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Bounded rationality

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https://www.readbyqxmd.com/read/28809485/dispersion-and-halogen-bonding-interactions-binding-of-the-axial-conformers-of-monohalo-and-%C3%A2-trans-1-2-dihalocyclohexanes-in-enantiopure-alleno-acetylenic-cages
#1
Cornelius Gropp, Tamara Husch, Nils Trapp, Markus Reiher, François Diederich
Enantiopure alleno-acetylenic cage (AAC) receptors with a resorcin[4]arene scaffold, from which four homochiral alleno-acetylenes converge to shape a cavity closed by a four-fold OH-hydrogen-bonding array, form a highly ordered porous network in the solid state. They enable the complexation and co-crystallization of otherwise non-crystalline small molecules. This paper analyzes the axial conformers of monohalo- and (±)-trans-1,2-dihalocyclohexanes, bound in the interior cavity of the AACs, on the atomic level in the solid state and in solution, accompanied by accurate calculations...
August 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28805809/x-ray-structures-of-endothelin-etb-receptor-bound-to-clinical-antagonist-bosentan-and-its-analog
#2
Wataru Shihoya, Tomohiro Nishizawa, Keitaro Yamashita, Asuka Inoue, Kunio Hirata, Francois Marie Ngako Kadji, Akiko Okuta, Kazutoshi Tani, Junken Aoki, Yoshinori Fujiyoshi, Tomoko Doi, Osamu Nureki
Endothelin receptors (ETRs) have crucial roles in vascular control and are targets for drugs designed to treat circulatory-system diseases and cancer progression. The nonpeptide dual-ETR antagonist bosentan is the first oral drug approved to treat pulmonary arterial hypertension. Here we report crystal structures of human endothelin ETB receptor bound to bosentan and to the ETB-selective analog K-8794, at 3.6-Å and 2.2-Å resolution, respectively. The K-8794-bound structure reveals the detailed water-mediated hydrogen-bonding network at the transmembrane core, which could account for the weak negative allosteric modulation of ETB by Na(+) ions...
August 14, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28802844/structural-basis-for-cullins-and-ring-component-inhibition-targeting-e3-ubiquitin-pathway-conductors-for-cancer-therapeutics
#3
Shagufta Shafique, Waqar Ali, Sonia Kanwal, Sajid Rashid
Cullin (CUL)-RING E3 ubiquitin ligases (CRLs) are attractive therapeutic targets as they regulate diverse biological processes important for cancer cell survival by conferring substrate selectivity for ubiquitination and degradation. Given the complexity of CRL complexes, steps toward the structure-based design of small-molecule inhibitors to modulate their activity have remained elusive. In this study, we explored the structural assembly and interaction details of closely related CUL scaffolds (CUL1, CUL2, CUL3, CUL4A, CUL4B, CUL5 and CUL7) with RBX1 to screen potent small molecules against CRLs...
August 9, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28799368/the-nature-of-the-chemical-bond-in-be2-be2-be2-and-be3
#4
Apostolos Kalemos
The present study focuses on the Be2+, Be2, Be2-, and Be3 species with the aim to unveil their bonding pattern. The ground states of the above molecules are examined mainly through multi reference configuration interaction methods using an aug-cc-pVQZ basis set. Previous work is scrutinized with an eye to the instability problems inherent in various Hartree-Fock schemes. Under this point of view, we rationalize previous findings and put them in a unified context of what and why should be done in similar hard to crack cases...
December 7, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28793191/structural-basis-of-analog-specificity-in-pkg-i-and-ii
#5
James C Campbell, Philipp Henning, Eugen Franz, Banumathi Sankaran, Friedrich W Herberg, Choel Kim
Cyclic GMP analogs, 8-Br, 8-pCPT, and PET-cGMP, have been widely used for characterizing cellular functions of cGMP dependent protein kinase (PKG) I and II isotypes. However, interpreting results obtained using these analogs has been difficult due to their low isotype specificity. Additionally each isotype has two binding sites with different cGMP affinities and analog selectivities, making understanding the molecular basis for isotype specificity of these compounds even more challenging. To determine isotype specificity of cGMP analogs and their structural basis, we generated the full-length regulatory domains of PKG I and II isotypes with each binding site disabled, determined their affinities for these analogs, and obtain co-crystal structures of both isotypes bound with cGMP analogs...
