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Bounded rationality

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https://www.readbyqxmd.com/read/27908829/exploring-the-binding-mechanism-of-heteroaryldihydropyrimidines-and-hepatitis-b-virus-capsid-combined-3d-qsar-and-molecular-dynamics
#1
Jing Tu, Jiao Jiao Li, Zhi Jie Shan, Hong Lin Zhai
The non-nucleoside drugs have been developed to treat HBV infection owing to their increased efficacy and lesser side effects, in which heteroaryldihydropyrimidines (HAPs) have been identified as effective inhibitors of HBV capsid. In this paper, the binding mechanism of HAPs targeting on HBV capsid protein was explored through three-dimensional quantitative structure-activity relationship, molecular dynamics and binding free energy decompositions. The obtained models of comparative molecular field analysis and comparative molecular similarity indices analysis enable the sufficient interpretation of structure-activity relationship of HAPs-HBV...
November 28, 2016: Antiviral Research
https://www.readbyqxmd.com/read/27899452/structural-basis-of-the-oncogenic-interaction-of-phosphatase-prl-1-with-the-magnesium-transporter-cnnm2
#2
Paula Giménez-Mascarell, Iker Oyenarte, Serge Hardy, Tilman Breiderhoff, Marchel Stuiver, Elie Kostantin, Tammo Diercks, Angel L Pey, June Ereño-Orbea, María Luz Martinez-Chantar, Reham Khalaf-Nazzal, Félix Claverie-Martín, Dominik Müller, Michel L Tremblay, Luis Alfonso Martínez-Cruz
Phosphatases of regenerating liver (PRLs), the most oncogenic of all protein tyrosine phosphatases (PTPs), play a critical role in metastatic progression of cancers. Recent findings established a new paradigm by uncovering that their association with magnesium transporters of the Cyclin M (CNNM) family causes intracellular magnesium levels that promotes oncogenic transformation. On the other hand, it has recently been highlighted essential roles of the CNNM family in regulation of the circadian rhythm, and reproduction...
November 29, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27893160/integrating-household-risk-mitigation-behavior-in-flood-risk-analysis-an-agent-based-model-approach
#3
Toon Haer, W J Wouter Botzen, Hans de Moel, Jeroen C J H Aerts
Recent studies showed that climate change and socioeconomic trends are expected to increase flood risks in many regions. However, in these studies, human behavior is commonly assumed to be constant, which neglects interaction and feedback loops between human and environmental systems. This neglect of human adaptation leads to a misrepresentation of flood risk. This article presents an agent-based model that incorporates human decision making in flood risk analysis. In particular, household investments in loss-reducing measures are examined under three economic decision models: (1) expected utility theory, which is the traditional economic model of rational agents; (2) prospect theory, which takes account of bounded rationality; and (3) a prospect theory model, which accounts for changing risk perceptions and social interactions through a process of Bayesian updating...
November 28, 2016: Risk Analysis: An Official Publication of the Society for Risk Analysis
https://www.readbyqxmd.com/read/27881238/rational-identification-of-natural-organic-compounds-to-target-the-intermolecular-interaction-between-foxm-and-dna-in-colorectal-cancer
#4
Chunling Dong, Peng Yan, Juxun Wang, Hailian Mu, Shuli Wang, Fangchun Guo
The oncogenic transcription factor forkhead box M (Foxm) is overexpressed in human colorectal cancer (CRC). Targeting the protein interaction with its cognate DNA has been established as an attractive approach to anti-CRC chemotherapy. State-of-the-art molecular dynamics (MD) simulations revealed that the Foxm adopts considerably different conformations to interact with and without its DNA partner; the holo conformation is tightly packed as a typical globulin configuration, whereas the apo form is locally unstructured that exhibits intrinsic disorder in DNA recognition helix, indicating that DNA binding can help the Foxm refolding...
November 9, 2016: Bioorganic Chemistry
https://www.readbyqxmd.com/read/27877103/neural-underpinnings-of-decision-strategy-selection-a-review-and-a-theoretical-model
#5
Szymon Wichary, Tomasz Smolen
In multi-attribute choice, decision makers use decision strategies to arrive at the final choice. What are the neural mechanisms underlying decision strategy selection? The first goal of this paper is to provide a literature review on the neural underpinnings and cognitive models of decision strategy selection and thus set the stage for a neurocognitive model of this process. The second goal is to outline such a unifying, mechanistic model that can explain the impact of noncognitive factors (e.g., affect, stress) on strategy selection...
