When small is different: The case of membranes inside tubes

Recently, classical elasticity theory for thin sheets was used to demonstrate the existence of a universal structural behavior describing the confinement of sheets inside cylindrical tubes. However, this kind of formalism was derived to describe macroscopic systems. A natural question is whether this behavior still holds at nanoscale. In this work, we have investigated through molecular dynamics simulations the structural behavior of graphene and boron nitride single layers confined into nanotubes. Our results show that the class of universality observed at macroscale is no longer observed at nanoscale. The origin of this discrepancy is addressed in terms of the relative importance of forces and energies at macro and nano scales. © 2012 Materials Research Society.

Kinetic parameters for thermal decomposition of supramolecular polymers derived from diclofenac-meglumine supramolecular adducts

Meglumine is an aminocarbohydrate able to form supramolecular adducts with organic acids. The recognition is based on hydrogen bonds and the structures resulting from the complexation have high solubility in water. This property has been exploited by the pharmaceutical industry in the improvement of existing drugs, and the successful example of this approach involves the poorly soluble non-steroidal anti-inflammatory drugs (NSAIDs). Investigation of the thermal behavior of adduct obtained from meglumine and the NSAID diclofenac revealed that a polymer-like material is formed from the self-assembly of diclofenac-meglumine adducts in the melt. This polymer showed a high molecular weight around 2.0×105kDa. The kinetic parameters for the thermal decomposition step of the polymer were determined by the Capela-Ribeiro non-linear isoconversional method. From data for the TG curves in nitrogen atmosphere and heating rates of 5, 10, 15 and 20°Cmin-1, the Eα and Bα terms could be determined, and consequently the pre-exponential factor, Aα, as well as the kinetic model, g(α). © 2012 Elsevier B.V.

Graphene to fluorographene and fluorographane: A theoretical study

We report here a fully reactive molecular dynamics study on the structural and dynamical aspects of the fluorination of graphene membranes (fluorographene). Our results show that fluorination tends to produce defective areas on the graphene membranes with significant distortions of carbon-carbon bonds. Depending on the amount of incorporated fluorine atoms, large membrane holes were observed due to carbon atom losses. These results may explain the broad distribution of the structural lattice parameter values experimentally observed. We have also investigated the effects of mixing hydrogen and fluorine atoms on the graphene functionalization. Our results show that, when in small amounts, the presence of hydrogen atoms produces a significant decrease in the rate of fluorine incorporation onto the membrane. On the other hand, when fluorine is the minority element, it produces a significant catalytic effect on the rate of hydrogen incorporation. We have also observed the spontaneous formation of new hybrid structures with different stable configurations (chair-like, zigzag-like and boat-like) which we named fluorographane. © 2013 IOP Publishing Ltd.

Biophysical characterization of the recombinant importin-α from neurospora crassa

Neurospora crassa has been widely used as a model organism and contributed to the development of biochemistry and molecular biology by allowing the identification of many metabolic pathways and mechanisms responsible for gene regulation. Nuclear proteins are synthesized in the cytoplasm and need to be translocated to the nucleus to exert their functions which the importin-α receptor has a key role for the classical nuclear import pathway. In an attempt to get structural information of the nuclear transport process in N. crassa, we present herein the cloning, expression, purification and structural studies with N-terminally truncated IMPα from N. crassa (IMPα-Nc). Circular dichroism analysis revealed that the IMPα-Nc obtained is correctly folded and presents a high structural conservation compared to other importins-α. Dynamic light scattering, analytical size-exclusion chromatography experiments and molecular dynamics simulations indicated that the IMPα-Nc unbound to any ligand may present low stability in solution. The IMPα-Nc theoretical model displayed high similarity of its inner concave surface, which binds the cargo proteins containing the nuclear localization sequences, among IMPα from different species. However, the presence of non-conserved amino acids relatively close to the NLS binding region may influence the binding specificity of IMPα-Nc to cargo proteins. Copyright © 2012 Bentham Science Publishers. All Rights Reserved.

Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the major component of the transcription machinery. The development of single-molecule techniques, such as magnetic and optical tweezers, atomic-force microscopy and single-molecule fluorescence, increased our understanding of the transcription process and complements traditional biochemical studies. Based on these studies, theoretical models have been proposed to explain and predict the kinetics of the RNAP during the polymerization, highlighting the results achieved by models based on the thermodynamic stability of the transcription elongation complex. However, experiments showed that if more than one RNAP initiates from the same promoter, the transcription behavior slightly changes and new phenomenona are observed. We proposed and implemented a theoretical model that considers collisions between RNAPs and predicts their cooperative behavior during multi-round transcription generalizing the Bai et al. stochastic sequence-dependent model. In our approach, collisions between elongating enzymes modify their transcription rate values. We performed the simulations in Mathematica® and compared the results of the single and the multiple-molecule transcription with experimental results and other theoretical models. Our multi-round approach can recover several expected behaviors, showing that the transcription process for the studied sequences can be accelerated up to 48% when collisions are allowed: the dwell times on pause sites are reduced as well as the distance that the RNAPs backtracked from backtracking sites. © 2013 Costa et al.

