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Protein contact prediction

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https://www.readbyqxmd.com/read/28641111/structural-insights-into-modulation-of-neurexin-neuroligin-trans-synaptic-adhesion-by-mdga1-neuroligin-2-complex
#1
Jung A Kim, Doyoun Kim, Seoung Youn Won, Kyung Ah Han, Dongseok Park, Eunju Cho, Nayoung Yun, Hyun Joo An, Ji Won Um, Eunjoon Kim, Jie-Oh Lee, Jaewon Ko, Ho Min Kim
Membrane-associated mucin domain-containing glycosylphosphatidylinositol anchor proteins (MDGAs) bind directly to neuroligin-1 (NL1) and neuroligin-2 (NL2), thereby respectively regulating excitatory and inhibitory synapse development. However, the mechanisms by which MDGAs modulate NL activity to specify development of the two synapse types remain unclear. Here, we determined the crystal structures of human NL2/MDGA1 Ig1-3 complex, revealing their stable 2:2 arrangement with three interaction interfaces. Cell-based assays using structure-guided, site-directed MDGA1 mutants showed that all three contact patches were required for the MDGA's negative regulation of NL2-mediated synaptogenic activity...
June 21, 2017: Neuron
https://www.readbyqxmd.com/read/28633528/the-binding-space-concept-a-new-approach-to-enhance-the-reliability-of-docking-scores-and-its-application-to-predicting-butyrylcholinesterase-bche-hydrolytic-activity
#2
Giulio Vistoli, Angelica Mazzolari, Bernard Testa, Alessandro Pedretti
Docking simulations are very popular approaches able to assess the capacity of a given ligand to interact with a target. Docking simulations are usually focused on a single best complex even though many studies showed that ligands retain a significant mobility within a binding pocket by assuming different binding modes all of which may contribute to the monitored ligand affinity. The present study describes an innovative concept, the binding space, which allows an exploration of the ligand mobility within the binding pocket by simultaneously considering several ligand poses as generated by docking simulations...
June 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28625135/studying-interactions-of-drugs-with-cell-membrane-nutrient-transporters-new-frontiers-of-proteoliposome-nanotechnology
#3
Mariafrancesca Scalise, Michele Galluccio, Lorena Pochini, Lara Console, Maria Barile, Nicola Giangregorio, Annamaria Tonazzi, Cesare Indiveri
Transport systems are hydrophobic proteins localized in cell membranes where they mediate transmembrane flow of nutrients, ions and any other compounds essential for cell metabolism. More than 400 transporters of the SoLuteCarrier (SLC) group are present in human cells. Transporters take contacts also with xenobiotics, thus mediating absorption and/or interaction with these exogenous compounds. Since drugs belong to xenobiotics, transporters gained interest also in drug discovery. Transporters differentially expressed in pathological conditions are exploited as drug targets...
June 15, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28623886/epsilon-cp-using-deep-learning-to-combine-information-from-multiple-sources-for-protein-contact-prediction
#4
Kolja Stahl, Michael Schneider, Oliver Brock
BACKGROUND: Accurately predicted contacts allow to compute the 3D structure of a protein. Since the solution space of native residue-residue contact pairs is very large, it is necessary to leverage information to identify relevant regions of the solution space, i.e. correct contacts. Every additional source of information can contribute to narrowing down candidate regions. Therefore, recent methods combined evolutionary and sequence-based information as well as evolutionary and physicochemical information...
June 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28604413/single-chain-factor-xii-a-new-form-of-activated-factor-xii
#5
Ivan Ivanov, Anton Matafonov, David Gailani
PURPOSE OF REVIEW: Exposure of blood to foreign surfaces induces reciprocal conversion of the plasma proteins factor XII (fXII) and plasma prekallikrein (PPK) to the proteases α-fXIIa and α-kallikrein. This process, called contact activation, has a range of effects on host defence mechanisms, including promoting coagulation. The nature of the triggering mechanism for contact activation is debated. One hypothesis predicts that fXII has protease activity, either intrinsically or upon surface-binding, that initiates contact activation...
June 9, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28599239/synthesis-structural-elucidation-antioxidant-ct-dna-binding-and-molecular-docking-studies-of-novel-chloroquinoline-derivatives-promising-antioxidant-and-anti-diabetic-agents
#6
S Murugavel, C S Jacob Prasanna Stephen, R Subashini, Dhanabalan AnanthaKrishnan
The synthesized novel chloroquinoline derivatives 1-(2-chloro-4-phenylquinolin-3-yl)ethanone (CPQE), 1-(2,6-dichloro-4-phenylquinolin-3-yl)ethanone (DCPQE), methyl 2,6-dichloro-4-phenylquinoline-3-carboxylate (MDCPQC),methyl 2-chloro-4-methylquinoline-3-carboxylate (MCMQC) were subjected to the elementary analysis like FT-IR, NMR and Mass spectra using GCMS. Also, single crystal X-ray diffraction study was executed for the compound MDCPQC. The crystal packing is stabilized by C-H…π and π-π interactions and also Chlorine-Chlorine short intermolecular contacts generating a three-dimensional supramolecular network...
