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molecular dynamics

Biplab Sarkar, Suresh K Verma, Javed Akhtar, Surya Prakash Netam, Sanjay Kr Gupta, Pritam Kumar Panda, Koel Mukherjee
With the enhancement of commercial manifestation of silver nanoparticles, concerned has risen on their accumulation in aquatic system and consequent effects on fish development and metabolism. In this study, experiments were conducted to assess the impacts of silver nanoparticles on early life cycles of fish considering Zebrafish (Danio rerio) as experimental model. Silver nanoparticles were synthesized through chemical reduction method and characterized through UV-visible spectroscopy, dynamic light scattering (DLS), and HR-TEM...
May 4, 2018: Chemosphere
Jiao Guan, Xin Yan, Yajing Zhao, Yinhe Sun, Xin Peng
The antimicrobial triclocarban (TCC) is frequently found in various personal care products (PCPs), and recent studies have demonstrated that it shows a high unintended biological activity on humans and wildlife. To evaluate the toxicity of TCC at the protein level, the effect of TCC on bovine serum albumin (BSA) has been investigated using various spectroscopic methods in combination with molecular modeling. Analysis of fluorescence quenching data of BSA revealed the formation of a ground state BSA-TCC complex with a binding constant of 2...
May 9, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Sameer Shakeel Ansari, Imtiyaz Yousuf, Farukh Arjmand, Mohammad Khursheed Siddiqi, Saeeda Naqvi
The intermolecular interaction of flufenamic acid (Hfluf) with two model proteins i.e., hemoglobin and lysozyme was explored using fluorescence, UV-vis, circular dichroism, DLS, and molecular docking techniques. The corroborative spectroscopic techniques suggested efficient binding of Hfluf to both the proteins. The S-V plot in Hb-Hfluf system showed positive deviation highlighting the presence of both static and dynamic quenching. Hence, ground state complex model and sphere of action quenching model were used for the study...
May 16, 2018: International Journal of Biological Macromolecules
Neda Esfandiari, Yahya Sefidbakht
Since Potato Virus X (PVX) is easily transmitted mechanically between their hosts, its control is difficult. We have previously reported new isolate of this virus (PVX-Iran, GenBank Accession number FJ461343). However, the molecular basis of resistance breaking activity and its relation to capsid protein structure are still not well-understood. SDS-PAGE, ELISA, Western blot and RT-PCR molecular examinations were performed on the inoculated plants Nicotiana benthamiana. The pathological symptoms were related to the PVX isolate...
May 16, 2018: International Journal of Biological Macromolecules
Andrey M Grishin, Kathryn R Barber, Ruo-Xu Gu, D Peter Tieleman, Gary S Shaw, Miroslaw Cygler
Gram-negative pathogens secrete effector proteins into human cells to modulate normal cellular processes and establish a bacterial replication niche. Shigella and pathogenic E. coli possess homologous effector kinases, OspG and NleH1/2, respectively. Upon translocation, OspG but not NleH binds to ubiquitin and a subset of E2~Ub conjugates, which was shown to activate its kinase activity. Here we show that OspG, having a minimal kinase fold, acquired a novel mechanism of regulation of its activity. Binding of the E2~Ub conjugate to OspG not only stimulates its kinase activity but also increases its optimal temperature for activity to match the human body temperature and stabilizes its labile C-terminal domain...
May 16, 2018: Journal of Molecular Biology
Sander J Wezenberg, Ben L Feringa
Stimuli-controlled motion at the molecular level has fascinated chemists already for several decades. Taking inspiration from the myriad of dynamic and machine-like functions in nature, a number of strategies have been developed to control motion in purely synthetic systems. Unidirectional rotary motion, such as is observed in ATP synthase and other motor proteins, remains highly challenging to achieve. Current artificial molecular motor systems rely on intrinsic asymmetry or a specific sequence of chemical transformations...
May 18, 2018: Nature Communications
Sherif M Reda, Murali Chandra
Recent clinical studies have revealed a new hypertrophic cardiomyopathy-associated mutation (F87L) in the central region of human cardiac troponin T (TnT). However, despite its implication in several incidences of sudden cardiac death in young and old adults, whether F87L is associated with cardiac contractile dysfunction is unknown. Because the central region of TnT is important for modulating the muscle length-mediated recruitment of new force-bearing cross-bridges (XBs), we hypothesize that the F87L mutation causes molecular changes that are linked to the length-dependent activation of cardiac myofilaments...
