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https://www.readbyqxmd.com/read/28110448/molecular-dynamics-exploration-of-the-binding-mechanism-and-properties-of-single-walled-carbon-nanotube-to-wt-and-mutant-vp35-fbp-region-of-ebola-virus
#1
Yan-Jun Zhang, Jing-Na Ding, Hui Zhong, Chang-Ping Sun, Ju-Guang Han
VP35 of Ebola viruses (EBOVs) is an attractive potential target because of its multifunction. All-atom molecular dynamics (MD) simulations and Molecular Mechanics Generalized Born surface area (MM/GBSA) energy calculations are performed to investigate the single-walled carbon nanotube (SWCNT) as an inhibitor in wild-type (WT) VP35 as well as in three primary mutants (K248A, I295A, and K248A/I295A) through docking the SWCNT in the first basic patch (FBP) of VP35. The SWCNTs of all the four systems effectively bind to the FBP...
January 21, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28110274/c4-photosynthesis-50-years-of-discovery-and-innovation
#2
EDITORIAL
Susanne von Caemmerer, Oula Ghannoum, Robert T Furbank
It is now over half a century since the biochemical characterization of the C4 photosynthetic pathway, and this special issue highlights the sheer breadth of current knowledge. New genomic and transcriptomic information shows that multi-level regulation of gene expression is required for the pathway to function, yet we know it to be one of the most dynamic examples of convergent evolution. Now, a focus on the molecular transition from C3-C4 intermediates, together with improved mathematical models, experimental tools and transformation systems, holds great promise for improving C4 photosynthesis in crops...
January 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28110185/computational-analysis-of-amsacrine-resistance-in-human-topoisomerase-ii-alpha-mutants-r487k-and-e571k-using-homology-modeling-docking-and-all-atom-molecular-dynamics-simulation-in-explicit-solvent
#3
Safaa Sader, Chun Wu
Amsacrine is an effective topoisomerase II enzyme inhibitor in acute lymphatic leukemia. Previous experimental studies have successfully identified two important mutations (R487K and E571K) conferring 100 and 25 fold resistance to Amsacrine respectively. Although the reduction of the cleavage ligand-DNA-protein ternary complex has been well thought as the major cause of drug resistance, the detailed energetic, structural and dynamic mechanisms remain to be elusive. In this study, we constructed human topoisomerase II alpha (hTop2α) homology model docked with Amsacrine based on crystal structure of human Top2β in complex with etoposide...
January 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28110184/structural-analysis-of-binding-functionality-of-folic-acid-peg-dendrimers-against-folate-receptor
#4
Diana Sampogna-Mireles, Ingrid D Araya-Durán, Valeria Márquez-Miranda, Jesús A Valencia-Gallegos, Fernando D González-Nilo
Dendrimers functionalized with folic acid (FA) are drug delivery systems that can selectively target cancer cells with folate receptors (FR-α) overexpression. Incorporation of polyethylene glycol (PEG) can enhance dendrimers solubility and pharmacokinetics, but ligand-receptor binding must not be affected. In this work we characterized, at atomic level, the binding functionality of conventional site-specific dendrimers conjugated with FA with PEG 750 or PEG 3350 as a linker. After Molecular Dynamics simulation, we observed that both PEG's did not interfere over ligand-receptor binding functionality...
January 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28110039/heat-induced-solubilization-of-curcumin-in-kinetically-stable-pluronic-p123-micelles-and-vesicles-an-exploit-of-slow-dynamics-of-the-micellar-restructuring-processes-in-the-aqueous-pluronic-system
#5
R Ganguly, A Kunwar, B Dutta, S Kumar, K C Barick, A Ballal, V K Aswal, P A Hassan
Wide therapeutic potential combined with low cost and negligible toxicity makes curcumin one of the most sought after drugs in recent times. Its poor aqueous solubility and low bioavailability are often overcome by using micelles and vesicles as its carriers. The substances that are commonly used for this purpose are a class of nonionic surfactants called pluronics. Solubilization of curcumin in aqueous systems of these surfactants is carried out by thin film hydration method presumably because slow dynamics of micellar restructuring processes in them creates hindrance for direct solubilization...
