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https://www.readbyqxmd.com/read/29340240/refining-amino-acid-hydrophobicity-for-dynamics-simulation-of-membrane-proteins
#1
Ronald D Hills
Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. Reassignment of select CG sidechain sites from the apolar to polar site type was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues...
2018: PeerJ
https://www.readbyqxmd.com/read/29339003/direct-recovery-of-bacillus-subtilis-xylanase-from-fermentation-broth-with-an-alcohol-salt-aqueous-biphasic-system
#2
Hui Suan Ng, Cindy Xin Yi Chai, Yin Hui Chow, Wai Leng Carmen Loh, Hip Seng Yim, Joo Shun Tan, John Chi-Wei Lan
Xylanase enzyme degrades linear polysaccharide β-1,4 xylan and the hemicellulose of the plant cell wall. There is a growing demand in finding a cost-effective alternative for industrial scale production of xylanase with high purity for pharmaceutical applications. In this study, an alcohol/salt aqueous biphasic system (ABS) was adopted to recover xylanase from the Bacillus subtilis fermentation broth. The effects of several ABS parameters such as types and concentrations of alcohols and salts (i.e., sulphate, phosphate, and citrate), amount of crude loading and pH of the system on the recovery of xylanase were investigated...
January 12, 2018: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/29323684/maximizing-the-absorption-of-small-cosolutes-inside-neutral-hydrogels-steric-exclusion-versus-hydrophobic-adhesion
#3
Luis Pérez-Mas, Alberto Martín-Molina, Manuel Quesada-Pérez, Arturo Moncho-Jordá
In this work the equilibrium absorption of nanometric cosolutes (which could represent drugs, reactants, small globular proteins and other kind of biomacromolecules) inside neutral hydrogels is studied. We specially focus on exploring, for different swelling states, the competition between the steric exclusion induced by the cross-linked polymer network constituting the hydrogel, and the solvent-induced short-range hydrophobic attraction between the polymer chains and the cosolute particle. For this purpose, the cosolute partition coefficient is calculated by means of coarse-grained grand canonical Monte Carlo simulations, and the results are compared to theoretical predictions based on the calculation of the excluded and binding volume around the polymer chains...
January 11, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29322928/constraint-based-perturbation-analysis-with-cluster-newton-method-a-case-study-of-personalized-parameter-estimations-with-irinotecan-whole-body-physiologically-based-pharmacokinetic-model
#4
Shun Asami, Daisuke Kiga, Akihiko Konagaya
BACKGROUND: Drug development considering individual varieties among patients becomes crucial to improve clinical development success rates and save healthcare costs. As a useful tool to predict individual phenomena and correlations among drug characteristics and individual varieties, recently, whole-body physiologically based pharmacokinetic (WB- PBPK) models are getting more attention. WB-PBPK models generally have a lot of drug-related parameters that need to be estimated, and the estimations are difficult because the observed data are limited...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29320854/a-highly-resolved-mercury-emission-inventory-of-chinese-coal-fired-power-plants
#5
Kaiyun Liu, Shuxiao Wang, Qingru Wu, Long Wang, Qiao Ma, Lei Zhang, Guoliang Li, Hezhong Tian, Lei Duan, Jiming Hao
As the largest coal consumer in China, the coal-fired power plants have come under increasing public concern in regard to atmospheric mercury pollution. This study developed an up-to-date and high-resolution mercury emission inventory of Chinese coal-fired power plants using a unit-based method that combined data from individual power plants, provincial coal characteristics, and industry removal efficiencies. National mercury emissions in 2015 were estimated at 73 tons, including 54 tons of elemental mercury, 18 tons of gaseous oxidized mercury and 1 ton of particle-bound mercury...
January 11, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29318251/environmental-fate-and-exposure-models-advances-and-challenges-in-21st-century-chemical-risk-assessment
#6
REVIEW
Antonio Di Guardo, Todd Gouin, Matthew MacLeod, Martin Scheringer
Environmental fate and exposure models are a powerful means to integrate information on chemicals, their partitioning and degradation behaviour, the environmental scenario and the emissions in order to compile a picture of chemical distribution and fluxes in the multimedia environment. A 1995 pioneering book, resulting from a series of workshops among model developers and users, reported the main advantages and identified needs for research in the field of multimedia fate models. Considerable efforts were devoted to their improvement in the past 25 years and many aspects were refined; notably the inclusion of nanomaterials among the modelled substances, the development of models at different spatial and temporal scales, the estimation of chemical properties and emission data, the incorporation of additional environmental media and processes, the integration of sensitivity and uncertainty analysis in the simulations...