June 1, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28595268/placental-biomarkers-for-assessing-fetal-health
#7
Irina Manokhina, Giulia F Del Gobbo, Chaini Konwar, Samantha L Wilson, Wendy P Robinson
The placenta is a multifunctional organ that regulates key aspects of pregnancy maintenance and fetal development. As the placenta is in direct contact with maternal blood, cellular products (DNA, RNA, proteins, etc.) from the placenta can enter maternal circulation by a variety of ways. The application of serum proteins and circulating placental derived DNA has been well demonstrated for the diagnosis of aneuploidy, and there is great interest in exploring the use of placental biomarkers for the prediction of a range of fetal health parameters...
June 8, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28592179/driving-forces-for-nonnative-protein-aggregation-and-approaches-to-predict-aggregation-prone-regions
#8
Gulsum Meric, Anne S Robinson, Christopher J Roberts
Nonnative protein aggregation is the process by which otherwise folded, monomeric proteins are converted to stable aggregates composed of protein chains that have undergone some degree of unfolding. Often, a conformational change is needed to allow certain sequences of amino acids-so-called aggregation-prone regions (APRs)-to form stable interprotein contacts such as β-sheet structures. In addition to APRs that are needed to stabilize aggregates, other factors or driving forces are also important in inducing aggregation in practice...
June 7, 2017: Annual Review of Chemical and Biomolecular Engineering
https://www.readbyqxmd.com/read/28590110/modeling-and-optimization-of-nldh-pvdf-ultrafiltration-nanocomposite-membrane-using-artificial-neural-network-genetic-algorithm-hybrid
#9
Samira Arefi-Oskoui, Alireza Khataee, Vahid Vatanpour
In this research, MgAl-CO32- nanolayered double hydroxide (NLDH) was synthesized through a facile co-precipitation method followed by a hydrothermal treatment. The prepared NLDHs were used as a hydrophilic nanofiller for improving the performance of the PVDF-based ultrafiltration membranes. The main objective of this research was to obtain the optimized formula of NLDH/PVDF nanocomposite membrane presenting the best performance using computational techniques as a cost-effective method. For this aim, an artificial neural network (ANN) model was developed for modeling and expressing the relationship between the performance of the nanocomposite (pure water flux, protein flux and flux recovery ratio) and the affecting parameters including the NLDH, PVP 29000 and polymer concentrations...
June 7, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28584445/a-comparative-molecular-docking-study-of-curcumin-and-methotrexate-to-dihydrofolate-reductase
#10
Yahya Hobani, Ahmed Jerah, Anil Bidwai
Interaction of curcumin (CUR) with the enzyme dihydrofolate reductase (DHFR) was studied by molecular docking using AutoDock 4.2 as the docking software application. AutoDock 4.2 software serves as a valid and acceptable docking application to study the interactions of small compounds with proteins. Interactions of curcumin with DHFR were compared to those of methotrexate (MTX), a known inhibitor of the enzyme. The calculated free energy of binding (ΔG binding) shows that curcumin (ΔG = -9.02 kcal/mol; Ki = 243 nM) binds with affinity comparable to or better than MTX (ΔG = -8...
2017: Bioinformation
https://www.readbyqxmd.com/read/28578104/assessing-food-allergy-risks-from-residual-peanut-protein-in-highly-refined-vegetable-oil
#11
W Marty Blom, Astrid G Kruizinga, Carina M Rubingh, Ben C Remington, René W R Crevel, Geert F Houben
Refined vegetable oils including refined peanut oil are widely used in foods. Due to shared production processes, refined non-peanut vegetable oils can contain residual peanut proteins. We estimated the predicted number of allergic reactions to residual peanut proteins using probabilistic risk assessment applied to several scenarios involving food products made with vegetable oils. Variables considered were: a) the estimated production scale of refined peanut oil, b) estimated cross-contact between refined vegetable oils during production, c) the proportion of fat in representative food products and d) the peanut protein concentration in refined peanut oil...
