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Bounded rationality

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https://www.readbyqxmd.com/read/28636281/aryl-and-heteroaryl-substituted-phenylalanines-as-ampa-receptor-ligands
#1
Ewa Szymańska, Paulina Chałupnik, Tommy N Johansen, Birgitte Nielsen, Ana Maria Cuñado Moral, Darryl S Pickering, Anna Więckowska, Katarzyna Kieć-Kononowicz
A series of racemic unnatural amino acids was rationally designed on the basis of recently published X-ray structures of the GluA2 LBD with bound phenylalanine-based antagonists. Twelve new diaryl- or aryl/heteroaryl-substituted phenylalanine derivatives were synthesized and evaluated in vitro in radioligand binding assays at native rat ionotropic glutamate receptors. The most interesting compound in this series, (RS)-2-amino-3-(3'-hydroxy-5-(1H-pyrazol-4-yl)-[1,1'-biphenyl]-3-yl)propanoic acid 7e, showed the binding affinity of 4...
June 21, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28628309/dissecting-orthosteric-contacts-for-a-reverse-fragment-based-ligand-design
#2
Arun Chandramohan, Nikhil Kumar Tulsian, Ganesh Srinivasan Anand
Orthosteric sites on proteins are formed typically from non-contiguous interacting sites in three dimensional space where the composite binding interaction of a biological ligand is mediated by multiple synergistic interactions of its constituent functional groups. Through these multiple interactions, ligands stabilize both the ligand binding site and the protein fold. However, relative energetic contributions of the individual contacts in these protein-ligand interactions are difficult to resolve. Deconvolution of the contributions of these various functional groups in natural inhibitors/ligand would greatly aid in iterative fragment-based drug discovery (FBDD)...
June 19, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28626916/unexpected-functions-of-angiotensin-converting-enzyme-beyond-its-enzymatic-activity
#3
REVIEW
Jean Martinez
Angiotensin converting enzyme (ACE) is a well-known enzyme, largely studied for its action on hypertension, as it produces angiotensin II from angiotensin I. This paper describes two original behaviours of ACE. We showed that ACE could hydrolyse gastrin, a neuropeptide from the gastrointestinal tract, releasing the C-terminal amidated dipeptide H-Asp-Phe-NH2 . This dipeptide is believed to be involved in the gastrin-induced acid secretion in the stomach. This hypothetic mechanism of action of gastrin resulted in a strategy to rationally design gastrin receptor antagonists...
June 19, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28606198/clinical-information-transfer-between-ems-staff-and-emergency-medicine-assistants-during-handover-of-trauma-patients
#4
Seyedeh Almas Fahim Yegane, Ali Shahrami, Hamid Reza Hatamabadi, Seyed-Mostafa Hosseini-Zijoud
Introduction Clinical handover by Emergency Medical Services (EMS) staff, as the first people who have contact with trauma patients, in the emergency department (ED), is very important. Therefore, effective communication to transfer clinical information about patients in a concise, rational, clear, and time-bound manner is essential. In Iran, the transfer of necessary information in clinical handover in EDs was carried out orally and without following standard instructions. This study aimed to audit the current clinical handover according to the Identify, Situation, Background, Assessment, and Recommendation (ISBAR) tool and survey the effect of training the ISBAR tool to Emergency Medicine Assistants (EMAs) and EMS staff on improvement of the clinical handover of patients to the ED...
June 13, 2017: Prehospital and Disaster Medicine
https://www.readbyqxmd.com/read/28601112/the-role-of-dysfunctional-myths-in-a-decision-making-process-under-bounded-rationality-a-complex-dynamical-systems-perspective
#5
Dimitrios Stamovlasis, Julie Vaiopoulou
The present study examines the factors influencing a decision-making process, with specific focus on the role of dysfunctional myths (DM). DM are thoughts or beliefs that are rather irrational, however influential to people's decisions. In this paper a decision-making process regarding the career choice of university students majoring in natural sciences and education (N=496) is examined by analyzing survey data taken via Career Decision Making Difficulties Questionnaire (CDDQ). The difficulty of making the choice and the certainty about one's decision were the state variables, while the independent variables were factors related to the lack of information or knowledge needed, which actually reflect a bounded rationality...
