keyword
MENU ▼
Read by QxMD icon Read
search

hydrophobic

keyword
https://www.readbyqxmd.com/read/28922636/effects-of-mutations-on-active-site-conformation-and-dynamics-of-rna-dependent-rna-polymerase-from-coxsackievirus-b3
#1
Hujun Shen, Mingsen Deng, Yachao Zhang
Recent crystal structures of RNA-dependent RNA polymerase (3D(pol)) from Coxsackievirus B3 (CVB3) revealed that a tyrosine mutation at Phe364 (F364Y) resulted in structures with open active site whereas a hydrophobic mutation at Phe364 (F364A) led to conformations with closed active site. Besides, the crystal structures showed that the F364W mutation had no preference between the open and closed active sites, similar to wild-type. In this paper, we present a molecular dynamics (MD) study on CVB3 3D(pol) in order to address some important questions raised by experiments...
September 12, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28922633/protein-extraction-into-the-bicontinuous-microemulsion-phase-of-a-water-sds-pentanol-dodecane-winsor-iii-system-effect-on-nanostructure-and-protein-conformation
#2
Douglas G Hayes, Ran Ye, Rachel N Dunlap, Matthew J Cuneo, Sai Venkatesh Pingali, Hugh M O'Neill, Volker S Urban
Bicontinuous microemulsions (BμEs), consisting of water and oil nanodomains separated by surfactant monolayers of near-zero curvature, are potentially valuable systems for purification and delivery of biomolecules, for hosting multiphasic biochemical reactions, and as templating media for preparing nanomaterials. We formed Winsor-III systems by mixing aqueous protein and sodium dodecyl sulfate (SDS) solutions with dodecane and 1-pentanol (cosurfactant) to efficiently extract proteins into the middle (BμE) phase...
September 7, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28922631/surface-modification-of-platelet-concentrate-bags-to-reduce-biofilm-formation-and-transfusion-sepsis
#3
Joels S T Wilson-Nieuwenhuis, Nina Dempsey-Hibbert, Christopher M Liauw, Kathryn A Whitehead
Bacterial contamination of blood products poses a major risk in transfusion medicine, including transfusions involving platelet products. Although testing systems are in place for routine screening of platelet units, the formation of bacterial biofilms in such units may decrease the likelihood that bacteria will be detected. This work determined the surface properties of p-PVC platelet concentrate bags and investigated how these characteristics influenced biofilm formation. Serratia marcescens and Staphylococcus epidermidis, two species commonly implicated in platelet contamination, were used to study biofilm growth...
September 7, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28922602/cucurbit-7-uril-induced-formation-of-fret-enabled-uni-lamellar-lipid-vesicles
#4
Shilpi Kushwaha, Arunava Maity, Monalisa Gangopadhyay, Sapna Ravindranathan, Pattuparambil R Rajamohanan, Amitava Das
A unique fluorescence resonance energy transfer (FRET) process is found to be operational in a unilamellar lipid self-assembly in the aqueous phase. A newly synthesized naphthyl based long chain lipid derivative [N-(naphthalene-1-ylmethyl)tetradecane-1-ammonium chloride, 14NA+] forms various self-assembled architectures in the aqueous phase. Controlled changes in lipid concentration lead to a transition of the self-assemblies from micelles to vesicles to rods. In the presence of cucurbit[7]uril (CB7), 14NA+ forms a host-guest [2]pseudorotaxane complex (CB7∋14NA+) and secondary interactions lead to the formation of a lipid bilayer with hydrophobic pockets situated in between the layers...
September 18, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28922505/enhancing-the-antimicrobial-activity-of-alamethicin-f50-5-by-incorporating-n-terminal-hydrophobic-triazole-substituents
#5
Sanjit Das, Khoubaib Ben Haj Salah, Emmanuel Wenger, Jean Martinez, Jules Kotarba, Vanessa Andreu, Nicolas Ruiz, Filippo Savini, Lorenzo Stella, Claude Didierjean, Baptiste Legrand, Nicolas Inguimbert
We propose a simple and efficient strategy to significantly improve the antibacterial activity of peptaibols and other antimicrobial peptides by N-terminal capping with 1,2,3-triazole bearing various hydrophobic substituents on C-4. We showed, herein, that such N-terminal insertions on alamethicin F50/5 could enhance its antimicrobial activity on gram-positive bacteria without modification of its overall three-dimensional structure. Indeed, while the native peptide and its analogues shared comparable helical contents, the crystal structure of one of the most active derivative showed a local slight distortion of the N-terminal extremity, which was also observed in solution using NMR spectroscopy...
