keyword
MENU ▼
Read by QxMD icon Read
search

MD simulation

keyword
https://www.readbyqxmd.com/read/28453549/idiosyncratic-recognition-of-uug-uua-codons-by-modified-nucleoside-5-taurinomethyluridine-%C3%AF-m5u-present-at-wobble-position-in-anticodon-loop-of-trnaleu-a-molecular-modeling-approach
#1
Asmita S Kamble, Prayagraj M Fandilolu, Susmit B Sambhare, Kailas D Sonawane
Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U) at the 'wobble' 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS). The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level. Hence, 50ns multiple molecular dynamics (MD) simulations of various anticodon stem loop (ASL) models of tRNALeu in presence and absence of τm5U34 along with UUG and UUA codons were performed to explore the dynamic behaviour of τm5U34 during codon recognition process...
2017: PloS One
https://www.readbyqxmd.com/read/28448807/alternative-sweeteners-influence-the-biomass-of-oral-biofilm
#2
Fathilah Abdul Razak, Baizatul Amirah Baharuddin, Elisya Farha Mohd Akbar, Amira Hanim Norizan, Nur Fazilah Ibrahim, Md Yusoff Musa
OBJECTIVE: Compact-structured oral biofilm accumulates acids that upon prolonged exposure to tooth surface, causes demineralisation of enamel. This study aimed to assess the effect of alternative sweeteners Equal Stevia(®), Tropicana Slim(®), Pal Sweet(®) and xylitol on the matrix-forming activity of plaque biofilm at both the early and established stages of formation. METHODS: Saliva-coated glass beads (sGB) were used as substratum for the adhesion of a mixed-bacterial suspension of Streptococcus mutans, Streptococcus sanguinis and Streptococcus mitis...
April 20, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28448138/idp-specific-force-field-ff14idpsff-improves-the-conformer-sampling-of-intrinsically-disordered-proteins
#3
Dong Song, Ray Luo, Hai-Feng Chen
Intrinsically disordered proteins (IDPs) or intrinsically disordered regions have not fixed tertiary structure, but play key roles in signal regulation, molecule recognition, and drug target. However it is difficult to study the structure and function of IDPs by traditional experimental methods because of their diverse conformations. Limitations of current generic protein force fields and solvent models were reported in the previous simulations of IDPs. We have also explored to overcome these limitations by developing ff99IDPs and ff14IDPs force fields to correct the dihedral distribution for eight disordered promoting residues often observed in IDPs and found encouraging improvements...
April 27, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28447543/human-egf-derived-direct-and-reverse-short-linear-motifs-conformational-dynamics-insight-into-the-receptor-binding-residues
#4
Nurbubu T Moldogazieva, Konstantin V Shaitan, Mikhail Yu Antonov, Innokenty M Mokhosoev, Olga V Levtsova, Аlexander A Terentiev
Short linear motifs (SLiMs) have been recognized to perform diverse functions in a variety of regulatory proteins through the involvement in protein-protein interactions, signal transduction, cell cycle regulation, protein secretion, etc. However, detailed molecular mechanisms underlying their functions including roles of definite amino acid residues remain obscure. In our previous studies, we demonstrated that conformational dynamics of amino acid residues in oligopeptides derived from regulatory proteins such as alpha-fetoprotein (AFP), carcino-embryonic antigen (CEA) and pregnancy specific β1-glycoproteins (PSGs) contributes greatly to their biological activities...
April 27, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28447461/diffusion-controlled-recrystallization-of-water-sorbed-into-poly-meth-acrylates-revealed-by-variable-temperature-mid-infrared-spectroscopy-and-molecular-dynamics-simulation
#5
Nobuhiro Yasoshima, Mizuki Fukuoka, Hiromi Kitano, Shigehiro Kagaya, Tatsuya Ishiyama, Makoto Gemmei-Ide
Recrystallization behaviors of water sorbed into four poly(meth)acrylates; poly(2-methoxyethyl acrylate) (PMEA), poly(tetrahydrofurfuryl acrylate) (PTHFA), poly(methyl acrylate) (PMA), and poly(methyl methacrylate) (PMMA), are investigated by variable-temperature mid-infrared (VT-MIR) spectroscopy and molecular dynamics (MD) simulation. VT-MIR spectra demonstrate that recrystallization temperatures of water sorbed into the polymers are positively correlated with their glass transition temperatures reported previously...