2016: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/27872191/structural-and-biochemical-analyses-reveal-the-mechanism-of-glutathione-s-transferase-pi-1-inhibition-by-the-anti-cancer-compound-piperlongumine
#6
Wayne Harshbarger, Sudershan Gondi, Scott B Ficarro, John Hunter, Durga Udayakumar, Deepak Gurbani, William Singer, Yan Liu, Lianbo Li, Jarrod A Marto, Kenneth D Westover
Glutathione S-transferase pi 1 (GSTP1), is frequently overexpressed in cancerous tumors and is a putative target of the plant compound piperlongumine (PL), which contains two reactive olefins and inhibits proliferation in cancer cells but not normal cells. PL exposure of cancer cells results in increased reactive oxygen species and decreased glutathione (GSH). This data in tandem with other information led to the conclusion that PL inhibits GSTP1, which forms covalent bonds between GSH and various electrophilic compounds, through covalent adduct formation at PLs C7-C8 olefin, while PLs C2-C3 olefin was postulated to react with GSH...
November 21, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27851940/a-coiled-coil-peptide-shaping-lipid-bilayers-upon-fusion
#7
Martin Rabe, Christopher Aisenbrey, Kristyna Pluhackova, Vincent de Wert, Aimee L Boyle, Didjay F Bruggeman, Sonja A Kirsch, Rainer A Böckmann, Alexander Kros, Jan Raap, Burkhard Bechinger
A system based on two designed peptides, namely the cationic peptide K, (KIAALKE)3, and its complementary anionic counterpart called peptide E, (EIAALEK)3, has been used as a minimal model for membrane fusion, inspired by SNARE proteins. Although the fact that docking of separate vesicle populations via the formation of a dimeric E/K coiled-coil complex can be rationalized, the reasons for the peptides promoting fusion of vesicles cannot be fully explained. Therefore it is of significant interest to determine how the peptides aid in overcoming energetic barriers during lipid rearrangements leading to fusion...
November 15, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27832071/approach-induced-biases-in-human-information-sampling
#8
Laurence T Hunt, Robb B Rutledge, W M Nishantha Malalasekera, Steven W Kennerley, Raymond J Dolan
Information sampling is often biased towards seeking evidence that confirms one's prior beliefs. Despite such biases being a pervasive feature of human behavior, their underlying causes remain unclear. Many accounts of these biases appeal to limitations of human hypothesis testing and cognition, de facto evoking notions of bounded rationality, but neglect more basic aspects of behavioral control. Here, we investigated a potential role for Pavlovian approach in biasing which information humans will choose to sample...
November 2016: PLoS Biology
https://www.readbyqxmd.com/read/27816496/advanced-endoscopy-imaging-in-inflammatory-bowel-diseases
#9
REVIEW
Ralf Kiesslich, Markus F Neurath
BACKGROUND AND AIMS: Rapid assessment of mucosal inflammation is of crucial importance for the initial diagnosis and the assessment of mucosal healing in inflammatory bowel diseases (IBD). Moreover, the identification of intraepithelial neoplasias in IBD is of key relevance for clinical management. Here, we systematically analyzed the utility of advanced endoscopic imaging techniques for optimized diagnosis in IBD. METHODS: PubMed/Medline, Web of Knowledge and Cochrane library were searched twice for diagnostic studies on advanced endoscopic imaging in IBD...
November 2, 2016: Gastrointestinal Endoscopy
https://www.readbyqxmd.com/read/27793987/the-amino-terminal-domain-of-the-androgen-receptor-co-opts-erk-docking-sites-in-elk1-to-induce-sustained-gene-activation-that-supports-prostate-cancer-cell-growth
#10
Rayna Rosati, Mugdha Patki, Venkatesh Chari, Selvakumar Dakshnamurthy, Thomas McFall, Janice Saxton, Benjamin L Kidder, Peter E Shaw, Manohar Ratnam
The ETS domain transcription factor ELK1 is in a repressive association with growth genes and is transiently activated through phosphorylation by ERK1/2. In prostate cancer (PCa) cells the androgen receptor (AR) is recruited by ELK1, via its amino-terminal domain (A/B), as a transcriptional co-activator, without ELK1 hyper-phosphorylation. Here we elucidate the structural basis of the interaction of AR with ELK1. The ELK1 polypeptide motifs required for co-activation by AR vs. those required for activation of ELK1 by ERK were systematically mapped using a mammalian two-hybrid system and confirmed using a co-immunoprecipitation assay...