January 17, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28109973/sleep-loss-and-structural-plasticity
#6
REVIEW
Cassandra C Areal, Simon C Warby, Valérie Mongrain
Wakefulness and sleep are dynamic states during which brain functioning is modified and shaped. Sleep loss is detrimental to many brain functions and results in structural changes localized at synapses in the nervous system. In this review, we present and discuss some of the latest observations of structural changes following sleep loss in some vertebrates and insects. We also emphasize that these changes are region-specific and cell type-specific and that, most importantly, these structural modifications have functional roles in sleep regulation and brain functions...
January 18, 2017: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/28109869/outcomes-infectiousness-and-transmission-dynamics-of-patients-with-extensively-drug-resistant-tuberculosis-and-home-discharged-patients-with-programmatically-incurable-tuberculosis-a-prospective-cohort-study
#7
Keertan Dheda, Jason D Limberis, Elize Pietersen, Jody Phelan, Aliasgar Esmail, Maia Lesosky, Kevin P Fennelly, Julian Te Riele, Barbara Mastrapa, Elizabeth M Streicher, Tania Dolby, Abdallah M Abdallah, Fathia Ben-Rached, John Simpson, Liezel Smith, Tawanda Gumbo, Paul van Helden, Frederick A Sirgel, Ruth McNerney, Grant Theron, Arnab Pain, Taane G Clark, Robin M Warren
BACKGROUND: The emergence of programmatically incurable tuberculosis threatens to destabilise control efforts. The aim of this study was to collect prospective patient-level data to inform treatment and containment strategies. METHODS: In a prospective cohort study, 273 South African patients with extensively drug-resistant tuberculosis, or resistance beyond extensively drug-resistant tuberculosis, were followed up over a period of 6 years. Transmission dynamics, infectiousness, and drug susceptibility were analysed in a subset of patients from the Western Cape using whole-genome sequencing (WGS; n=149), a cough aerosol sampling system (CASS; n=26), and phenotypic testing for 18 drugs (n=179)...
January 18, 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/28109815/a-novel-biocompatible-drug-delivery-system-of-chitosan-temozolomide-nanoparticles-loaded-pcl-pu-nanofibers-for-sustained-delivery-of-temozolomide
#8
Mohammad Irani, Gity Mir Mohamad Sadeghi, Ismaeil Haririan
In the present study, the anticancer drug temozolomide (TMZ) was initially loaded into the chitosan (CS) nanoparticles and synthesized CS/TMZ nanoparticles were incorporated into the synthesized poly (ε-caprolactone diol) based polyurethane (PCL-Diol-b-PU) nanofibers. The synthesized nanoparticles and nanofibers were characterized using dynamic light scattering, transmission electron microscopy, X-ray powder diffraction and scanning electron microscopy. The obtained results revealed that the CS/TMZ nanoparticles were successfully embedded into the PCL-Diol-b-PU nanofibers...
