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Protein contact prediction

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https://www.readbyqxmd.com/read/28523153/pleural-pressure-theory-revisited-a-role-for-capillary-equilibrium
#1
Aaron R Casha, Roberto Caruana-Gauci, Alexander Manche, Marilyn Gauci, Stanley Chetcuti, Luca Bertolaccini, Marco Scarci
BACKGROUND: Theories elucidating pleural pressures should explain all observations including the equal and opposite recoil of the chest wall and lungs, the less than expected pleural hydrostatic gradient and its variation at lobar margins, why pleural pressures are negative and how pleural fluid circulation functions. METHODS: A theoretical model describing equilibrium between buoyancy, hydrostatic forces, and capillary forces is proposed. The capillary equilibrium model described depends on control of pleural fluid volume and protein content, powered by an active pleural pump...
April 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28512576/applications-of-contact-predictions-to-structural-biology
#2
REVIEW
Felix Simkovic, Sergey Ovchinnikov, David Baker, Daniel J Rigden
Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are important for protein structure or function can lead to covariance between the two positions. Recent methodological advances allow much more accurate contact predictions to be derived from this evolutionary covariance signal. The practical application of contact predictions has largely been confined to structural bioinformatics, yet, as this work seeks to demonstrate, the data can be of enormous value to the structural biologist working in X-ray crystallo-graphy, cryo-EM or NMR...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28510698/xsult-a-web-server-for-structural-annotation-and-representation-of-sequence-structure-alignments
#3
Bernardo Ochoa-Montaño, Tom L Blundell
The web server XSuLT, an enhanced version of the protein alignment annotation program JoY, formats a submitted multiple-sequence alignment using three-dimensional (3D) structural information in order to assist in the comparative analysis of protein evolution and in the optimization of alignments for comparative modelling and construct design. In addition to the features analysed by JoY, which include secondary structure, solvent accessibility and sidechain hydrogen bonds, XSuLT annotates each amino acid residue with residue depth, chain and ligand interactions, inter-residue contacts, sequence entropy, root mean square deviation and secondary structure and disorder prediction...
May 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28510212/supercoiling-biases-the-formation-of-loops-involved-in-gene-regulation
#4
REVIEW
Laura Finzi, David Dunlap
The function of DNA as a repository of genetic information is well-known. The post-genomic effort is to understand how this information-containing filament is chaperoned to manage its compaction and topological states. Indeed, the activities of enzymes that transcribe, replicate, or repair DNA are regulated to a large degree by access. Proteins that act at a distance along the filament by binding at one site and contacting another site, perhaps as part of a bigger complex, create loops that constitute topological domains and influence regulation...
November 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28505149/distinct-dna-binding-surfaces-in-the-atpase-and-linker-domains-of-mutl%C3%AE-determine-its-substrate-specificities-and-exert-separable-functions-in-meiotic-recombination-and-mismatch-repair
#5
Corentin Claeys Bouuaert, Scott Keeney
Mlh1-Mlh3 (MutLγ) is a mismatch repair factor with a central role in formation of meiotic crossovers, presumably through resolution of double Holliday junctions. MutLγ has DNA binding, nuclease, and ATPase activities, but how these relate to one another and to in vivo functions are unclear. Here, we combine biochemical and genetic analyses to characterize Saccharomyces cerevisiae MutLγ. Limited proteolysis and atomic force microscopy showed that purified recombinant MutLγ undergoes ATP-driven conformational changes...
May 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28486528/identification-and-characterization-of-a-neutralizing-monoclonal-antibody-that-provides-complete-protection-against-yersinia-pestis
#6
Weicen Liu, Jun Ren, Jinlong Zhang, Xiaohong Song, Shuling Liu, Xiangyang Chi, Yi Chen, Zhonghua Wen, Jianmin Li, Wei Chen
Yersinia pestis (Y. pestis) has caused an alarming number of deaths throughout recorded human history, and novel prophylactics and therapeutics are necessary given its potential as a bioweapon. Only one monoclonal antibody has been identified to date that provides complete protection against Y. pestis. Here, we describe a second novel murine monoclonal antibody (F2H5) that provided complete protection against Y. pestis 141 infection when administered prophylactically to Balb/c mice (100 μg intravenously). We humanized F2H5, characterized its ability to bind to the Y...
2017: PloS One
https://www.readbyqxmd.com/read/28472330/dynomics-dynamics-of-structural-proteome-and-beyond
#7
Hongchun Li, Yuan-Yu Chang, Ji Young Lee, Ivet Bahar, Lee-Wei Yang
DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core of the portal is a newly developed server, ENM 1.0, which permits users to efficiently generate information on the collective dynamics of any structure in PDB format, user-uploaded or database-retrieved...