October 28, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27791120/structural-flexibility-at-a-major-conserved-antibody-target-on-hepatitis-c-virus-e2-antigen
#11
Leopold Kong, David E Lee, Rameshwar U Kadam, Tong Liu, Erick Giang, Travis Nieusma, Fernando Garces, Netanel Tzarum, Virgil L Woods, Andrew B Ward, Sheng Li, Ian A Wilson, Mansun Law
Hepatitis C virus (HCV) is a major cause of liver disease, affecting over 2% of the world's population. The HCV envelope glycoproteins E1 and E2 mediate viral entry, with E2 being the main target of neutralizing antibody responses. Structural investigations of E2 have produced templates for vaccine design, including the conserved CD81 receptor-binding site (CD81bs) that is a key target of broadly neutralizing antibodies (bNAbs). Unfortunately, immunization with recombinant E2 and E1E2 rarely elicits sufficient levels of bNAbs for protection...
October 24, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27790811/influence-of-label-and-charge-density-on-the-association-of-the-therapeutic-monoclonal-antibodies-trastuzumab-and-cetuximab-conjugated-to-anionic-fluorophores
#12
Jutta Pauli, Marieke Pochstein, Andrea Haase, Joanna Napp, Andreas Luch, Ute Resch-Genger
The design of bright and functional dye-protein conjugates requires hydrophilic and stable fluorophores with high molar absorption coefficients and high fluorescence quantum yields, which must not be prone to dimerization, as well as conservation of protein function and suppression of protein association. Although many synthetic dyes meet these needs, the influence of dye charge on bioconjugate performance is commonly neglected. This encouraged us to assess the spectroscopic properties, antibody functionality, binding behavior, folding, and association of conjugates of the therapeutic antibodies trastuzumab and cetuximab with the red cyanine dyes S0586, S2381, and 6SIDCC (bearing two, three, and six sulfonate groups, respectively)...
October 28, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27790627/microarray-screening-of-guillain-barr%C3%A3-syndrome-sera-for-antibodies-to-glycolipid-complexes
#13
Susan K Halstead, Gabriela Kalna, Mohammad B Islam, Israt Jahan, Quazi D Mohammad, Bart C Jacobs, Hubert P Endtz, Zhahirul Islam, Hugh J Willison
OBJECTIVE: To characterize the patterns of autoantibodies to glycolipid complexes in a large cohort of Guillain-Barré syndrome (GBS) and control samples collected in Bangladesh using a newly developed microarray technique. METHODS: Twelve commonly studied glycolipids and lipids, plus their 66 possible heteromeric complexes, totaling 78 antigens, were applied to polyvinylidene fluoride-coated slides using a microarray printer. Arrays were probed with 266 GBS and 579 control sera (2 μL per serum, diluted 1/50) and bound immunoglobulin G detected with secondary antibody...
December 2016: Neurology® Neuroimmunology & Neuroinflammation
https://www.readbyqxmd.com/read/27788161/fabrication-of-co-mn-3o4-rgo-composite-for-lithium-ion-battery-anode-by-a-one-step-hydrothermal-process-with-h2o2-as-additive
#14
Zuohua Li, Yanhui Cui, Jun Chen, Lianlin Deng, Junwei Wu
Binary transition metal oxides have been regarded as one of the most promising candidates for high-performance electrodes in energy storage devices, since they can offer high electrochemical activity and high capacity. Rational designing nanosized metal oxide/carbon composite architectures has been proven to be an effective way to improve the electrochemical performance. In this work, the (Co,Mn)3O4 spinel was synthesized and anchored on reduced graphene oxide (rGO) nanosheets using a facile and single hydrothermal step with H2O2 as additive, no further additional calcination required...