August 9, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28789529/structure-dynamics-and-electron-transfer-of-azurin-bound-to-gold-electrode
#6
Anna Rita Bizzarri, Chiara Baldacchini, Salvatore Cannistraro
Blue copper redox protein Azurin (AZ) constitutes an ideal active element for building bio-nano-optoelectronic devices based on the intriguing interplay among its electron transfer (ET), vibrational and optical properties. A full comprehension of its dynamical and functional behaviour is required for efficient applications. Here, AZ bound to gold electrode via its disulphide bridge was investigated by a Molecular Dynamics simulation approach taking into account for gold electron polarization which provides a more realistic description of the protein-gold interaction...
August 9, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28782358/iron-redox-transformations-in-the-presence-of-natural-organic-matter-effect-of-calcium
#7
Chao Jiang, Shikha Garg, T David Waite
The effects of calcium on iron redox transformations in acidic non-irradiated and irradiated Suwannee River Fulvic Acid (SRFA) solutions are investigated in this study. Our results reveal that, even though calcium is redox-inert, it affects the redox transformations of iron with increased Fe(III) reduction rates under irradiated conditions and decreased Fe(II) oxidation rates in the dark in the presence compared to the absence of calcium. While the exact mechanism via which the Fe(III) reduction rate under irradiated conditions is impacted by calcium addition is not clear, the formation of more photo-labile weakly complexed Fe(III)SRFA is most consistent with our experimental results...
August 7, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28780303/computational-analysis-of-asp519-and-glu665-mutations-of-coagulation-factor-fviiia-implications-for-enhanced-binding-affinity-of-a2-domain
#8
Shenna Shearin, Divi Venkateswarlu
The A2-domain of blood coagulation factor VIIIa is non-covalently bound to the A1 and A3 domains via weak intermolecular interactions. Functional instability due to rapid dissociation of A2-domain from the active FVIII in blood presents a major hurdle for the therapeutic applications of FVIIIa to treat Hemophilia-A. To identify the ideal hot-spot residues at the interface of A2 and A1/A3 domains that could enhance the structural stability of FVIIIa, we performed a comprehensive computational mutagenesis study of two A2-domain residues, Asp519 and Glu665, that interface the A1 and A3-domains...
July 29, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28761383/on-the-dynamics-of-disobedience-experimental-investigations-of-defying-unjust-authority
#9
Piero Bocchiaro, Philip Zimbardo
Across six Experimental conditions with university student participants (N=600), we examined some of the dynamics underlying expressed defiance to unjust authority. Results revealed disobedience was best enacted by participants low in right-wing authoritarianism and was more likely to occur when: 1) in physical proximity of other rebels, 2) the authority made two demanding requests instead of one, and 3) there had been an earlier opposition to injustice. Results are discussed within the theoretical framework of bounded rationality...
2017: Psychology Research and Behavior Management
https://www.readbyqxmd.com/read/28750513/a-dna-walker-as-a-fluorescence-signal-amplifier
#10
Dongfang Wang, Carolin Vietz, Tim Schröder, Guillermo Acuna, Birka Lalkens, Philip Tinnefeld
Sensing nucleic acids typically involves the recognition of a specific sequence and reporting by, for example, a fluorogenic reaction yielding one activated dye molecule per detected nucleic acid. Here, we show that after binding to a DNA origami track a bound DNA target (a "DNA walker") can release the fluorescence of many molecules by acting as the catalyst of an enzymatic nicking reaction. As the walking kinetics sensitively depends on the walker sequence, the resulting brightness distribution of DNA origamis is a sequence fingerprint with single-nucleotide sensitivity...