July 2017: Nonlinear Dynamics, Psychology, and Life Sciences
https://www.readbyqxmd.com/read/28587923/generation-and-validation-of-intracellular-ubiquitin-variant-inhibitors-for-usp7-and-usp10
#6
Wei Zhang, Maria A Sartori, Taras Makhnevych, Kelly E Federowicz, Xiaohui Dong, Li Liu, Satra Nim, Aiping Dong, Jingsong Yang, Yanjun Li, Dania Haddad, Andreas Ernst, Dirk Heerding, Yufeng Tong, Jason Moffat, Sachdev S Sidhu
Post-translational modification of the p53 signaling pathway plays an important role in cell cycle progression and stress-induced apoptosis. Indeed, a large body of work has shown that dysregulation of p53 and its E3 ligase MDM2 by the ubiquitin-proteasome system (UPS) promotes carcinogenesis and malignant transformation. Thus, drug discovery efforts have focused on the restoration of wild-type p53 activity or inactivation of oncogenic mutant p53 by targeted inhibition of UPS components, particularly key deubiquitinases (DUBs) of the ubiquitin-specific protease (USP) class...
June 3, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28578565/conditional-network-assembly-and-targeted-protein-retention-via-environmentally-responsive-engineered-%C3%AE-roll-peptides
#7
Beyza Bulutoglu, Sarah J Yang, Scott Banta
Stimulus-responsive biomaterials have applications in many areas of biotechnology, such as tissue engineering, drug delivery, and bioelectrocatalysis. The intrinsically disordered repeat-in-toxin (RTX) domain is a conformationally dynamic peptide that gains β-roll secondary structure when bound to calcium ions. A smart hydrogel platform was constructed by genetically fusing two rationally designed mutant RTX domains: first, a mutant peptide with hydrophobic interfaces capable of calcium-dependent network assembly, and second, another mutant that conditionally binds the model target protein lysozyme...
June 15, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28557467/thanks-coefficient-alpha-we-ll-take-it-from-here
#8
Daniel McNeish
Empirical studies in psychology commonly report Cronbach's alpha as a measure of internal consistency reliability despite the fact that many methodological studies have shown that Cronbach's alpha is riddled with problems stemming from unrealistic assumptions. In many circumstances, violating these assumptions yields estimates of reliability that are too small, making measures look less reliable than they actually are. Although methodological critiques of Cronbach's alpha are being cited with increasing frequency in empirical studies, in this tutorial we discuss how the trend is not necessarily improving methodology used in the literature...
May 29, 2017: Psychological Methods
https://www.readbyqxmd.com/read/28554189/structure-of-the-human-multidrug-transporter-abcg2
#9
Nicholas M I Taylor, Ioannis Manolaridis, Scott M Jackson, Julia Kowal, Henning Stahlberg, Kaspar P Locher
ABCG2 is a constitutively expressed ATP-binding cassette (ABC) transporter that protects many tissues against xenobiotic molecules. Its activity affects the pharmacokinetics of commonly used drugs and limits the delivery of therapeutics into tumour cells, thus contributing to multidrug resistance. Here we present the structure of human ABCG2 determined by cryo-electron microscopy, providing the first high-resolution insight into a human multidrug transporter. We visualize ABCG2 in complex with two antigen-binding fragments of the human-specific, inhibitory antibody 5D3 that recognizes extracellular loops of the transporter...
May 29, 2017: Nature
https://www.readbyqxmd.com/read/28549582/crystal-structure-of-spsb2-in-complex-with-a-rational-designed-rgd-containing-cyclic-peptide-inhibitor-of-spsb2-inos-interaction
#10
Tingting You, Yuhui Wang, Kefa Li, Danting Zhang, Huan Wei, Yanhong Luo, Hua Li, Yongzhi Lu, Xunchen Su, Zhihe Kuang
SPRY domain-containing SOCS box protein 2 (SPSB2) is a negative regulator of inducible nitric oxide synthase (iNOS) that modulates the lifetime of iNOS and thus the levels of nitric oxide (NO) production. Inhibitors that can disrupt the endogenous SPSB2-iNOS interaction and augment NO production have potential as novel antimicrobial and anticancer drugs. In this study, we have designed a cyclic peptide (cR8), containing an RGD motif and the SPSB2 binding motif (DINNNV). ITC and chemical shift perturbation showed that cR8 binds to the iNOS binding site on SPSB2 with a Kd of 671 nM, and saturation transfer difference NMR showed that cR8 binds to αvβ3 integrin-expressing cells...
