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https://www.readbyqxmd.com/read/27915021/poly-aspartic-acid-with-adjustable-ph-dependent-solubility
#1
Csaba Németh, Benjámin Gyarmati, Timur Abdullin, Krisztina László, András Szilágyi
Poly(aspartic acid) (PASP) derivatives with adjustable pH-dependent solubility were synthesized and characterized to establish the relationship between their structure and solubility in order to predict their applicability as a basic material for enteric coatings. Polysuccinimide, the precursor of PASP, was modified with short chain alkylamines, and the residual succinimide rings were subsequently opened to prepare the corresponding PASP derivatives. Study of the effects of the type and concentration of the side groups on the pH-dependent solubility of PASP showed that solubility can be adjusted by proper selection of the chemical structure...
November 30, 2016: Acta Biomaterialia
https://www.readbyqxmd.com/read/27914044/the-framework-of-computational-protein-design
#2
Ilan Samish
Computational protein design (CPD) has established itself as a leading field in basic and applied science with a strong coupling between the two. Proteins are computationally designed from the level of amino acids to the level of a functional protein complex. Design targets range from increased thermo- (or other) stability to specific requested reactions such as protein-protein binding, enzymatic reactions, or nanotechnology applications. The design scheme may encompass small regions of the proteins or the entire protein...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27912110/structures-and-mechanisms-of-crispr-rna-guided-effector-nucleases
#3
REVIEW
Hiroshi Nishimasu, Osamu Nureki
In the prokaryotic CRISPR-Cas adaptive immune systems, a CRISPR RNA (crRNA) assembles with multiple or single Cas proteins to form crRNA ribonucleoprotein (crRNP) effector complexes, responsible for the destruction of invading genetic elements. Although the mechanisms of target recognition and cleavage by the crRNP effectors are quite diverse among the different types of CRISPR-Cas systems, the basic action principles of these crRNA-guided effector nucleases are highly conserved. In all of the crRNP effectors, the repeat-derived invariant and spacer-derived variable segments of the crRNA are recognized by the Cas protein(s) in sequence-dependent and sequence-independent manners, respectively, with the spacer-derived guide segment available for base pairing with target nucleic acids...
November 29, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27911494/determining-functional-aptamer-protein-interaction-by-biolayer-interferometry
#4
Xinhui Lou, Martin Egli, Xianbin Yang
Short single-stranded nucleic acids called aptamers are widely being explored as recognition molecules of high affinity and specificity for binding a wide range of target molecules, particularly protein targets. In biolayer interferometry (BLI), a simple Dip-and-Read approach in which the aptamer-coated biosensors are dipped into microplate wells is used to study the interactions between an aptamer and its target protein. Here we describe the protocol for the analysis of the interaction between a well-characterized anti-thrombin RNA aptamer with thrombin (Basic Protocol)...
December 1, 2016: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/27911042/orderly-layered-zr-benzylphosphonate-nanohybrids-for-efficient-acid-base-mediated-bifunctional-cascade-catalysis
#5
Hu Li, Zhen Fang, Jian He, Song Yang
The development of functional metal-organic materials being robust and active for bifunctional/cascade catalysis is of great significance. Herein, a series of mesoporous and orderly layered nanohybrids were synthesized for the first time via simple and template-free assembly of ortho-, meta-, or para-xylylenediphosphonates (o-, p-, or m-PhP) with zirconium. It was found that m-PhPZr nanoparticles (20-50 nm) with mesopores centered at 7.9 nm and high Lewis acid/base site ratio (1:0.7) showed prominent performance under mild conditions (as low as 82 ºC) in transfer hydrogenation of carbonyl compounds including bio-aldehydes to alcohols with near quantative yields and little Zr leaching...
December 2, 2016: ChemSusChem
https://www.readbyqxmd.com/read/27909924/tailor-made-biocatalysts-based-on-scarcely-studied-acidic-horseradish-peroxidase-for-biodegradation-of-reactive-dyes
#6
Barbara S Janović, Milica Lj Mićić Vićovac, Zoran M Vujčić, Miroslava T Vujčić
Peroxidases (EC 1.11.1.7) have enormous biotechnological applications. Usage of more abundant, basic isoforms of peroxidases in diagnostic kits and/or in immunochemistry has led to under exploitation and disregard of horseradish peroxidase (HRP) acidic isoforms. Therefore, acidic horseradish peroxidase (HRP-A) isoenzyme was used for the preparation of a biocatalyst with improved ability in dye decolorization. Ten biocatalysts were prepared by covalent binding of enzyme to chitosan and alginate, adsorption followed by cross-linking on inorganic support (aluminum oxide), and encapsulation in spherical calcium alginate beads via polyethylene glycol...