August 7, 2017: Nano Letters
https://www.readbyqxmd.com/read/28743912/structural-basis-for-dolichylphosphate-mannose-biosynthesis
#11
Rosaria Gandini, Tom Reichenbach, Tien-Chye Tan, Christina Divne
Protein glycosylation is a critical protein modification. In biogenic membranes of eukaryotes and archaea, these reactions require activated mannose in the form of the lipid conjugate dolichylphosphate mannose (Dol-P-Man). The membrane protein dolichylphosphate mannose synthase (DPMS) catalyzes the reaction whereby mannose is transferred from GDP-mannose to the dolichol carrier Dol-P, to yield Dol-P-Man. Failure to produce or utilize Dol-P-Man compromises organism viability, and in humans, several mutations in the human dpm1 gene lead to congenital disorders of glycosylation (CDG)...
July 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28737432/integrin-targeted-nano-sized-polymeric-systems-for-paclitaxel-conjugation-a-comparative-study
#12
Anat Eldar-Boock, Rachel Blau, Claudia Ryppa, Hemda Baabur-Cohen, Ariel Many, María J Vicent, Felix Kratz, Joaquin Sanchis, Ronit Satchi-Fainaro
The generation of rationally-designed polymer therapeutics via the conjugation of low molecular weight anti-cancer drugs to water-soluble polymeric nanocarriers aims to improve the therapeutic index. Here, we focus on applying polymer therapeutics to target two cell compartments simultaneously - tumor cells and angiogenic endothelial cells. Comparing different polymeric backbones carrying the same therapeutic agent and targeting moiety may shed light on any correlation between the choice of polymer and the anti-cancer activity of the conjugate...
July 24, 2017: Journal of Drug Targeting
https://www.readbyqxmd.com/read/28735000/application-of-pharmacometrics-and-quantitative-systems-pharmacology-to-cancer-therapy-the-example-of-luminal-a-breast-cancer
#13
REVIEW
Brett Fleisher, Ashley N Brown, Sihem Ait-Oudhia
Breast cancer (BC) is the most common cancer in women, and the second most frequent cause of cancer-related deaths in women worldwide. It is a heterogeneous disease composed of multiple subtypes with distinct morphologies and clinical implications. Quantitative systems pharmacology (QSP) is an emerging discipline bridging systems biology with pharmacokinetics (PK) and pharmacodynamics (PD) leveraging the systematic understanding of drugs' efficacy and toxicity. Despite numerous challenges in applying computational methodologies for QSP and mechanism-based PK/PD models to biological, physiological, and pharmacological data, bridging these disciplines has the potential to enhance our understanding of complex disease systems such as BC...
July 19, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28731321/conjugation-dependent-interaction-of-folic-acid-with-folate-binding-protein
#14
Rachel Leah Merzel, Carolina Frey, Junjie Chen, Rachel Garn, Mallory A van Dongen, Casey A Dougherty, Ananda Kandaluru, Philip S Low, E Neil G Marsh, Mark M Banaszak Holl
Serum proteins play a critical role in the transport, uptake, and efficacy of targeted drug therapies, and here we investigate the interactions between folic acid-polymer conjugates and serum folate binding protein (FBP), the soluble form of the cellular membrane-bound folate receptor. We demonstrate that both choice of polymer and method of ligand conjugation affect the interactions between folic acid-polymer conjugates and serum FBP, resulting in changes in the folic acid-induced protein aggregation process...
July 21, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28730671/many-faces-of-rationality-implications-of-the-great-rationality-debate-for-clinical-decision-making
#15
Benjamin Djulbegovic, Shira Elqayam
Given that more than 30% of healthcare costs are wasted on inappropriate care, suboptimal care is increasingly connected to the quality of medical decisions. It has been argued that personal decisions are the leading cause of death, and 80% of healthcare expenditures result from physicians' decisions. Therefore, improving healthcare necessitates improving medical decisions, ie, making decisions (more) rational. Drawing on writings from The Great Rationality Debate from the fields of philosophy, economics, and psychology, we identify core ingredients of rationality commonly encountered across various theoretical models...
