Thereza Amélia Soares da Silva.

A large fraction of the proteome of various organisms corresponds to polypeptides that do not form a defined three-dimensional structure. An entirely disordered polypeptide is known as an intrinsically disordered protein (IDP), and a segment of a protein that devoids a stable three-dimensional structure is called an intrinsically disordered region (IDR). It is increasingly recognized that IDRs are not simply passive disordered segments that connect well-folded domains, but they display biological functions themselves such as molecular recognition. IDPs and IDRs participate in a wide range of relevant cellular processes such as signal transduction pathways, RNA metabolism, and DNA packaging. However, the lack of a well-defined native structure leads to significant conceptual and methodological challenges in characterizing the structure or structural ensemble of IDPs and IDRs. Disordered proteins populate a diverse set of conformations with exceptional spatio-temporal heterogeneity and extraordinary conformational flexibility. For this reason, the elucidation of the functional mechanisms of IDPs and IDRs presupposes a full description of their structural dynamics. In this context, we propose to dissect the energy landscape of a series of biologically relevant IDPs and IDRs through an iterative approach that combines new computational algorithms and established experimental techniques, such as in-solution Small-angle X-ray scattering (SAXS), synchrotron radiation circular dichroism (SRCD), heteronuclear multidimensional Nuclear Magnetic Resonance (NMR) spectroscopy and video-microscopy of giant unilamellar vesicles (GUVs). The computational component of this proposal relies on two methods (and associated open-source codes) developed by our groups. The Energy Landscape Visualization Method (ELViM) was conceived as a multidimensional scaling method for describing protein-folding ensembles with great potential for investigating molecular mechanisms. Because the method does not depend on reaction coordinates or native reference structures, it is well-suited to tackle IDPs and IDRs. In contrast, the Surface Assessment Via grid Evaluation (SuAVE) method accounts for the effect of curvature in the calculations of structural properties of chemical interfaces regardless of the chemical composition, symmetry, and level of atom coarseness. The proposed research will contribute to better describing the structure ensemble of molecules that do not have a stable well-characterized structure and that display broad conformational distributions. By doing so, the joint research group will work to decipher how protein plasticity modulates function, thus allowing us to infer key factors that trigger diseases such as Parkinson, diabetes Mellitus and cancers, among others. The project will also contribute to the training of skilled individuals in the areas of computational biophysics and integrated structural biology, with emphasis on NMR, SRCD and SAXS.

Bolsa de Pesquisador do Exterior para o Prof. Wilfred van Gunsteren, ETHZ, Suiça

Bolsa de doutorado no exterior (BEPE) para Diane Lima

Bolsa de Doutorado de Diane Lima - PPQG-USP

Our main goal is to understand the physicochemical interactions modulating the attachment processes of infectious bacteria onto model surfaces designed to repel such attachment. We will approach this important problem from a molecular perspective, integrating the experimental characterization of polymer surfaces and computational simulations of bacterial surface onto such polymers. We will create well-defined abiotic model surfaces with a range of different chemistries through surface polymerization techniques. We will perform detailed chemical characterization of the model surfaces and bacterial surfaces. We will perform computational simulations for the interface between bacterial membranes and selected model surfaces exhibiting the desired functionalities.

O presente projeto propõe a aplicação de metodologias e protocolos computacionais para a elucidação das bases moleculares de doenças infecciosas, e para o desenvolvimento de moléculas com novas funcionalidades imunorreativas ou antibióticas. Esta proposta é parte de 02 projetos de cooperação científica prévios na área de bionanotecnologia e adesão bacteriana envolvendo a Ohio State University, USA e a University of Umeå, Suécia.

