in terms of finding lower energy conformations. In the final, third section we have implemented a Monte Carlo (MC) based conformer searching approach into Gaussian03. This enables high level quantum mechanics/molecular mechanics (QM/MM) potentials to be used in docking molecules in a protein active site. This program was tested on two Zn2+ ion-containing complexes, carbonic anhydrase II and cytidine deaminase. The effects of different QM region definitions were explored in both systems. A consecutive and a parallel docking approach were used to study the volume of the active site explored by the MC search algorithm. In case of the carbonic anhydrase II complex, we have used 1,2-difluorobenzene as a ligand to explore the favourable interactions within the binding site. With the cytidine deaminase complex, we have evaluated the ability of the approach to discriminate the native pose from other higher energy conformations during the exploration of the active site of the protein. We find from our initial calculations, that our program is able to perform a conformational search in both cases, and the effect of QM region definition is noticeable, especially in the description of the hydrophobic interactions within the carbonic anhydrase II system. Our approach is also able to find poses of the cytidine deaminase ligand within 1 Å of the native pose.

L’obtention, dans des conditions douces, sélectives et de chimie durable de molécules ciblées est aujourd’hui un enjeu majeur. Les métalloenzymesartificielles représentent une voie d’investigation importante, car en jouant, par exemple, sur la seconde sphère de coordination,il est possible de modifier fortement la réactivité de ces systèmes bio-inspirés. Le développement de cette chimie suppose une connaissanceapprofondie des différentes étapes du mécanisme de la réaction envisagée. Pour cela, la chimie théorique est essentielle à la rationalisation dela réactivité chimique mais elle souffre encore de nombreuses insuffisances pour les systèmes que nous nous proposons d’étudier.Dans ce travail, nous avons choisi d’étudier la superoxyde réductase, enzyme détoxifiante du radical superoxyde. Si de nombreuses expérimentalessont disponibles détaillant certains intermédiaires, le mécanisme précis est peu documenté. Le but a été de mettre en place uneméthodologie complète allant du développement de paramètres MM spécifiques à l’étude de la réactivité par métadynamiques QM/MM.Le développement de paramètres MM pour le site actif à fer a permis son étude en dynamique MM donnant des informations sur la conformationsdu squelette peptidique ainsi que l’interaction avec les molécules de solvant. De part la nature du fer, une description QM du site actifà été nécessaire via l’utilisation de DFT hybride. Les métadynamiques QM/MM ont permis quant à elles d’explorer les chemins réactionnelset de caractériser les espèces ainsi formées et les énergies d’activations.Cette méthodologie a permis la compréhension en premier lieu de la réactivité native de la forme sauvage et elle a aussi permis d’explorer lesréactivités nouvelles des mutations de la SOR permettant ainsi de définir le rôle crucial de la seconde sphère de coordination. / Obtaining targeted molecules under gentle, selective and sustainable conditions is still a major challenge. Artificial metalloenzymes are animportant line of enquiry, because by playing, for example, with the second sphere of coordination, it is possible to strongly modify thereactivity of these bio-inspired systems. The development of this chemistry presupposes a thorough knowledge of the different stages of themechanism of the reaction under study. For this reason, theoretical chemistry is essential to rationalize chemical reactivity, but it still suffersfrom many shortcomings for the systems we propose to study.In this work, we study the superoxide reductase, a detoxifying enzyme of the superoxide radical. While many experiments are available detailingsome intermediates, the precise mechanism is not well documented. The aim was to implement a complete methodology ranging from thedevelopment of specific MM parameters to the study of reactivity by QM/MM metadynamics.The development of MM parameters for the iron active site allowed its study by MM dynamics giving informations on the conformation ofthe peptide backbone as well as on the interaction with solvent molecules. Due to the nature of the iron, a QM description of the active sitewas required using hybrid DFT. QM/MM metadynamics have allowed us to explore reaction pathways and to characterize the compoundsformed to obtain the needed activation energies. This methodology made it possible to understand the native reactivity of the wild form ofthe SOR, but also to explore the new reactivity of the mutations of the SOR and thus to define the crucial role of the second coordination sphere.

