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https://www.readbyqxmd.com/read/30098527/the-challenge-of-synthetic-biology-synthetic-darwinism-and-the-aperiodic-crystal-structure
#1
REVIEW
Nilesh B Karalkar, Steven A Benner
'Grand Challenges' offer ways to discover flaws in existing theory without first needing to guess what those flaws are. Our grand challenge here is to reproduce the Darwinism of terran biology, but on molecular platforms different from standard DNA. Access to Darwinism distinguishes the living from the non-living state. However, theory suggests that any biopolymer able to support Darwinism must (a) be able to form Schrödinger's `aperiodic crystal', where different molecular components pack into a single crystal lattice, and (b) have a polyelectrolyte backbone...
August 8, 2018: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/30098457/redox-regulation-of-grpel2-nucleotide-exchange-factor-for-mitochondrial-hsp70-chaperone
#2
Svetlana Konovalova, Xiaonan Liu, Pooja Manjunath, Sundar Baral, Nirajan Neupane, Taru Hilander, Yang Yang, Diego Balboa, Mügen Terzioglu, Liliya Euro, Markku Varjosalo, Henna Tyynismaa
Mitochondria are central organelles to cellular metabolism. Their function relies largely on nuclear-encoded proteins that must be imported from the cytosol, and thus the protein import pathways are important for the maintenance of mitochondrial proteostasis. Mitochondrial HSP70 (mtHsp70) is a key component in facilitating the translocation of proteins through the inner membrane into the mitochondrial matrix. Its protein folding cycle is regulated by the nucleotide-exchange factor GrpE, which triggers the release of folded proteins by ATP rebinding...
August 4, 2018: Redox Biology
https://www.readbyqxmd.com/read/30098361/identification-of-chemically-diverse-gaba-a-agonists-as-potential-anti-epileptic-agents-using-structure-guided-virtual-screening-admet-quantum-mechanics-and-clinical-validation-through-off-target-analysis
#3
Pakhuri Mehta, Shubham Srivastava, Manish Sharma, Inderpal Singh, Ruchi Malik
Development of resistance against existing anti-epileptic drugs has alarmed the scientific innovators to find novel potential chemical starting points for the treatment of epilepsy and GABAA inhibition is a promising drug target strategy against epilepsy. The crystal structure of a subtype-selective β3-homopentameric ligand-gated ion channel of GABAA receptor has been used for the first time for screening the Asinex library for discovery of GABAA agonists as potential anti-epileptic agents. Co-crystallized ligand established the involvement of part of the β7-β8 loop (Glu155 and Tyr157) and β9-β10 loop (Phe200 and Tyr205) residues as the crucial amino acids in effective binding, an essential feature, being hydrogen bond or ionic interaction with Glu155 residue...
August 8, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/30098248/-identification-of-compound-heterozygous-mutations-p-gly400val-and-p-arg532ter-of-the-f11-gene-in-a-chinese-patient-with-hereditary-factor-xi-deficiency
#4
Kuangyi Shu, Kai Xu, Fanfan Li, Tao Chen, Jie Liu, Susu Jin, Jingjing Guo, Zhaohua Zhang, Minghua Jiang
OBJECTIVE: To investigate the phenotype and genotype defect characteristics of a Chinese patient with hereditary factor XI deficiency. METHODS: The activated partial thromboplastin time (APTT), prothrombin time (PT), FXI activity (FXI:C) of the proband and his relatives were measured by a clotting method using automatic coagulation analyzer. FXI antigen (FXI:Ag) was assayed by enzyme-linked immunosorbent assay (ELISA). Fifteen exons of the F11 gene were amplified by PCR and sequenced...
August 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/30098128/a-miniaturized-solid-phase-extraction-adsorbent-of-calix-4-arene-functionalized-graphene-oxide-polydopamine-coated-cellulose-acetate-for-the-analysis-of-aflatoxins-in-corn
#5
Piyaluk Nurerk, Warapon Bunkoed, Proespichaya Kanatharana, Opas Bunkoed
A calix[4]arene-functionalized graphene oxide/polydopamine-coated cellulose acetate adsorbent was fabricated for the preconcentration of aflatoxins. The highly porous developed adsorbent does not produce the high back pressure that normally occurs in particles packed cartridges and its large surface area helps to improve adsorption. The highly efficient adsorption of aflatoxins by the hybrid adsorbent is facilitated via hydrogen bonding and hydrophobic and π-π interactions. Polymerization time, amount of calix[4]arene-functionalized graphene oxide, type and volume of desorption solvent, sample pH, sample volume and sample flow rate were optimized...
