Read by QxMD icon Read

Function* structur* model*

Fumiaki Shima, Hirokazu Narita, Ayami Hiura, Hiroshi Shimoda, Mitsuru Akashi
There is considerable global demand for three-dimensional (3D) functional tissues which mimic our native organs and tissues for use as in vitro drug screening systems and in regenerative medicine. In particular, there has been an increasing number of patients who suffer from arterial diseases such as arteriosclerosis. As such, in vitro 3D arterial wall models that can evaluate the effects of novel medicines and a novel artificial graft for the treatment are required. In our previous study, we reported the rapid construction of 3D tissues by employing a Layer-by-Layer (LbL) technique and revealed their potential applications in the pharmaceutical fields and tissue engineering...
October 25, 2016: Journal of Biomedical Materials Research. Part A
Bethany G Caulkins, Robert P Young, Ryan A Kudla, Chen Yang, Thomas J Bittbauer, Baback Bastin, Eduardo Hilario, Li Fan, Michael J Marsella, Michael F Dunn, Leonard J Mueller
Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5'-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography - the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry - to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established...
October 25, 2016: Journal of the American Chemical Society
Anna Starzyk, Michał Wojciechowski, Marek Cieplak
We perform molecular dynamics simulations for a simple coarse-grained model of a protein placed inside of a softly repulsive sphere of radius R. The protein is surrounded either by a number of same molecules or a number of spherical crowding particles that immitate other biomolecules such as the osmolytes. The two descriptions are shown to lead to distinct results when testing thermal stability as assessed by studying the unfolding times as a function of temperature. We consider three examples of proteins and show that crowding increases the thermal stability provided the inter-protein or protein-crowder interactions are repulsive...
October 25, 2016: Physical Biology
Steven G Thomas, Natalie S Poulter, Danai Bem, Brenda Finney, Laura M Machesky, Stephen P Watson
A dynamic, properly organised actin cytoskeleton is critical for the production and haemostatic function of platelets. The Wiskott Aldrich Syndrome protein (WASp) and Actin-Related Proteins 2 & 3 Complex (Arp2/3 complex) are critical mediators of actin polymerisation and organisation in many cell types. In platelets and megakaryocytes, these proteins have been shown to be important for proper platelet production and function. The cortactin family of proteins (Cttn & HS1) are known to regulate WASp-Arp2/3-mediated actin polymerisation in other cell types and so here we address the role of these proteins in platelets using knockout mouse models...
October 25, 2016: Platelets
P Kovalenko, A T DiCioccio, J D Davis, M Li, M Ardeleanu, Nmh Graham, R Soltys
An exploratory population pharmacokinetic model for functional dupilumab was developed. Data from healthy volunteers and patients with atopic dermatitis (AD) receiving intravenous or subcutaneous doses were integrated. The data included 197 participants (2,518 measurements of dupilumab in serum) from six phase I and II studies. The data were analyzed using stochastic approximation expectation-maximization and importance sampling methods. The best structural model was a two-compartment model with parallel linear and Michaelis-Menten elimination from the central compartment...
October 25, 2016: CPT: Pharmacometrics & Systems Pharmacology
Igor V Tetko, Uko Maran, Alexander Tropsha
Thousands of (Quantitative) Structure-Activity Relationships (Q)SAR models have been described in peer-reviewed publications; however, this way of sharing seldom makes models available for the use by the research community outside of the developer's laboratory. Conversely, on-line models allow broad dissemination and application representing the most effective way of sharing the scientific knowledge. Approaches for sharing and providing on-line access to models range from web services created by individual users and laboratories to integrated modeling environments and model repositories...
October 25, 2016: Molecular Informatics
Phuc Van Pham, Ngoc Bich Vu, Thuy Thi-Thanh Dao, Ha Thi-Ngan Le, Lan Thi Phi, Ngoc Kim Phan
Endothelial progenitor cells (EPCs) play an important role in angiogenesis. However, they exist in limited numbers in the human body. This study was aimed to produce EPCs, for autologous transplantation, using direct reprogramming of skin fibroblasts under GMP-compliant conditions. Fibroblasts were collected and cultured from the skin in DMEM/F12 medium supplemented with 5% activated platelet-rich plasma and 1% antibiotic-antimycotic solution. They were then transfected with mRNA ETV2 and incubated in culture medium under hypoxia (5% oxygen) for 14 d...