Den ökande koldioxidhalten i atmosfären har lett till ett ökat intresse för användning av solljus, ett exempel är inom kemi. Att använda ljus i kemi kan leda till nya och intressanta kemiska reaktioner och kan tillämpas i användningsområden som exempelvis fotokatalys och fotovoltaik. Genom att kombinera de kraftfulla egenskaperna av ljus i kemi med den höga selektivitet som karaktäriserar proteiner kan intressanta och kraftfulla maskinerier erhållas, så kallade fotoaktiva proteiner. Att studera de fotoinducerade beteendena i fotoaktiva proteiner är däremot icke-trivialt eftersom många utmaningar uppstår från ett experimentellt och teoretiskt perspektiv. Denna uppsats fokuserar på det teoretiska perspektivet. Simulationer av beteenden hos fotoaktiva proteiner leder till utmaningar relaterade till den stora variationen av tids- och längdskalor involverade, där allt ifrån ultrasnabba och lokaliserade excitationsprocesser till storskaliga strukturförändringar som utspelar sig på större tidsskalor. Detta, tillsammans med det faktum att det inte finns en "svart låda" som vi kan använda för nya teoretiska studier motiverar ett försiktigt tillvägagångssätt för teoretiska studier av fotoaktiva proteiner. I detta projekt görs en teoretisk undersökning av två nyligen framställda fotosensibiliserande proteiner (PSP2 och PSP3). De skapades för att härma huvudprocesserna av fotosyntesen i plantor. Fotosensibiliserande proteinerna skiljer sig med en enda aminosyra (position 203), som är en aspartat i PSP2 och en tyrosin i PSP3. Även fast proteinerna är strukturellt lika så uppvisar de olika fotoinducerade beteenden. Målet med denna studie är att klargöra för de mekanistiska detaljerna bakom dessa olikheter. Som ett första steg i att teoretiskt studera PSP2 och PSP3 upprättar vi ett protokoll för teoretisk förberedelse av proteinerna. Detta protokoll används sedan för att teoretiskt undersöka fotofysiken i dessa två proteiner med hjälp av kvantmekaniska/ molekylär mekaniska simuleringar. Våra resultat ger en första ordningens kartläggning av de exciterade tillstånden i de två proteinerna. Vi erhåller en intressant laddningsöverföring tillstånd i PSP3 som involverar tyrosinen och proteinets kromofor, med en energi lägre än det tillstånd ansvarig för absorption av ljus. Denna laddningsöverföring saknas i PSP2 och kan därför vara anledningen till de olika fotoinducerade beteendena i proteinerna. Detta kräver dock fortsatta studier av de två systemen. / The increase of carbon dioxide levels in the atmosphere have resulted in an increasing interest in using solar light for different purposes, one being chemistry. The introduction of light in chemistry can drive new and exciting chemical reactions, finding applications in many fields such as photocatalysis and photovoltaics. Combining the aspects of light in chemistry together with the high selectivity that characterizes proteins make for interesting and powerful machineries, so-called photoactive proteins. However, studying the behaviors of photoactive proteins is a non-trivial task and many challenges arise from both an experimental and a theoretical point of view. This thesis takes a theoretical perspective. The challenges associated with simulating photoactive protein behavior originate from the wide range of time and length scales involved, ranging from ultrafast and localized excitation processes to large-scale structural changes occurring on longer timescales. This, together with the fact that there is no black box that we can use for novel theoretical studies of photoactive proteins motivates a careful approach for theoretical studies of photoactive proteins. In this project, we conduct a theoretical investigation of two photosensitizer proteins (PSP2 and PSP3), recently engineered to capture the essence of plant photosynthesis. The photosensitizer proteins differ by only one residue (position 203), which is an aspartate in PSP2 while a tyrosine in PSP3. Although structurally similar, the proteins demonstrate different photoinduced behaviors. This study aims to shed light on the mechanistic details underlying these differences. As a first step to study PSP2 and PSP3 computationally, we develop a computational protocol for protein preparation. The protocol is then used for a theoretical investigation of the photophysics of the two proteins using quantum mechanics/molecular mechanics simulations. Our results provide a first mapping of the electronic-state manifold of the two proteins. We find an intriguing charge-transfer state in PSP3, involving the tyrosine and the protein chromophore, located below bright state responsible for light absorption. This state is absent in PSP2 and could therefore be the reason for the different photoinduced behavior of the two proteins. However, this requires further studies of the two systems.