January 18, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28109442/label-free-and-standard-free-absolute-quantitative-proteomics-using-the-total-protein-and-proteomic-ruler-approaches
#9
J R Wiśniewski
Understanding biological systems and their variation upon stimuli requires knowledge on their composition, primarily including information on organization and dynamics of proteomes. The total protein approach (TPA) is a label- and standard-free method for absolute protein quantitation of proteins using large-scale proteomic data. The method relies on the assumption that the total MS signal from all identified proteins in the dataset reflects-in a biochemical sense-the total protein and the MS signal from a single protein corresponds its abundance in the studied sample...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28109426/wgcna-application-to-proteomic-and-metabolomic-data-analysis
#10
G Pei, L Chen, W Zhang
Progresses in mass spectrometric instrumentation and bioinformatics identification algorithms made over the past decades allow quantitative measurements of relative or absolute protein/metabolite amounts in cells in a high-throughput manner, which has significantly expedited the exploration into functions and dynamics of complex biological systems. However, interpretation of high-throughput data is often restricted by the limited availability of suitable computational methods and enough statistical power. While many computational methodologies have been developed in the past decades to address the issue, it becomes clear that network-focused rather than individual gene/protein-focused strategies would be more appropriate to obtain a complete picture of cellular responses...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28109326/from-the-evolution-of-protein-sequences-able-to-resist-self-assembly-to-the-prediction-of-aggregation-propensity
#11
F Bemporad, M Ramazzotti
Folding of polypeptide chains into biologically active entities is an astonishingly complex process, determined by the nature and the sequence of residues emerging from ribosomes. While it has been long believed that evolution has pressed genomes so that specific sequences could adopt unique, functional three-dimensional folds, it is now clear that complex protein machineries act as quality control system and supervise folding. Notwithstanding that, events such as erroneous folding, partial folding, or misfolding are frequent during the life of a cell or a whole organism, and they can escape controls...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28109305/medical-pluralism-and-livestock-health-ethnomedical-and-biomedical-veterinary-knowledge-among-east-african-agropastoralists
#12
Mark A Caudell, Marsha B Quinlan, Robert J Quinlan, Douglas R Call
BACKGROUND: Human and animal health are deeply intertwined in livestock dependent areas. Livestock health contributes to food security and can influence human health through the transmission of zoonotic diseases. In low-income countries diagnosis and treatment of livestock diseases is often carried out by household members who draw upon both ethnoveterinary medicine (EVM) and contemporary veterinary biomedicine (VB). Expertise in these knowledge bases, along with their coexistence, informs treatment and thus ultimately impacts animal and human health...
January 21, 2017: Journal of Ethnobiology and Ethnomedicine
https://www.readbyqxmd.com/read/28109249/parameter-estimation-in-large-scale-systems-biology-models-a-parallel-and-self-adaptive-cooperative-strategy
#13
David R Penas, Patricia González, Jose A Egea, Ramón Doallo, Julio R Banga
BACKGROUND: The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear dynamic models. Global optimization methods can be used to solve this type of problems but the associated computational cost is very large. Moreover, many of these methods need the tuning of a number of adjustable search parameters, requiring a number of initial exploratory runs and therefore further increasing the computation times...
January 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28109242/local-spin-dynamics-of-iron-oxide-magnetic-nanoparticles-dispersed-in-different-solvents-with-variable-size-and-shape-a-1-h-nmr-study
#14
M Basini, T Orlando, P Arosio, M F Casula, D Espa, S Murgia, C Sangregorio, C Innocenti, A Lascialfari
Colloidal magnetic nanoparticles (MNPs) based on a nearly monodisperse iron oxide core and capped by oleic acid have been used as model systems for investigating the superparamagnetic spin dynamics by means of magnetometry measurements and nuclear magnetic resonance ((1)H NMR) relaxometry. The key magnetic properties (saturation magnetization, coercive field, and frequency dependent "blocking" temperature) of MNPs with different core size (3.5 nm, 8.5 nm, and 17.5 nm), shape (spherical and cubic), and dispersant (hexane and water-based formulation) have been determined...
January 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28109228/vibronic-eigenstates-and-the-geometric-phase-effect-in-the-2-e%C3%A2-state-of-no3
#15
Wolfgang Eisfeld, Alexandra Viel
The (2)E″ state of NO3, a prototype for the Jahn-Teller effect, has been an enigma and a challenge for a long time for both experiment and theory. We present a detailed theoretical study of the vibronic quantum dynamics in this electronic state, uncovering the effects of tunnelling, geometric phase, and symmetry. To this end, 45 vibronic levels of NO3 in the (2)E″ state are determined accurately and analyzed thoroughly. The computation is based on a high quality diabatic potential representation of the two-sheeted surface of the (2)E″ state developed by us [W...