Modelling polymers with side chains: MEH-PPV and P3HT

Modelling polymers with side chains is always a challenge once the degrees of freedom are very high. In this study, we present a successful methodology to model poly[2-methoxy-5-(2′-ethyl-hexyloxy)-p-phenylenevinylene] (MEH-PPV) and poly[3-hexylthiophene] (P3HT) in solutions, taking into account the influence of side chains on the polymer conformation. Molecular dynamics and semi-empirical quantum mechanical methods were used for structure optimisation and evaluation of optical properties. The methodology allows to describe structural and optical characteristics of the polymers in a satisfactory way, as well as to evaluate some usual simplifications adopted for modelling these systems. Effective conjugation lengths of 8-14.6 and 21 monomers were obtained for MEH-PPV and P3HT, respectively, in accordance with experimental findings. In addition, anti/syn conformations of these polymers could be predicted based on intrinsic interactions of the lateral branches. © 2013 Copyright Taylor and Francis Group, LLC.

Developing descriptors to predict mechanical properties of nanotubes

Descriptors and quantitative structure property relationships (QSPR) were investigated for mechanical property prediction of carbon nanotubes (CNTs). 78 molecular dynamics (MD) simulations were carried out, and 20 descriptors were calculated to build quantitative structure property relationships (QSPRs) for Young's modulus and Poisson's ratio in two separate analyses: vacancy only and vacancy plus methyl functionalization. In the first analysis, C N2/CT (number of non-sp2 hybridized carbons per the total carbons) and chiral angle were identified as critical descriptors for both Young's modulus and Poisson's ratio. Further analysis and literature findings indicate the effect of chiral angle is negligible at larger CNT radii for both properties. Raman spectroscopy can be used to measure CN2/C T, providing a direct link between experimental and computational results. Poisson's ratio approaches two different limiting values as CNT radii increases: 0.23-0.25 for chiral and armchair CNTs and 0.10 for zigzag CNTs (surface defects <3%). In the second analysis, the critical descriptors were CN2/CT, chiral angle, and MN/CT (number of methyl groups per total carbons). These results imply new types of defects can be represented as a new descriptor in QSPR models. Finally, results are qualified and quantified against experimental data. © 2013 American Chemical Society.

Intermolecular interactions of the malate synthase of Paracoccidioides spp

Background: The fungus Paracoccidioides spp is the agent of paracoccidioidomycosis (PCM), a pulmonary mycosis acquired by the inhalation of fungal propagules. Paracoccidioides malate synthase (PbMLS) is important in the infectious process of Paracoccidioides spp because the transcript is up-regulated during the transition from mycelium to yeast and in yeast cells during phagocytosis by murine macrophages. In addition, PbMLS acts as an adhesin in Paracoccidioides spp. The evidence for the multifunctionality of PbMLS indicates that it could interact with other proteins from the fungus and host. The objective of this study was to identify and analyze proteins that possibly bind to PbMLS (PbMLS-interacting proteins) because protein interactions are intrinsic to cell processes, and it might be possible to infer the function of a protein through the identification of its ligands. Results: The search for interactions was performed using an in vivo assay with a two-hybrid library constructed in S. cerevisiae; the transcripts were sequenced and identified. In addition, an in vitro assay using pull-down GST methodology with different protein extracts (yeast, mycelium, yeast-secreted proteins and macrophage) was performed, and the resulting interactions were identified by mass spectrometry (MS). Some of the protein interactions were confirmed by Far-Western blotting using specific antibodies, and the interaction of PbMLS with macrophages was validated by indirect immunofluorescence and confocal microscopy. In silico analysis using molecular modeling, dynamics and docking identified the amino acids that were involved in the interactions between PbMLS and PbMLS-interacting proteins. Finally, the interactions were visualized graphically using Osprey software. Conclusion: These observations indicate that PbMLS interacts with proteins that are in different functional categories, such as cellular transport, protein biosynthesis, modification and degradation of proteins and signal transduction. These data suggest that PbMLS could play different roles in the fungal cell. © 2013 de Oliveira et al.; licensee BioMed Central Ltd.