October 24, 2016: In Vitro Cellular & Developmental Biology. Animal
Hamidreza Kavianpour, Mahdi Vasighi
Nowadays, having knowledge about cellular attributes of proteins has an important role in pharmacy, medical science and molecular biology. These attributes are closely correlated with the function and three-dimensional structure of proteins. Knowledge of protein structural class is used by various methods for better understanding the protein functionality and folding patterns. Computational methods and intelligence systems can have an important role in performing structural classification of proteins. Most of protein sequences are saved in databanks as characters and strings and a numerical representation is essential for applying machine learning methods...
October 24, 2016: Amino Acids
Aung Kyaw Lwin, Edoardo Bertolini, Mario Enrico Pè, Andrea Zuccolo
Transposable elements (TEs) are the most abundant genetic material for almost all eukaryotic genomes. Their effects on the host genomes range from an extensive size variation to the regulation of gene expression, altering gene function and creating new genes. Because of TEs pivotal contribute to the host genome structure and regulation, their identification and characterization provide a wealth of useful data for gaining an in-depth understanding of host genome functioning. The giant reed (Arundo donax) is a perennial rhizomatous C3 grass, octadecaploid, with an estimated nuclear genome size of 2744 Mbp...
October 24, 2016: Molecular Genetics and Genomics: MGG
James W N Steenberg, Andrew A Millward, David J Nowak, Pamela J Robinson, Alexis Ellis
The benefits derived from urban forest ecosystems are garnering increasing attention in ecological research and municipal planning. However, because of their location in heterogeneous and highly-altered urban landscapes, urban forests are vulnerable and commonly suffer disproportionate and varying levels of stress and disturbance. The objective of this study is to assess and analyze the spatial and temporal changes, and potential vulnerability, of the urban forest resource in Toronto, Canada. This research was conducted using a spatially-explicit, indicator-based assessment of vulnerability and i-Tree Forecast modeling of temporal changes in forest structure and function...
October 24, 2016: Environmental Management
José J Baldoví, Yan Duan, Carlos Bustos, Salvador Cardona-Serra, Pierre Gouzerh, Richard Villanneau, Geoffrey Gontard, Juan M Clemente-Juan, Alejandro Gaita-Ariño, Carlos Giménez-Saiz, Anna Proust, Eugenio Coronado
Polyoxometalate (POM) chemistry has recently offered excellent examples of single ion magnets (SIMs) and molecular spin qubits. Compared with conventional coordination compounds, POMs provide rigid and highly symmetric coordination sites. However, all POM-based SIMs reported to date exhibit a very limited range of possibilities for chemical processability. We present herein two new families of POM-based SIMs which are soluble in organic solvents: [Ln(β-Mo8O26)2](5-) {Ln(III) = Tb, Dy, Ho, Er, Tm and Yb} and the functionalised POMs [Ln{Mo5O13(OMe)4NNC6H4-p-NO2}2](3-) {Ln(III) = Tb, Dy, Ho, Er, Yb and Nd}...
October 25, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
Min Xiao, Haitao Ge, Budhachandra S Khundrakpam, Junhai Xu, Gleb Bezgin, Yuan Leng, Lu Zhao, Yuchun Tang, Xinting Ge, Seun Jeon, Wenjian Xu, Alan C Evans, Shuwei Liu
Functional neuroimaging studies have indicated the involvement of separate brain areas in three distinct attention systems: alerting, orienting, and executive control (EC). However, the structural correlates underlying attention remains unexplored. Here, we utilized graph theory to examine the neuroanatomical substrates of the three attention systems measured by attention network test (ANT) in 65 healthy subjects. White matter connectivity, assessed with diffusion tensor imaging deterministic tractography was modeled as a structural network comprising 90 nodes defined by the automated anatomical labeling (AAL) template...
2016: Frontiers in Behavioral Neuroscience
Link R Swanson
Predictive processing (PP) is a paradigm in computational and cognitive neuroscience that has recently attracted significant attention across domains, including psychology, robotics, artificial intelligence and philosophy. It is often regarded as a fresh and possibly revolutionary paradigm shift, yet a handful of authors have remarked that aspects of PP seem reminiscent of the work of 18th century philosopher Immanuel Kant. To date there have not been any substantive discussions of how exactly PP links back to Kant...
2016: Frontiers in Systems Neuroscience
Da-Qing Jiang, Tian-Xiang Gu, Zhao-Fa Xu, Shuang Liu, Xue-Yuan Li
OBJECTIVE: To investigate whether heart tissue-derived extracellular matrix (ECM) promotes the differentiation of cardiosphere-derived cells (CDCs) implanted in rat infracted myocardium to improve the cardiac structure and function. METHODS: Rat CDCs were cultured by cardiac explant methods, and ECM was prepared by decelluariztion method. In a Wistar rat model of acute myocardial infarction established by ligating the left anterior descending branch, IMDM solution, ECM suspension, 10(6) CDCs in IMDM solution, or 10(6) CDCs in ECM suspension were injected into the infracted rat myocardium (6 rats in each group)...
