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https://www.readbyqxmd.com/read/28538738/solid-phase-synthesis-cyclization-and-site-specific-functionalization-of-aziridine-containing-tetrapeptides
#1
Benjamin K W Chung, Christopher J White, Andrei K Yudin
Cyclic tetrapeptides comprise a potent and selective class of molecules with a wide range of biological activities, including the phytotoxic activity of tentoxin and the histone deacetylase (HDAC) inhibitory effects of chlamydocin. The incorporation of a functional aziridine group within cyclic peptides enables their conformational control and allows for late-stage and site-selective functionalization of these molecules, thereby creating the potential for covalent protein labeling. This protocol describes the solid-phase synthesis, cyclization, and site-specific structural modification of aziridine-containing tetrapeptides...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28538735/ensemble-cryo-em-elucidates-the-mechanism-of-translation-fidelity
#2
Anna B Loveland, Gabriel Demo, Nikolaus Grigorieff, Andrei A Korostelev
Gene translation depends on accurate decoding of mRNA, the structural mechanism of which remains poorly understood. Ribosomes decode mRNA codons by selecting cognate aminoacyl-tRNAs delivered by elongation factor Tu (EF-Tu). Here we present high-resolution structural ensembles of ribosomes with cognate or near-cognate aminoacyl-tRNAs delivered by EF-Tu. Both cognate and near-cognate tRNA anticodons explore the aminoacyl-tRNA-binding site (A site) of an open 30S subunit, while inactive EF-Tu is separated from the 50S subunit...
May 24, 2017: Nature
https://www.readbyqxmd.com/read/28538729/cryo-em-structure-of-the-activated-glp-1-receptor-in-complex-with-a-g-protein
#3
Yan Zhang, Bingfa Sun, Dan Feng, Hongli Hu, Matthew Chu, Qianhui Qu, Jeffrey T Tarrasch, Shane Li, Tong Sun Kobilka, Brian K Kobilka, Georgios Skiniotis
Glucagon-like peptide 1 (GLP-1) is a hormone with essential roles in regulating insulin secretion, carbohydrate metabolism and appetite. GLP-1 effects are mediated through binding to the GLP-1 receptor (GLP-1R), a class B G-protein-coupled receptor (GPCR) that signals primarily through the stimulatory G protein Gs. Class B GPCRs are important therapeutic targets; however, our understanding of their mechanism of action is limited by the lack of structural information on activated and full-length receptors. Here we report the cryo-electron microscopy structure of the peptide-activated GLP-1R-Gs complex at near atomic resolution...
May 24, 2017: Nature
https://www.readbyqxmd.com/read/28538549/impact-of-evolving-radiation-therapy-techniques-on-implant-based-breast-reconstruction
#4
Horatiu Muresan, Gretl Lam, Benjamin T Cooper, Carmen A Perez, Alexes Hazen, Jamie P Levine, Pierre B Saadeh, Mihye Choi, Nolan S Karp, Daniel J Ceradini
BACKGROUND: Patients undergoing implant-based reconstruction in the setting of postmastectomy radiation therapy suffer from increased complications and inferior outcomes compared with those not irradiated, but advances in radiation delivery have allowed for more nuanced therapy. The authors investigated whether these advances impact patient outcomes in implant-based breast reconstruction. METHODS: Retrospective chart review identified all implant-based reconstructions performed at a single institution from November of 2010 to November of 2013...
June 2017: Plastic and Reconstructive Surgery
https://www.readbyqxmd.com/read/28538397/quality-of-reporting-of-multivariable-logistic-regression-models-in-chinese-clinical-medical-journals
#5
Ying-Ying Zhang, Xiao-Bin Zhou, Qiu-Zhen Wang, Xiao-Yan Zhu
Multivariable logistic regression (MLR) has been increasingly used in Chinese clinical medical research during the past few years. However, few evaluations of the quality of the reporting strategies in these studies are available.To evaluate the reporting quality and model accuracy of MLR used in published work, and related advice for authors, readers, reviewers, and editors.A total of 316 articles published in 5 leading Chinese clinical medical journals with high impact factor from January 2010 to July 2015 were selected for evaluation...
