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# molecular dynamics

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#1
Minseok Kim, Tansol Park, Zhongtang Yu
The gastrointestinal (GI) tract, including the rumen and the other intestinal segments of cattle, harbors a diverse, complex, and dynamic microbiome that drives feed digestion and fermentation in cattle, determining feed efficiency and output of pollutants. This microbiome also plays an important role in affecting host health. Research has been conducted for more than a century to understand the microbiome and its relationship to feed efficiency and host health. The traditional cultivation-based research elucidated some of the major metabolism, but studies using molecular biology techniques conducted from late 1980's to the late early 2000's greatly expanded our view of the diversity of the rumen and intestinal microbiome of cattle...
August 22, 2017: Asian-Australasian Journal of Animal Sciences
#2
Jiyong Park, Sunny Chun, Thomas A Bobik, Kendall N Houk, Todd O Yeates
Bacterial microcompartments are giant protein-based organelles that encapsulate special metabolic pathways in diverse bacteria. Structural and genetic studies indicate that metabolic substrates enter these microcompartments by passing through the central pores in hexameric assemblies of shell proteins. Limiting the escape of toxic metabolic intermediates created inside the microcompartments would confer a selective advantage for the host organism. Here, we report the first molecular dynamics (MD) simulation studies to analyze small-molecule transport across a microcompartment shell...
August 22, 2017: Journal of Physical Chemistry. B
#3
Katerina Bartova, Lucie Čechová, Eliska Prochazkova, Ondrej Socha, Zlatko Janeba, Martin Dracinsky
Intramolecular hydrogen bonds (IMHBs) in 5-azopyrimidines are investigated by NMR spectroscopy and DFT computations that involve nuclear quantum effects. A series of substituted 5-phenylazopyrimidines with one or two hydrogen bond donors able to form IMHBs with the azo group is prepared by azo coupling. The barrier of interconversion between two rotamers of the compounds with two possible IMHBs is determined by variable temperature NMR spectroscopy and it is demonstrated that the barrier is significantly affected by intramolecular charge transfer...
August 22, 2017: Journal of Organic Chemistry
#4
Heng Deng, Yuan Dong, Jheng-Wun Su, Cheng Zhang, Yunchao Xie, Chi Zhang, Matthew R Maschmann, Yuyi Lin, Jian Lin
Responsive materials with functions of forming three-dimensional (3D) origami and/or kirigami structures have a broad range of applications in bioelectronics, metamaterials, microrobotics, and microelectromechanical (MEMS) systems. To realize such functions, building blocks of actuating components usually possess localized inhomogeneous so that they respond differently to external stimuli. Previous fabrication strategies lie in localizing non-swellable or less-swellable guest components in their swellable host polymers to reduce swelling ability...
August 22, 2017: ACS Applied Materials & Interfaces
#5
G Naaresh Reddy, Rakesh Parida, Santanab Giri
Inorganic superhalogens are commonly used as anionic counterparts in Li-ion batteries. In an endeavour to prepare better electrolytes, we have modelled the anionic part with different organic heterocyclic-based superhalogens. First principles calculations on those organic superhalogens reveal that the Li-binding energy is at par with that of the Li-salt of a common electrolyte. Out of five different halogen free organic heterocycles, Li[C3BN2(NO2)4] and Li[C2BNO(NO2)3] are found to be mostly suitable as electrolytes in Li-ion batteries...
August 22, 2017: Chemical Communications: Chem Comm
#6
Thomas R Vincent, James Canham, Masatsugu Toyota, Marieta Avramova, Sam T Mugford, Simon Gilroy, Anthony J Miller, Saskia Hogenhout, Dale Sanders
Calcium ions are predicted to be key signaling entities during biotic interactions, with calcium signaling forming an established part of the plant defense response to microbial elicitors and to wounding caused by chewing insects, eliciting systemic calcium signals in plants. However, the role of calcium in vivo during biotic stress is still unclear. This protocol describes the use of a genetically-encoded calcium sensor to detect calcium signals in plants during feeding by a hemipteran pest. Hemipterans such as aphids pierce a small number of cells with specialized, elongated sucking mouthparts, making them the ideal tool to study calcium dynamics when a plant is faced with a biotic stress, which is distinct from a wounding response...
August 15, 2017: Journal of Visualized Experiments: JoVE
#7
Ivan Haralampiev, Holger A Scheidt, Daniel Huster, Peter Müller
Sterols play a unique role for the structural and dynamical organization of membranes. The current study reports data on the membrane properties of the phytosterol (3β,5α,22E)-stigmasta-7,22-dien-3-β-ol (α-spinasterol), which represents an important component of argan oil and have not been investigated so far in molecular detail. In particular, the impact of α-spinasterol on the structure and organization of lipid membranes was investigated and compared with those of cholesterol. Various membrane parameters such as the molecular packing of the phospholipid fatty acyl chains, the membrane permeability toward polar molecules, and the formation of lateral membrane domains were studied...