May 18, 2018: Journal of General Physiology
Richard D Mortensen, Regan P Moore, Stephanie M Fogerson, Hellen Y Chiou, Chimdindu V Obinero, Neel K Prabhu, Angela H Wei, Janice M Crawford, Daniel P Kiehart
Cell sheet morphogenesis characterizes key developmental transitions and homeostasis, in vertebrates and throughout phylogeny, including gastrulation, neural tube formation and wound healing. Dorsal closure, a process during Drosophila embryogenesis, has emerged as a model for cell sheet morphogenesis. ∼140 genes are currently known to affect dorsal closure and new genes are identified each year. Many of these genes were identified in screens that resulted in arrested development. Dorsal closure is remarkably robust and many questions regarding the molecular mechanisms involved in this complex biological process remain...
May 18, 2018: G3: Genes—Genomes—Genetics
Laura E Jennings, Matthias Schiedel, David S Hewings, Sarah Picaud, Corentine M C Laurin, Paul A Bruno, Joseph P Bluck, Amy R Scorah, Larissa See, Jessica K Reynolds, Mustafa Moroglu, Ishna N Mistry, Amy Hicks, Pavel Guzanov, James Clayton, Charles N G Evans, Giulia Stazi, Philip C Biggin, Anna K Mapp, Ester M Hammond, Philip G Humphreys, Panagis Filippakopoulos, Stuart J Conway
Ligands for the bromodomain and extra-terminal domain (BET) family of bromodomains have shown promise as useful therapeutic agents for treating a range of cancers and inflammation. Here we report that our previously developed 3,5-dimethylisoxazole-based BET bromodomain ligand (OXFBD02) inhibits interactions of BRD4(1) with the RelA subunit of NF-κB, in addition to histone H4. This ligand shows a promising profile in a screen of the NCI-60 panel but was rapidly metabolised (t½  = 39.8 min). Structure-guided optimisation of compound properties led to the development of the 3-pyridyl-derived OXFBD04...
May 15, 2018: Bioorganic & Medicinal Chemistry
Simon R Harris, Michelle J Cole, Gianfranco Spiteri, Leonor Sánchez-Busó, Daniel Golparian, Susanne Jacobsson, Richard Goater, Khalil Abudahab, Corin A Yeats, Beatrice Bercot, Maria José Borrego, Brendan Crowley, Paola Stefanelli, Francesco Tripodo, Raquel Abad, David M Aanensen, Magnus Unemo
BACKGROUND: Traditional methods for molecular epidemiology of Neisseria gonorrhoeae are suboptimal. Whole-genome sequencing (WGS) offers ideal resolution to describe population dynamics and to predict and infer transmission of antimicrobial resistance, and can enhance infection control through linkage with epidemiological data. We used WGS, in conjunction with linked epidemiological and phenotypic data, to describe the gonococcal population in 20 European countries. We aimed to detail changes in phenotypic antimicrobial resistance levels (and the reasons for these changes) and strain distribution (with a focus on antimicrobial resistance strains in risk groups), and to predict antimicrobial resistance from WGS data...
May 15, 2018: Lancet Infectious Diseases
Ulla König, Evmorfia Psarra, Olga Guskova, Eva Bittrich, Klaus-Jochen Eichhorn, Martin Müller, Petra B Welzel, Manfred Stamm, Petra Uhlmann
The development of bioengineered surface coatings with stimuli-responsive properties is beneficial for a number of biomedical applications. Environmentally responsive and switchable polymer brush systems have a great potential to create such smart biointerfaces. This study focuses on the bioconjugation of cell-instructive peptides, containing the arginine-glycine-aspartic acid tripeptide sequence (RGD motif), onto well-defined polymer brush films. Herein, the highly tailored end-grafted homo polymer brushes are either composed of the polyelectrolyte poly(acrylic) acid (PAA), providing the reactive carboxyl functionalities, or of the temperature-responsive poly(N-isopropylacrylamide) (PNIPAAm)...
May 18, 2018: Biointerphases
Pankaj Kr Mishra, Vincent Bettaque, Oriol Vendrell, Robin Santra, Ralph Welsch
Ultrashort, high-intensity THz pulses, e.g., created at free-electron laser facilities, allow for direct investigation as well as the driving of intermolecular modes in liquids like water and thus will deepen our understanding of the hydrogen bonding network. In this work, the temperature-jump (T-jump) of water induced by THz radiation is simulated for ten different THz frequencies in the range from 3 to 30 THz and five different pulse intensities in the range from 1 × 1011 to 5 × 1012 W/cm2 employing both ab initio molecular dynamics (AIMD) and force field molecular dynamics (FFMD) approaches...