January 9, 2018: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/29317668/hygroscopic-coating-of-sulfuric-acid-shields-oxidant-attack-on-the-atmospheric-pollutant-benzo-a-pyrene-bound-to-model-soot-particles
#7
Debajyoti Ray, Tara Shankar Bhattacharya, Abhijit Chatterjee, Achintya Singha, Sanjay K Ghosh, Sibaji Raha
Substantial impacts on climate have been documented for soot‒sulfuric acid (H2SO4) interactions in terms of optical and hygroscopic properties of soot aerosols. However, the influence of H2SO4 on heterogeneous chemistry on soot remains unexplored. Additionally, oxidation rate coefficients for polycyclic aromatic hydrocarbons intrinsic to the atmospheric particles evaluated in laboratory experiments seem to overestimate their degradation in ambient atmosphere, possibly due to matrix effects which are hitherto not mimicked in laboratory experiments...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29315781/bioconcentration-model-for-non-ionic-polar-and-ionizable-organic-compounds-in-amphipod
#8
Ciara Chun Chen, Dave Ta Fu Kuo
This study presents a bioconcentration model for non-ionic, polar, and ionizable organic compounds in amphipod based on first-order kinetics. Uptake rate constant k1 is modeled as log k1=10.81logKOW+0.15 (root mean square error, RMSE = 0.52). Biotransformation rate constant kM is estimated using an existing polyparameter linear free energy relationship model. Respiratory elimination k2 is calculated as modeled k1 over theoretical biota-water partition coefficient Kbiow considering the contributions of lipid, protein, carbohydrate and water...
January 9, 2018: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/29315700/binding-affinity-and-decontamination-of-dermal-decontamination-gel-to-model-chemical-warfare-agent-simulants
#9
Yachao Cao, Akram Elmahdy, Hanjiang Zhu, Xiaoying Hui, Howard Maibach
Six chemical warfare agent simulants (trimethyl phosphate, dimethyl adipate, 2-chloroethyl methyl sulfide, diethyl adipate, chloroethyl phenyl sulfide and diethyl sebacate) were studied in in vitro human skin to explore relationship between dermal penetration/absorption and the mechanisms of simulant partitioning between stratum corneum (SC) and water as well as between dermal decontamination gel (DDGel) and water. Both binding affinity to and decontamination of simulants using DDGel were studied. Partition coefficients of six simulants between SC and water (Log PSC/w ) and between DDGel and water (Log PDDGel/w ) were determined...
January 7, 2018: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/29311084/intrapulmonary-pharmacokinetics-of-relebactam-a-novel-%C3%AE-lactamase-inhibitor-dosed-in-combination-with-imipenem-cilastatin-in-healthy-subjects
#10
Matthew L Rizk, Elizabeth G Rhee, Patricia A Jumes, Mark H Gotfried, Tian Zhao, Eric Mangin, Sheng Bi, Cynthia M Chavez-Eng, Zufei Zhang, Joan R Butterton
This Phase I study assessed the intrapulmonary pharmacokinetic profiles of relebactam (MK-7655), a novel ß-lactamase inhibitor, and imipenem. Sixteen healthy subjects received 250 mg relebactam with 500 mg imipenem/cilastatin, given IV every 6 hours for 5 doses, and were randomized to bronchoscopy/broncho-alveolar lavage at 0.5, 1, 1.5, or 3 hours after the last dose (4 subjects per time point). Both drugs penetrated the epithelial lining fluid (ELF) to a similar degree, with profiles similar in shape to the corresponding plasma profiles and apparent terminal half-lives in plasma and ELF, respectively, of 1...