August 22, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
#8
Gregory L Dignon, Gül H Zerze, Jeetain Mittal
Amyloid aggregates are characteristic of many serious diseases such as Alzheimer's Disease, Parkinson's and Type II Diabetes, and commonly involve intrinsically disordered proteins (IDPs), those that populate an ensemble of conformations rather than a single folded structure in isolation. Human Islet Amyloid Polypeptide (hIAPP or amylin) is an amyloidogenic IDP implicated in pancreatic $\beta$-cell death during the pathogenesis of Type II Diabetes. The target of amylin's toxic activity is thought to be the cell's lipid membrane, which may also act as a catalyst for aggregation...
August 22, 2017: Journal of Physical Chemistry. B
#9
Ling Zhang, Hanzi Sun, Zhen Chen, Zhengsheng Liu, Niu Huang, Feng Qian
Novel "pairs" of drugs possessing pharmacological synergies could be encapsulated into polymeric micelles and exert superb therapeutic effects in vivo upon intravenous administration, with the prerequisite that the micelles remain stable. NADP(H) quinone oxidoreductase 1 (NQO1) inhibitors, such as β-lapachone (LPC) and tanshinone IIA (THA) are structurally and pharmacologically similar molecules that are both poorly water soluble, crystallize extremely fast, and demonstrate synergistic anticancer effect when used together with paclitaxel (PTX)...
August 22, 2017: Molecular Pharmaceutics
#10
Milan Delor, Dannielle G McCarthy, Benjamin L Cotts, Trevor D Roberts, Rodrigo Noriega, David D Devore, Sukrit Mukhopadhyay, Timothy S De Vries, Naomi S Ginsberg
Solid-state solvation (SSS) is a solid-state analogue of solvent-solute interactions in the liquid state. Although it could enable exceptionally fine control over the energetic properties of solid-state devices, its molecular mechanisms have remained largely unexplored. We use ultrafast transient absorption and optical Kerr effect spectroscopies to independently track and correlate both the excited-state dynamics of an organic emitter and the polarization anisotropy relaxation of a small polar dopant embedded in an amorphous polystyrene matrix...
August 22, 2017: Journal of Physical Chemistry Letters
#11
GiovanniMaria Piccini, Daniela Polino, Michele Parrinello
We have studied the cyclization reaction of deprotonated 4-chloro-1-butanethiol to tetrahydrothiophene by means of well-tempered metadynamics. To properly select the collective variables, we used the recently proposed variational approach to conformational dynamics within the framework of metadyanmics. This allowed us to select the appropriate linear combinations from a set of collective variables representing the slow degrees of freedom that best describe the slow modes of the reaction. We performed our calculations at three different temperatures, namely, 300, 350, and 400 K...
August 22, 2017: Journal of Physical Chemistry Letters
#12
Franco P Bonafé, Bálint Aradi, Mengxue Guan, Oscar A Douglas-Gallardo, Chao Lian, Sheng Meng, Thomas Frauenheim, Cristián G Sánchez
We present the first real-time atomistic simulation on the quantum dynamics of icosahedral silver nanoparticles under strong laser pulses, using time dependent density functional theory (TDDFT) molecular dynamics. We identify the emergence of sub-picosecond breathing-like radial oscillations starting immediately after laser pulse excitation, with increasing amplitude as the field intensity increases. The ultrafast dynamic response of nanoparticles to laser excitation points to a new mechanism other than equilibrium electron-phonon scattering previously assumed, which takes a much longer timescale...
August 22, 2017: Nanoscale
#13
Alexey V Shvetsov, Yana A Zabrodskaya, Peter A Nekrasov, Vladimir V Egorov
In this study we present molecular dynamics simulations of the antiviral drug triazavirine, that affects formation of amyloid-like fibrils of the model peptide (SI). According to our simulations, triazavirine is able to form linear supramolecular structures which can act as shields and prevent interactions between SI monomers. This model, as validated by simulations, provides an adequate explanation of triazavirine's mechanism of action as it pertains to SI peptide fibril formation.