Fetal-Maternal Interactions in the Synepitheliochorial Placenta Using the eGFP Cloned Cattle Model

Background: To investigate mechanisms of fetal-maternal cell interactions in the bovine placenta, we developed a model of transgenic enhanced Green Fluorescent Protein (t-eGFP) expressing bovine embryos produced by nuclear transfer (NT) to assess the distribution of fetal-derived products in the bovine placenta. In addition, we searched for male specific DNA in the blood of females carrying in vitro produced male embryos. Our hypothesis is that the bovine placenta is more permeable to fetal-derived products than described elsewhere. Methodology/Principal Findings: Samples of placentomes, chorion, endometrium, maternal peripheral blood leukocytes and blood plasma were collected during early gestation and processed for nested-PCR for eGFP and testis-specific Y-encoded protein (TSPY), western blotting and immunohistochemistry for eGFP detection, as well as transmission electron microscopy to verify the level of interaction between maternal and fetal cells. TSPY and eGFP DNA were present in the blood of cows carrying male pregnancies at day 60 of pregnancy. Protein and mRNA of eGFP were observed in the trophoblast and uterine tissues. In the placentomes, the protein expression was weak in the syncytial regions, but intense in neighboring cells on both sides of the fetal-maternal interface. Ultrastructurally, our samples from t-eGFP expressing NT pregnancies showed to be normal, such as the presence of interdigitating structures between fetal and maternal cells. In addition, channels-like structures were present in the trophoblast cells. Conclusions/Significance: Data suggested that there is a delivery of fetal contents to the maternal system on both systemic and local levels that involved nuclear acids and proteins. It not clear the mechanisms involved in the transfer of fetal-derived molecules to the maternal system. This delivery may occur through nonclassical protein secretion; throughout transtrophoblastic-like channels and/or by apoptotic processes previously described. In conclusion, the bovine synepitheliochorial placenta displays an intimate fetal-maternal interaction, similar to other placental types for instance human and mouse. © 2013 Pereira et al.

The effects of pinning on critical currents of superconducting films

Using molecular dynamics simulations, we analyze the effects of artificial periodic arrays of pinning sites on the critical current of superconducting thin films as a function of vortex density. We analyze two types of periodic pinning array: hexagonal and Kagomé. For the Kagome pinning network we make calculations using two directions of transport current: along and perpendicular to the main axis of the lattice. Our results show that the hexagonal pinning array presents higher critical currents than the Kagomé and random pinning configuration for all vortex densities. In addition, the Kagomé networks show anisotropy in their transport properties. © 2012 Springer Science+Business Media, LLC.

Critical currents and melting temperature of a two-dimensional vortex lattice with periodic pinning

The critical current and melting temperature of a vortex system are analyzed. Calculations are made for a two-dimensional film at finite temperature with two kinds of periodic pinning: hexagonal and Kagomé. A transport current parallel and perpendicular to the main axis of the pinning arrays is applied and molecular dynamics simulations are used to calculate the vortex velocities to obtain the critical currents. The structure factor and displacements of vortices at zero transport current are used to obtain the melting temperature for both pinning arrays. The critical currents are higher for the hexagonal pinning lattice and anisotropic for both pinning arrays. This anisotropy is stronger with temperature for the hexagonal array. For the Kagomé pinning lattice, our analysis shows a multi stage phase melting; that is, as we increase the temperature, each different dynamic phase melts before reaching the melting temperature. Both the melting temperature and critical currents are larger for the hexagonal lattice, indicating the role for the interstitial vortices in decreasing the pinning strength. © 2012 Springer Science+Business Media New York.

Analyzing the effect of homogeneous frustration in protein folding

The energy landscape theory has been an invaluable theoretical framework in the understanding of biological processes such as protein folding, oligomerization, and functional transitions. According to the theory, the energy landscape of protein folding is funneled toward the native state, a conformational state that is consistent with the principle of minimal frustration. It has been accepted that real proteins are selected through natural evolution, satisfying the minimum frustration criterion. However, there is evidence that a low degree of frustration accelerates folding. We examined the interplay between topological and energetic protein frustration. We employed a Cα structure-based model for simulations with a controlled nonspecific energetic frustration added to the potential energy function. Thermodynamics and kinetics of a group of 19 proteins are completely characterized as a function of increasing level of energetic frustration. We observed two well-separated groups of proteins: one group where a little frustration enhances folding rates to an optimal value and another where any energetic frustration slows down folding. Protein energetic frustration regimes and their mechanisms are explained by the role of non-native contact interactions in different folding scenarios. These findings strongly correlate with the protein free-energy folding barrier and the absolute contact order parameters. These computational results are corroborated by principal component analysis and partial least square techniques. One simple theoretical model is proposed as a useful tool for experimentalists to predict the limits of improvements in real proteins. © 2013 Wiley Periodicals, Inc.

Análise vibracional do α-tocoferol

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estudo do efeito da adição de frustração no enovelamento de proteínas utilizando modelos baseados em estruturas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Análise conformacional dos petídeos protonectina e protonectina (1-6), isolados e em associação, em mistura TFE-água

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)