August 10, 2018: Journal of Separation Science
https://www.readbyqxmd.com/read/30097974/papain-loaded-poly-%C3%AE%C2%B5-caprolactone-nanoparticles-in-silico-and-in-vitro-studies
#6
Yasemin Budama-Kilinc, Rabia Cakir-Koc, Serda Kecel-Gunduz, Tolga Zorlu, Yagmur Kokcu, Bilge Bicak, Zeynep Karavelioglu, Aysen E Ozel
Papain is a protease enzyme with therapeutic properties that are very valuable for medical applications. Poly(ε-caprolactone) (PCL) is an ideal polymeric carrier for controlled drug delivery systems due to its low biodegradability and its high biocompatibility. In this study, the three-dimensional structure and action mechanism of papain were investigated by in vitro and in silico experiments using molecular dynamics (MD) and molecular docking methods to elucidate biological functions. The results showed that the size of papain-loaded PCL nanoparticles (NPs) and the polydispersity index (PDI) of the NPs were 242...
August 10, 2018: Journal of Fluorescence
https://www.readbyqxmd.com/read/30097092/aminofutalosine-synthase-mqne-a-new-catalytic-motif-in-radical-sam-enzymology
#7
Sumedh Joshi, Dmytro Fedoseyenko, Nilkamal Mahanta, Tadhg P Begley
Aminofutalosine synthase (MqnE) is a radical SAM enzyme involved in the futalosine-dependent menaquinone biosynthetic pathway. Its ability to add the 5'-deoxyadenosyl radical to the substrate-rather than abstract a hydrogen atom-and to catalyze radical addition to a stable benzene ring gives it a unique place in the radical SAM superfamily and required the development of new strategies for trapping radical intermediates. This chapter describes the methodologies used for enzyme overexpression, purification, and in vitro reconstitution...
2018: Methods in Enzymology
https://www.readbyqxmd.com/read/30096992/adsorption-process-of-tetrachloroethylene-pce-on-network-growth-ring
#8
Huang Wanyi, Zhong Dan, Yuan Yixing, Ma Wencheng, Yuan Yuan, Liu Bohan
This study was undergone to investigate the adsorption characteristics of tetrachloroethylene (PCE) on water supply network growth ring. According to the chemical composition of real network growth ring, iron oxide mixture containing synthesized goethite and lepidocrocite was applied as simulated growth ring. The adsorption mechanism was studied in terms of adsorption kinetic, isotherm, thermodynamic and FTIR spectroscopy experiments. The results demonstrate that competition could take place only between PCE and the co-present organic non-ionic compound, while inorganic salt had no discernible effect on PCE adsorption...
August 10, 2018: Environmental Technology
https://www.readbyqxmd.com/read/30096806/discovery-of-4-5-dihydro-1-h-thieno-2-3-2-3-thiepino-4-5-c-pyrazole-3-carboxamide-derivatives-as-the-potential-epidermal-growth-factor-receptors-for-tyrosine-kinase-inhibitors
#9
Jia Ke, Qi Lu, Xin Wang, Rui Sun, Zhe Jin, Xiaoyi Zhan, Jianshu Hu, David Chi-Cheong Wan, Chun Hu
The epidermal growth factor receptors (EGFRs), in which overexpression (known as upregulation) or overactivity have been associated with a number of cancers, has become an attractive molecular target for the treatment of selective cancers. We report here the design and synthesis of a novel series of 4,5-dihydro-1 H -thieno [2',3':2,3]thiepino[4,5-c]pyrazole-3-carboxamide derivatives and the screening for their inhibitory activity on the EGFR high-expressing human A549 cell line using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)...
August 8, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/30096627/rational-in-silico-design-of-novel-%C3%AE-glucosidase-inhibitory-peptides-and-in-vitro-evaluation-of-promising-candidates
#10
Mohammed Auwal Ibrahim, Megan J Bester, Albert W Neitz, Anabella R M Gaspar
Treatment of type 2 diabetes is achieved through the inhibition of carbohydrate hydrolyzing enzymes such as α-glucosidase and α-amylase. The present study was conducted to identify novel α-glucosidase inhibitory peptides and to validate the α-glucosidase and α-amylase inhibitory activities of two promising candidates. A total of 4210 potential α-glucosidase inhibitory peptides with 3-5 amino acid residues were designed and individually subjected to in silico simulated gastrointestinal (GIT) digestion using the BIOPEP database...