A aquisição de novos equipamentos multiusuários objetiva a melhoria da capacidade analítica do dQF de maneira a atender as demandas tecnológicas (pesquisa) e educacionais (formação de recursos humanos) de forma integrada às necessidades locais, regionais, bem como de laboratórios de outras regiões do país. Os equipamentos pleiteados visam a inovação regional através do desenvolvimento de uma nova área de pesquisa na região. Salientamos que os equipamentos solicitados serão instalados em locais físicos já existentes do Departamento de Química Fundamental da UFPE. A presente proposta tem como objetivo geral o aperfeiçoamento da infra-estrutura multiusuário do DQF nas suas instalações já existentes. Como objetivos específicos espera-se:

1. Ampliação e diversificação do parque de equipamentos multiusuários da Central Analítica; 2. Inovação regional através do desenvolvimento de uma nova área de pesquisa no Nordeste; 3. Fortalecimento do programa de pós-graduação em Química e programas associados através da diversificação do portfolio de pesquisa e ensino.

Este projeto visa integrar competências individuais dos pesquisadores das duas equipes envolvidas (USP/Capital e UFPE), com especialidades em modelagem, simulação e caracterização de sistemas biológicos, em uma rede de Biologia Computacional. As equipes são compostas por docentes das Ciências Exatas e da Terra e Ciências Biológicas e Biomédicas, sendo 5 físicos, 4 químicos, 2 biólogos, 1 farmacêutico e 1 cientista da computação, totalizando 13 docentes (9 da USP e 4 da UFPE). Como o projeto é inerentemente teórico daremos destaque apenas às atividades que serão desenvolvidas pelos pesquisadores teóricos, porém a participação de pesquisadores experimentais é fundamental, tanto em fornecer/colaborar com os dados experimentais como também nas discussões científicas e acadêmicas; e na participação na formação de recursos humanos com uma visão ampliada entre teorias e experimentos. Dentre os 8 docentes teóricos temos um grupo multidisciplinar com 4 físicos (USP), 2 biólogos (UFPE), 1 químico (UFPE) e 1 cientista da computação (USP). Essa composição mostra uma complementaridade de perfil acadêmico entre as duas equipes, pois a equipe da UFPE é voltada às áreas mais biológicas (Biologia e Bioquímica) e da USP voltada às áreas mais exatas (Biofísica e Bioinformática). Esse perfil das equipes envolvidas reflete, em parte, o quadro de docentes teóricos de ambas as instituições, entretanto contribuirá com informações complementares na formação de recursos humanos e com uma visão crítica nas discussões acadêmicas voltadas à integração das Ciências Biológicas às Ciências Exatas e da Terra na área de Biologia Computacional, propiciadas com a formação da rede. Fizemos a opção de montar inicialmente uma equipe pequena para garantir a qualidade e eficiência nas discussões científicas e acadêmicas. Todos esses docentes são bolsistas de produtividade do CNPq (1 no nível 1A, 2 no nível 1C e 5 no nível 2); com uma média de 5 orientandos em nível de pós-graduação (total de 26 doutorandos e 14 mestrandos) e cerca de 3 em outros níveis (12 pós-doutores, 6 graduandos em IC e 2 estudantes do ensino médio em Pré-IC); e uma média de mais de 6 trabalhos publicados/docente-ano nos últimos 5 anos (entre 2008-2013). Esses indicadores mostram a excelência e a grande capacidade de produção de conhecimento científico e formação de recursos humanos do grupo de docentes teóricos envolvidos neste projeto. Adicionalmente, esse projeto irá propiciar uma integração de duas grandes universidades das regiões Nordeste e Sudeste do país e aproximar academicamente duas regiões tão distantes geograficamente.