May 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28538206/spectroscopic-far-or-terahertz-mid-infrared-and-raman-investigation-thermal-analysis-and-biological-activity-of-piplartine
#6
Anubha Srivastava, T Karthick, B D Joshi, Rashmi Mishra, Poonam Tandon, A P Ayala, Javier Ellena
Research in the field of medicinal plants including Piper species like long pepper (Piper longum L.- Piperaceae) is increasing all over the world due to its use in traditional and Ayurvedic medicine. Piplartine (piperlongumine, 5,6-dihydro-1-[(2E)-1-oxo-3-(3,4,5-trimethoxyphenyl)-2-propenyl]-2(1H)-pyridinone), a biologically active alkaloid/amide was isolated from the phytochemical investigations of Piper species, as long pepper. This alkaloid has cytotoxic, anti-fungal, anti-diabetic, anti-platelet aggregation, anti-tumoral, anxiolytic, anti-depressant, anti-leishmanial, and genotoxic activities, but, its anticancer property is the most promising and has been widely explored...
May 5, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28538165/the-complexity-in-herpesvirus-entry
#7
REVIEW
Karthik Sathiyamoorthy, Jia Chen, Richard Longnecker, Theodore S Jardetzky
Enveloped viruses have evolved diverse transmembrane proteins and protein complexes to enable host cell entry by regulating and activating membrane fusion in a target cell-specific manner. In general terms, the entry process requires a receptor binding step, an activation step and a membrane fusion step, which can be encoded within a single viral protein or distributed among multiple viral proteins. HIV and influenza virus, for example, encode all of these functions in a single trimeric glycoprotein, HIV env or influenza virus hemagglutinin (HA)...
May 21, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28538154/effect-of-ca-2-to-sphingomyelin-investigated-by-sum-frequency-generation-vibrational-spectroscopy
#8
Rong-Juan Feng, Lu Lin, Yi-Yi Li, Ming-Hua Liu, Yuan Guo, Zhen Zhang
The interactions between Ca(2+) ions and sphingomyelin play crucial roles in a wide range of cellular activities. However, little is known about the molecular details of the interactions at interfaces. In this work, we investigated the interactions between Ca(2+) ions and egg sphingomyelin (ESM) Langmuir monolayers at the air/water interface by subwavenumber high-resolution broadband sum frequency generation vibrational spectroscopy (HR-BB-SFG-VS). We show that Ca(2+) ions can induce ordering of the acyl chains in the ESM monolayer...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538148/active-site-pka-determination-for-photoactive-yellow-protein-rationalizes-slow-ground-state-recovery
#9
Nur Alia Oktaviani, Trijntje J Pool, Yuichi Yoshimura, Hironari Kamikubo, Ruud M Scheek, Mikio Kataoka, Frans A A Mulder
The ability to avoid blue-light radiation is crucial for bacteria to survive. In Halorhodospira halophila, the putative receptor for this response is known as photoactive yellow protein (PYP). Its response to blue light is mediated by changes in the optical properties of the chromophore para-coumaric acid (pCA) in the protein active site. PYP displays photocycle kinetics with a strong pH dependence for ground-state recovery, which has remained enigmatic. To resolve this problem, a comprehensive pKa determination of the active-site residues of PYP is required...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538095/high-resolution-structures-of-the-amyloid-%C3%AE-1-42-dimers-from-the-comparison-of-four-atomistic-force-fields
#10
Viet Hoang Man, Phuong Hoang Nguyen, Philippe Derreumaux
The dimer of the amyloid-beta peptide Aβ of 42 residues is the smallest toxic species in Alzheimer's disease, but its equilibrium structures are unknown. Here we determined the equilibrium ensembles generated by the four atomistic OPLS-AA, CHARMM22*, AMBER99sb-ildn and AMBERsb14 force fields with the TIP3P water model. Based on 144 microsecond replica exchange molecular dynamics simulations (with 750 ns per replica), we find that the four force fields lead to random coil ensembles with calculated cross-collision sections, hydrodynamics properties and small-angle X-ray scattering profiles independent on the force field...