January 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28109221/charge-and-energy-migration-in-molecular-clusters-a-stochastic-schr%C3%A3-dinger-equation-approach
#16
Thomas Plehn, Volkhard May
The performance of stochastic Schrödinger equations for simulating dynamic phenomena in large scale open quantum systems is studied. Going beyond small system sizes, commonly used master equation approaches become inadequate. In this regime, wave function based methods profit from their inherent scaling benefit and present a promising tool to study, for example, exciton and charge carrier dynamics in huge and complex molecular structures. In the first part of this work, a strict analytic derivation is presented...
January 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28109218/efficient-algorithm-for-multiconfiguration-pair-density-functional-theory-with-application-to-the-heterolytic-dissociation-energy-of-ferrocene
#17
Andrew M Sand, Donald G Truhlar, Laura Gagliardi
The recently developed multiconfiguration pair-density functional theory (MC-PDFT) combines multiconfiguration wave function theory with a density functional that depends on the on-top pair density of an electronic system. In an MC-PDFT calculation, there are two steps: a conventional multiconfiguration self-consistent-field (MCSCF) calculation and a post-MCSCF evaluation of the energy with an on-top density functional. In this work, we present the details of the MC-PDFT algorithm that avoids steeply scaling steps that are present in other post-self-consistent-field multireference calculations of dynamic correlation energy...
January 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28109215/interplay-between-alkyl-chain-asymmetry-and-cholesterol-addition-in-the-rigid-ion-pair-amphiphile-bilayer-systems
#18
Fong-Yin Huang, Chi-Cheng Chiu
Ion pair amphiphile (IPA), a molecular complex composed of a pair of cationic and anionic surfactants, has been proposed as a novel phospholipid substitute. Controlling the physical stability of IPA vesicles is important for its application developments such as cosmetic and drug deliveries. To investigate the effects of IPA alkyl chain combinations and the cholesterol additive on the structural and mechanical properties of IPA vesicular bilayers, we conducted a series of molecular dynamics studies on the hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS) and dodecyltrimethylammonium-hexadecylsulfate (DTMA-HS) IPA bilayers with cholesterol...
January 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28108530/use-of-performance-metrics-for-the-measurement-of-universal-coverage-for-maternal-care-in-mexico
#19
Edson Serván-Mori, David Contreras-Loya, Octavio Gomez-Dantés, Gustavo Nigenda, Sandra G Sosa-Rubí, Rafael Lozano
This study provides evidence for those working in the maternal health metrics and health system performance fields, as well as those interested in achieving universal and effective health care coverage. Based on the perspective of continuity of health care and applying quasi-experimental methods to analyse the cross-sectional 2009 National Demographic Dynamics Survey (n = 14 414 women), we estimated the middle-term effects of Mexico's new public health insurance scheme, Seguro Popular de Salud (SPS) (vs women without health insurance) on seven indicators related to maternal health care (according to official guidelines): (a) access to skilled antenatal care (ANC); (b) timely ANC; (c) frequent ANC; (d) adequate content of ANC; (e) institutional delivery; (f) postnatal consultation and (g) access to standardized comprehensive antenatal and postnatal care (or the intersection of the seven process indicators)...
January 20, 2017: Health Policy and Planning
https://www.readbyqxmd.com/read/28108494/the-rich-club-organization-in-rat-functional-brain-network-to-balance-between-communication-cost-and-efficiency
#20
Xia Liang, Li-Ming Hsu, Hanbing Lu, Akira Sumiyoshi, Yong He, Yihong Yang
Network analyses of structural connectivity in the brain have highlighted a set of highly connected hubs that are densely interconnected, forming a "rich-club" substrate in diverse species. Here, we demonstrate the existence of rich-club organization in functional brain networks of rats. Densely interconnected rich-club regions are found to be distributed in multiple brain modules, with the majority located within the putative default mode network. Rich-club members exhibit high wiring cost (as measured by connection distance) and high metabolic running cost (as surrogated by cerebral blood flow), which may have evolved to achieve high network communications to support efficient brain functions...
January 19, 2017: Cerebral Cortex
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