May 24, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28542609/potent-and-selective-inhibition-of-pathogenic-viruses-by-engineered-ubiquitin-variants
#11
Wei Zhang, Ben A Bailey-Elkin, Robert C M Knaap, Baldeep Khare, Tim J Dalebout, Garrett G Johnson, Puck B van Kasteren, Nigel J McLeish, Jun Gu, Wenguang He, Marjolein Kikkert, Brian L Mark, Sachdev S Sidhu
The recent Middle East respiratory syndrome coronavirus (MERS-CoV), Ebola and Zika virus outbreaks exemplify the continued threat of (re-)emerging viruses to human health, and our inability to rapidly develop effective therapeutic countermeasures. Many viruses, including MERS-CoV and the Crimean-Congo hemorrhagic fever virus (CCHFV) encode deubiquitinating (DUB) enzymes that are critical for viral replication and pathogenicity. They bind and remove ubiquitin (Ub) and interferon stimulated gene 15 (ISG15) from cellular proteins to suppress host antiviral innate immune responses...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28530741/thionine-graphene-oxide-covalent-hybrid-and-its-interaction-with-light
#12
Ewelina Krzyszkowska, Justyna Walkowiak-Kulikowska, Sven Stienen, Aleksandra Wojcik
Graphene oxide sheets (GO) were covalently functionalized with thionine molecules. The obtained hybrid material, Th-GO, was characterized by means of scanning electron microscopy (SEM), Auger electron spectroscopy (AES), Fourier transform infrared spectroscopy (FTIR) and Raman spectroscopy. Subsequently, the interaction of light with the free dye molecules and with dye molecules bound to the graphene oxide sheets was probed via UV-Vis spectroscopy, fluorescence spectroscopy and femtosecond pump-probe spectroscopy...
June 7, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28522117/characterization-of-cu-ii-reconstituted-acc-oxidase-using-experimental-and-theoretical-approaches
#13
Nadia El Bakkali-Tahéri, Sybille Tachon, Maylis Orio, Sylvain Bertaina, Marlène Martinho, Viviane Robert, Marius Réglier, Thierry Tron, Pierre Dorlet, A Jalila Simaan
1-Aminocyclopropane-1-carboxylic acid oxidase (ACCO) is a non heme iron(II) containing enzyme that catalyzes the final step of the ethylene biosynthesis in plants. The iron(II) ion is bound in a facial triad composed of two histidines and one aspartate (H177, D179 and H234). Several active site variants were generated to provide alternate binding motifs and the enzymes were reconstituted with copper(II). Continuous wave (cw) and pulsed Electron Paramagnetic Resonance (EPR) spectroscopies as well as Density Functional Theory (DFT) calculations were performed and models for the copper(II) binding sites were deduced...
June 1, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28511016/structural-and-biochemical-insights-into-dimethylsulfoniopropionate-cleavage-by-cofactor-bound-dddk-from-the-prolific-marine-bacterium-pelagibacter
#14
Nicholas J Schnicker, Saumya M De Silva, Jonathan D Todd, Mishtu Dey
Enormous amounts of the organic osmolyte dimethylsulfoniopropionate (DMSP) are produced in marine environments where bacterial DMSP lyases cleave it, yielding acrylate and the climate-active gas dimethyl sulfide (DMS). SAR11 bacteria are the most abundant clade of heterotrophic bacteria in the oceans and play a key role in DMSP catabolism. An important environmental factor affecting DMS generation via DMSP lyases is the availability of metal ions because they are essential cofactors for many of these enzymes...
May 30, 2017: Biochemistry
https://www.readbyqxmd.com/read/28505196/unveiling-a-novel-transient-druggable-pocket-in-bace-1-through-molecular-simulations-conformational-analysis-and-binding-mode-of-multisite-inhibitors
#15
Ornella Di Pietro, Jordi Juárez-Jiménez, Diego Muñoz-Torrero, Charles A Laughton, F Javier Luque
The critical role of BACE-1 in the formation of neurotoxic ß-amyloid peptides in the brain makes it an attractive target for an efficacious treatment of Alzheimer's disease. However, the development of clinically useful BACE-1 inhibitors has proven to be extremely challenging. In this study we examine the binding mode of a novel potent inhibitor (compound 1, with IC50 80 nM) designed by synergistic combination of two fragments-huprine and rhein-that individually are endowed with very low activity against BACE-1...
