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https://www.readbyqxmd.com/read/28524918/urotensin-ii-peptidomimetic-incorporating-a-non-reducible-1-5-triazole-disulfide-bond-reveals-a-pseudo-irreversible-covalent-binding-mechanism-to-the-urotensin-g-protein-coupled-receptor
#1
Salvatore Pacifico, Aidan Kerckhoffs, Andrew J Fallow, Rachel E Foreman, Remo Guerrini, John McDonald, David G Lambert, Andrew G Jamieson
The urotensin-II receptor (UTR) is a class A GPCR that predominantly binds to the pleiotropic cyclic peptide urotensin-II (U-II). U-II is constrained by a disulfide bridge that induces a β-turn structure and binds pseudo-irreversibly to UTR and is believed to result in a structural rearrangement of the receptor. However, it is not well understood how U-II binds pseudo-irreversibly and the nature of the reorganization of the receptor that results in G-protein activation. Here we describe a series of U-II peptidomimetics incorporating a non-reducible disulfide bond structural surrogate to investigate the feasibility that native U-II binds to the G protein-coupled receptor through disulfide bond shuffling as a mechanism of covalent interaction...
May 19, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28524201/a-computational-framework-for-distinguishing-direct-versus-indirect-interactions-in-human-functional-protein-protein-interaction-networks
#2
Suyu Mei, Erik K Flemington, Kun Zhang
Recognition of indirect interactions is instrumental to in silico reconstruction of signaling pathways and sheds light on the exploration of unknown physical paths between two indirectly interacting genes. However, very limited computational methods have explicitly exploited the indirect interactions with experimental evidence thus far. In this work, we attempt to distinguish direct versus indirect interactions in human functional protein-protein interaction (PPI) networks via a predictive l2-regularized logistic regression model built on the experimental data...
May 19, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28521203/3d-full-field-quantification-of-cell-induced-large-deformations-in-fibrillar-biomaterials-by-combining-non-rigid-image-registration-with-label-free-second-harmonic-generation
#3
Alvaro Jorge-Peñas, Hannelore Bové, Kathleen Sanen, Marie-Mo Vaeyens, Christian Steuwe, Maarten Roeffaers, Marcel Ameloot, Hans Van Oosterwyck
To advance our current understanding of cell-matrix mechanics and its importance for biomaterials development, advanced three-dimensional (3D) measurement techniques are necessary. Cell-induced deformations of the surrounding matrix are commonly derived from the displacement of embedded fiducial markers, as part of traction force microscopy (TFM) procedures. However, these fluorescent markers may alter the mechanical properties of the matrix or can be taken up by the embedded cells, and therefore influence cellular behavior and fate...
May 10, 2017: Biomaterials
https://www.readbyqxmd.com/read/28520105/large-scale-computational-models-of-liver-metabolism-how-far-from-the-clinics
#4
REVIEW
Tanja Cvitanović, Matthias C Reichert, Miha Moškon, Miha Mraz, Frank Lammert, Damjana Rozman
Understanding the dynamics of human liver metabolism is fundamental for effective diagnosis and treatment of liver diseases in general and the metabolism of drugs in particular. This knowledge can be obtained with systems biology/medicine approaches that account for the complexity of hepatic responses and their systemic consequences in other organs. Computational modelling can reveal hidden principles of the system by classification of individual components, analysing their interactions and simulating the effects that are difficult to investigate experimentally...
May 18, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28516454/a-multiscale-computational-modelling-approach-predicts-mechanisms-of-female-sex-risk-in-the-setting-of-arousal-induced-arrhythmias
#5
Pei-Chi Yang, Laura L Perissinotti, Fernando López-Redondo, Yibo Wang, Kevin R DeMarco, Mao-Tsuen Jeng, Igor Vorobyov, Robert D Harvey, Junko Kurokawa, Sergei Y Noskov, Colleen E Clancy
Female sex is a risk factor for inherited and acquired Long-QT associated Torsade de Pointes (TdP) arrhythmias, and sympathetic discharge is a major factor in triggering TdP in female Long-QT syndrome patients. We used a combined experimental and computational approach to predict 'the perfect storm' of hormone concentration, IKr block, and sympathetic stimulation that induces arrhythmia in females with inherited and acquired Long-QT. More specifically, we developed mathematical models of acquired and inherited Long-QT syndrome in male and female ventricular human myocytes by combining effects of a hormone and a hERG blocker dofetilide or hERG mutations...
May 18, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28515901/experimental-identification-and-computational-characterization-of-a-novel-extracellular-metalloproteinase-produced-by-clostridium-sordellii
#6
Michael J Aldape, Aoxiang Tao, Dustin D Heeney, Eric R McIndoo, John M French, Dong Xu
Clostridium sordellii is a lethal pathogen for both animals and humans. Severe capillary leakage, toxic shock syndrome, and an extreme leukemoid reaction (LR), are hallmark features of C. sordellii infections and contribute to its high mortality rate. Here we report the discovery of a previously unknown and uncharacterized metalloproteinase of C. sordellii (referred as Mcs1) that cleaves human vascular cell adhesion molecule (VCAM)-1 in vitro, an adhesion molecule critical to hematopoietic precursor retention and leukocyte diapedesis...