July 20, 2017: Journal of Evaluation in Clinical Practice
https://www.readbyqxmd.com/read/28727236/structural-and-electronic-flexibility-in-hydrides-of-zintl-phases-with-tetrel-hydrogen-and-tetrel-tetrel-bonds
#16
Henry Auer, Holger Kohlmann
The hydrogenation of Zintl phases enables the formation of new structural entities with main group element-hydrogen bonds in the solid state. The hydrogenation of SrSi, BaSi and BaGe yields the hydrides SrSiH5/3-x, BaSiH5/3-x and BaGeH5/3-x, whose crystal structures were solved by a combination of X-ray, neutron and electron diffraction. Layers of connected HSr4 (HBa4) tetrahedra containing hydride ions alternate with layers of infinite single- and double-chain polyanions, where hydrogen atoms are covalently bound to silicon and germanium...
July 20, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28714688/design-of-a-chemical-probe-for-the-bromodomain-and-plant-homeodomain-finger-containing-brpf-family-of-proteins
#17
Niall Igoe, Elliott D Bayle, Cynthia Tallant, Oleg Fedorov, Julia C Meier, Pavel Savitsky, Catherine Rogers, Yannick Morias, Sarah Scholze, Helen Boyd, Danen Cunoosamy, David M Andrews, Anne Cheasty, Paul E Brennan, Susanne Müller, Stefan Knapp, Paul V Fish
The bromodomain and PHD finger-containing (BRPF) family are scaffolding proteins important for the recruitment of histone acetyltransferases of the MYST family to chromatin. Here we describe NI-57 (16) as new pan-BRPF chemical probe of the bromodomain (BRD) of the BRPFs. Inhibitor 16 preferentially bound the BRD of BRPF1 and BRD1 over BRPF3, whereas binding to BRD9 was weaker. 16 has excellent selectivity over non-class IV BRD proteins. Target engagement of BRPF1B and BRD1 with 16 was demonstrated in nanoBRET and FRAP assays...
July 17, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28695571/australian-lobbyist-registers-are-not-serving-the-purposes-they-were-designed-for
#18
Narelle Robertson, Kypros Kypri, Julia Stafford, Mike Daube, Michelle Avery, Peter Miller
INTRODUCTION AND AIMS: There is widespread concern about the nature, extent and impacts of lobbying by industries selling unhealthy commodities, which threatens public health and undermines important democratic processes. In the last decade, all Australian jurisdictions (except the Northern Territory) have established lobbyist registers with the stated objective of increasing the capacity of government and the public to scrutinise lobbying. Our aim was to assess whether the registers are fulfilling this objective...
July 11, 2017: Drug and Alcohol Review
https://www.readbyqxmd.com/read/28689476/the-role-of-music-therapy-in-rehabilitation-improving-aphasia-and-beyond
#19
Simona Leonardi, Alberto Cacciola, Rosaria De Luca, Bianca Aragona, Veronica Andronaco, Demetrio Milardi, Placido Bramanti, Rocco Salvatore Calabrò
Music is part of the human nature, and it is also philogenically relevant to language evolution. Language and music are bound together in the enhancement of important social functions, such as communication, cooperation and social cohesion. In the last few years, there has been growing evidence that music and music therapy may improve communication skills (but not only) in different neurological disorders. One of the plausible reasons concerning the rational use of sound and music in neurorehabilitation is the possibility to stimulate brain areas involved in emotional processing and motor control, such as the fronto-parietal network...
July 10, 2017: International Journal of Neuroscience
https://www.readbyqxmd.com/read/28684739/dna-binding-strength-increases-the-processivity-and-activity-of-a-y-family-dna-polymerase
#20
Jing Wu, Alexandra de Paz, Bradley M Zamft, Adam H Marblestone, Edward S Boyden, Konrad P Kording, Keith E J Tyo
DNA polymerase (pol) processivity, i.e., the bases a polymerase extends before falling off the DNA, and activity are important for copying difficult DNA sequences, including simple repeats. Y-family pols would be appealing for copying difficult DNA and incorporating non-natural dNTPs, due to their low fidelity and loose active site, but are limited by poor processivity and activity. In this study, the binding between Dbh and DNA was investigated to better understand how to rationally design enhanced processivity in a Y-family pol...
July 6, 2017: Scientific Reports
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