April 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28447346/a-charge-equilibration-formalism-for-treating-charge-transfer-effects-in-md-simulations-application-to-water-clusters
#6
Sudipta Kumar Sinha, Mohit Mehta, Sandeep Patel
Conventional classical force fields by construction do not explicitly partition intermolecular interactions to include polarization and charge transfer effects, whereas fully quantum mechanical treatments allow a means to effect this dissection (although not uniquely due to the lack of a charge transfer operator). Considering the importance of polarization in a variety of systems, a particular class of classical models, charge equilibration models, have been extensively developed to study those systems; since these types of interaction models are inherently based on movement of charge throughout a system, they are natural platform for including polarization and charge transfer effects within the context of molecular simulations...
June 15, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28446025/medicinal-plant-phytochemicals-and-their-inhibitory-activities-against-pancreatic-lipase-molecular-docking-combined-with-molecular-dynamics-simulation-approach
#7
Bilal Ahmed, Usman Ali Ashfaq, Muhammad Usman Mirza
Obesity is the worst health risk worldwide, which is linked to a number of diseases. Pancreatic lipase is considered as an affective cause of obesity and can be a major target for controlling the obesity. The present study was designed to find out best phytochemicals against pancreatic lipase through molecular docking combined with molecular dynamics (MD) simulation. For this purpose, a total of 3770 phytochemicals were docked against pancreatic lipase and ranked them on the basis of binding affinity. Finally, 10 molecules (Kushenol K, Rosmarinic acid, Reserpic acid, Munjistin, Leachianone G, Cephamycin C, Arctigenin, 3-O-acetylpadmatin, Geniposide and Obtusin) were selected that showed strong bonding with the pancreatic lipase...
April 26, 2017: Natural Product Research
https://www.readbyqxmd.com/read/28445765/in-line-monitoring-and-optimization-of-powder-flow-in-a-simulated-continuous-process-using-transmission-near-infrared-spectroscopy
#8
Md Anik Alam, Zhenqi Shi, James K Drennen, Carl A Anderson
In-line monitoring of continuous powder flow is an integral part of the continuous manufacturing process of solid oral dosage forms in the pharmaceutical industry. Specifically, monitoring downstream from loss-in-weight (LIW) feeders and/or continuous mixers provides important data about the state of the process. Such measurements support control of the process and thereby enhance product quality. Near Infrared Spectroscopy (NIRS) is a potential PAT tool to monitor the homogeneity of a continuous powder flow stream in pharmaceutical manufacturing...
April 23, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28445231/the-effects-of-multi-day-vs-single-pre-exercise-nitrate-supplement-dosing-on-simulated-cycling-time-trial-performance-and-skeletal-muscle-oxygenation
#9
Edward Jo, Michelle Fischer, Alexandra T Auslander, Alan Beigarten, Bruce Daggy, Ken Hansen, Lisa Kessler, Adam Osmond, Hong Wang, Rachel Wes
A transient augmentation in the metabolic efficiency of skeletal muscle is the purported basis for dietary nitrate supplementation amongst competitive and recreational athletes alike. Previous studies support the ergogenic effects of nitrate supplementation as findings indicated improved microvascular blood flow, exercise economy, and performance with relatively short-term supplementation. As with most ergogenic aids, the optimum duration of supplementation prior to performance or competition, i.e. loading phase, is a critical determinant for efficacy...
April 18, 2017: Journal of Strength and Conditioning Research
https://www.readbyqxmd.com/read/28444908/micelles-of-the-chiral-biocompatible-surfactant-1r-2s-dodecyl-2-hydroxy-1-methyl-2-phenylethyl-dimethylammonium-bromide-dmeb-molecular-dynamics-and-fragmentation-patterns-in-gas-phase
#10
David Bongiorno, Serena Indelicato, Leopoldo Ceraulo, Ugo Perricone, Valentina Calabrese, Anna Maria Almerico, Vincenzo Turco Liveri, Marco Tutone
RATIONALE: The study of self-assembly process of surfactant molecules in gas phase is of actually interest for several theoretical and technological reasons related to their possible exploitation as drug carriers, protein shields and cleaning agents in gas phase. METHODS: Stability and fragmentation patterns of singly and multiply charged (either positively or negatively) aggregates of the surfactant (1R,2S)-dodecyl(2-hydroxy-1-methyl-2-phenylethyl) dimethyl ammonium bromide (DMEB) in gas phase have been studied by ion mobility mass spectrometry and tandem mass spectrometry...