May 18, 2018: Journal of Physical Chemistry. A
Neil A Mehta, Deborah A Levin
Molecular dynamics (MD) electrospray simulations of 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM-BF_{4}) ion liquid were performed with the goal of evaluating the influence of long-range Coulomb models on ion emission characteristics. The direct Coulomb (DC), shifted force Coulomb sum (SFCS), and particle-particle particle-mesh (PPPM) long-range Coulomb models were considered in this work. The DC method with a sufficiently large cutoff radius was found to be the most accurate approach for modeling electrosprays, but, it is computationally expensive...
March 2018: Physical Review. E
Patricia Ternes, Evy Salcedo, Marcia C Barbosa
The slip of a fluid layer in contact with a solid confining surface is investigated for different temperatures and densities using molecular dynamic simulations. We show that for an anomalous waterlike fluid the slip goes as follows: for low levels of shear, defect slip appears and is related to the particle exchange between the fluid layers; at high levels of shear, global slip occurs and is related to the homogeneous distribution of the fluid in the confining surfaces. The oscillations in the transition velocity from defect to global slip are shown to be associated with changes in the layering distribution in the anomalous fluid...
March 2018: Physical Review. E
Adarsh K Chaurasia, Andrew M Rukangu, Michael K Philen, Gary D Seidel, Eric C Freeman
In the current paper, phospholipid bilayers are modeled using coarse-grained molecular dynamics simulations with the MARTINI force field. The extracted molecular trajectories are analyzed using Fourier analysis of the undulations and orientation vectors to establish the differences between the two approaches for evaluating the bending modulus. The current work evaluates and extends the implementation of the Fourier analysis for molecular trajectories using a weighted horizon-based averaging approach. The effect of numerical parameters in the analysis of these trajectories is explored by conducting parametric studies...
March 2018: Physical Review. E
Subhajit Paul, Subir K Das
Via event-driven molecular dynamics simulations we study kinetics of clustering in assemblies of inelastic particles in various space dimensions. We consider two models, viz., the ballistic aggregation model (BAM) and the freely cooling granular gas model (GGM), for each of which we quantify the time dependence of kinetic energy and average mass of clusters (that form due to inelastic collisions). These quantities, for both the models, exhibit power-law behavior, at least in the long time limit. For the BAM, corresponding exponents exhibit strong dimension dependence and follow a hyperscaling relation...
March 2018: Physical Review. E
Ankush Aggarwal
Virus capsids are protein shells that protect the virus genome, and determination of their mechanical properties has been a topic of interest because of their potential use in nanotechnology and therapeutics. It has been demonstrated that stresses exist in virus capsids, even in their equilibrium state, due to their construction. These stresses, termed "prestresses" in this study, closely affect the capsid's mechanical behavior. Three methods-shape-based metric, atomic force microscope indentation, and molecular dynamics-have been proposed to determine the capsid elastic properties without fully accounting for prestresses...
March 2018: Physical Review. E
Marwa Kchaou, Pierre Alcouffe, Sivasurender Chandran, Philippe Cassagnau, Günter Reiter, Samer Al Akhrass
Using dewetting as a characterization tool, we demonstrate that physical properties of thin polymer films can be regulated and tuned by employing variable processing conditions. For different molecular weights, the variable behavior of polystyrene films of identical thickness, prepared along systematically altered pathways, became predictable through a single parameter P, defined as the ratio of time required over time available for the equilibration of polymers. In particular, preparation-induced residual stresses, the corresponding relaxation times as well as the rupture probability of such films (of identical thickness) varied by orders of magnitude following scaling relations with P...
March 2018: Physical Review. E
Guillermo Rodrigo
Gene expression programs in living cells are highly dynamic due to spatiotemporal molecular signaling and inherent biochemical stochasticity. Here we study a mechanism based on molecule-to-molecule variability at the RNA level for the generation of bursts of protein production, which can lead to heterogeneity in a cell population. We develop a mathematical framework to show numerically and analytically that genes regulated post transcriptionally by small RNA molecules can exhibit such bursts due to different states of translation activity (on or off), mostly revealed in a regime of few molecules...
March 2018: Physical Review. E
Parth Rakesh Desai, Shayandev Sinha, Siddhartha Das
We employ molecular dynamics (MD) simulations and develop scaling theories to quantify the equilibrium behavior of polyelectrolyte (PE) brush bilayers (BBLs) in the weakly interpenetrated regime, which is characterized by d_{0}<d_{g}<2d_{0}, where d_{g} is the gap between the opposing plates where the PE brushes are grafted and d_{0} is the unperturbed height of a PE brush grafted at a single plate. Scaling predictions establish that, for the weakly interpenetrated osmotic PE BBLs δ∼N^{1/2}(2-d_{g}/d_{0})^{1/2} (where δ is the interpenetration length and N is the number of Kuhn segments in PE brush)...
March 2018: Physical Review. E
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