September 18, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28922156/soluble-oligomers-require-a-ganglioside-to-trigger-neuronal-calcium-overload
#6
Roberta Cascella, Elisa Evangelisti, Alessandra Bigi, Matteo Becatti, Claudia Fiorillo, Massimo Stefani, Fabrizio Chiti, Cristina Cecchi
An altered distribution of membrane gangliosides (GM), including GM1, has recently been reported in the brains of Alzheimer's disease (AD) patients. Moreover, amyloid-positive synaptosomes obtained from AD brains were found to contain high-density GM1 clusters, suggesting a pathological significance of GM1 increase at presynaptic neuritic terminals in AD. Here, we show that membrane GM1 specifically recruits small soluble oligomers of the 42-residue form of amyloid-β peptide (Aβ42), with intracellular flux of Ca2+ ions in primary rat hippocampal neurons and in human neuroblastoma cells...
September 8, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28921974/the-hydrophobic-effect-and-the-role-of-cosolvents
#7
Nico F A van der Vegt, Divya Nayar
Cosolvents modulate aqueous solubility, hydrophobic interactions, and the stability and function of most proteins in the living cell. Our molecular-level understanding of cosolvent effects is incomplete, not only at the level of complex systems such as proteins, but also at the level of very fundamental interactions that underlie the hydrophobic effect. This Feature Article discusses cosolvent effects on the aqueous solubility of nonpolar solutes, hydrophobic interactions, and hydrophobic self-assembly/collapse of aqueous polymers, recently studied with molecular dynamics simulations...
September 18, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28921952/nano-air-seeds-trapped-in-mesoporous-janus-nanoparticles-facilitate-cavitation-and-enhance-ultrasound-imaging
#8
Konstantin Tamarov, Andrey Sviridov, Wujun Xu, Markus Malo, Valery Andreev, Victor Yu Timoshenko, Vesa-Pekka Lehto
The current contrast agents utilized in ultrasound (US) imaging are based on microbubbles which, however, suffer from a short lifetime in the systemic circulation. The present study introduces a new type of contrast agents for US imaging based on bioresorbable Janus nanoparticles (NPs) that are able to generate microbubbles in situ under US radiation for extended time. The Janus NPs were fabricated from porous silicon (PSi) that was modified via a nanostopper technique. The technique was exploited to prepare PSi NPs which had hydrophobic pore walls (inner face) while the external surfaces of the NPs (outer face) were hydrophilic...
September 18, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28921601/is-2-hydroxypropyl-%C3%AE-cyclodextrin-a-suitable-carrier-for-central-administration-of-%C3%AE-9-tetrahydrocannabinol-preclinical-evidence
#9
R Agabio, F Sanna, C Lobina, M Monduzzi, V Nairi, F Cugia, S Mameli, G M Pisanu, G L Gessa, M R Melis
Preclinical Research Δ(9) -Tetrahydrocannabinol (THC) is a hydrophobic compound that has a potent antinociceptive effect in animals after intrathecal (IT) or intracerebroventricular (ICV) administration. The lack of a suitable solvent precludes its IT administration in humans. 2-Hydroxypropyl-β-cyclodextrin (HPβCD) increases the water solubility of hydrophobic drugs and is approved for IT administration in humans. To investigate whether HPβCD might be a suitable carrier for ICV administration of THC in rats, two formulations containing THC complexed with HPβCD (30 and 135 μg of THC per animal) and vehicle were administered to Wistar rats...