December 1, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27908754/cyclic-citrullinated-mbp87-99-peptide-stimulates-t-cell-responses-implications-in-triggering-disease
#7
Vasso Apostolopoulos, George Deraos, Minos-Timotheos Matsoukas, Stephanie Day, Lily Stojanovska, Theodore Tselios, Maria-Eleni Androutsou, John Matsoukas
Amino acid mutations to agonist peptide epitopes of myelin proteins have been used to modulate immune responses and experimental autoimmune encephalomyelitis (EAE, animal model of multiple sclerosis). Such amino acid alteration are termed, altered peptide ligands (APL). We have shown that the agonist myelin basic protein (MBP) 87-99 epitope (MBP87-99) with crucial T cell receptor (TCR) substitutions at positions 91 and 96 (K(91),P(96) (TCR contact residues) to R(91),A(96); [R(91),A(96)]MBP87-99) results in altered T cell responses and inhibits EAE symptoms...
November 19, 2016: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/27907110/electrospray-ionization-efficiency-is-dependent-on-different-molecular-descriptors-with-respect-to-solvent-ph-and-instrumental-configuration
#8
Andreas Kiontke, Ariana Oliveira-Birkmeier, Andreas Opitz, Claudia Birkemeyer
Over the past decades, electrospray ionization for mass spectrometry (ESI-MS) has become one of the most commonly employed techniques in analytical chemistry, mainly due to its broad applicability to polar and semipolar compounds and the superior selectivity which is achieved in combination with high resolution separation techniques. However, responsiveness of an analytical method also determines its suitability for the quantitation of chemical compounds; and in electrospray ionization for mass spectrometry, it can vary significantly among different analytes with identical solution concentrations...
2016: PloS One
https://www.readbyqxmd.com/read/27906631/mitochondrial-purine-and-pyrimidine-metabolism-and-beyond
#9
Liya Wang
Carefully balanced deoxynucleoside triphosphate (dNTP) pools are essential for both nuclear and mitochondrial genome replication and repair. Two synthetic pathways operate in cells to produce dNTPs, e.g., the de novo and the salvage pathways. The key regulatory enzymes for de novo synthesis are ribonucleotide reductase (RNR) and thymidylate synthase (TS), and this process is considered to be cytosolic. The salvage pathway operates both in the cytosol (TK1 and dCK) and the mitochondria (TK2 and dGK). Mitochondrial dNTP pools are separated from the cytosolic ones owing to the double membrane structure of the mitochondria, and are formed by the salvage enzymes TK2 and dGK together with NMPKs and NDPK in postmitotic tissues, while in proliferating cells the mitochondrial dNTPs are mainly imported from the cytosol produced by the cytosolic pathways...
December 2016: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/27904094/design-and-synthesis-of-functional-molecules-based-on-complexation-and-their-biological-applications
#10
Yosuke Hisamatsu
 In this review, we introduce the development of supermolecules, host-guest complexes, and metal complexes formed from the combination of non-covalent interactions and/or coordination bonds, as well as their biological applications. An adenine selective host molecule 1 provides a correctly oriented array of complementary hydrogen bonding sites for the adenine nucleobase. Furthermore, the new DDAA (D: hydrogen bond donor, A: hydrogen bond acceptor) module 4 and ADDA module 7 have been developed as quadruple hydrogen-bonding modules...
2016: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/27902924/simple-mechanisms-of-early-life-simulation-model-on-the-origin-of-semi-cells
#11
Adrian Klein, Martin Bock, Wolfgang Alt
The development of first cellular structures played an important role in the early evolution of life. Early evolution of life probably took place on a molecular level in a reactive environment. The iron-sulfur theory postulates the formation of cell-like structures on catalytic surfaces. Experiments show that H2S together with FeS and other metallic centers drive auto-catalytic surface reactions, in which organic molecules such as pyruvic and amino acids occur. It is questionable which mechanisms are needed to form cell-like structures under these conditions...
