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https://www.readbyqxmd.com/read/28735170/effects-of-different-solvents-on-the-conformations-of-apoptotic-cytochrome-c-structural-insights-from-molecular-dynamics-simulation
#1
Gurusamy Muneeswaran, Subramanian Kartheeswaran, Kaliappan Muthukumar, Christopher D Dharmaraj, Chandran Karunakaran
Cytochrome c (cyt-c) upon binding with cardiolipin acquires peroxidase activity and is strictly connected to the pathogenesis of many human diseases including neurodegenerative and cardiovascular diseases. Interaction of cyt-c with cardiolipin mimics partial unfolding/conformational changes of cyt-c in different solvent environments. Dynamic pictures of these conformational changes of cyt-c are crucial in understanding their physiological roles in mitochondrial functions. Therefore, atomistic molecular dynamics (MD) simulations have been carried out to investigate the effect of different solvents (water, urea/water, MeOH and DMSO) on the structure and conformations of apoptotic cyt-c (Fe(3+))...
July 14, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28734204/molecular-dynamics-of-conformation-specific-dopamine-transporter-inhibitor-complexes
#2
Bernandie Jean, Christopher K Surratt, Jeffry D Madura
The recreational psychostimulant cocaine inhibits dopamine reuptake from the synapse, resulting in excessive stimulation of postsynaptic dopamine receptors in brain areas associated with reward and addiction. Cocaine binds to and stabilizes the outward- (extracellular-) facing conformation of the dopamine transporter (DAT) protein, while the low abuse potential DAT inhibitor benztropine prefers the inward- (cytoplasmic-) facing conformation. A correlation has been previously postulated between psychostimulant abuse potential and preference for the outward-facing DAT conformation...
July 11, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28733595/how-cholesteryl-ester-transfer-protein-can-also-be-a-potential-triglyceride-transporter
#3
Venkat R Chirasani, Sanjib Senapati
CETP transfers cholesteryl esters (CEs) and triglycerides (TGs) between different lipoproteins and came in limelight as a drug-target against CVD. In the search for detailed mechanism of lipid transfer through CETP, enormous effort is devoted employing crystallographic, cryo-EM, and Molecular Dynamics (MD) studies. However, these studies primarily focused on CE-bound CETP structure and CE transfer mechanism. With the reported correlation that CETP looses significant CE transfer activity upon inhibiting TG transfer, it is of tremendous importance to understand the structure and dynamics of TG-bound CETP...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733203/in-silico-pharmacogenetic-approach-the-natalizumab-case-study
#4
Francesca Cavaliere, Enrico Montanari, Andrew Emerson, Annamaria Buschini, Pietro Cozzini
Natalizumab is a humanized monoclonal antibody to α4β1 integrin and is approved for the treatment of Multiple Sclerosis. In patients there is a great variation in drug response and there is much evidence that genetic contributors play an important role in defining an individual's susceptibility. Natalizumab binds to α4-residues Gln-152, Lys-201, Lys256, and these seem to be essential for its activity. Studies on a range of species in disease model have showed a loss of reactivity when any one of those three residues were different to human...
July 18, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28731858/a-generalized-approach-for-measuring-relationships-among-genes
#5
Lijun Wang, Md Asif Ahsan, Ming Chen
Several methods for identifying relationships among pairs of genes have been developed. In this article, we present a generalized approach for measuring relationships between any pairs of genes, which is based on statistical prediction. We derive two particular versions of the generalized approach, least squares estimation (LSE) and nearest neighbors prediction (NNP). According to mathematical proof, LSE is equivalent to the methods based on correlation; and NNP is approximate to one popular method called the maximal information coefficient (MIC) according to the performances in simulations and real dataset...
July 21, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28731776/predicting-flory-huggins-%C3%AF-from-simulations
#6
Wenlin Zhang, Enrique D Gomez, Scott T Milner
We introduce a method, based on a novel thermodynamic integration scheme, to extract the Flory-Huggins χ parameter as small as 10^{-3}kT for polymer blends from molecular dynamics (MD) simulations. We obtain χ for the archetypical coarse-grained model of nonpolar polymer blends: flexible bead-spring chains with different Lennard-Jones interactions between A and B monomers. Using these χ values and a lattice version of self-consistent field theory (SCFT), we predict the shape of planar interfaces for phase-separated binary blends...
July 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28731695/how-rhodopsin-tunes-the-equilibrium-between-protonated-and-deprotonated-forms-of-the-retinal-chromophore
#7
Siri Camee van Keulen, Alicia Solano, Ursula Rothlisberger
Rhodopsin is a photoactive G-protein-coupled receptor (GPCR) that converts dim light into a signal for the brain, leading to eyesight. Full activation of this GPCR is achieved after passing through several steps of the protein's photoactivation pathway. Key events of rhodopsin activation are the initial cis-trans photoisomerisation of the covalently bound retinal moiety followed by conformational rearrangements and deprotonation of the chromophore's protonated Schiff base (PSB), which ultimately lead to full activation in the meta II state...