May 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28472263/a-deep-learning-framework-for-improving-long-range-residue-residue-contact-prediction-using-a-hierarchical-strategy
#8
Dapeng Xiong, Jianyang Zeng, Haipeng Gong
Motivation: Residue-residue contacts are of great value for protein structure prediction, since contact information, especially from those long-range residue pairs, can significantly reduce the complexity of conformational sampling for protein structure prediction in practice. Despite progresses in the past decade on protein targets with abundant homologous sequences, accurate contact prediction for proteins with limited sequence information is still far from satisfaction. Methodologies for these hard targets still need further improvement...
May 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449647/pear1-is-not-a-major-susceptibility-gene-for-cardiovascular-disease-in-a-flemish-population
#9
Wen-Yi Yang, Thibault Petit, Nicholas Cauwenberghs, Zhen-Yu Zhang, Chang-Sheng Sheng, Lutgarde Thijs, Erika Salvi, Benedetta Izzi, Christophe Vandenbriele, Fang-Fei Wei, Yu-Mei Gu, Lotte Jacobs, Lorena Citterio, Simona Delli Carpini, Cristina Barlassina, Daniele Cusi, Marc F Hoylaerts, Peter Verhamme, Tatiana Kuznetsova, Jan A Staessen
BACKGROUND: Platelet Endothelial Aggregation Receptor 1 (PEAR1), a membrane protein highly expressed in platelets and endothelial cells, plays a role in platelet contact-induced activation, sustained platelet aggregation and endothelial function. Previous reports implicate PEAR1 rs12041331 as a variant influencing risk in patients with coronary heart disease. We investigated whether genetic variation in PEAR1 predicts cardiovascular outcome in a white population. METHODS: In 1938 participants enrolled in the Flemish Study on Environment, Genes and Health Outcomes (51...
April 27, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28447801/droplets-on-microdecorated-surfaces-evolution-of-the-polygonal-contact-line
#10
Alok Kumar, Rishi Raj
Interaction of liquids with surfaces is ubiquitous in our physical environment as well as many engineering applications. Recent advances on this topic have not only provided us with valuable insight into nature's design, but also enabled improved fluidic manipulation for liquid-based printing applications such as biomicroarrays for protein and DNA sequencing, multicolor polymer-based LED displays, inkjet printing, and solder droplet printing, among others. For example, droplet contact lines, which are typically circular on a smooth and homogeneous surface, when deposited on a microdecorated surface may take various common polygonal shapes such as squares, rectangles, hexagons, octagons and dodecagons...
May 4, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28447708/protein-collapse-is-encoded-in-the-folded-state-architecture
#11
Himadri S Samanta, Pavel I Zhuravlev, Michael Hinczewski, Naoto Hori, Shaon Chakrabarti, D Thirumalai
Folded states of single domain globular proteins are compact with high packing density. The radius of gyration, Rg, of both the folded and unfolded states increase as N(ν) where N is the number of amino acids in the protein. The values of the Flory exponent ν are, respectively, ≈⅓ and ≈0.6 in the folded and unfolded states, coinciding with those for homopolymers. However, the extent of compaction of the unfolded state of a protein under low denaturant concentration (collapsibility), conditions favoring the formation of the folded state, is unknown...
April 27, 2017: Soft Matter
https://www.readbyqxmd.com/read/28446903/simulating-intestinal-growth-conditions-enhances-toxin-production-of-enteropathogenic-bacillus-cereus
#12
Nadja Jeßberger, Corinna Rademacher, Viktoria M Krey, Richard Dietrich, Ann-Katrin Mohr, Maria-Elisabeth Böhm, Siegfried Scherer, Monika Ehling-Schulz, Erwin Märtlbauer
Bacillus cereus is a ubiquitous bacterial pathogen increasingly reported to be the causative agent of foodborne infections and intoxications. Since the enterotoxins linked to the diarrheal form of food poising are foremost produced in the human intestine, the toxic potential of enteropathogenic B. cereus strains is difficult to predict from studies carried out under routine cultivation procedures. In this study, toxigenic properties of a panel of strains (n = 19) of diverse origin were compared using cell culture medium pre-incubated with CaCo-2 cells to mimic intestinal growth conditions...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28441034/thrombus-formation-at-high-shear-rate
#13
Lauren D C Casa, David N Ku
The final common pathway in myocardial infarction and ischemic stroke is occlusion of blood flow from a thrombus forming under high shear rates in arteries. A high-shear thrombus forms rapidly and is distinct from the slow formation of coagulation that occurs in stagnant blood. Thrombosis at high shear rates depends primarily on the long protein von Willebrand factor (vWF) and platelets, with hemodynamics playing an important role in each stage of thrombus formation, including vWF binding, platelet adhesion, platelet activation, and rapid thrombus growth...
April 24, 2017: Annual Review of Biomedical Engineering
https://www.readbyqxmd.com/read/28439455/the-evolution-of-logic-circuits-for-the-purpose-of-protein-contact-map-prediction
#14
Samuel D Chapman, Christoph Adami, Claus O Wilke, Dukka B Kc
Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset...