November 27, 2016: Bio Systems
https://www.readbyqxmd.com/read/27902502/zika-virus-and-patient-blood-management
#12
Lawrence T Goodnough, Marisa B Marques
Sporadic Zika virus infections had only occurred in Africa and Asia until an outbreak in Micronesia (Oceania) in 2007. In 2013 to 2014, several outer Pacific Islands reported local outbreaks. Soon thereafter, the virus was likely introduced in Brazil from competing athletes from French Polynesia and other countries that participated in a competition there. Transmission is thought to have occurred through mosquito bites and spread to the immunologically naive population. Being also a flavivirus, the Zika virus is transmitted by the Aedes mosquito that is endemic in South and Central America that is also the vector of West Nile virus, dengue, and chikungunya...
November 29, 2016: Anesthesia and Analgesia
https://www.readbyqxmd.com/read/27900234/n-terminal-derivatization-with-structures-having-high-proton-affinity-for-discrimination-between-leu-and-ile-residues-in-peptides-by-high-energy-collision-induced-dissociation
#13
Atsushi Kitanaka, Masahiro Miyashita, Ayumi Kubo, Takaya Satoh, Michisato Toyoda, Hisashi Miyagawa
De novo sequencing is still essential in the identification of peptides and proteins from unexplored organisms whose sequence information is not available. One of the remaining problems in de novo sequencing is discrimination between Leu and Ile residues. The discrimination is possible based on differences in side chain fragmentation between Leu and Ile under high-energy collision-induced dissociation (HE-CID) conditions. However, this is observed only when basic residues, such as Arg and Lys, are present near the N- or C-terminal end...
2016: Mass Spectrometry
https://www.readbyqxmd.com/read/27899501/unraveling-fungal-radiation-resistance-regulatory-networks-through-the-genome-wide-transcriptome-and-genetic-analyses-of-cryptococcus-neoformans
#14
Kwang-Woo Jung, Dong-Hoon Yang, Min-Kyu Kim, Ho Seong Seo, Sangyong Lim, Yong-Sun Bahn
The basidiomycetous fungus Cryptococcus neoformans has been known to be highly radiation resistant and has been found in fatal radioactive environments such as the damaged nuclear reactor at Chernobyl. To elucidate the mechanisms underlying the radiation resistance phenotype of C. neoformans, we identified genes affected by gamma radiation through genome-wide transcriptome analysis and characterized their functions. We found that genes involved in DNA damage repair systems were upregulated in response to gamma radiation...
November 29, 2016: MBio
https://www.readbyqxmd.com/read/27898784/effect-of-metal-ions-on-the-formation-of-trichloronitromethane-during-chlorination-of-catechol-and-nitrite
#15
Guojuan Gan, Rongwu Mei, Lin Qiu, Huachang Hong, Qingjun Wang, Asit Mazumder, Shikai Wu, Xiangliang Pan, Yan Liang
Catechol, nitrite, and dissolved metals are ubiquitous in source drinking water. Catechol and nitrite have been identified as precursors for halonitromethanes (HNMs), but the effect of metal ions on HNM formation during chlorination remains unclear. The main objective of this study was to investigate the effect of metal ions (Fe, Ti, Al) on the formation of trichloronitromethane (TCNM) (the most representative HNM species in disinfected water) on chlorinating catechol and nitrite. Trichloronitromethane was extracted by methyl tert-butyl ether and detected by gas chromatography...
November 2016: Journal of Environmental Quality
https://www.readbyqxmd.com/read/27898012/hydrodechlorination-of-tetrachloromethane-over-palladium-catalysts-supported-on-mixed-mgf%C3%A2-mgo-carriers
#16
Magdalena Bonarowska, Maria Wojciechowska, Maciej Zieliński, Angelika Kiderys, Michał Zieliński, Piotr Winiarek, Zbigniew Karpiński
Pd/MgO, Pd/MgF₂ and Pd/MgO-MgF₂ catalysts were investigated in the reaction of CCl₄ hydrodechlorination. All the catalysts deactivated in time on stream, but the degree of deactivation varied from catalyst to catalyst. The MgF₂-supported palladium with relatively large metal particles appeared the best catalyst, characterized by good activity and selectivity to C₂-C₅ hydrocarbons. Investigation of post-reaction catalyst samples allowed to find several details associated with the working state of hydrodechlorination catalysts...