March 2, 2017: RSC Advances
https://www.readbyqxmd.com/read/28515787/a-computational-approach-for-the-functional-classification-of-the-epigenome
#7
Francesco Gandolfi, Anna Tramontano
BACKGROUND: In the last decade, advanced functional genomics approaches and deep sequencing have allowed large-scale mapping of histone modifications and other epigenetic marks, highlighting functional relationships between chromatin organization and genome function. Here, we propose a novel approach to explore functional interactions between different epigenetic modifications and extract combinatorial profiles that can be used to annotate the chromatin in a finite number of functional classes...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28511665/clone-temporal-centrality-measures-for-incomplete-sequences-of-graph-snapshots
#8
Moritz Hanke, Ronja Foraita
BACKGROUND: Different phenomena like the spread of a disease, social interactions or the biological relation between genes can be thought of as dynamic networks. These can be represented as a sequence of static graphs (so called graph snapshots). Based on this graph sequences, classical vertex centrality measures like closeness and betweenness centrality have been extended to quantify the importance of single vertices within a dynamic network. An implicit assumption for the calculation of temporal centrality measures is that the graph sequence contains all information about the network dynamics over time...
May 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28511148/computational-studies-of-membrane-proteins-from-sequence-to-structure-to-simulation
#9
REVIEW
Phillip J Stansfeld
In this review, I discuss the recent advances in computational approaches to studying membrane protein structures, covering the latest methods for predicting a protein structure from its amino acid sequence, through to methods for assessing the structural dynamics and lipid interactions within molecular simulations of complex biological membranes. These approaches have not only benefited from advances in the computational software and architectures, but have also been assisted by a prodigious rise in the number of both the molecular sequences and experimentally determined membrane protein structures...
May 13, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28509865/detecting-and-classifying-human-touches-in-a-social-robot-through-acoustic-sensing-and-machine-learning
#10
Fernando Alonso-Martín, Juan José Gamboa-Montero, José Carlos Castillo, Álvaro Castro-González, Miguel Ángel Salichs
An important aspect in Human-Robot Interaction is responding to different kinds of touch stimuli. To date, several technologies have been explored to determine how a touch is perceived by a social robot, usually placing a large number of sensors throughout the robot's shell. In this work, we introduce a novel approach, where the audio acquired from contact microphones located in the robot's shell is processed using machine learning techniques to distinguish between different types of touches. The system is able to determine when the robot is touched (touch detection), and to ascertain the kind of touch performed among a set of possibilities: stroke, tap, slap, and tickle (touch classification)...
May 16, 2017: Sensors
https://www.readbyqxmd.com/read/28509533/a-low-cost-label-free-biosensing-bimetallic-cellulose-strip-with-silar-synthesized-silver-core-gold-shell-nanoparticle-structures
#11
Wansun Kim, Jae-Chul Lee, Gi-Ja Lee, Hun-Kuk Park, Anbok Lee, Samjin Choi
We introduce a label-free biosensing cellulose strip sensor with surface-enhanced Raman spectroscopy (SERS)-encoded bimetallic core@shell nanoparticles. Bimetallic nanoparticles consisting of a synthesis of core Ag nanoparticles (AgNP) and a synthesis of shell gold nanoparticles (AuNPs) were fabricated on a cellulose substrate by two-stage successive ionic layer absorption and reaction (SILAR) techniques. The bimetallic nanoparticle-enhanced localized surface plasmon resonance (LSPR) effects were theoretically verified by computational calculations with finite element models of optimized bimetallic nanoparticles interacting with an incident laser source...
May 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28507154/information-socialtaxis-and-efficient-collective-behavior-emerging-in-groups-of-information-seeking-agents
#12
Ehud D Karpas, Adi Shklarsh, Elad Schneidman
Individual behavior, in biology, economics, and computer science, is often described in terms of balancing exploration and exploitation. Foraging has been a canonical setting for studying reward seeking and information gathering, from bacteria to humans, mostly focusing on individual behavior. Inspired by the gradient-climbing nature of chemotaxis, the infotaxis algorithm showed that locally maximizing the expected information gain leads to efficient and ethological individual foraging. In nature, as well as in theoretical settings, conspecifics can be a valuable source of information about the environment...
May 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28506700/synergistic-antimutagenic-effect-of-isothiocyanates-against-varied-mutagens
#13
Geetanjali Rampal, Tarunpreet Singh Thind, Rohit Arora, Adarsh Pal Vig, Saroj Arora
Although plant foods provide an array of nutrients in the human diet, our knowledge of how these nutrients are interacting among each other, at molecular level, is limited. Among these, glucosinolates are the most important secondary metabolites, which are readily hydrolyzed to a variety of products including isothiocyanates. The current study emphasizes on the antimutagenic potential of three isothiocyanates (ITCs) viz. allyl, benzyl and 3-butenyl ITCs (individually and in binary combinations) in Ames Salmonella histidine reversion assay using S...
