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Protein contact prediction

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https://www.readbyqxmd.com/read/28722347/foxo3-longevity-interactome-on-chromosome-6
#1
Timothy A Donlon, Brian J Morris, Randi Chen, Kamal H Masaki, Richard C Allsopp, D Craig Willcox, Ayako Elliott, Bradley J Willcox
FOXO3 has been implicated in longevity in multiple populations. By DNA sequencing in long-lived individuals, we identified all single nucleotide polymorphisms (SNPs) in FOXO3 and showed 41 were associated with longevity. Thirteen of these had predicted alterations in transcription factor binding sites. Those SNPs appeared to be in physical contact, via RNA polymerase II binding chromatin looping, with sites in the FOXO3 promoter, and likely function together as a cis-regulatory unit. The SNPs exhibited a high degree of LD in the Asian population, in which they define a specific longevity haplotype that is relatively common...
July 19, 2017: Aging Cell
https://www.readbyqxmd.com/read/28720122/enhance-the-performance-of-current-scoring-functions-with-the-aid-of-3d-protein-ligand-interaction-fingerprints
#2
Jie Liu, Minyi Su, Zhihai Liu, Jie Li, Yan Li, Renxiao Wang
BACKGROUND: In structure-based drug design, binding affinity prediction remains as a challenging goal for current scoring functions. Development of target-biased scoring functions provides a new possibility for tackling this problem, but this approach is also associated with certain technical difficulties. We previously reported the Knowledge-Guided Scoring (KGS) method as an alternative approach (BMC Bioinformatics, 2010, 11, 193-208). The key idea is to compute the binding affinity of a given protein-ligand complex based on the known binding data of an appropriate reference complex, so the error in binding affinity prediction can be reduced effectively...
July 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28715501/diversity-and-distribution-of-nuclease-bacteriocins-in-bacterial-genomes-revealed-using-hidden-markov-models
#3
Connor Sharp, James Bray, Nicholas G Housden, Martin C J Maiden, Colin Kleanthous
Bacteria exploit an arsenal of antimicrobial peptides and proteins to compete with each other. Three main competition systems have been described: type six secretion systems (T6SS); contact dependent inhibition (CDI); and bacteriocins. Unlike T6SS and CDI systems, bacteriocins do not require contact between bacteria but are diffusible toxins released into the environment. Identified almost a century ago, our understanding of bacteriocin distribution and prevalence in bacterial populations remains poor. In the case of protein bacteriocins, this is because of high levels of sequence diversity and difficulties in distinguishing their killing domains from those of other competition systems...
July 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28704961/extraction-of-pathogenesis-related-proteins-and-phenolics-in-sauvignon-blanc-as-affected-by-grape-harvesting-and-processing-conditions
#4
Bin Tian, Roland Harrison, James Morton, Marlene Jaspers, Simon Hodge, Claire Grose, Mike Trought
Thaumatin-like proteins (TLPs) and chitinases are the two main groups of pathogenesis-related (PR) proteins found in wine that cause protein haze formation. Previous studies have found that phenolics are also involved in protein haze formation. In this study, Sauvignon Blanc grapes were harvested and processed in two vintages (2011 and 2012) by three different treatments: (1) hand harvesting with whole bunch press (H-WB); (2) hand harvesting with destem/crush and 3 h skin contact (H-DC-3); and (3) machine harvesting with destem/crush and 3 h skin contact (M-DC-3)...
July 12, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28689580/a-molecular-modeling-based-method-to-predict-elution-behavior-and-binding-patches-of-proteins-in-multimodal-chromatography
#5
Suvrajit Banerjee, Siddharth Parimal, Steven M Cramer
Multimodal (MM) chromatography provides a powerful means to enhance the selectivity of protein separations by taking advantage of multiple weak interactions that include electrostatic, hydrophobic and van der Waals interactions. In order to increase our understanding of such phenomena, a computationally efficient approach was developed that combines short molecular dynamics simulations and continuum solvent based coarse-grained free energy calculations in order to study the binding of proteins to Self Assembled Monolayers (SAM) presenting MM ligands...