May 24, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28537745/deciphering-cryptic-binding-sites-on-proteins-by-mixed-solvent-molecular-dynamics
#11
S Roy Kimura, Haipeng Hu, Anatoly M Ruvinsky, Woody B Sherman, Angelo D Favia
In recent years, molecular dynamics simulations of proteins in explicit mixed-solvents have been applied to various problems in protein biophysics and drug discovery, including protein folding, protein surface characterization, fragment screening, allostery, and druggability assessment. In this study, we perform a systematic study on how mixtures of organic solvent probes in water can reveal cryptic ligand binding pockets that are not evident in crystal structures of apo proteins. We examine a diverse set of eight PDB proteins that show pocket opening induced by ligand binding and investigate whether solvent MD simulations on the apo structures can induce the binding site observed in the holo structures...
May 24, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28537739/modeling-the-effect-of-polymer-chain-stiffness-on-the-behavior-of-polymer-nanocomposites
#12
José Javier Burgos-Mármol, Óscar Álvarez-Machancoses, Alessandro Patti
Due to their central role in industrial formulations spanning from food packaging to smart coatings, polymer nanocomposites have been the object of a remarkable attention over the last two decades. Incorporating nanoparticles (NPs) to a polymer matrix modifies the conformation and mobility of the polymer chains at the NP-polymer interface and can potentially provide materials with enhanced properties as compared to pristine polymers. To this end, it is crucial to predict and control the ability of NPs to diffuse and achieve a good dispersion in the polymer matrix...
May 24, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28537728/antimalarial-inhibitors-targeting-serine-hydroxymethyltransferase-shmt-with-in-vivo-efficacy-and-analysis-of-their-binding-mode-based-on-x-ray-cocrystal-structures
#13
Geoffrey Schwertz, Matthias C Witschel, Matthias Rottmann, Roger Bonnert, Ubolsree Leartsakulpanich, Penchit Chitnumsub, Aritsara Jaruwat, Wanwipa Ittarat, Anja Schäfer, Raphael A Aponte, Susan A Charman, Karen L White, Abhijit Kundu, Surajit Sadhukhan, Mel Lloyd, Gail M Freiberg, Myron Srikumaran, Marc Siggel, Adrian Zwyssig, Pimchai Chaiyen, François Diederich
Target-based approaches towards new antimalarial treatments are highly valuable to prevent resistance development. We report several series of pyrazolopyran-based inhibitors targeting the enzyme serine hydroxymethyltransferase (SHMT), designed to improve microsomal metabolic stability and to identify suitable candidates for in vivo efficacy evaluation. The best ligands inhibited Plasmodium falciparum (Pf) and Arabidopsis thaliana (At) SHMT in target assays and PfNF54 strains in cell-based assays with values in the low nanomolar range (3...
May 24, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28535338/a-flexible-lithium-ion-fiber-battery-by-regularly-stacking-two-dimensional-titanium-oxide-nanosheets-hybridized-with-reduced-graphene-oxide
#14
Tatsumasa Hoshide, Yuanchuan Zheng, Junyu Hou, Zhiqiang Wang, Qingwen Li, Zhigang Zhao, Renzhi Ma, Takayoshi Sasaki, Fengxia Geng
Increasing interest has recently been devoted to developing small, rapid, and portable electronic devices; thus, it is becoming critically important to provide matching light and flexible energy-storage systems to power them. To this end, compared with the inevitable drawbacks of being bulky, heavy, and rigid for traditional planar sandwiched structures, linear fiber-shaped lithium-ion batteries (LIB) have become increasingly important owing to their combined superiorities of miniaturization, adaptability, and weavability, the progress of which is heavily dependent on developing new fiber-shaped electrodes...
May 23, 2017: Nano Letters
https://www.readbyqxmd.com/read/28535337/overall-structural-model-of-ns5a-protein-from-hepatitis-c-virus-and-modulation-by-mutations-confering-resistance-of-virus-replication-to-cyclosporin-a
#15
Aurelie Badillo, Veronique Brechot, Stephane Sarrazin, François-Xavier Cantrelle, Frederic Delolme, Marie-Laure Fogeron, Jennifer Molle, Roland Montserret, Anja Bockmann, Ralf Bartenschlager, Volker Lohmann, Guy Lippens, Sylvie Ricard-Blum, Xavier Hanoulle, Francois Penin
Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is a RNA-binding phosphoprotein composed of a N-terminal membrane anchor (AH), a structured domain 1 (D1) and two intrinsically disordered domains (D2 and D3). The knowledge of the functional architecture of this multifunctional protein remains limited. We report here that NS5A-D1D2D3 produced in a wheat germ cell-free system is obtained under a highly phosphorylated state. Its NMR analysis revealed that these phosphorylations do not change the disordered nature of D2 and D3 domains but increase the number of conformers due to partial phosphorylations...