January 8, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29305056/salting-in-counter-current-chromatography-separation-of-tanshinones-based-on-room-temperature-ionic-liquids
#11
Yanyan Wang, Lihong Zhang, Xiuyun Guo, Shihua Wu
Ionic liquids have been widely used for the extraction and separation of bioactive natural and synthetic mixtures. In this study, we provided an updated example by using an ionic liquid-based salting-in counter-current chromatography (CCC) strategy for the separation of hydrophobic tanshinones without subsequent column chromatography purification. Several ionic liquids such as 1-allyl-3-methylimidazolium chloride ([AMIM]Cl), 1-methallyl-3-methylimidazolium chloride ([MAMIM]Cl) and 1-butyl-3-ethylimidazolium chloride [BMIM]Cl could significantly decrease the partition coefficients (K) of tanshinones in the selected two-phase solvent composed of hexane-ethyl acetate-methanol-ionic liquid aqueous solution (5:5:6:4, v/v)...
December 26, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29303519/teaching-an-old-scaffold-new-recognition-tricks-oligopyrrolamide-antagonists-of-iapp-aggregation
#12
Sunil Kumar, Maria C Vogel, Andrew D Hamilton
A library of N-substituted oligopyrrolamides was designed to modulate the aggregation kinetics of islet amyloid polypeptide (IAPP). IAPP is a hormonal peptide, co-secreted with insulin in the pancreatic β-cells. IAPP samples a variety of conformations, starting from a native random coil to membrane-associated α-helical intermediates and eventually terminates in the amyloid plaques rich in β-sheet structures. A growing body of evidence suggests that membrane bound α-helical intermediates are the key cytotoxic species that impair the functionality and viability of β-cells and contribute to the onset of type 2 diabetes mellitus (DM2)...
January 5, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29301457/diffusion-of-energetic-compounds-through-biological-membrane-application-of-classical-md-and-cosmomic-approximations
#13
Anastasiia Golius, Leonid Gorb, Olexander Isayev, Jerzy Leszczynski
Computational studies of the potential biological impact of several energetic compounds were performed. The most commonly used explosives were considered in the present studies: trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 2,4-dinitroanisole (DNAN), and 5-Nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO). The effect of such factors as ionic strength and presence of DMSO in the water solution on the structure of the membrane were considered using the POPC lipid bilayer as an example. Molecular dynamics (MD) simulations revealed that, even on a short-time scale, the influence of those additives is noticeable, and therefore those factors should always be taken into account...
January 4, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29291579/a-rapid-quantification-method-for-the-screening-indicator-for-%C3%AE-thalassemia-with-near-infrared-spectroscopy
#14
Jiemei Chen, Lijun Peng, Yun Han, Lijun Yao, Jing Zhang, Tao Pan
Near-infrared (NIR) spectroscopy combined with chemometrics was applied to rapidly analyse haemoglobin A2 (HbA2) for β-thalassemia screening in human haemolysate samples. The relative content indicator HbA2 was indirectly quantified by simultaneous analysis of two absolute content indicators (Hb and Hb∙HbA2). According to the comprehensive prediction effect of the multiple partitioning of calibration and prediction sets, the parameters were optimized to achieve modelling stability, and the preferred models were validated using the samples not involved in modelling...
December 27, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29289283/the-presence-and-partitioning-behavior-of-flame-retardants-in-waste-leachate-and-air-particles-from-norwegian-waste-handling-facilities
#15
Nicolas A O Morin, Patrik L Andersson, Sarah E Hale, Hans Peter H Arp
Flame retardants in commercial products eventually make their way into the waste stream. Herein the presence of flame retardants in Norwegian landfills, incineration facilities and recycling sorting/defragmenting facilities is investigated. These facilities handled waste electrical and electronic equipment (WEEE), vehicles, digestate, glass, combustibles, bottom ash and fly ash. The flame retardants considered included polybrominated diphenyl ethers (∑BDE-10) as well as dechlorane plus, polybrominated biphenyls, hexabromobenzene, pentabromotoluene and pentabromoethylbenzene (collectively referred to as ∑FR-7)...