October 20, 2016: Nan Fang Yi Ke da Xue Xue Bao, Journal of Southern Medical University
David B MacManus, Baptiste Pierrat, Jeremiah G Murphy, Michael D Gilchrist
The brain is a complex organ made up of many different functional and structural regions consisting of different types of cells such as neurons and glia, as well as complex anatomical geometries. It is hypothesized that the different regions of the brain exhibit significantly different mechanical properties which may be attributed to the diversity of cells within individual brain regions. The regional viscoelastic properties of P56 mouse brain tissue, up to 70 μm displacement, are presented and discussed in the context of traumatic brain injury, particularly how the different regions of the brain respond to mechanical loads...
October 21, 2016: Acta Biomaterialia
Castrese Morrone, Riccardo Miggiano, Mario Serpe, Alberto Massarotti, Anna Valenti, Giovanni Del Monaco, Mosè Rossi, Franca Rossi, Menico Rizzi, Giuseppe Perugino, Maria Ciaramella
BACKGROUND: Alkylated DNA-protein alkyltransferases (AGTs) are conserved proteins that repair alkylation damage in DNA by using a single-step mechanism leading to irreversible alkylation of the catalytic cysteine in the active site. Trans-alkylation induces inactivation and destabilization of the protein, both in vitro and in vivo, likely triggering conformational changes. A complete picture of structural rearrangements occurring during the reaction cycle is missing, despite considerable interest raised by the peculiarity of AGT reaction, and the contribution of a functional AGT in limiting the efficacy of chemotherapy with alkylating drugs...
October 21, 2016: Biochimica et Biophysica Acta
William A Cantara, Erik D Olson, Karin Musier-Forsyth
In addition to their role in correctly attaching specific amino acids to cognate tRNAs, aminoacyl-tRNA synthetases (aaRS) have been found to possess many alternative functions and often bind to and act on other nucleic acids. In contrast to the well-defined 3D structure of tRNA, the structures of many of the other RNAs recognized by aaRSs have not been solved. Despite advances in the use of X-ray crystallography (XRC), nuclear magnetic resonance (NMR) spectroscopy and cryo-electron microscopy (cryo-EM) for structural characterization of biomolecules, significant challenges to solving RNA structures still exist...
October 21, 2016: Methods: a Companion to Methods in Enzymology
V S Kokhan, M I Matveeva, A S Bazyan, V S Kudrin, A Mukhametov, A S Shtemberg
Space flight factors (SFF) significantly affect the operating activity of astronauts during deep space missions. In contrast to an orbital flight, leaving the Earth's magnetic field is fraught with the dangers of exposure to ionizing radiation and more specifically, the high-energy nuclei component of galactic cosmic rays. Microgravity, just another critical non-radiation factor, significantly affects the normal functioning of the CNS. Some morphological structures of the brain, such as the prefrontal cortex and the hippocampus, that are rich in monoaminergic and acetylcholinergic neurones, are the most sensitive to the effects of ionizing radiation and non-radiation spaceflight factors (SFF)...
October 21, 2016: Behavioural Brain Research
Mohammad T Mazhab-Jafari, Alexis Rohou, Carla Schmidt, Stephanie A Bueler, Samir Benlekbir, Carol V Robinson, John L Rubinstein
Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V1 region drives proton translocation through the membrane-embedded VO region via rotation of a rotor subcomplex. Variability in the structure of the intact enzyme has prevented construction of an atomic model for the membrane-embedded motor of any rotary ATPase. We induced dissociation and auto-inhibition of the V1 and VO regions of the V-ATPase by starving the yeast Saccharomyces cerevisiae, allowing us to obtain a ~3...
October 24, 2016: Nature
Juke S Lolkema, Dirk Jan Slotboom
The recently determined crystal structure of the bacterial Na(+)-citrate symporter CitS provides unexpected structural and mechanistic insights. The protein has a fold that has not been seen in other proteins, but the oligomeric state, domain organization and proposed transport mechanism strongly resemble those of the sodium-dicarboxylate symporter vcINDY, and the putative exporters YdaH and MtrF, thus hinting at convergence in structure and function. CitS and the related proteins are predicted to translocate their substrates by an elevator-like mechanism, in which a compact transport domain slides up and down through the membrane while the dimerization domain is stably anchored...
October 21, 2016: Current Opinion in Structural Biology
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"