August 7, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/30096472/role-of-zein-incorporation-on-hydrophobic-drug-loading-capacity-and-colloidal-stability-of-phospholipid-nanoparticles
#11
Soon-Seok Hong, Raj Kumar Thapa, Jin-Hee Kim, Soo-Yeon Kim, Jong Oh Kim, Jin-Ki Kim, Han-Gon Choi, Soo-Jeong Lim
Liposome, phosphatidylcholine nanoparticle (PC-NP), is an attractive colloidal carrier of hydrophobic drugs but its clinical development is often limited by low drug-loading capacity and the physical instability. Zein is a water-insoluble amphiphilic protein obtained from the corn. We herein investigated a possibility to develop zein-phosphatidylcholine hybrid nanoparticle (Z/PC-NP) as an advanced hydrophobic drug carrier. By employing the conventional liposome preparation method with the addition of zein, Z/PC-NP were produced...
August 2, 2018: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/30096238/growth-of-au-pd2sn-nanorods-via-galvanic-replacement-and-their-catalytic-performance-on-hydrogenation-and-sonogashira-coupling-reactions
#12
Raquel Nafria, Zhishan Luo, Maria Ibáñez, Sara Martí-Sànchez, Xiaoting Yu, María de la Mata, Jordi Llorca, Jordi Arbiol, Maksym V Kovalenko, Arnald Grabulosa, Guillermo Muller, Andreu Cabot
Colloidal Pd2Sn and Au-Pd2Sn nanorods (NRs) with tuned size were produced by the reduction of Pd and Sn salts in the presence of size- and shape-controlling agents and the posterior growth of Au tips through a galvanic replacement reaction. Pd2Sn and Au-Pd2Sn NRs exhibited high catalytic activity toward quasi-homogeneous hydrogenation of alkenes (styrene and 1-octene) and alkynes (phenylacetylene and 1-octyne) in dichloromethane (DCM). Au-Pd2Sn NRs showed higher activity than Pd2Sn for 1-octene, 1-octyne and phenylacetylene...
August 10, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/30095924/catalytic-reaction-mechanism-for-drug-metabolism-in-human-carboxylesterase-1-cocaine-hydrolysis-pathway
#13
Jianzhuang Yao, Xiabin Chen, Fang Zheng, Chang-Guo Zhan
Carboxylesterase-1 (CE-1) is a crucial enzyme responsible for metabolism/activation/inactivation of xenobiotics (therapeutic agents, prodrugs, abused drugs, and organophosphorus nerve agents etc.) and also involved in many other biological processes. In this study, we performed extensive computational modeling and simulations to understand the fundamental reaction mechanism of cocaine hydrolysis catalyzed by CE-1, revealing that CE-1-catalyzed cocaine hydrolysis follows a novel reaction pathway with only two reaction steps: a single-step acylation process and a single-step deacylation process...
August 10, 2018: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/30095910/rational-design-and-structure-validation-of-a-novel-peptide-inhibitor-of-the-adenomatous-polyposis-coli-apc-rho-guanine-nucleotide-exchange-factor-4-asef-interaction
#14
Xiuyan Yang, Jie Zhong, Qiufen Zhang, Jinxing Qian, Kun Song, Cong Ruan, Jianrong Xu, Ke Ding, Jian Zhang
In colorectal cancer, adenomatous polyposis coli (APC) interacts with Rho guanine nucleotide exchange factor 4 (Asef), thereby stimulating aberrant colorectal cancer cell migration. Consequently, the APC-Asef interaction represents a promising therapeutic target to mitigate colorectal cancer migration. In this study, we adopted the rational design strategy involved introducing intramolecular hydrogen bonds and optimizing the lipophilic substituents to improve binding affinity of peptides, leading to the discovery of MAI-400, the best-known inhibitor to date of the APC-Asef interaction (Kd = 0...
August 10, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/30095900/structure-based-design-leads-to-potent-and-orally-bioavailable-inverse-agonists-of-ror%C3%AE-t
#15
Frank Narjes, Yafeng Xue, Stefan von Berg, Jesper Malmberg, Antonio Llinas, Roine I Olsson, Johan Jirholt, Hanna Grindebacke, Agnes Leffler, Nafizal Hossain, Matti Lepistö, Linda Thunberg, Hanna Leek, Anna Aagaard, Jane McPheat, Eva L Hansson, Elisabeth Back, Stefan Tångefjord, Rongfeng Chen, Yao Xiong, Ge Hongbin, Thomas Hansson
Retinoic acid receptor-related orphan receptor γt (RORγt), has been identified as the master regulator of TH 17 cell function and development, making it an attractive target for the treatment of autoimmune diseases by a small molecule approach. Herein we describe our investigations on a series of 4-aryl-thienyl acetamides, which were guided by insights from X-ray co-crystal structures. Efforts in targeting the co-factor recruitment site from the 4-aryl group on the thiophene led to a series of potent binders, with nanomolar activity in a primary human TH 17 cell assay...