2017: PeerJ
https://www.readbyqxmd.com/read/28430949/capturing-non-local-interactions-by-long-short-term-memory-bidirectional-recurrent-neural-networks-for-improving-prediction-of-protein-secondary-structure-backbone-angles-contact-numbers-and-solvent-accessibility
#15
Rhys Heffernan, Yuedong Yang, Kuldip Paliwal, Yaoqi Zhou
Motivation: The accuracy of predicting protein local and global structural properties such as secondary structure and solvent accessible surface area has been stagnant for many years because of the challenge of accounting for non-local interactions between amino acid residues that are close in three-dimensional structural space but far from each other in their sequence positions. All existing machine-learning techniques relied on a sliding window of 10-20 amino acid residues to capture some "short to intermediate" non-local interactions...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28403479/the-gard-platform-for-potency-assessment-of-skin-sensitizing-chemicals
#16
Kathrin S Zeller, Andy Forreryd, Tim Lindberg, Robin Gradin, Aakash Chawade, Malin Lindstedt
Contact allergy induced by certain chemicals is a common health concern, and several alternative methods have been developed to fulfill the requirements of European legislation with regard to hazard assessment of potential skin sensitizers. However, validated methods, which provide information about the potency of skin sensitizers, are still lacking. The cell-based assay Genomic Allergen Rapid Detection (GARD), targeting key event 3, dendritic cell activation, of the skin sensitizer AOP, uses gene expression profiling and a machine learning approach for the prediction of chemicals as sensitizers or non-sensitizers...
April 12, 2017: ALTEX
https://www.readbyqxmd.com/read/28383913/an-ensemble-based-protocol-for-the-computational-prediction-of-helix-helix-interactions-in-g-protein-coupled-receptors-using-coarse-grained-molecular-dynamics
#17
Nojood A Altwaijry, Michael Baron, David W Wright, Peter V Coveney, Andrea Townsend-Nicholson
The accurate identification of the specific points of interaction between G protein-coupled receptor (GPCR) oligomers is essential for the design of receptor ligands targeting oligomeric receptor targets. A coarse-grained molecular dynamics computer simulation approach would provide a compelling means of identifying these specific protein-protein interactions and could be applied both for known oligomers of interest and as a high-throughput screen to identify novel oligomeric targets. However, to be effective, this in silico modeling must provide accurate, precise, and reproducible information...
May 9, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28383276/predicting-the-initial-steps-of-salt-stable-cowpea-chlorotic-mottle-virus-capsid-assembly-with-atomistic-force-fields
#18
Zoltan Antal, Janos Szoverfi, Szilard N Fejer
Computational prediction of native protein-protein interfaces still remains a challenging task. In virus capsids, each protein unit is in contact with copies of itself through several interfaces. The relative strengths of the different contacts affect the dynamics of the assembly, especially if the process is hierarchical. We investigate the dimerization of the salt-stable cowpea chlorotic mottle virus (CCMV) capsid protein using a combination of different computational tools. The best predictions of dimer configurations provided by blind docking with ZDOCK are rescored using geometry optimization with the Amber and Rosetta force fields...
April 24, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28383141/the-use-of-human-umbilical-vein-endothelial-cells-huvecs-as-an-in-vitro-model-to-assess-the-toxicity-of-nanoparticles-to-endothelium-a-review
#19
REVIEW
Yi Cao, Yu Gong, Liangliang Liu, Yiwei Zhou, Xin Fang, Cao Zhang, Yining Li, Juan Li
With the rapid development of nanotechnologies, nanoparticles (NPs) are increasingly produced and used in many commercial products, which could lead to the contact of human blood vessels with NPs. Thus, it is necessary to understand the adverse effects of NPs to relevant cells lining human blood vessels, especially endothelial cells (ECs) that cover the lumen of blood vessels. Human umbilical vein endothelial cells (HUVECs) are among one of the most popular models used for ECs in vitro. In the present review, we discussed studies that have used HUVECs as a model to investigate the EC-NP interactions, the toxic effects of NPs on ECs and the mechanisms...
April 6, 2017: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/28378120/comprehensive-analysis-of-the-in-vitro-and-ex-ovo-hemocompatibility-of-surface-engineered-iron-oxide-nanoparticles-for-biomedical-applications
#20
Florian Schlenk, Sebastian Werner, Martin Rabel, Franziska Jacobs, Christian Bergemann, Joachim H Clement, Dagmar Fischer
A set of biomedically relevant iron oxide nanoparticles with systematically modified polymer surfaces was investigated regarding their interaction with the first contact partners after systemic administration such as blood cells, blood proteins, and the endothelial blood vessels, to establish structure-activity relationships. All nanoparticles were intensively characterized regarding their physicochemical parameters. Cyto- and hemocompatibility tests showed that (1) the properties of the core material itself were not relevant in short-term incubation studies, and (2) toxicities increased with higher polymer mass, neutral = anionic < cationic surface charge and charge density, as well as agglomeration...
April 4, 2017: Archives of Toxicology
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