1,720,986 research outputs found
Cosolvent, ions, and temperature effects on the structural properties of cecropin A-Magainin 2 hybrid peptide in solutions
No full textAntimicrobial peptides are promising alternative to traditional antibiotics and antitumor drugs for the battle against new antibiotic resistant bacteria strains and cancer maladies. The study of their structural and dynamics properties at physiological conditions can help to understand their stability, delivery mechanisms, and activity in the human body. In this article, we have used molecular dynamics simulations to study the effects of solvent environment, temperature, ions concentration, and peptide concentration on the structural properties of the antimicrobial hybrid peptide Cecropin A-Magainin 2. In TFE/water mixtures, the structure of the peptide retained α-helix contents and an average hinge angle in close agreement with the experimental NMR and CD measurements reported in literature. Compared to the TFE/water mixture, the peptide simulated at the same ionic concentration lost most of its α-helix structure. The increase of peptide concentration at both 300 and 310 K resulted in the peptide aggregation. The peptides in the complex retained the initial N-ter α-helix segment during all the simulation. The α-helix stabilization is further enhanced in the high salt concentration simulations. The peptide aggregation was not observed in TFE/water mixture simulations and, the peptide aggregate, obtained from the water simulation, simulated in the same conditions did dissolve within few tens of nanoseconds. The results of this study provide insights at molecular level on the structural and dynamics properties of the CA-MA peptide at physiological and membrane mimic conditions that can help to better understand its delivery and interaction with biological interfaces
Coating mechanisms of single-walled carbon nanotube by linear polyether surfactants: Insights from computer simulations
Full text linkThe noncovalent coating of carbon-based nanomaterials, such as carbon nanotubes, has important applications in nanotechnology and nanomedicine. The molecular modeling of this process can clarify its mechanism and provide a tool for the design of novel materials. In this paper, the coating mechanism of single-walled carbon nanotubes (SWCNT) in aqueous solutions by 1,2-dimethoxyethane oxide (DME), 1,2-dimethoxypropane oxide (DMP), poly(ethylene oxide) (PEO), poly(propylene oxide) (PPO) pentamers, and L64 triblock copolymer chains have been studied using molecular dynamics (MD) simulations. The results suggest a preferential binding to the SWCNT surface of the DMP molecules with respect to DME mainly driven by their difference in hydrophobicity. For the longer pentamers, it depends by the chain conformation. PPO isomers with radius of gyration larger than PEO pentamers bind more tightly than those with more compact conformation. In the case of the L64 triblock copolymer, the coating of the SWCNT surface produces a shell of PPO blocks with the PEO chains protruding into bulk water as expected from the so-called nonwrapping binding mechanism of SWCNT. In addition, the polymer coating, in qualitative agreement with experimental evidence on the poor capability of the L64 to disperse SWCNT, do not prevent the formation of CNT aggregates. © 2014 American Chemical Society
Spontaneous insertion of carbon nanotube bundles inside biomembranes: A hybrid particle-field coarse-grained molecular dynamics study
Full text linkThe processes of CNTs bundle formation and insertion/rearrangement inside lipid bilayers, as models of cellular membranes, is described and analyzed in details using simulations on the microsecond scale. Molecular Dynamics simulations employing hybrid particle-field models (MD-SCF) show that during the insertion process lipid molecules coat bundles surfaces. The distortions of bilayers are more pronounced for systems undergoing to insertion of bundles made of longer CNTs. In particular, when the insertion occurs in perpendicular orientation, adsorption of lipids on CNTs surfaces promotes a transient poration. This result suggests mechanism of membrane disruption operated by bundles causing the formation of solvent-rich pockets. © 2014 Elsevier B.V. All rights reserved
Dynamical aspects of TEM-1 β-Lactamase probed by molecular dynamics
No full textThe dynamical aspects of the fully hydrated TEM-1 β-lactamase have been determined by a 5ns Molecular Dynamics simulation. Starting from the crystallographic coordinates, the protein shows a relaxation in water with an overall root mean square deviation from the crystal structure increasing up to 0.17 nm, within the first nanosecond. Then a plateau is reached and the molecule fluctuates around an equilibrium conformation. The results obtained in the first nanosecond are in agreement with those of a previous simulation (Diaz et al., J. Am. Chem. Soc., (2003) 125, 672-684). The successive equilibrium conformation in solution shows an increased mobility characterized by the following aspects. A flap-like translational motion anchores the Ω-loop to the body of the enzyme. A relevant part of the backbone dynamics implies a rotational motion of one domain relative to the other. The water molecules in the active site can exchange with different residence times. The H-bonding networks formed by the catalytic residues are frequently interrupted by water molecules that could favour proton transfer reactions. An additional simulation, where the aspartyl dyad D214-D233 was considered fully deprotonated, shows that the active site is destabilized. © Springer 2005
Characterization of liquid behaviour by means of local density fluctuations
No full textBy means of principle component analysis of the local density fluctuations, as revealed by molecular dynamics simulations, we obtain detailed information on the relevant local density fluxes and corresponding spatial patterns
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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