December 2017: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/29287380/improving-the-extraction-of-l-phenylalanine-by-the-use-of-ionic-liquids-as-adjuvants-in-aqueous-biphasic-systems
#16
Hongpeng Yang, Li Chen, Cunshan Zhou, Xiaojie Yu, Abu ElGasim A Yagoub, Haile Ma
Polyethylene glycol (PEG) is widely used in the polymer-salt systems. However, the low polarity of the PEG-rich phase limits the application of aqueous biphasic systems (ABS). To overcome this disadvantage, a small quantity of ionic liquid (IL) was used as an adjuvant in ABS to enlarge the polarity range. Therefore, an innovative study involving addition of 4wt% imidazolium-based ILs to the PEG 600/NaH2PO4 ABS, aiming at controlling the phase behavior and extraction ability, was carried out. The phase diagrams, the tie-lines and the partitioning behavior of l-phenylalanine and ILs were studied in these systems...
April 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29283449/oxaprozin-prodrug-as-safer-nonsteroidal-anti-inflammatory-drug-synthesis-and-pharmacological-evaluation
#17
Jaya P Peesa, Lakshmana R Atmakuri, Prasanna R Yalavarthi, Basaveswara R Mandava Venkata, Arun Rasheed, Vengalrao Pachava
Oxaprozin is a popular non-steroidal anti-inflammatory drug (NSAID) and its chronic oral use is clinically restricted due to its gastrointestinal (GI) complications. In order to circumvent the GI complications, oxaprozin was amended as a prodrug in a one-pot reaction using N,N-carbonyldiimidazole as an activating agent. Dextran of average molecular weight (60,000-90,000 Da) was exploited as a carrier in the process of oxaprozin prodrug production by esterification. The structural profiles of the synthesized oxaprozin prodrug were characterized by FT-IR and NMR spectroscopy...
December 28, 2017: Archiv der Pharmazie
https://www.readbyqxmd.com/read/29281280/extraction-of-gd3-and-uo22-ions-using-polystyrene-grafted-dibenzo-crown-ether-db18c6-with-octanol-and-nitrobenzene-a-molecular-dynamics-study
#18
Praveen Kumar Sappidi, Sadanandam Namsani, Sk Musharaf Ali, Jayant Kumar Singh
Atomistic molecular dynamics (MD) simulations are performed in order to derive thermodynamic properties important to understand the extraction of gadolinium (Gd3+) and uranium dioxide (UO2) with dibenzo crown ether (DBCE) in nitrobenzene (NB) and octanol (OCT) solvents. The effect of polystyrene graft length, on DBCE, on the binding behavior of Gd3+ and UO22+ is investigated for the first time. Our simulation results demonstrate that the binding of Gd and UO2 on to the oxygens of crown ethers is favorable for polystyrene grafted crown ether in the organic solvents OCT and NB...
December 27, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29273000/age-based-partitioning-of-individual-genomic-inbreeding-levels-in-belgian-blue-cattle
#19
Marina Solé, Ann-Stephan Gori, Pierre Faux, Amandine Bertrand, Frédéric Farnir, Mathieu Gautier, Tom Druet
BACKGROUND: Inbreeding coefficients can be estimated either from pedigree data or from genomic data, and with genomic data, they are either global or local (when the linkage map is used). Recently, we developed a new hidden Markov model (HMM) that estimates probabilities of homozygosity-by-descent (HBD) at each marker position and automatically partitions autozygosity in multiple age-related classes (based on the length of HBD segments). Our objectives were to: (1) characterize inbreeding with our model in an intensively selected population such as the Belgian Blue Beef (BBB) cattle breed; (2) compare the properties of the model at different marker densities; and (3) compare our model with other methods...
December 22, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29251499/incorporation-of-metals-into-calcite-in-a-deep-anoxic-granite-aquifer
#20
Henrik Drake, Frédéric Adrien Mathurin, Thomas Zack, Thorsten Schäfer, Nick Roberts, Martin W Whitehouse, Andreas Karlsson, Curt Broman, Mats Åström
Understanding metal scavenging by calcite in deep aquifers in granite is of importance for deciphering and modelling hydrochemical fluctuations and water-rock interaction in the upper crust, and for retention mechanisms associated with underground repositories for toxic wastes. Metal scavenging into calcite has generally been established in laboratory or in natural environments that cannot be unreservedly applied to conditions in deep crystalline rocks - an environment of broad interest for nuclear waste repositories...
December 18, 2017: Environmental Science & Technology
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