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Protein contact prediction

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https://www.readbyqxmd.com/read/28811207/anion-%C3%AF-interactions-in-active-centers-of-superoxide-dismutases
#1
Vesna R Ribić, Srđan Đ Stojanović, Mario V Zlatović
We investigated 1060 possible anion-π interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-π interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-π interactions. Anion-π interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-π interactions using ab initio calculations...
August 12, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28806086/role-of-electrostatics-in-protein-rna-binding-the-global-vs-the-local-energy-landscape
#2
Zhaleh Ghaemi, Irisbel Guzman, David Gnutt, Zaida Luthey-Schulten, Martin Gruebele
U1A protein - stem loop 2 RNA association is a basic step in the assembly of the spliceosomal U1 small nuclear ribonucleoprotein. Long-range electrostatic interactions due to the positive charge of U1A are thought to provide high binding affinity for the negatively charged RNA. Short range interactions, such as hydrogen bonds and contacts between RNA bases and protein side chains, favor a specific binding site. Here, we propose that electrostatic interactions are as important as local contacts in biasing the protein-RNA energy landscape towards a specific binding site...
August 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28805214/the-low-populated-folding-intermediate-of-a-mutant-of-the-fyn-sh3-domain-identified-by-a-simple-model
#3
Jing Wu, Guojun Chen, Zhuqing Zhang, Ping Zhang, Tao Chen
Experimental studies indicate that the A39V/N53P/V55L Fyn SH3 domain folds from the unfolded state to the native state via a low-populated on-pathway intermediate, whereas the folding of the wildtype is two-state-like. To get insights into the biophysical basis of their different folding mechanisms, we used native-centric models with and without additional transferrable, sequence-dependent nonnative hydrophobic interactions to study the folding behaviors of the Fyn SH3 domain and its mutant. The pure native-centric model predicts that both the wildtype and the mutant fold in a two-state manner, without any detectable intermediate...
August 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28801570/the-buckling-instability-of-aggregating-red-blood-cells
#4
Daniel Flormann, Othmane Aouane, Lars Kaestner, Christian Ruloff, Chaouqi Misbah, Thomas Podgorski, Christian Wagner
Plasma proteins such as fibrinogen induce the aggregation of red blood cells (RBC) into rouleaux, which are responsible for the pronounced shear thinning behavior of blood, control the erythrocyte sedimentation rate (ESR) - a common hematological test - and are involved in many situations of physiological relevance such as structuration of blood in the microcirculation or clot formation in pathological situations. Confocal microscopy is used to characterize the shape of RBCs within rouleaux at equilibrium as a function of macromolecular concentration, revealing the diversity of contact zone morphology...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28799172/protein-structure-prediction-making-awsem-awsem-er-by-adding-evolutionary-restraints
#5
Brian J Sirovetz, Nicholas P Schafer, Peter G Wolynes
Protein sequences have evolved to fold into functional structures, resulting in families of diverse protein sequences that all share the same overall fold. One can harness protein family sequence data to infer likely contacts between pairs of residues. In the current study, we combine this kind of inference from coevolutionary information with a coarse-grained protein force field ordinarily used with single sequence input, the Associative memory, Water mediated, Structure and Energy Model (AWSEM), to achieve improved structure prediction...
August 11, 2017: Proteins
https://www.readbyqxmd.com/read/28791516/nlscore-a-novel-quantitative-algorithm-based-on-3-dimensional-structural-determinants-to-predict-the-probability-of-nuclear-localization-in-proteins-containing-classical-nuclear-localization-signals
#6
P S Hari, T S Sridhar, R Pravin Kumar
The presence of a nuclear localization signal (NLS) in proteins can be inferred by the presence of a stretch of basic amino acids (KRKK). These NLSs are termed classical NLS (cNLS). However, only a fraction of proteins containing the cNLS pattern are transported into the nucleus by binding to importin α. Hence, there must exist, additional structural determinants that guide the appropriate interaction between putative NLSs containing cargo and importin α. Using 52 protein structures containing cNLS obtained from RCSB PDB, we assembled a training set and a validation set such that both sets were comprised of a combination of proteins with proven nuclear localization and ones that were non-nuclear...
August 9, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28764156/improved-serodiagnostic-sensitivity-of-strip-test-for-latent-tuberculosis
#7
Songsri Kasempimolporn, Wichit Thaveekarn, Kanyanat Promrungreang, Orawan Khow, Supatsorn Boonchang, Visith Sitprija
INTRODUCTION: Diagnosis of Latent Tuberculosis Infection (LTBI) is difficult due to no clinical manifestations. Cases of LTBI are mostly sputum negative. The World Health Organization recommends the Tuberculin Skin Test (TST) as the current diagnostic standard for LTBI. Our previously developed serologic strip test for LTBI detection had suboptimal sensitivity. Additional Mycobacteriumtuberculosis (MTB) latency-associated antigens may improve the detection rate of LTBI. AIM: The present study aimed to optimize sensitivity of existing strip test...
June 2017: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/28722347/foxo3-longevity-interactome-on-chromosome-6
#8
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
#9
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
#10
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 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
#11
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
#12
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
#13
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
#14
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...
August 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28665408/groel-actively-stimulates-folding-of-the-endogenous-substrate-protein-pepq
#15
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
#16
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...
July 2017: EBioMedicine
https://www.readbyqxmd.com/read/28641111/structural-insights-into-modulation-of-neurexin-neuroligin-trans-synaptic-adhesion-by-mdga1-neuroligin-2-complex
#17
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
#18
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
#19
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
#20
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
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