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Structure prediction

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
Helga Myrseth, Guy Notelaers
The aim of the present study was to improve the weaknesses of the three-dimensional Gambling Motives Questionnaire and to examine the psychometric properties and factor structure of the Gambling Motives Questionnaire-Revised. The Gambling Motives Questionnaire was administered to a sample of 418 gamblers (92% men, mean age 19.5years). Participants completed the Gambling Motives Questionnaire and an additional item tapping boredom, as well as a variety of measures of gambling behavior and gambling problems as criterion measures...
October 14, 2016: Addictive Behaviors
Money Gupta, Rashi Chauhan, Yamuna Prasad, Gulshan Wadhwa, Chakresh Kumar Jain
The lack of complete treatments and appearance of multiple drug-resistance strains of Burkholderia cepacia complex (Bcc) are causing an increased risk of lung infections in cystic fibrosis patients. Bcc infection is a big risk to human health and demands an urgent need to identify new therapeutics against these bacteria. Network biology has emerged as one of the prospective hope in identifying novel drug targets and hits. We have applied protein-protein interaction methodology to identify new drug-target candidates (orthologs) in Burkhloderia cepacia GG4, which is an important strain for studying the quorum-sensing phenomena...
October 8, 2016: Computational Biology and Chemistry
Thomas Schmidt, Alan J Situ, Tobias S Ulmer
The solvation of membrane proteins by both lipids and water makes their membrane immersion difficult to predict and the choice of a membrane mimic challenging. To characterize protein-lipid contacts and bicelle membrane mimics, we examined protein-lipid cross-relaxation of integrin αIIb and β3(A711P) transmembrane helices in isotropic phospholipid bicelles (q=0.5 and 0.7). Long-chain bicelle lipids dominated contacts with central helix segments, whereas both short- and long-chain lipids contacted the terminal turns of each helix in corroboration of the mixed bicelle model...
October 24, 2016: Journal of Physical Chemistry Letters
Florent Xavier Smit, Jurriaan A Luiken, Peter G Bolhuis
We performed replica exchange molecular dynamics and forward flux sampling simulations of hexapeptide VQIINK and VQIVYK systems, also known as, respectively, fragments PHF6* and PHF6 from tau protein. Part of the microtubule binding region, these fragments are known to be aggregation prone, and at least one of them is a prerequisite for fibril formation of the tau protein. Using a coarse-grained force field, we establish the phase behavior of both fragments, and investigate the nucleation kinetics for the conversion into a β-sheet fibril...
October 24, 2016: Journal of Physical Chemistry. B
Martin Paparella, Annamaria Colacci, Miriam N Jacobs
An approach for a systematic description of the uncertainties and complexity of the standard animal testing and assessment approach for carcinogenicity is explored by using a draft OECD Guidance document that was originally developed for reporting defined in vitro approaches to testing and assessment (OECD, 2016). The format is suitable for this re-purposing and it appears that the potential multitude of approaches for integrating and interpreting data from standard animal testing may ultimately be conceptually similar to the challenge of integrating relevant in vitro and in silico data...
October 24, 2016: ALTEX
Jasper L A Vleugels, Joep E G IJspeert, Yark Hazewinkel, Manon van der Vlugt, Paul Fockens, Lianne Koens, Evelien Dekker
BACKGROUND: Optical diagnosis of diminutive (1 to 5 mm) polyps could result in a more cost-effective colonoscopy practice. Previous optical diagnosis studies did not incorporate the differentiation of sessile serrated polyps (SSPs). This study aimed to evaluate the impact of optical diagnosis of diminutive SSPs on the overall performance of endoscopic polyp differentiation in daily colonoscopy practice. METHODS: Endoscopy data were prospectively collected between 2011 and 2014 in a colonoscopy center...