November 25, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27897117/enantiomeric-resolution-of-rs-naproxen-and-application-of-s-naproxen-in-the-direct-and-indirect-enantioseparation-of-racemic-compounds-by-liquid-chromatography-a-review
#17
Sonika Batra, Ravi Bhushan
(S)-Naproxen (Npx), an α-aryl propionic acid derivative, belongs to class of Non-Steroidal Anti-Inflammatory Drugs and is easily available in pure (S)-form. (S)-Npx has been used as a chiral selector for chromatographic separation of a variety of racemates, using both direct and indirect methods, and has been found to be useful and successful as a basic chiral moiety. This review article describes methods for enantioseparation of (RS)-Npx, development of chiral stationary phases based on (S)-Npx and preparation of novel chiral derivatizing reagents synthesized from (S)-Npx along with their application for enantioseparation of several pharmaceutically important racemates...
November 28, 2016: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/27896590/improvement-in-thermal-stability-of-sucralose-by-%C3%AE-cyclodextrin-metal-organic-frameworks
#18
Nana Lv, Tao Guo, Botao Liu, Caifen Wang, Vikaramjeet Singh, Xiaonan Xu, Xue Li, Dawei Chen, Ruxandra Gref, Jiwen Zhang
PURPOSE: To explain thermal stability enhancement of an organic compound, sucralose, with cyclodextrin based metal organic frameworks. METHODS: Micron and nanometer sized basic CD-MOFs were successfully synthesized by a modified vapor diffusion method and further neutralized with glacial acetic acid. Sucralose was loaded into CD-MOFs by incubating CD-MOFs with sucralose ethanol solutions. Thermal stabilities of sucralose-loaded basic CD-MOFs and neutralized CD-MOFs were investigated using thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and high performance liquid chromatography with evaporative light-scattering detection (HPLC-ELSD)...
November 28, 2016: Pharmaceutical Research
https://www.readbyqxmd.com/read/27896130/studies-of-the-autoinhibitory-segment-comprising-residues-31-60-of-the-prodomain-of-pcsk9-possible-implications-for-the-mechanism-underlying-gain-of-function-mutations
#19
Lene Wierød, Jamie Cameron, Thea Bismo Strøm, Trond P Leren
Proprotein convertase subtilisin/kexin type 9 (PCSK9) binds to the low density lipoprotein receptor (LDLR) at the cell surface and is internalized as a complex with the LDLR. In the acidic milieu of the sorting endosome, PCSK9 remains bound to the LDLR and prevents the LDLR from folding over itself to adopt a closed conformation. As a consequence, the LDLR fails to recycle back to the cell membrane. Even though it is the catalytic domain of PCSK9 that interacts with the LDLR at the cell surface, the structurally disordered segment consisting of residues 31-60 and which is rich in acidic residues, has a negative effect both on autocatalytic cleavage and on the activity of PCSK9 towards the LDLR...
December 2016: Molecular Genetics and Metabolism Reports
https://www.readbyqxmd.com/read/27893705/gephyrin-binding-peptides-visualize-postsynaptic-sites-and-modulate-neurotransmission
#20
Hans Michael Maric, Torben Johann Hausrat, Franziska Neubert, Nils Ole Dalby, Sören Doose, Markus Sauer, Matthias Kneussel, Kristian Strømgaard
γ-Aminobutyric acid type A and glycine receptors are the major mediators of fast synaptic inhibition in the human central nervous system and are established drug targets. However, all drugs targeting these receptors bind to the extracellular ligand-binding domain of the receptors, which inherently is associated with perturbation of the basic physiological action. Here we pursue a fundamentally different approach, by instead targeting the intracellular receptor-gephyrin interaction. First, we defined the gephyrin peptide-binding consensus sequence, which facilitated the development of gephyrin super-binding peptides and later effective affinity probes for the isolation of native gephyrin...
November 28, 2016: Nature Chemical Biology
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