May 12, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28504943/towards-multimodal-human-robot-interaction-to-enhance-active-participation-of-users-in-gait-rehabilitation
#14
Kai Gui, Honghai Liu, Dingguo Zhang
Robotic exoskeletons for physical rehabilitation have been utilized for retraining patients suffering from paraplegia and enhancing motor recovery in recent years. However, users are not voluntarily involved in most systems. This work aims to develop a locomotion trainer with multiple gait patterns, which can be controlled by the active motion intention of users. A multimodal human-robot interaction (HRI) system is established to enhance subject's active participation during gait rehabilitation, which includes cognitive human-robot interaction (cHRI) and physical human-robot interaction (pHRI)...
May 11, 2017: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/28504004/experimental-and-computational-studies-on-the-binding-of-diazinon-to-human-serum-albumin
#15
Fataneh Jafari, Setareh Samadi, Amin Nowroozi, Komail Sadrjavadi, Sajad Moradi, Mohammad Reza Ashrafi-Kooshk, Mohsen Shahlaei
In the present research, the binding properties of Diazinon (DZN), as an organophosphorus herbicide, to human serum albumin (HSA) were investigated using combination of spectroscopic, electrochemistry and molecular modeling techniques. Changes in the UV-Vis and FT-IR spectra were observed upon ligand binding along with a significant degree of tryptophan fluorescence quenching on complex formation. The obtained results from spectroscopic and electrochemistry experiments along with the computational studies suggest that DZN binds to residues located in subdomains IIA of HSA with binding constant about 1410...
May 15, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28503145/a-neural-dynamic-architecture-for-concurrent-estimation-of-object-pose-and-identity
#16
Oliver Lomp, Christian Faubel, Gregor Schöner
Handling objects or interacting with a human user about objects on a shared tabletop requires that objects be identified after learning from a small number of views and that object pose be estimated. We present a neurally inspired architecture that learns object instances by storing features extracted from a single view of each object. Input features are color and edge histograms from a localized area that is updated during processing. The system finds the best-matching view for the object in a novel input image while concurrently estimating the object's pose, aligning the learned view with current input...
2017: Frontiers in Neurorobotics
https://www.readbyqxmd.com/read/28499419/across-proteome-modeling-of-dimer-structures-for-the-bottom-up-assembly-of-protein-protein-interaction-networks
#17
Surabhi Maheshwari, Michal Brylinski
BACKGROUND: Deciphering complete networks of interactions between proteins is the key to comprehend cellular regulatory mechanisms. A significant effort has been devoted to expanding the coverage of the proteome-wide interaction space at molecular level. Although a growing body of research shows that protein docking can, in principle, be used to predict biologically relevant interactions, the accuracy of the across-proteome identification of interacting partners and the selection of near-native complex structures still need to be improved...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28498321/bdnf-binds-its-pro-peptide-with-high-affinity-and-the-common-val66met-polymorphism-attenuates-the-interaction
#18
Koichi Uegaki, Haruko Kumanogoh, Toshiyuki Mizui, Takatsugu Hirokawa, Yasuyuki Ishikawa, Masami Kojima
Most growth factors are initially synthesized as precursors then cleaved into bioactive mature domains and pro-domains, but the biological roles of pro-domains are poorly understood. In the present study, we investigated the pro-domain (or pro-peptide) of brain-derived neurotrophic factor (BDNF), which promotes neuronal survival, differentiation and synaptic plasticity. The BDNF pro-peptide is a post-processing product of the precursor BDNF. Using surface plasmon resonance and biochemical experiments, we first demonstrated that the BDNF pro-peptide binds to mature BDNF with high affinity, but not other neurotrophins...
May 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28494725/computational-methods-for-predicting-ncrna-protein-interactions
#19
Shao-Wu Zhang, Xiao-Nan Fan
BACKGROUND: RNA-protein interactions (RPIs) play an important role in many cellular processes. In particular, noncoding RNA-protein interactions (ncRPIs) are involved in various gene regulations and human complex diseases. High-throughput experiments have provided a large number of valuable information about ncRPIs, but these experiments are expensive and time-consuming. Therefore, some computational approaches have been developed to predict ncRPIs efficiently and effectively. METHODS: In this work, we will describe the recent advance of predicting ncRPIs from the following aspects: i) the dataset construction; ii) the sequence and structural feature representation, and iii) the machine learning algorithm...
May 9, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28490417/accelerating-digital-mental-health-research-from-early-design-and-creation-to-successful-implementation-and-sustainment
#20
David C Mohr, Aaron R Lyon, Emily G Lattie, Madhu Reddy, Stephen M Schueller
Mental health problems are common and pose a tremendous societal burden in terms of cost, morbidity, quality of life, and mortality. The great majority of people experience barriers that prevent access to treatment, aggravated by a lack of mental health specialists. Digital mental health is potentially useful in meeting the treatment needs of large numbers of people. A growing number of efficacy trials have shown strong outcomes for digital mental health treatments. Yet despite their positive findings, there are very few examples of successful implementations and many failures...
May 10, 2017: Journal of Medical Internet Research
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