September 18, 2017: Drug Development Research
https://www.readbyqxmd.com/read/28921549/%C3%AE-flucs-brighter-photinus-pyralis-firefly-luciferases-identified-by-surveying-consecutive-single-amino-acid-deletion-mutations-in-a-thermostable-variant
#10
Lisa M Halliwell, Amit P Jathoul, Jack P Bate, Harley L Worthy, James C Anderson, Dafydd D Jones, James A H Murray
The bright bioluminescence catalysed by Photinus pyralis firefly luciferase (Fluc) enables a vast array of life science research such as bioimaging in live animals and sensitive in vitro diagnostics. The effectiveness of such applications is improved using engineered enzymes that to date have been constructed using amino acid substitutions. We describe ΔFlucs: consecutive single amino acid deletion mutants within 6 loop structures of the bright and thermostable x11 Fluc. Deletion mutations are a promising avenue to explore new sequence and functional space and isolate novel mutant phenotypes...
September 16, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28921438/purification-methods-for-recombinant-factor-viii-expressed-in-human-liver-sk-hep-cells
#11
Vladimir Granovski, Mario Soares Abreu-Neto, Dimas Tadeu Covas
Coagulation factor VIII is one of the largest proteins attempted to be expressed in recombinant form. A very complex and labile protein which has a very short half-live and need a fast and efficient purification chain. Here, we describe a simple purification sequence using multimodal Capto MMC, affinity FVIII select and ion exchange SP-Fastflow chromatography steps without subjecting the target molecule to mechanical and temperature stress, separating impurities from rFVIII using net charge, hydrophobicity, and affinity of the molecules...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28921397/a-binding-block-ion-selective-mechanism-revealed-by-a-na-k-selective-channel
#12
Jie Yu, Bing Zhang, Yixiao Zhang, Cong-Qiao Xu, Wei Zhuo, Jingpeng Ge, Jun Li, Ning Gao, Yang Li, Maojun Yang
Mechanosensitive (MS) channels are extensively studied membrane protein for maintaining intracellular homeostasis through translocating solutes and ions across the membrane, but its mechanisms of channel gating and ion selectivity are largely unknown. Here, we identified the YnaI channel as the Na(+)/K(+) cation-selective MS channel and solved its structure at 3.8 Å by cryo-EM single-particle method. YnaI exhibits low conductance among the family of MS channels in E. coli, and shares a similar overall heptamer structure fold with previously studied MscS channels...
September 18, 2017: Protein & Cell
https://www.readbyqxmd.com/read/28921373/released-fraction-of-polychlorinated-biphenyls-from-soil-biosolid-system-using-a-leaching-procedure-and-its-comparison-with-bioavailable-fraction-determined-by-wheat-plant-uptake
#13
Lourdes Jachero, Claudio Leiva, Inés Ahumada, Pablo Richter
The bioavailability of polychlorinated biphenyls (PCBs) in soils amended with biosolids was estimated using an aqueous leaching process of the compounds combined with rotating disk sorptive extraction (RDSE), and compared with bioavailability determined through of PCB absorption in wheat plants growing in the same soil-biosolid matrix. The matrices consisted of soil amended with biosolids at doses of 30, 90, and 200 Mg/ha, which increase concomitantly the organic matter content of the matrix. Considering that PCBs were natively absent in both the biosolids and soil used, the compounds were spiked in the biosolids and aged for 10 days...
September 18, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28921302/comparative-evolutionary-genomics-of-corynebacterium-with-special-reference-to-codon-and-amino-acid-usage-diversities
#14
Shilpee Pal, Indrani Sarkar, Ayan Roy, Pradeep K Das Mohapatra, Keshab C Mondal, Arnab Sen
The present study has been aimed to the comparative analysis of high GC composition containing Corynebacterium genomes and their evolutionary study by exploring codon and amino acid usage patterns. Phylogenetic study by MLSA approach, indel analysis and BLAST matrix differentiated Corynebacterium species in pathogenic and non-pathogenic clusters. Correspondence analysis on synonymous codon usage reveals that, gene length, optimal codon frequencies and tRNA abundance affect the gene expression of Corynebacterium...