2016: PloS One
https://www.readbyqxmd.com/read/27777586/structural-stability-transitions-and-interactions-within-soxyzcd-thiosulphate-from-sulfurimonas-denitrificans-an-in-silico-molecular-outlook-for-maintaining-environmental-sulphur-cycle
#15
Sujay Ray, Arundhati Banerjee
Thiosulphate oxidation (an essential mechanism) serves to maintain the global sulphur cycle. Earlier experimental and computational studies dealt with environmental thiosulphate oxidation but none dealt with thiosulphate oxidation from deep ocean belts. Wet-laboratory experimental research shows that epsilon-proteobacteria Sulfurimonas denitrificans possess sox (sulphur-oxidizing) operon and perform thiosulphate oxidation efficiently underneath the oceans. From this specific sox operon, SoxCD complex recycles the thiosulphate-bound SoxY from SoxYZ complex to balance the environmental sulphur cycle...
2016: Journal of Biophysics
https://www.readbyqxmd.com/read/27770412/lipase-activation-and-stabilization-in-room-temperature-ionic-liquids
#16
Joel L Kaar
Widespread interest in the use of room-temperature ionic liquids (RTILs) as solvents in anhydrous biocatalytic reactions has largely been met with underwhelming results. Enzymes are frequently inactivated in RTILs as a result of the influence of solvent on the enzyme's microenvironment, be it through interacting with the enzyme or enzyme-bound water molecules. The purpose of this chapter is to present a rational approach to mediate RTIL-enzyme interactions, which is essential if we are to realize the advantages of RTILs over conventional solvents for biocatalysis in full...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27767076/direct-and-indirect-mechanisms-of-klk4-inhibition-revealed-by-structure-and-dynamics
#17
Blake T Riley, Olga Ilyichova, Mauricio G S Costa, Benjamin T Porebski, Simon J de Veer, Joakim E Swedberg, Itamar Kass, Jonathan M Harris, David E Hoke, Ashley M Buckle
The kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (~1 Å) resolution, as well as with bound nickel...
October 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27762089/improvement-of-ligand-affinity-and-thermodynamic-properties-by-nmr-based-evaluation-of-local-dynamics-and-surface-complementarity-in-the-receptor-bound-state
#18
Yumiko Mizukoshi, Koh Takeuchi, Misa Arutaki, Yuji Tokunaga, Takeshi Takizawa, Hiroyuki Hanzawa, Ichio Shimada
The thermodynamic properties of a ligand in the bound state affect its binding specificity. Strict binding specificity can be achieved by introducing multiple spatially defined interactions, such as hydrogen bonds and van der Waals interactions, into the ligand-receptor interface. These introduced interactions are characterized by restricted local dynamics and improved surface complementarity in the bound state. In this study, we experimentally evaluated the local dynamics and the surface complementarity of weak-affinity ligands in the receptor-bound state by forbidden coherence transfer analysis in free-bound exchange systems (Ex-FCT), using the interaction between a ligand, a myocyte-enhancer factor 2A (MEF2A) docking peptide, and a receptor, p38α, as a model system...
November 14, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27746512/looking-across-and-looking-beyond-the-knowledge-frontier-intellectual-distance-novelty-and-resource-allocation-in-science
#19
Kevin J Boudreau, Eva C Guinan, Karim R Lakhani, Christoph Riedl
Selecting among alternative projects is a core management task in all innovating organizations. In this paper, we focus on the evaluation of frontier scientific research projects. We argue that the "intellectual distance" between the knowledge embodied in research proposals and an evaluator's own expertise systematically relates to the evaluations given. To estimate relationships, we designed and executed a grant proposal process at a leading research university in which we randomized the assignment of evaluators and proposals to generate 2,130 evaluator-proposal pairs...
October 2016: Management Science
https://www.readbyqxmd.com/read/27746191/in-silico-analysis-of-the-binding-of-anthelmintics-to-caenorhabditis-elegansp-glycoprotein-1
#20
Marion A David, Stéphane Orlowski, Roger K Prichard, Shaima Hashem, François André, Anne Lespine
Macrocyclic lactones (ML) are important anthelmintics used in animals and humans against parasite nematodes, but their therapeutic success is compromised by the spread of ML resistance. Some ABC transporters, such as p-glycoproteins (Pgps), are selected and overexpressed in ML-resistant nematodes, supporting a role for some drug efflux proteins in ML resistance. However, the role of such proteins in ML transport remains to be clarified at the molecular level. Recently, Caenorhabditis elegans Pgp-1 (Cel-Pgp-1) has been crystallized, and its drug-modulated ATPase function characterized in vitro revealed Cel-Pgp-1 as a multidrug transporter...
September 15, 2016: International Journal for Parasitology, Drugs and Drug Resistance
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