Leandro Oliveira Bortot

WeFold: A coopetition for protein structure prediction

The protein structure prediction problem continues to elude scientists. Despite the introduction of many methods, only modest gains were made over the last decade for certain classes of prediction targets. To address this challenge, a social‐media based worldwide collaborative effort, named WeFold, was undertaken by 13 labs. During the collaboration, the laboratories were simultaneously competing with each other. Here, we present the first attempt at “coopetition” in scientific research applied to the protein structure prediction and refinement problems. The coopetition was possible by allowing the participating labs to contribute different components of their protein structure prediction pipelines and create new hybrid pipelines that they tested during CASP10. This manuscript describes both successes and areas needing improvement as identified throughout the first WeFold experiment and discusses the efforts that are underway to advance this initiative. A footprint of all contributions and structures are publicly accessible at http://www.wefold.org. Proteins 2014; 82:1850–1868.

A mono-objective evolutionary algorithm for Protein Structure Prediction in structural and energetic contexts

The Protein Structure Prediction (PSP) problem is concerned about the prediction of the native structure of a protein from its amino acid sequence. PSP is a challenging and computationally open problem. Therefore, several researches and methodologies have been developed for it. This paper presents the application of protpred-GROMACS, an evolutionary framework for PSP, in structural and energetic contexts. The performance of mono-objective algorithm was compared with other methodologies, such as multi-objective evolutionary algorithm, coarse grained monte carlo and replica exchange molecular dynamics.

A Synthetic MUC1 Glycopeptide Bearing βGalNAc-Thr as a Tn Antigen Isomer Induces the Production of Antibodies against Tumor Cells

This study presents the synthesis of the novel protected O‐glycosylated amino acid derivatives 1 and 2, containing βGalNAc‐SerOBn and βGalNAc‐ThrOBn units, respectively, as mimetics of the natural Tn antigen (αGalNAc‐Ser/Thr), along with the solid‐phase assembly of the glycopeptides NHAcSer‐Ala‐Pro‐Asp‐Thr[αGalNAc]‐Arg‐Pro‐Ala‐Pro‐Gly‐BSA (3‐BSA) and NHAcSer‐Ala‐Pro‐Asp‐Thr[βGalNAc]‐Arg‐Pro‐Ala‐Pro‐Gly‐BSA (4‐BSA), bearing αGalNAc‐Thr or βGalNAc‐Thr units, respectively, as mimetics of MUC1 tumor mucin glycoproteins. According to ELISA tests, immunizations of mice with βGalNAc‐glycopeptide 4‐BSA induced higher sera titers (1:320 000) than immunizations with αGalNAc‐glycopeptide 3‐BSA (1:40 000). Likewise, flow cytometry assays showed higher capacity of the obtained anti‐glycopeptide 4‐BSA antibodies to recognize MCF‐7 tumor cells. Cross‐recognition between immunopurified anti‐βGalNAc antibodies and αGalNAc‐glycopeptide and vice versa was also verified. Lastly, molecular dynamics simulations and surface plasmon resonance (SPR) showed that βGalNAc‐glycopeptide 4 can interact with a model antitumor monoclonal antibody (SM3). Taken together, these data highlight the improved immunogenicity of the unnatural glycopeptide 4‐BSA, bearing βGalNAc‐Thr as Tn antigen isomer.

Membrane vesiculation induced by proteins of the dengue virus envelope studied by molecular dynamics simulations

Abstract Biological membranes are continuously remodeled in the cell by specific membrane-shaping machineries to form, for example, tubes and vesicles. We examine fundamental mechanisms involved in the vesiculation processes induced by a cluster of envelope (E) and membrane (M) proteins of the dengue virus (DENV) using molecular dynamics simulations and a coarse-grained model. We show that an arrangement of three E-M heterotetramers (EM3) works as a bending unit and an ordered cluster of five such units generates a closed vesicle, reminiscent of the virus budding process. In silico mutagenesis of two charged residues of the anchor helices of the envelope proteins of DENV shows that Arg-471 and Arg-60 are fundamental to produce bending stress on the membrane. The fine-tuning between the size of the EM3 unit and its specific bending action suggests this protein unit is an important factor in determining the viral particle size.

Baccharis dracunculifolia DC (Asteraceae) selectively modulates the effector functions of human neutrophils

To examine whether the hydroalcoholic extract from Baccharis dracunculifolia leaves (BdE) modulates the human neutrophil oxidative metabolism, degranulation, phagocytosis and microbial killing capacity.