July 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28731353/altering-dna-programmable-colloidal-crystallization-paths-by-modulating-particle-repulsion
#8
Mary X Wang, Jeffrey D Brodin, Jaime A Millan, Soyoung E Seo, Martin Girard, Monica Olvera de la Cruz, Byeongdu Lee, Chad A Mirkin
Colloidal crystal engineering with DNA can be used to realize precise control over nanoparticle (NP) arrangement. Here, we investigate a case of DNA-based assembly where the properties of DNA as a polyelectrolyte brush are employed to alter a hybridization-driven NP crystallization pathway. Using the coassembly of DNA-conjugated proteins and spherical gold nanoparticles (AuNPs) as a model system, we explore how steric repulsion between noncomplementary, neighboring NPs due to overlapping DNA shells can influence their ligand-directed behavior...
July 21, 2017: Nano Letters
https://www.readbyqxmd.com/read/28731083/mutable-polyelectrolyte-tube-arrays-mesoscale-modeling-and-lateral-force-microscopy
#9
Steven W Cranford, Lin Han, Christine Ortiz, Markus J Buehler
In this study, the pH-dependent friction of layer-by-layer assemblies of poly(allylamine hydrochloride) and poly(acrylic acid) (PAH/PAA) are quantified for microtube array structures via experimental and simulated lateral force microscopy (LFM). A novel coarse-grain tube model is developed, utilizing a molecular dynamics (MD) framework with a Hertzian soft contact potential (such that F ∼ δ(3/2)) to allow the efficient dynamic simulation of 3D arrays consisting of hundreds of tubes at micrometer length scales...
July 21, 2017: Soft Matter
https://www.readbyqxmd.com/read/28730431/protocols-for-molecular-dynamics-simulations-of-rna-nanostructures
#10
Taejin Kim, Wojciech K Kasprzak, Bruce A Shapiro
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730215/energetics-and-diffusion-of-liquid-water-and-hydrated-ions-through-nanopores-in-graphene-ab-initio-molecular-dynamics-simulation
#11
Raúl Guerrero-Avilés, Walter Orellana
The energetics and diffusion of water molecules and hydrated ions (Na(+), Cl(-)) passing through nanopores in graphene are addressed by dispersion-corrected density functional theory calculations and ab initio molecular dynamics (MD) simulations. Pores of about 0.8 nm in diameter with different pore-edge passivations, with (H) and (O, H) atoms, were considered. Our MD simulations show a water flux through the hydroxylated pores of about one H2O molecule every three picoseconds, in close agreement with recent experiments that estimated a water flux of three molecules per picosecond through pores of ∼1 nm...
July 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28729760/structural-insight-into-the-binding-of-c60-derivatives-with-enoyl-pyruvate-transferase-from-helicobacter-pylori
#12
Mohammad Teimouri, Muhammad Junaid, Abbas Khan, Houjin Zhang
Helicobacter pylori (H. pylori) is a human pathogen associated with acute gastritis and peptic ulcer. The MurA enzyme is an important drug target for the identification of ligands with improved efficacy and acceptable pharmaco-kinetic properties. We developed a homology model of H. Pylori MurA followed by refinement and molecular dynamics (MD) simulations. A total of 16 C60-derivatives were docked and its docking score were compared. Some of the known inhibitors were also similarly characterized and compared...
2017: Bioinformation
https://www.readbyqxmd.com/read/28729534/uv-activated-zno-films-on-a-flexible-substrate-for-room-temperature-o2-and-h2o-sensing
#13
Christopher B Jacobs, Artem B Maksov, Eric S Muckley, Liam Collins, Masoud Mahjouri-Samani, Anton Ievlev, Christopher M Rouleau, Ji-Won Moon, David E Graham, Bobby G Sumpter, Ilia N Ivanov
We demonstrate that UV-light activation of polycrystalline ZnO films on flexible polyimide (Kapton) substrates can be used to detect and differentiate between environmental changes in oxygen and water vapor. The in-plane resistive and impedance properties of ZnO films, fabricated from bacteria-derived ZnS nanoparticles, exhibit unique resistive and capacitive responses to changes in O2 and H2O. We propose that the distinctive responses to O2 and H2O adsorption on ZnO could be utilized to statistically discriminate between the two analytes...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28728523/structural-insights-into-the-binding-of-small-ligand-molecules-to-a-g-quadruplex-dna-located-in-the-hiv-1-promoter
#14
Petar M Mitrasinovic
Targeting guanine (G)-rich DNA sequences, folded into non-canonical G-quadruplex (G4) structures, by small ligand molecules is a promising strategy for gene therapy of various diseases. There is experimental proposal that, among eight studied ligands, nitidine chloride - NC and a benzo phenanthridine derivative - BPD have the highest binding affinities for such a sequence (5'-T(1)G(2)G(3)C(4)C(5)T(6)G(7)G(8)G(9)C(10)G(11)G(12)G(13)A(14)C(15)T(16)G(17)G(18)G(19)-3') in the HIV-1 promoter, indicating that an anti-HIV-1 prodrug may regulate the expression of the promoter...
