Structured and Unstructured Binding of an Intrinsically Disordered Protein as Revealed by Atomistic Simulations

Intrinsically disordered proteins (IDPs) are a set of proteins that lack a definite secondary structure in solution. IDPs can acquire tertiary structure when bound to their partners; therefore, the recognition process must also involve protein folding. The nature of the transition state (TS), structured or unstructured, determines the binding mechanism. The characterization of the TS has become a major challenge for experimental techniques and molecular simulations approaches since diffusion, recognition, and binding is coupled to folding. In this work we present atomistic molecular dynamics (MD) simulations that sample the free energy surface of the coupled folding and binding of the transcription factor c-myb to the cotranscription factor CREB binding protein (CBP). This process has been recently studied and became a model to study IDPs. Despite the plethora of available information, we still do not know how c-myb binds to CBP. We performed a set of atomistic biased MD simulations running a total of 15.6 μs. Our results show that c-myb folds very fast upon binding to CBP with no unique pathway for binding. The process can proceed through both structured or unstructured TS's with similar probabilities. This finding reconciles previous seemingly different experimental results. We also performed Go-type coarse-grained MD of several structured and unstructured models that indicate that coupled folding and binding follows a native contact mechanism. To the best of our knowledge, this is the first atomistic MD simulation that samples the free energy surface of the coupled folding and binding processes of IDPs.Fil: Ithuralde, Raúl Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Roitberg, Adrián. University of Florida; Estados UnidosFil: Turjanski, Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentin

Experiencia relevante de vinculación universidad-industria

Reconociendo la convergencia como una tendencia transformadora, alineándonos con las áreas estratégicas definidas por el MinCyT en el Plan Estratégico 2020 y eligiendo hacer foco en el sector de la salud, Fluxit S.A y el grupo de bioinformática estructural de la Facultad de Ciencias Exactas y Naturales de la Universidad de Buenos Aires, vimos la oportunidad de avanzar hacia una mayor colaboración público-privada, con el objetivo de formar un equipo de trabajo conjunto, que se complemente, para el desarrollo de proyectos bioinformáticos orientados especialmente a la medicina personalizada. Fortaleciendo las actividades entre la industria, el sector científico-tecnológico y el Estado en su rol de articulador entre las empresas y las instituciones científico-tecnológicas; estimulando lo que se conoce como la triple hélice.Sociedad Argentina de Informática e Investigación Operativa (SADIO

Experiencia relevante de vinculación universidad-industria

Reconociendo la convergencia como una tendencia transformadora, alineándonos con las áreas estratégicas definidas por el MinCyT en el Plan Estratégico 2020 y eligiendo hacer foco en el sector de la salud, Fluxit S.A y el grupo de bioinformática estructural de la Facultad de Ciencias Exactas y Naturales de la Universidad de Buenos Aires, vimos la oportunidad de avanzar hacia una mayor colaboración público-privada, con el objetivo de formar un equipo de trabajo conjunto, que se complemente, para el desarrollo de proyectos bioinformáticos orientados especialmente a la medicina personalizada. Fortaleciendo las actividades entre la industria, el sector científico-tecnológico y el Estado en su rol de articulador entre las empresas y las instituciones científico-tecnológicas; estimulando lo que se conoce como la triple hélice.Sociedad Argentina de Informática e Investigación Operativa (SADIO

Accelerating Protein-Protein Docking using a Graphics Processing Unit (GPU)

Solving the structure of protein-protein complexes is one of the most important tasks in structural biology. Even though there has been great progress in recent years there still a small number of protein complexes structures deposited in the Protein Data Bank in comparison to isolated partners. In this sense, the computational prediction of protein complexes starting from the unbound structures, protein-protein Docking algorithms, has emerged as a reasonable alternative. Many docking programs employ Fast Fourier Transform (FFT) correlations as an efficient search strategy. We describe an implementation of a protein-protein docking program based on FFT surface complementarity that runs entirely on a Graphics Processing Unit (GPU), including grid generation, rotation and scoring. We evaluate its performance, and show that it can be up to 13 times faster than conventional CPU based implementations.Sociedad Argentina de Informática e Investigación Operativ

Solvents to Fragments to Drugs: MD Applications in Drug Design

Simulations of molecular dynamics (MD) are playing an increasingly important role in structure-based drug discovery (SBDD). Here we review the use of MD for proteins in aqueous solvation, organic/aqueous mixed solvents (MDmix) and with small ligands, to the classic SBDD problems: Binding mode and binding free energy predictions. The simulation of proteins in their condensed state reveals solvent structures and preferential interaction sites (hot spots) on the protein surface. The information provided by water and its cosolvents can be used very effectively to understand protein ligand recognition and to improve the predictive capability of well-established methods such as molecular docking. The application of MD simulations to the study of the association of proteins with drug-like compounds is currently only possible for specific cases, as it remains computationally very expensive and labor intensive. MDmix simulations on the other hand, can be used systematically to address some of the common tasks in SBDD. With the advent of new tools and faster computers we expect to see an increase in the application of mixed solvent MD simulations to a plethora of protein targets to identify new drug candidates

Omics data integration facilitates target selection for new antiparasitic drugs against TriTryp infections

Introduction:Trypanosoma cruzi, Trypanosoma brucei, and Leishmania spp., commonly referred to as TriTryps, are a group of protozoan parasites that cause important human diseases affecting millions of people belonging to the most vulnerable populations worldwide. Current treatments have limited efficiencies and can cause serious side effects, so there is an urgent need to develop new control strategies. Presently, the identification and prioritization of appropriate targets can be aided by integrative genomic and computational approaches.Methods: In this work, we conducted a genome-wide multidimensional data integration strategy to prioritize drug targets. We included genomic, transcriptomic, metabolic, and protein structural data sources, to delineate candidate proteins with relevant features for target selection in drug development.Results and Discussion: Our final ranked list includes proteins shared by TriTryps and covers a range of biological functions including essential proteins for parasite survival or growth, oxidative stress-related enzymes, virulence factors, and proteins that are exclusive to these parasites. Our strategy found previously described candidates, which validates our approach as well as new proteins that can be attractive targets to consider during the initial steps of drug discovery