August 10, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/30095260/isotopic-effects-on-intermolecular-and-intramolecular-structure-and-dynamics-in-hydrogen-deuterium-and-tritium-liquids-normal-liquid-and-weakly-and-strongly-cooled-liquids
#16
Kiharu Abe, Shutaro Yamaoka, Kim Hyeon-Deuk
Differences in properties such as phase-transition temperature and transport coefficients among liquids of different isotopic compositions, hydrogen, deuterium and tritium, should originate from their differently pronounced nuclear quantum effects (NQEs) rather than from any subtle difference in the electronic interaction potentials. Accurate and efficient determination of structural and dynamical isotopic effects in the quantum liquids still remains as one of the challenging problems in condensed-phase physics...
August 10, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/30095200/characterization-of-the-two-conformations-adopted-by-the-t3ss-inner-membrane-protein-prgk
#17
Julien R C Bergeron, Jacob A Brockerman, Marija Vuckovic, Wanyin Deng, Mark Okon, Brett B Finlay, Lawrence P McIntosh, Natalie C J Strynadka
The pathogenic bacterium Salmonella enterica serovar typhimurium utilizes two type III secretion systems (T3SS) to inject effector proteins into target cells upon infection. The T3SS secretion apparatus (the injectisome) is a large macromolecular assembly composed of over twenty proteins, many in highly oligomeric states. A sub-structure of the injectisome, termed the basal body, spans both membranes and the periplasmic space of the bacterium. It is primarily composed of three integral membranes proteins, InvG, PrgH, and PrgK, that form ring structures through which components are secreted...
August 10, 2018: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/30095189/direct-synthesis-of-heavy-grignard-reagents-challenges-limitations-and-derivatization
#18
Matthias Westerhausen, Alexander Koch, Quentin Dufrois, Marino Wirgenings, Helmar Görls, Sven Krieck, Michel Etienne, Georg Pohnert
The synthesis of organocalcium compounds (heavy Grignard reagents) via the reduction of organyl halides with calcium powder succeeds straightforwardly for organic bromides and iodides that are bound at sp2-hybridized carbon atoms. Extension of this strategy to alkyl halides is very limited and only the reduction of trialkylsilylmethyl bromides and iodides with activated calcium allows the isolation of corresponding heavy Grignard reagents. Substitution of only one hydrogen atom of the methylene moiety by a phenyl or methyl group directs this reduction toward the Wurtz-type coupling and the formation of calcium halide and the corresponding C-C coupling product...
August 10, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/30094722/lacidipine-amorphous-solid-dispersion-based-on-hot-melt-extrusion-good-miscibility-enhanced-dissolution-and-favorable-stability
#19
Long Xi, Hang Song, Yunzhi Wang, Haoshi Gao, Qiang Fu
The present study aimed to increase the in vitro dissolution rate of lacidipine, a poorly water-soluble drug, by formulating amorphous solid dispersions (ASDs) using hot-melt extrusion (HME). Differential scanning calorimetry, powder X-ray diffraction, polarized light microscopy, and Fourier transform infrared were used to characterize the optimal formulations and evaluate the physical stability for the stress test. Film-casting method and hot-stage microscopy were applied to study the miscibility of lacidipine and the drug carriers...
August 9, 2018: AAPS PharmSciTech
https://www.readbyqxmd.com/read/30094474/terahertz-electric-field-induced-membrane-electroporation-by-molecular-dynamics-simulations
#20
Jingchao Tang, Hairong Yin, Jialu Ma, Wenfei Bo, Yang Yang, Jin Xu, Yiyao Liu, Yubin Gong
In this paper, the membrane electroporation induced by the terahertz electric field is simulated by means of the molecular dynamics method. The influences of the waveform and frequency of the applied terahertz electric field on the electroporation and the unique features of the process of the electroporation with the applied terahertz electric field are given. It shows that whether the electroporation can happen depends on the waveform of the applied terahertz electric field when the magnitude is not large enough...
August 9, 2018: Journal of Membrane Biology
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