June 23, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28688220/assessment-of-the-protein-interaction-between-coagulation-factor-xii-and-corn-trypsin-inhibitor-by-molecular-docking-and-biochemical-validation
#6
Badraldin K Hamad, Monika Pathak, Rosa Manna, Peter M Fischer, Jonas Emsley, Lodewijk V Dekker
BACKGROUND: Corn trypsin inhibitor (CTI) has selectivity for serine proteases coagulation factor XII (FXII) and trypsin. CTI is in widespread use as a reagent that specifically inhibits the intrinsic pathway of blood coagulation but not the extrinsic pathway. OBJECTIVES: To investigate the molecular basis of FXII inhibition by CTI. METHODS: We performed molecular docking of CTI, using its known crystal structure, with a model of the activated FXII (FXIIa) protease domain...
July 8, 2017: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/28668253/expression-and-secretion-of-the-giardia-duodenalis-variant-surface-protein-9b10a-by-transfected-trophozoites-causes-damage-to-epithelial-cell-monolayers-mediated-by-protease-activity
#7
Ariana Cabrera-Licona, Eduardo Solano-González, Rocío Fonseca-Liñán, Ma Luisa Bazán-Tejeda, Raúl Argüello-García, Rosa Ma Bermúdez-Cruz, Guadalupe Ortega-Pierres
Giardia duodenalis is the protozoan parasite responsible for most cases of parasitic diarrhea worldwide. The pathogenic mechanisms of giardiasis have not yet been fully characterized. In this context parasite's excretory/secretory products have been related to the damage induced by the parasite on enterocytes. Among these is the Variable Surface Proteins (VSPs) family involved in antigenic variation and in the induction of protective response. In proteomic analyses carried out to identify the proteases with high molecular weight secreted by Giardia trophozoites during the initial phase of interaction with IEC-6 cell monolayers we identified the VSP9B10A protein...
June 28, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28665408/groel-actively-stimulates-folding-of-the-endogenous-substrate-protein-pepq
#8
Jeremy Weaver, Mengqiu Jiang, Andrew Roth, Jason Puchalla, Junjie Zhang, Hays S Rye
Many essential proteins cannot fold without help from chaperonins, like the GroELS system of Escherichia coli. How chaperonins accelerate protein folding remains controversial. Here we test key predictions of both passive and active models of GroELS-stimulated folding, using the endogenous E. coli metalloprotease PepQ. While GroELS increases the folding rate of PepQ by over 15-fold, we demonstrate that slow spontaneous folding of PepQ is not caused by aggregation. Fluorescence measurements suggest that, when folding inside the GroEL-GroES cavity, PepQ populates conformations not observed during spontaneous folding in free solution...
June 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/28655597/identification-of-host-proteins-predictive-of-early-stage-mycobacterium-tuberculosis-infection
#9
Charles M Bark, Ameur M Manceur, LaShaunda L Malone, Mary Nsereko, Brenda Okware, Harriet K Mayanja, Moses L Joloba, Isabelle Rajotte, Marija Mentinova, Phyla Kay, Seydina Lo, Patrick Tremblay, Catherine M Stein, W Henry Boom, Eustache Paramithiotis
The objective of this study was to identify blood-based protein biomarkers of early stage Mycobacterium tuberculosis (Mtb) infection. We utilized plasma and serum specimens from TB patients and their contacts (age≥12) enrolled in a household contact study in Uganda. In the discovery phase cross-sectional samples from 104 HIV-uninfected persons classified as either active TB, latent Mtb infection (LTBI), tuberculin skin test (TST) converters, or persistent TST-negative were analyzed. Two hundred eighty-nine statistically significant (false discovery rate corrected p<0...
June 20, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28641111/structural-insights-into-modulation-of-neurexin-neuroligin-trans-synaptic-adhesion-by-mdga1-neuroligin-2-complex
#10
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/binding-space-concept-a-new-approach-to-enhance-the-reliability-of-docking-scores-and-its-application-to-predicting-butyrylcholinesterase-hydrolytic-activity
#11
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...
July 10, 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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
Samira Arefi-Oskoui, Alireza Khataee, Vahid Vatanpour
In this research, MgAl-CO3(2-) nanolayered double hydroxide (NLDH) was synthesized through a facile coprecipitation 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 membrane (pure water flux, protein flux and flux recovery ratio) and the affecting parameters including the NLDH, PVP 29000 and polymer concentrations...
June 23, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28584445/a-comparative-molecular-docking-study-of-curcumin-and-methotrexate-to-dihydrofolate-reductase
#19
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
#20
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
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