Computational resources for simulations of Antimicrobial Polymeric Surfaces and Biological Membranes

Medical devices can give rise to difficult infections if they become colonized by bacteria. They can also influence and affect mammalian cells in their surrounding in a variety of ways. Consequently, medical devices need to display very poor adhesion of bacteria whilst being mammalian cell friendly. So understanding how both types of organisms behave on, or in close proximity of surfaces is important. The interactions between cells and a surface will be highly governed by physicochemical properties of both the cell and the substrate surface. Thus a better fundamental understanding of these interactions should allow our society to design better medical surfaces. The proposed project will study the interactions between a range of different well characterized polymeric surfaces with Pseudomonas aeruginosa bacteria and human keratinocytes (epithelial cells). Epithelial cells are relevant to this work as they are very often in contact with medical devices, and epidermal stem cells are an important type of epithelial cells implicated in wound healing, for example. We will study the interactions both experimentally and through molecular dynamics simulations to obtain a detailed understanding of the processes that influence the attachment or repulsion between a cell and an abiotic surface for both bacterial cells and mammalian cells. The results from this project are expected to be of great importance for the biomaterials field and influence the way we design biomaterials surfaces.

O objetivo deste projeto e investigar a enzima 3-hidroxi-quinurenina transaminase como alvo para compostos 1,2,4-oxadiazois com atividade larvicida visando a elucidação do mecanismo molecular de atividade destes compostos.

Nesse projeto, cálculos de dinâmica molecular a nível atomístico em conjunto com dados de ressonância magnética nuclear (RNM) (e.g., NOEs, J-Couplings, RCDs) serão utilizados para estudar as interações que regem a adsorção de biomoléculas na superfície de nanomateriais e superfícies minerais, bem como o empacotamento e a interaçã de polissacarídeos com complexos moleculares. Serão endereçados i) a dinâmica funcional e estabilidade estrutural dos biopolímeros na interface com o nanomaterial, ii) as mudanças conformacionais em função da interação com a nanopartícula ou superfiície mineral, iii) a identificação de sítios de ligação à materiais na superfície dos biopolímeors, e iv) a caracterização do arranjo molecular (assembly) das biomoléculas na superfície do nanomaterial quando adsorvidas.

In the present proposal, computational simulations coupled to NMR spectroscopy will be used to investigate the conformational heterogeneity of phospholamban and its effect on the regulation of Ca2+ uptake by Ca-ATPASE. The long-term goal of this effort is to establish the conformational transition mechanism that enables this process.

Electron and proton transfer reactions will be studied for two constituents of oxygenic photosynthesis, hydrogenases and the photosynthetic reaction center of Blastochloris viridis. We will use electron transfer simulation methodologies based on Marcus? theory, and classical molecular dynamics simulation to sample representative molecular environments for the electron transfer between redox sites, the simulation of proton hopping using the semi-classical QHOP and QM/MM methodologies, and thermodynamic integration to evaluate relative free energies of the possible redox states of the reaction center complex and hydrogenases. Ultimately, our research aims to provide a detailed molecular-level characterization and understanding of microbial processes that may play an important role in biological light harvesting and hydrogen production. The proposed research project will take advantage of the computational chemistry software system NWChem which, in addition to a wide range of electronic structure capabilities for density functional theory and ab initio molecular orbital theory calculations, also supports molecular dynamics (MD) calculations with a variety of empirical (classical mechanical) force fields for the simulation of macromolecular and solution systems.

The specific hypothesis behind the proposed research is that a denatured, unfolded, inactive protein may be able to be renatured, refolded, re-activated and stabilized in a Functionalized Nanoporous Support, which thereby plays a role as a molecular crowding environment and a confined space for the protein. Besides molecular crowding and confinement theory and modeling, this hypothesis is based on our following experimental observations: First, we have entrapped three different enzymes in functionalized mesoporous silica (FMS) with pore sizes as large as tens of nanometers and demonstrated that they exhibit enhanced stability and higher activity than the enzymes free in solution, which are either from our own recombinant expression or commercial sources. Second, enzyme specific activity can be increased or decreased to a large extent by changing protein loading density in FMS; Third, we found that FMS and chaotropic agents can act synergistically to enhance enzyme activity. Based on these observations, we see that FMS may have functioned as a molecular crowding environment and a confinement space to promote renaturation and re-activation of the denatured protein.