May 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28535068/a-conformal-lithium-fluoride-protection-layer-on-three-dimensional-lithium-by-non-hazardous-gaseous-reagent-freon
#16
Dingchang Lin, Yayuan Liu, Wei Chen, Guangmin Zhou, Kai Liu, Bruce S Dunn, Yi Cui
Research on lithium (Li) metal chemistry has been rapidly gaining momentum nowadays not only because of the appealing high theoretical capacity, but also its indispensable role in the next-generation Li-S and Li-air batteries. However, two root problems of Li metal, namely high reactivity and infinite relative volume change during cycling, bring about numerous other challenges that impede its practical applications. In the past, extensive studies have targeted these two root causes by either improving interfacial stability or constructing a stable host...
May 23, 2017: Nano Letters
https://www.readbyqxmd.com/read/28535051/structural-properties-of-nonionic-monorhamnolipid-aggregates-in-water-studied-by-classical-molecular-dynamics-simulations
#17
Elango Munusamy, Charles M Luft, Jeanne E Pemberton, Steven D Schwartz
Molecular dynamics simulations were carried out to investigate the structure and stabilizing factors of aggregates of the nonionic form of the most common congener of monorhamnolipids, α-rhamnopyranosyl-β-hydroxydecanoyl-β-hydroxydecanoate (Rha- C10-C10), in water. Aggregates of size ranging from 5 monomers to 810 monomers were observed in the simulation forming spherical and ellipsoidal structures, a torus like structure and a unilamellar vesicle. The effects of hydrophobic chain conformation and alignment in the aggregate, role of H-bonds between monomer...
May 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28534912/prediction-on-the-light-assisted-exfoliation-of-multilayered-arsenene-by-the-photo-isomerization-of-azobenzene
#18
Jun Zhao, Chunyan Liu, Wanlin Guo, Jing Ma
The exfoliation of gray arsenic into single- or few-layered arsenene is a challenge of utmost importance. We propose here that the conformational change in the photo-isomerization of azobenzene-based photochromes might be used to promote the exfoliation of multilayered arsenene. Our density functional theory calculations show that the trans-to-cis conformational change can lead to an increase of the adjacent interlayer distance of arsenene from 6.59 Å to 11.07 Å. Starting from the transition state, the azobenzene molecule can be isomerized into the more stable trans form based on further ab initio molecular dynamics simulations...
May 23, 2017: Nanoscale
https://www.readbyqxmd.com/read/28534783/nahal-flex-a-numerical-and-alphabetical-hinge-detection-algorithm-for-flexible-protein-structure-alignment
#19
Samira Fotoohifiroozabadi, Mohd Saberi Mohamad, Safaai Deris
Flexible proteins are proteins that have conformational changes in their structures. Protein flexibility analysis is critical for classifying and understanding protein functionality. For that analysis, the hinge areas where proteins show flexibility must be detected. To detect the location of the hinges, previous methods have utilized the three-dimensional (3D) structure of proteins, which is highly computational. To reduce the computational complexity, this study proposes a novel text-based method using structural alphabets (SAs) for detecting the hinge position, called NAHAL-Flex...
May 17, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28534625/reaction-mechanisms-of-the-atomic-layer-deposition-of-tin-oxide-thin-films-using-tributyltin-ethoxide-and-ozone
#20
Charith E Nanayakkara, Guo Liu, Abraham Vega, Charles L Dezelah, Ravindra K Kanjolia, Yves J Chabal
Uniform and conformal deposition of tin oxide thin films is important for several applications in electronics, gas sensing and transparent conducting electrodes. Thermal Atomic layer deposition (ALD) is often best suited for these applications, but its implementation requires a mechanistic understanding of the initial nucleation and subsequent ALD processes. To this end, in-situ FTIR and ex-situ XPS have been used to explore the ALD of tin oxide films using tributyltin ethoxide and ozone on an OH-terminated, SiO2-passivated Si(111) substrate...
May 23, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
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