September 18, 2017: Genetica
https://www.readbyqxmd.com/read/28921106/kinetic-stability-of-membrane-proteins
#15
REVIEW
F Luis González Flecha
Although membrane proteins constitute an important class of biomolecules involved in key cellular processes, study of the thermodynamic and kinetic stability of their structures is far behind that of soluble proteins. It is known that many membrane proteins become unstable when removed by detergent extraction from the lipid environment. In addition, most of them undergo irreversible denaturation, even under mild experimental conditions. This process was found to be associated with partial unfolding of the polypeptide chain exposing hydrophobic regions to water, and it was proposed that the formation of kinetically trapped conformations could be involved...
September 18, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28921081/site-saturation-mutagenesis-of-mutant-l-asparaginase-ii-signal-peptide-hydrophobic-region-for-improved-excretion-of-cyclodextrin-glucanotransferase
#16
Abbas Ismail, Rosli Md Illias
The excretion of cyclodextrin glucanotransferase (CGTase) into the culture medium offers significant advantages over cytoplasmic expression. However, the limitation of Escherichia coli is its inability to excrete high amount of CGTase outside the cells. In this study, modification of the hydrophobic region of the N1R3 signal peptide using site-saturation mutagenesis improved the excretion of CGTase. Signal peptide mutants designated M9F, V10L and A15Y enhanced the excretion of CGTase three-fold and demonstrated two-fold higher secretion rate than the wild type...
September 18, 2017: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28920989/half-sandwich-ru-ii-acylthiourea-complexes-dna-hsa-binding-anti-migration-and-cell-death-in-a-human-breast-tumor-cell-line
#17
Legna Colina-Vegas, Liany Luna-Dulcey, Ana M Plutín, Eduardo E Castellano, Marcia R Cominetti, Alzir A Batista
Organometallic ruthenium complexes as potential anticancer agents have been explored due to their suitable properties, such as stability in the solid state and in solution, water solubility and low toxicity. In this study, eight metal complexes of this class were synthesized, characterized and their important biological activities against a human breast tumor cell line (MDA-MB-231) were studied. Complexes 1-8 were obtained in good yields and have been characterized by satisfactory elemental analyses, IR, 1D and 2D (1)H and (13)C{(1)H} NMR, UV-Vis spectroscopy, cyclic voltammetry, ESI-MS and X-ray diffractometry (1, 2, 3 and 6)...
September 18, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28920983/unified-elucidation-of-the-entropy-driven-and-opposed-hydrophobic-effects
#18
Masahiro Kinoshita, Tomohiko Hayashi
The association of nonpolar solutes is generally believed to be entropy driven, which has been shown to be true for the contact of small molecules, ellipsoids, and plates. However, it has been reported with surprise that a model cavity-ligand binding is entropy opposed. How can these apparently conflicting behaviors be elucidated? Here, we calculate the potential of mean force between hard-sphere solutes with various diameters in water and its entropic and enthalpic components using a statistical-mechanical theory for molecular liquids...
September 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28920164/purification-and-characterization-of-a-naringinase-from-cryptococcus-albidus
#19
Nataliya Borzova, Olena Gudzenko, Lyudmila Varbanets
Naringinase which was extracted from the fermented broth of Cryptococcus albidus was purified about 42-folds with yield 0.7% by sulfate fractionation and chromatography on Toyopearl HW-60, Fractogel DEAE-650-s, and Sepharose 6B columns. Molecular weight of protein determined by gel filtration and SDS-PAGE was 50 kDa. Naringinase of C. albidus includes high content of the dicarbonic and hydrophobic amino acids. Enzyme contains also carbohydrate component, represented by mannose, galactose, rhamnose, ribose, arabinose, xylose, and glucose...
September 18, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28920092/thermogelling-properties-of-purified-poloxamer-407
#20
Amir Fakhari, Marta Corcoran, Alexander Schwarz
Poloxamers are triblock copolymers with a center block of hydrophobic polypropylene oxide (PPO) flanked by two hydrophilic polyethyleneoxide (PEO) blocks. Among this family of copolymers, poloxamer 407 is a non-ionic surfactant with reversible gelation properties above a particular polymer concentration and a particular temperature. Easy preparation of poloxamer 407 based sterile injectable formulations have made this copolymer a good candidate for drug delivery, specifically when controlled release of the drug is required...
August 2017: Heliyon
keyword
keyword
112061
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"