April 26, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/28443917/hydrogen-purification-performance-of-a-nanoporous-hexagonal-boron-nitride-membrane-molecular-dynamics-and-first-principle-simulations
#11
Masoud Darvish Ganji, Razieh Dodangeh
Membranes have attracted much attention for the efficient separation of gas mixtures, due to their specific structural and unique properties. In this work, density functional theory (DFT) and molecular dynamic (MD) simulations have been employed to evaluate the performance of nanoporous hexagonal boron nitride (h-BN) monolayers for hydrogen purification. Various porous membranes were designed, and full structural relaxation was carried out by using DFT calculations and then MD simulations to investigate the H2 purification performance of the nanoporous h-BN membranes...
April 26, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28443905/predicting-oligomer-polymer-compatibility-and-the-impact-on-nanoscale-segregation-in-thin-films
#12
Elise F D Sabattié, Jos Tasche, Mark R Wilson, Maximilian W A Skoda, Arwel Hughes, Torsten Lindner, Richard L Thompson
Compatibility between oligomers and polymers was systematically assessed using differential scanning calorimetry (DSC) and was correlated with similarity in saturation and solubility parameter. These measurements enabled validation of detailed volume of mixing calculations using Statistical Association Fluid Theory (SAFT-γ Mie) and molecular dynamics (MD) simulations, which can be used to predict behaviour beyond the experimentally accessible conditions. These simulations confirmed that squalane is somewhat more compatible with poly(isoprene), "PI" than poly(butadiene), "PB", and further enabled prediction of the temperature dependence of compatibility...
April 26, 2017: Soft Matter
https://www.readbyqxmd.com/read/28441910/mechanical-features-of-various-silkworm-crystalline-considering-hydration-effect-via-molecular-dynamics-simulations
#13
Yoonjung Kim, Myeongsang Lee, Hyunsung Choi, Inchul Baek, Jae In Kim, Sungsoo Na
Silk materials are receiving significant attention as base materials for various functional nanomaterials and nanodevices, due to its exceptionally high mechanical properties, biocompatibility, and degradable characteristics. Although crystalline silk regions are composed of various repetitive motifs with differing amino acid sequences, how the effect of humidity works differently on each of the motifs and their structural characteristics remains unclear. We report molecular dynamics (MD) simulations on various silkworm fibroins composed of major motifs (i...
April 25, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28441487/the-isomeric-preference-of-an-atypical-dopamine-transporter-inhibitor-contributes-to-its-selection-of-the-transporter-conformation
#14
Ara M Abramyan, Sebastian Stolzenberg, Zheng Li, Claus J Loland, Frank Noé, Lei Shi
Cocaine, a widely abused psychostimulant, inhibits the dopamine transporter (DAT) by trapping the protein in an outward-open conformation, whereas atypical DAT inhibitors such as benztropine have low abuse liability and prefer less outward-open conformations. Here, we use a spectrum of computational modeling and simulation approaches to obtain the underlying molecular mechanism in atomistic detail. Interestingly, our quantum mechanical calculations and molecular dynamics (MD) simulations suggest that a benztropine derivative JHW007 prefers a different stereoisomeric conformation of tropane in binding to DAT compared to that of a cocaine derivative, CFT...
April 25, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28440827/molecular-dynamics-investigations-of-membrane-bound-cyp2c19-polymorphisms-reveal-distinct-mechanisms-for-peripheral-variants-by-long-range-effects-on-the-enzymatic-activity
#15
Ying-Lu Cui, Rong-Ling Wu
Increasing sophistication in methods used to account for human polymorphisms in susceptibility to drug metabolism has been one of the success stories in the prevention of adverse drug reactions. Genetic polymorphisms in drug-metabolizing enzymes can affect enzyme activity and cause differences in treatment response or drug toxicity. CYP2C19 is one of the most highly polymorphic CYP enzymes and acts on 10-15% of drugs in current clinical use. Despite the number of experimental analyses carried out for this system, the detailed structural basis for altered catalytic properties of polymorphic CYP2C19 variants remains unexplained at the atomic level...