October 21, 2016: Journal of Clinical Gastroenterology
Cinzia Pizzi, Mattia Ornamenti, Simone Spangaro, Simona E Rombo, Laxmi Parida
Entropy, being closely related to repetitiveness and compressibility, is a widely used information-related measure to assess the degree of predictability of a sequence. Entropic profiles are based on information theory principles, and can be used to study the under-/over-representation of subwords, by also providing information about the scale of conserved DNA regions. Here we focus on the algorithmic aspects related to entropic profiles. In particular, we propose linear time algorithms for their computation that rely on suffix-based data structures, more specifically on the truncated suffix tree (TST) and on the enhanced suffix array (ESA)...
October 21, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Stavros Karakalos, Yun-Fei Xu, Fairoja Cheenicode Kabeer, Wei Chen, Juan Carlos F Rodriguez-Reyes, Alexandre Tkatchenko, Efthimios Kaxiras, Robert J Madix, Cynthia M Friend
Enhancing the selectivity of catalytic processes has potential for substantially increasing the sustainability of chemical production. Herein, we establish relationships between reaction selectivity and molecular structure for a homologous series of key intermediates for oxidative coupling of alcohols on gold using a combination of experiment and theory. We establish a scale of binding for molecules with different alkyl structures and chain lengths and thereby demonstrate the critical nature of non-covalent van der Waals interactions in determining the selectivity by modulating the stability of key reaction intermediates bound to the surface...
October 24, 2016: Journal of the American Chemical Society
Dan Liu, Qisong Wang, Xin Liu, Ruixin Niu, Yan Zhang, Jinwei Sun
Accurately measuring the oil content and salt content of crude oil is very important for both estimating oil reserves and predicting the lifetime of an oil well. There are some problems with the current methods such as high cost, low precision, and difficulties in operation. To solve these problems, we present a multifunctional sensor, which applies, respectively, conductivity method and ultrasound method to measure the contents of oil, water, and salt. Based on cross sensitivity theory, these two transducers are ideally integrated for simplifying the structure...
October 21, 2016: Sensors
Eugenio Ivorra, Samuel Verdu, Antonio J Sánchez, Raúl Grau, José M Barat
A technique that combines the spatial resolution of a 3D structured-light (SL) imaging system with the spectral analysis of a hyperspectral short-wave near infrared system was developed for freshness predictions of gilthead sea bream on the first storage days (Days 0-6). This novel approach allows the hyperspectral analysis of very specific fish areas, which provides more information for freshness estimations. The SL system obtains a 3D reconstruction of fish, and an automatic method locates gilthead's pupils and irises...
October 19, 2016: Sensors
Jian Zhang, Haiting Chai, Bo Gao, Guifu Yang, Zhiqiang Ma
Heme is an essential biomolecule that widely exists in numerous extant organisms. Accurately identifying heme binding residues (HEMEs) is of great importance in disease progression and drug development. In this study, a novel predictor named HEMEsPred was proposed for predicting HEMEs. First, several sequence- and structure-based features, including amino acid composition, motifs, surface preferences and secondary structure, were collected to construct feature matrices. Second, a novel fast-adaptive ensemble learning scheme was designed to overcome the serious class-imbalance problem as well as to enhance the prediction performance...
October 4, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Andreas Widder, Christian Kuehn
In this paper, we focus on the influence of heterogeneity and stochasticity of the population on the dynamical structure of a basic susceptible-infected-susceptible (SIS) model. First we prove that, upon a suitable mathematical reformulation of the basic reproduction number, the homogeneous system and the heterogeneous system exhibit a completely analogous global behaviour. Then we consider noise terms to incorporate the fluctuation effects and the random import of the disease into the population and analyse the influence of heterogeneity on warning signs for critical transitions (or tipping points)...
October 1, 2016: Mathematical Biosciences and Engineering: MBE
Qihua Huang, Hao Wang
The question of the effects of environmental toxins on ecological communities is of great interest from both environmental and conservational points of view. Mathematical models have been applied increasingly to predict the effects of toxins on a variety of ecological processes. Motivated by the fact that individuals with different sizes may have different sensitivities to toxins, we develop a toxin-mediated size-structured model which is given by a system of first order fully nonlinear partial differential equations (PDEs)...