August 22, 2017: Journal of Biomolecular Structure & Dynamics
#14
REVIEW
Matthew J Webber, Robert Langer
The rational design of drug delivery approaches leveraging supramolecular chemistry (i.e., "chemistry beyond the molecule") has garnered significant interest in recent years toward improving therapeutics. By using specific, dynamic, and tunable non-covalent interactions, engineered approaches to drug delivery can be realized. Certain benefits to this approach are molecular-level control of composition, improved routes for incorporating and targeting drugs, and new strategies to create delivery devices that respond to a variety of physiologic indicators...
August 22, 2017: Chemical Society Reviews
#15
Fritz Lehnert, Stefan G Mayr
Despite a high technical relevance and 35 years of observation, self-organized morphogenesis of nanoporous sponge-like amorphous structures during exposure of selected covalent materials to energetic ions is still insufficiently understood. Due to the presence and absence of these effects in amorphous Ge and Si, respectively, the Ge-Si alloy system constitutes an ideal testbed to track down the underlying physics at the atomic scale. This is realized within the present study by a combination of tailored experiments and extensive molecular dynamics computer modeling...
August 22, 2017: Physical Chemistry Chemical Physics: PCCP
#16
Yutaro Yamada, Hiroki Konno, Katsuya Shimabukuro
In this study, we present a new technique called correlative atomic force and transmission electron microscopy (correlative AFM/TEM) in which a targeted region of a sample can be observed under AFM and TEM. The ultimate goal of developing this new technique is to provide a technical platform to expand the fields of AFM application to complex biological systems such as cell extracts. Recent advances in the time resolution of AFM have enabled detailed observation of the dynamic nature of biomolecules. However, specifying molecular species, by AFM alone, remains a challenge...
2017: Biophysics and Physicobiology
#17
Yan Sun, Minxiao Wang, Leilei Li, Li Zhou, Xiaocheng Wang, Ping Zheng, Haiyan Yu, Chaolun Li, Song Sun
Deep-sea mussels of the genus Bathymodiolus are numerically dominant macrofauna in many cold seep and hydrothermal vent ecosystems worldwide, and they depend on organic carbon produced by symbionts present in the epithelial cells of the gills. Although Bathymodiolus platifrons represents typical methanotrophic endosymbiosis, our understanding of molecular mechanisms of methane oxidization and carbon fixation is still in its infancy. Moreover, the laboratory maintenance of B. platifrons and the symbiont abundance dynamics during maintenance has not been reported...
2017: PeerJ
#18
Daniel R Amor, Raúl Montañez, Salva Duran-Nebreda, Ricard Solé
A major force contributing to the emergence of novelty in nature is the presence of cooperative interactions, where two or more components of a system act in synergy, sometimes leading to higher-order, emergent phenomena. Within molecular evolution, the so called hypercycle defines the simplest model of an autocatalytic cycle, providing major theoretical insights on the evolution of cooperation in the early biosphere. These closed cooperative loops have also inspired our understanding of how catalytic loops appear in ecological systems...
August 21, 2017: PLoS Computational Biology
#19
Wesley M Botello-Smith, Abdelaziz Alsamarah, Payal Chatterjee, Chen Xie, Jerome J Lacroix, Jijun Hao, Yun Luo
Type 1 Serine/Threonine Kinase Receptors (STKR1) transduce a wide spectrum of biological signals mediated by TGF-β superfamily members. The STKR1 activity is tightly controlled by their regulatory glycine-serine rich (GS) domain adjacent to the kinase domain. Despite decades of studies, it remains unknown how physiological or pathological GS domain modifications are coupled to STKR1 kinase activity. Here, by performing molecular dynamics simulations and free energy calculation of Activin-Like Kinase 2 (ALK2), we found that GS domain phosphorylation, FKBP12 dissociation, and disease mutations all destabilize a D354-R375 salt-bridge, which normally acts as an electrostatic lock to prevent coordination of adenosine triphosphate (ATP) to the catalytic site...
August 21, 2017: PLoS Computational Biology
#20
Emmanuelle Bignon, Marco Marazzi, Vanessa Besancenot, Hugo Gattuso, Guillaume Drouot, Christophe Morell, Leif A Eriksson, Stephanie Grandemange, Elise Dumont, Antonio Monari
Nonsteroidal 2-arylproprionic acids are widely used, over-the-counter, anti-inflammatory drugs. Photosensitivity is a commonly overlooked adverse effect of these drugs. Based on the combined use of cell viability assays and molecular modeling, we prove and rationalize the photochemical pathways triggering photosensitization for two drugs, ibuprofen and ketoprofen. As its parent compound benzophenone, ketoprofen produces singlet oxygen, upon triplet manifold population. However, ibuprofen and ketoprofen photodissociate and hence may generate two highly reactive radicals...
August 21, 2017: Scientific Reports
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