In silico assessment of S100A12 monomer and dimer structural dynamics: implications for the understanding of its metal-induced conformational changes

Changes in the concentration of different ions modulate several cellular processes, such as Ca2+ and Zn2+ in inflammation. Upon activation of immune system effector cells, the intracellular Ca2+ concentration rises propagating the activation signal, leading to degranulation and generation of reactive oxygen species, which increases the Zn2+ intracellular concentration as a consequence of the cellular antioxidant machinery. In this context, S100A12 is of special interest because it is a pro-inflammatory protein expressed in neutrophils whose structure and function are modulated by both Ca2+ and Zn2+. The current hypothesis about its mechanism of action was built based on biochemical and crystallographic data. However, there are missing connections between molecular structure and the way in which many events are concatenated at the triggering and along the inflammatory process. In this work we use molecular dynamics simulations to describe how variations in Zn2+ and Ca2+ concentrations modulate the structural dynamics of the calcium-free S100A12 dimer and monomer, which was not considered a part of the mechanism of action before. Our results suggest that (i) Zn2+ have a determinant role in the dimerization step, as well as in the unbinding of the Na+ complexed to the N-terminal EF-hand; (ii) the N-terminal EF-hand domain is the first to bind Ca2+, and not the C-terminal, as usually accepted; and that (iii) Ca2+ modulates the structural dynamics of H-III.

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research.

The 3-phenylcoumarin derivative 6,7-dihydroxy-3-[3′,4′-methylenedioxyphenyl]-coumarin downmodulates the FcγR- and CR-mediated oxidative metabolism and elastase release in human neutrophils: Possible mechanisms underlying inhibition of the formation and release of neutrophil extracellular traps

ABSTRACT In this study, we report the ability of a set of eight 3‐phenylcoumarin derivatives bearing 6,7‐ or 5,7‐dihydroxyl groups, free or acetylated, bound to the benzopyrone moiety, to modulate the effector functions of human neutrophils. In general, (i) 6,7‐disubstituted compounds (5, 6, 19, 20) downmodulated the Fc&ggr; receptor‐mediated neutrophil oxidative metabolism more strongly than 5,7‐disubstituted compounds (21, 22, 23, 24), and (ii) hydroxylated compounds (5, 19, 21, 23) downmodulated this neutrophil function more effectively than their acetylated counterparts (6, 20, 22, 24, respectively). Compounds 5 (6,7‐dihydroxy‐3‐[3′,4′‐methylenedioxyphenyl]‐coumarin) and 19 (6,7‐dihydroxy‐3‐[3′,4′‐dihydroxyphenyl]‐coumarin) effectively downmodulated the neutrophil oxidative metabolism elicited via Fc&ggr; and/or complement receptors. Compound 5 also downmodulated the immune complex‐stimulated phagocytosis, degranulation of elastase, and production and release of neutrophil extracellular traps, as well as the human neutrophil chemotaxis towards n‐formyl‐methionyl‐leucyl‐phenylalanine, without altering the expression level of formyl peptide receptor type 1. Both compounds 5 and 19 did not impair the neutrophil capacity to recognize and kill Candida albicans. Docking calculations revealed that compounds 5 and 19 directly interacted with three catalytic residues – Gln‐91, His‐95, and Arg‐239 – inside the myeloperoxidase active site. Together, these findings indicate that (i) inhibition of reactive oxygen species generation and degranulation of elastase are closely associated with downmodulation of release of neutrophil extracellular traps; and (ii) compound 5 can be a prototype for the development of novel immunomodulating drugs to treat immune complex‐mediated inflammatory diseases. Graphical abstract Figure. No caption available. Highlights3‐PD 5 downmodulates neutrophil ROS generation, phagocytosis, and degranulation.3‐PD 5 downmodulates the production and release of neutrophil extracellular traps.3‐PD 5 downmodulates neutrophil chemotaxis towards fMLP but not FPR1 expression.3‐PD 5 is not cytotoxic to neutrophils and does not interfere with microbial killing.3‐PD 5 directly interacts with three catalytic residues of myeloperoxidase.

Multi-Objective Evolutionary Algorithm NSGA-II for Protein Structure Prediction using Structural and Energetic Properties

The Protein Structure Prediction (PSP) problem is concerned about the prediction of the native tertiary structure of a protein in respect to its amino acids sequence. PSP is a challenging and computationally open problem. Therefore, several researches and methodologies have been developed for it. In this way, developers are working to integrate frameworks in order to improve their capabilities and make their use more straightforward. This paper presents the application of NSGA-II algorithm using structural and energetic properties of protein. The implementation of this algorithm is based on ProtPred-GROMACS (2PG), an evolutionary framework for PSP. This framework is the integration between ProtPred and GROMACS. Six proteins were used to measure the capacity of ab initio predictions. The results were interesting since in all cases the native-like topology was obtained.