August 1, 2016: Mathematical Biosciences and Engineering: MBE
Wojciech Pulawski, Michal Jamroz, Michal Kolinski, Andrzej Kolinski, Sebastian Kmiecik
The CABS coarse-grained model is a well-established tool for modeling globular proteins (predicting their structure, dynamics and interactions). Here we introduce an extension of CABS representation and force field (CABS-membrane) to the modeling of the effect of biological membrane environment on the structure of membrane proteins. We validate the CABS-membrane model in folding simulations of 10 short helical membrane proteins not using any knowledge about their structure. The simulations start from random protein conformations placed outside the membrane environment and allow for full flexibility of the modeled proteins during their spontaneous insertion into the membrane...
October 24, 2016: Journal of Chemical Information and Modeling
Laurent Pedesseau, Daniel Sapori, Boubacar Traore, Roberto Robles, Hong-Hua Fang, Maria Antonietta Loi, Hsinhan Tsai, Wanyi Nie, Jean-Christophe Blancon, Amanda Neukirch, Sergei Tretiak, Aditya D Mohite, Claudine Katan, Jacky Even, Mikaël Kepenekian
Layered halide hybrid organic-inorganic perovskites (HOP) have been the subject of intense investigation before the rise of three-dimensional (3D) HOP and their impressive performance in solar cells. Recently, layered HOP have also been proposed as attractive alternatives for photostable solar cells and revisited for light-emitting devices. In this review, we combine classical solid-state physics concepts with simulation tools based on density functional theory to overview the main features of the optoelectronic properties of layered HOP...
October 24, 2016: ACS Nano
Ben Zercher, Todd A Hopkins
Materials that emit circularly polarized light have application in several important industries. Because they show large optical activity and emit sharp visible light transitions, europium complexes are often exploited in applications that require circularly polarized luminescence (CPL). Chiral and coordinating ionic liquids based on prolinate, valinate, and aspartate anions are used to induce CPL from a simple achiral europium triflate salt. The sign of the induced CPL is dependent on the handedness (l vs d) of the amino acid anion...
October 24, 2016: Inorganic Chemistry
Yuanyuan Zhou, Miao Li, Yijing Guo, Heng Lu, Jinsheng Song, Zhishan Bo, Hua Wang
With the efficient synthesis of the crucial dibenzopyran building block, a series of PDBPTBT polymers containing different alkyl side chains and/or fluorine substitution were designed and synthesized via the microwave assisted Suzuki polycondensation. Quantum chemistry calculations based on density functional theory indicated that different substitutions have significant impacts on the planarity and rigidity of the polymer backbones. Interestingly, the alkyloxy chains of PDBPTBT-4 tend to stay in the same plane with the benzothiadiazole unit, but the others appear to be out of plane...
October 24, 2016: ACS Applied Materials & Interfaces
Jiangping Xu, Jun Li, Yi Yang, Ke Wang, Nan Xu, Jingyi Li, Ruijing Liang, Lei Shen, Xiaolin Xie, Juan Tao, Jintao Zhu
Although high-boiling non-solvent induced macrophase separation in emulsion droplets has been widely applied for the fabrication of polymeric capsules, precise control of their structures remains a great challenge. Herein, block copolymer capsules with tunable shell structures were fabricated by employing a non-solvent as a liquid template in emulsion droplets. The properties of the non-solvents dictate the phase separation sequence in the droplets and the capsule formation mechanism. Two different pathways for capsule formation were observed, and could be applied to predict the shell structure...
October 24, 2016: Angewandte Chemie
Ezgi Yalçıntaş, Andreas C Scheinost, Xavier Gaona, Marcus Altmaier
The mechanisms for the reduction and uptake of Tc by magnetite (Fe3O4) and mackinawite (FeS) are investigated using X-ray absorption spectroscopy (XANES and EXAFS), in combination with thermodynamic calculations of the Tc/Fe systems and accurate characterization of the solution properties (pHm, pe, [Tc]). Batch sorption experiments were performed under strictly anoxic conditions using freshly prepared magnetite and mackinawite in 0.1 M NaCl solutions with varying initial Tc(vii) concentrations (2 × 10(-5) and 2 × 10(-4) M) and Tc loadings (400-900 ppm)...
October 24, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
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