April 25, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28440650/comprehensive-computational-and-experimental-analysis-of-biomaterial-towards-the-behavior-of-imidazolium-based-ionic-liquids-an-interplay-between-hydrophilic-and-hydrophobic-interactions
#16
Reddicherla Umapathi, Suresh B Vepuri, Pannuru Venkatesu, Mahmoud E S Soliman
To provide insights into the aggregation behavior, hydration tendency and variation in phase transition temperature produced by the addition of ionic liquids (ILs) to poly(N-isopropylacrylamide) (PNIPAM) aqueous solution, systematic physicochemical studies, and molecular dynamic simulations were carried out. The influence of ILs possessing same [Cl]- anion and a set of cation [Cnmim]+ with increasing alkyl chain length such as 1-ethyl-3-methylimidazolium ([Emim]+), 1-allyl-3-methylimidazolium ([Amim]+), 1-butyl-3-methylimidazolium ([Bmim]+), 1-hexyl-3-methylimidazolium ([Hmim]+), 1-benzyl-3-methylimidazolium ([Bzmim]+), and 1- decyl-3-methylimidazolium ([Dmim] +) on the phase transition of PNIPAM was monitored by the aid of UV-visible absorption spectra, fluorescence intensity spectra, viscosity (ɳ), dynamic light scattering (DLS) and Fourier transform infrared (FTIR) spectroscopy...
April 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28440638/dielectric-relaxation-of-the-ionic-liquid-1-ethyl-3-methylimidazolium-ethylsulfate-microwave-and-far-ir-properties
#17
Nilesh Ramchandra Dhumal, Johannes Kiefer, David Andrew Turton, Klaas Wynne, Hyung J Kim
Dielectric relaxation of the ionic liquid, 1-ethyl-3-methylimidazolium ethylsulfate (EMI(+)ETS(-)), is studied using molecular dynamics (MD) simulations. The collective dynamics of polarization arising from cations and anions are examined. Character- istics of the rovibrational and translational components of polarization dynamics are analyzed to understand their respective roles in the microwave and terahertz regions of dielectric relaxation. The MD results are compared with the experimental low- frequency spectrum of EMI(+)ETS(-), obtained via ultrafast optical Kerr effect (OKE) measurements...
April 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28440384/theoretical-and-numerical-analysis-of-nano-actuators-based-on-grafted-polyelectrolytes-in-an-electric-field
#18
N V Brilliantov, Yu A Budkov, C Seidel
We analyze, theoretically and by means of molecular dynamics (MD) simulations, the generation of mechanical force by a polyelectrolyte (PE) chain grafted to a plane and exposed to an external electric field; the free end of the chain is linked to a deformable target body. Varying the field, one can alter the length of the non-adsorbed (bulk) part of the chain and hence the deformation of the target body and the arising force. We focus on the impact of added salt on the magnitude of the generated force, which is especially important for applications...
April 25, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28439742/exploration-of-the-binding-affinities-between-ecdysone-agonists-and-ecr-usp-by-docking-and-mm-pb-gbsa-approaches
#19
Xueping Hu, Jin Xie, Song Hu, Li Zhang, Yanhong Dong
Ecdysone receptor (EcR) is a significant target in the identification of new environmentally friendly pesticides. There are two types of ecdysone agonists: steroidal ecdysone agonists and dibenzoylhydrazines (DBHs). In this study, various modeling methods (homology modeling, molecular docking, MD simulation, binding free energy calculation, and per-residue binding free energy decomposition) were utilized to study the different binding mechanisms of two types of ecdysone agonists. Our theoretical results indicated that the relative binding potencies of DBHs can be ranked sufficiently accurately using the MOE docking method...
May 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28437616/neural-network-and-nearest-neighbour-algorithms-for-enhancing-sampling-of-molecular-dynamics
#20
Raimondas Galvelis, Yuji Sugita
The free energy calculations of complex chemical and biological systems with molecular dynamics (MD) are inefficient due to multiple local minima separated by high-energy barriers. The minima can be escaped using an enhanced sampling method such as metadynamics, which apply bias (i.e. importance sampling) along a set of collective variables (CV), but the maximum number of CVs (or dimensions) is severely limited. We propose a high-dimensional bias potential method (NN2B) based on two machine learning algorithms: the nearest neighbour density estimator (NNDE) and the artificial neural network (ANN) for the bias potential approximation...
April 24, 2017: Journal of Chemical Theory and Computation
keyword
keyword
73321
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"