July 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28727843/atomistic-modeling-of-alternating-access-of-a-mitochondrial-adp-atp-membrane-transporter-with-molecular-simulations
#15
Koichi Tamura, Shigehiko Hayashi
The mitochondrial ADP/ATP carrier (AAC) is a membrane transporter that exchanges a cytosolic ADP for a matrix ATP. Atomic structures in an outward-facing (OF) form which binds an ADP from the intermembrane space have been solved by X-ray crystallography, and revealed their unique pseudo three-fold symmetry fold which is qualitatively different from pseudo two-fold symmetry of most transporters of which atomic structures have been solved. However, any atomic-level information on an inward-facing (IF) form, which binds an ATP from the matrix side and is fixed by binding of an inhibitor, bongkrekic acid (BA), is not available, and thus its alternating access mechanism for the transport process is unknown...
2017: PloS One
https://www.readbyqxmd.com/read/28727426/fully-atomistic-a%C3%AE-40-and-a%C3%AE-42-oligomers-in-water-observation-of-pore-like-conformations
#16
Matthew John Voelker, Bogdan Barz, Brigita Urbanc
Oligomers formed by amyloid β-protein (Aβ) are central to Alzheimer's disease (AD) pathology, yet their structure remains elusive. Of the two predominant Aβ alloforms, Aβ40 and Aβ42, the latter is more strongly associated with AD. Here, we structurally characterized Aβ40 and Aβ42 monomers through pentamers which were converted from previously derived coarse-grained (DMD4B-HYDRA) simulations into all-atom conformations and subjected to explicit-solvent MD. Free energy landscapes revealed that structural differences between Aβ40 and Aβ42 conformations increase with oligomer order up to trimers...
July 20, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28726921/molecular-dynamics-simulations-and-in-vitro-analysis-of-the-crmp2-thiol-switch
#17
Daniel Möller, Manuela Gellert, Walter Langel, Christopher Horst Lillig
The collapsin response mediator protein CRMP2 (gene: DPYSL2) is crucial for neuronal development. The homotetrameric CRMP2 complex is regulated via two mechanisms: first by phosphorylation and second by the reduction and oxidation of the Cys504 residues of two adjacent subunits. Here, we have analysed the effects of this redox switch on the protein in vitro combined with force field molecular dynamics (MD). Earlier X-ray data reveal the structure of the rigid body of the molecule but lack the flexible C-terminus with the important sites for phosphorylation and redox regulation...
July 20, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28726898/probe-location-dependent-resonance-energy-transfer-at-lipid-water-interfaces-comparison-between-the-gel-and-fluid-phase-of-lipid-bilayer
#18
Moirangthem Kiran Singh, Mohammad Firoz Khan, Him Shweta, Sobhan Sen
Despite significant interest in understanding the role of the local dielectric environment and lipid-bilayer fluidity/rigidity in resonance energy transfer between chromophores at lipid/water interfaces, a comprehensive approach to quantify such environmental dependence on energy transfer is missing - primarily because of the scarcity of suitable probes. Here we present the results on multi-chromophoric Förster resonance energy transfer (FRET) from a series of 4-aminophthalimide-based molecules (4AP-Cn; n = 2-10, 12) of different lipophilicity (donors), which reside at different depths across the lipid/water interfaces, to rhodamine-6G (Rh6G; acceptor) molecules that stay in a water-rich region near the lipid headgroups...
July 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28726688/energy-efficient-and-fast-reversal-of-a-fixed-skyrmion-2-terminal-memory-with-spin-current-assisted-by-voltage-controlled-magnetic-anisotropy
#19
Dhritiman Bhattacharya, Md Mamun Al Rashid, Jayasimha Atulasimha
Recent work [1,2] suggests that ferromagnetic reversal with spin transfer torque (STT) requires more current in a system in the presence of DMI than switching a typical ferromagnet of the same dimensions and perpendicular magnetic anisotropy (PMA). However, DMI promotes stabilization of skyrmions and we report that when the perpendicular anisotropy is modulated (reduced) for both the skyrmion and ferromagnet, it takes much smaller current to reverse the fixed skyrmion than to reverse the ferromagnet in the same time, or the skyrmion reverses much faster than the ferromagnet at similar levels of current...
July 20, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28725531/computational-insights-into-materials-and-interfaces-for-capacitive-energy-storage
#20
REVIEW
Cheng Zhan, Cheng Lian, Yu Zhang, Matthew W Thompson, Yu Xie, Jianzhong Wu, Paul R C Kent, Peter T Cummings, De-En Jiang, David J Wesolowski
Supercapacitors such as electric double-layer capacitors (EDLCs) and pseudocapacitors are becoming increasingly important in the field of electrical energy storage. Theoretical study of energy storage in EDLCs focuses on solving for the electric double-layer structure in different electrode geometries and electrolyte components, which can be achieved by molecular simulations such as classical molecular dynamics (MD), classical density functional theory (classical DFT), and Monte-Carlo (MC) methods. In recent years, combining first-principles and classical simulations to investigate the carbon-based EDLCs has shed light on the importance of quantum capacitance in graphene-like 2D systems...
July 2017: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
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