May 31, 2017: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/28573570/the-sticky-patch-model-of-crystallization-and-modification-of-proteins-for-enhanced-crystallizability
#12
Zygmunt S Derewenda, Adam Godzik
Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28571639/longitudinal-outcomes-of-patients%C3%A2-with%C3%A2-single-ventricle-after%C3%A2-the%C3%A2-fontan%C3%A2-procedure
#13
Andrew M Atz, Victor Zak, Lynn Mahony, Karen Uzark, Nicholas D'agincourt, David J Goldberg, Richard V Williams, Roger E Breitbart, Steven D Colan, Kristin M Burns, Renee Margossian, Heather T Henderson, Rosalind Korsin, Bradley S Marino, Kaitlyn Daniels, Brian W McCrindle
BACKGROUND: Multicenter longitudinal objective data for survival into adulthood of patients who have undergone Fontan procedures are lacking. OBJECTIVES: This study sought to describe transplant-free survival and explore relationships between laboratory measures of ventricular performance and functional status over time. METHODS: Exercise testing, echocardiography, B-type natriuretic peptide, functional health assessment, and medical history abstraction were repeated 9...
June 6, 2017: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/28570708/designing-small-molecules-to-target-cryptic-pockets-yields-both-positive-and-negative-allosteric-modulators
#14
Kathryn M Hart, Katelyn E Moeder, Chris M W Ho, Maxwell I Zimmerman, Thomas E Frederick, Gregory R Bowman
Allosteric drugs, which bind to proteins in regions other than their main ligand-binding or active sites, make it possible to target proteins considered "undruggable" and to develop new therapies that circumvent existing resistance. Despite growing interest in allosteric drug discovery, rational design is limited by a lack of sufficient structural information about alternative binding sites in proteins. Previously, we used Markov State Models (MSMs) to identify such "cryptic pockets," and here we describe a method for identifying compounds that bind in these cryptic pockets and modulate enzyme activity...
2017: PloS One
https://www.readbyqxmd.com/read/28544811/differential-protein-expression-in-exosomal-samples-taken-from-trauma-patients
#15
Ron B Moyron, Amber Gonda, Matthew J Selleck, Xian Luo-Owen, Richard D Catalano, Thomas O'Callahan, Carlos Garberoglio, David Turay, Nathan R Wall
Traumatic Brain Injuries (TBI) are among the most misdiagnosed and underreported types of head trauma. The potential long-term impact of undiagnosed or incorrectly identified concussions and other head injuries are potentially devastating, as evidenced by the increasing societal burden exhibited by soldiers returning from combat and athletes in contact sports. Concussions and TBI are notoriously difficult to correctly diagnose and prognosis for these injuries is poorly understood. In order to increase the likelihood of successful diagnosis, treatment, and prediction of outcomes, a definitive differential diagnosis will need to be established...
May 25, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28542325/membrane-protein-contact-and-structure-prediction-using-co-evolution-in-conjunction-with-machine-learning
#16
Pedro L Teixeira, Jeff L Mendenhall, Sten Heinze, Brian Weiner, Marcin J Skwark, Jens Meiler
De novo membrane protein structure prediction is limited to small proteins due to the conformational search space quickly expanding with length. Long-range contacts (24+ amino acid separation)-residue positions distant in sequence, but in close proximity in the structure, are arguably the most effective way to restrict this conformational space. Inverse methods for co-evolutionary analysis predict a global set of position-pair couplings that best explain the observed amino acid co-occurrences, thus distinguishing between evolutionarily explained co-variances and these arising from spurious transitive effects...
2017: PloS One
https://www.readbyqxmd.com/read/28542178/uncovering-direct-and-indirect-molecular-determinants-of-chromatin-loops-using-a-computational-integrative-approach
#17
Raphaël Mourad, Lang Li, Olivier Cuvier
Chromosomal organization in 3D plays a central role in regulating cell-type specific transcriptional and DNA replication timing programs. Yet it remains unclear to what extent the resulting long-range contacts depend on specific molecular drivers. Here we propose a model that comprehensively assesses the influence on contacts of DNA-binding proteins, cis-regulatory elements and DNA consensus motifs. Using real data, we validate a large number of predictions for long-range contacts involving known architectural proteins and DNA motifs...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28535189/predicting-accurate-contacts-in-thousands-of-pfam-domain-families-using-pconsc3
#18
Mirco Michel, Marcin J Skwark, David Menéndez Hurtado, Magnus Ekeberg, Arne Elofsson
Motivation: A fewyears ago it was shown that by using amaximumentropy approach to describe couplings between columns in a multiple sequence alignment it is possible to significantly increase the accuracy of residue contact predictions. For very large protein families with more than 1000 effective sequences the accuracy is sufficient to produce accurate models of proteins as well as complexes. Today, for about half of all Pfam domain families no structure is known, but unfortunately most of these families have at most a few hundred members, i...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28523153/pleural-pressure-theory-revisited-a-role-for-capillary-equilibrium
#19
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
#20
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
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