2017: PloS One
https://www.readbyqxmd.com/read/28493700/effect-of-fluorination-on-the-competition-of-halogen-bonding-and-hydrogen-bonding-complexes-of-fluoroiodomethane-with-dimethyl-ether-and-trimethylamine
#16
Yannick Geboes, Frank De Proft, Wouter A Herrebout
To further rationalize the competition between halogen and hydrogen bonding, a combined experimental and theoretical study on the weakly bound molecular complexes formed between the combined halogen bond/hydrogen bond donor fluoroiodomethane and the Lewis bases dimethyl ether and trimethylamine (in standard and fully deuterated form) is presented. The experimental data are obtained by recording infrared and Raman spectra of mixtures of the compounds in liquid krypton, at temperatures between 120 and 156 K. The experiments are supported by ab initio calculations at the MP2/aug-cc-pVDZ-PP level, statistical thermodynamics and Monte Carlo free energy perturbation calculations...
May 18, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28488849/solution-conformations-and-dynamics-of-substrate-bound-cytochrome-p450-mycg
#17
Drew R Tietz, Larissa M Podust, David H Sherman, Thomas C Pochapsky
MycG is a P450 monooxygenase that catalyzes the sequential hydroxylation and epoxidation of mycinamicin IV (M-IV), the last two steps in the biosynthesis of mycinamicin II, a macrolide antibiotic isolated from Micromonospora griseorubida. The crystal structure of MycG with M-IV bound was previously determined but showed the bound substrate in an orientation that did not rationalize the observed regiochemistry of M-IV hydroxylation. Nuclear magnetic resonance paramagnetic relaxation enhancements provided evidence of an orientation of M-IV in the MycG active site more compatible with the observed chemistry, but substrate-induced changes in the enzyme structure were not characterized...
May 30, 2017: Biochemistry
https://www.readbyqxmd.com/read/28485587/strategic-design-of-2-2-bipyridine-derivatives-to-modulate-metal-amyloid-%C3%AE-aggregation
#18
Yonghwan Ji, Hyuck Jin Lee, Minjeong Kim, Geewoo Nam, Shin Jung C Lee, Jaeheung Cho, Cheol-Min Park, Mi Hee Lim
The complexity of Alzheimer's disease (AD) stems from the inter-relation of multiple pathological factors upon initiation and progression of the disease. To identify the involvement of metal-bound amyloid-β (metal-Aβ) aggregation in AD pathology, among the pathogenic features found in the AD-affected brain, small molecules as chemical tools capable of controlling metal-Aβ aggregation were developed. Herein, we report a new class of 2,2'-bipyridine (bpy) derivatives (1-4) rationally designed to be chemical modulators toward metal-Aβ aggregation over metal-free Aβ analogue...
May 9, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28484972/radical-generation-from-the-gas-phase-activation-of-ionized-lipid-ozonides
#19
Shane R Ellis, Huong T Pham, Marc In Het Panhuis, Adam J Trevitt, Todd W Mitchell, Stephen J Blanksby
Reaction products from the ozonolysis of unsaturated lipids at gas-liquid interfaces have the potential to significantly influence the chemical and physical properties of organic aerosols in the atmosphere. In this study, the gas-phase dissociation behavior of lipid secondary ozonides is investigated using ion-trap mass spectrometry. Secondary ozonides were formed by reaction between a thin film of unsaturated lipids (fatty acid methyl esters or phospholipids) with ozone before being transferred to the gas phase as [M + Na](+) ions by electrospray ionization...
May 8, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28484952/the-anchoring-bias-reflects-rational-use-of-cognitive-resources
#20
REVIEW
Falk Lieder, Thomas L Griffiths, Quentin J M Huys, Noah D Goodman
Cognitive biases, such as the anchoring bias, pose a serious challenge to rational accounts of human cognition. We investigate whether rational theories can meet this challenge by taking into account the mind's bounded cognitive resources. We asked what reasoning under uncertainty would look like if people made rational use of their finite time and limited cognitive resources. To answer this question, we applied a mathematical theory of bounded rationality to the problem of numerical estimation. Our analysis led to a rational process model that can be interpreted in terms of anchoring-and-adjustment...
May 8, 2017: Psychonomic Bulletin & Review
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