Geobiology of Andean Microbial Ecosystems Discovered in Salar de Atacama, Chile

The Salar de Atacama in the Chilean Central Andes harbors unique microbial ecosystems due to extreme environmental conditions, such as high altitude, low oxygen pressure, high solar radiation, and high salinity. Combining X-ray diffraction analyses, scanning electron microscopy and molecular diversity studies, we have characterized twenty previously unexplored Andean microbial ecosystems in eight different lakes and wetlands from the middle-east and south-east regions of this salt flat. The mats and microbialites studied are mainly formed by calcium carbonate (aragonite and calcite) and halite, whereas the endoevaporites are composed predominantly of gypsum and halite. The carbonate-rich mats and microbialites are dominated by Bacteroidetes and Proteobacteria phyla. Within the phylum Proteobacteria, the most abundant classes are Alphaproteobacteria, Gammaproteobacteria and Deltaproteobacteria. While in the phylum Bacteroidetes, the most abundant classes are Bacteroidia and Rhodothermia. Cyanobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia phyla are also wellrepresented in the majority of these systems. Gypsum endoevaporites, on the contrary, are dominated by Proteobacteria, Bacteroidetes, and Euryarchaeota phyla. The Cyanobacteria phylum is also abundant in these systems, but it is less represented in comparison to mats and microbialites. Regarding the eukaryotic taxa, diatoms are key structural components in most of the microbial ecosystems studied. The genera of diatoms identified were Achnanthes, Fallacia, Halamphora, Mastogloia, Navicula, Nitzschia, and Surirella. Normally, in the mats and microbialites, diatoms form nano-globular carbonate aggregates with filamentous cyanobacteria and other prokaryotic cells, suggesting their participation in the mineral precipitation process. This work expands our knowledge of the microbial ecosystems inhabiting the extreme environments from the Central Andes region, which is important to ensure their protection and conservation.Centro de Investigaciones Geológica

Interacción de la melatonina con radicales libres

El objetivo de este trabajo de tesis fue el estudio a nivel molecular de la interacción de la melatonina (N-acetil-S-metoxitriptamina) con dos radicales libres de relevancia biológica, el radical oxhidrilo (OH·) y el óxido nítrico (NO). Para el desarrollo del presente trabajo se analizaron estas interacciones químicas desde un enfoque teórico, mediante técnicas de simulación computacional, desde un enfoque experimental, a través del estudio de las mismas en condiciones aisladas y controladas, y a través de la evaluación de los alcances fisiológicos de las reacciones propuestas. Para evaluar las interacciones con los diferentes blancos se analizó, en primer término, la superficie de energía potencial de la melatonina mediante técnicas de dinámica molécular basadas en campos de fuerzas clásicos y métodos semiempíricos. Se prestó especial atención a los aspectos relacionados con su libertad conformacional en vacío y en solución acuosa. Asimismo, se analizó la dependencia de las propiedades moleculares con la conformación. La reacción con el radical oxhidrilo se estudió mediante técnicas de estructura electrónica, evaluando los posibles mecanismos de reacción y realizando una exhaustiva caracterización de los intermediarios. El estudio de la interacción con NO se puede dividir en dos partes: i) la identificación y caracterización de los productos de reacción y la elucidación de los mecanismos operantes en diversos medios; y ii) el estudio del efecto de la melatonina sobre la biosíntesis de NO en la retina de hámster. Finalmente, mediante el uso de técnicas de resonancia magnética nuclear y de dinámica molecular, se realizó un estudio detallado de la interacción entre la melatonina y la calmodulina, una proteína con probado efecto estimulatorio en la biosíntesis del NO.The goal of this thesis was the study at a molecular level of the interactions of melatonin (N-Acetyl-5-metoxytriptamine) with two free radicals of biological relevance, hydroxyl (OH·) radical and nitric oxide (NO). The evaluation of the different interactions has been performed by a theoretical approach using molecular modeling tools; through the study of these reactions in isolated and controlled conditions, and finally by the evaluation of their physiological relevance. In order to evaluate the interactions with these different targets, the potential energy surface of melatonin has been analyzed by classical molecular dynamics and semiempirical electronic structure methodologies. Special attention has been paid to the conformational behavior in vacuum and aqueous solution. Moreover, the influence of conformation on several properties has been studied. The reaction with OH· has been analyzed with electronic structure methods. Feasible reaction mechanisms have been evaluated along with a thorough characterization of the intermediates. The research on the interaction with NO consisted of: i) the identification and characterization of the products, and the elucidation of the mechanisms operative in different environments ii) by the analysis of the effect of melatonin on NO biosynthesis in the hamster retina. Finally, by means of nuclear magnetic resonance and molecular dynamics techniques, a detailed study of the interaction of melatonin with calmodulin, a stimulatory protein of NO biosynthesis has been carried out.Fil:Turjanski, Adrián G.. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina

Changes in structure upon phosphorylation.

<p>(A) and (B) Structure of the Wild Type showing polar and charged inter protein interactions respectively. (C) and (D) depict the interactions of the15pSer and charged interactions respectively. (E) and (F) depict the interactions of the 18pThr and charged interactions respectively. (G and H) depict the interactions of the 20pSer and charged interactions respectively.</p