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Protein interface prediction

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https://www.readbyqxmd.com/read/29159598/etox-allies-an-automated-pipeline-for-linear-interaction-energy-based-simulations
#1
Luigi Capoferri, Marc van Dijk, Ariën S Rustenburg, Tsjerk A Wassenaar, Derk P Kooi, Eko A Rifai, Nico P E Vermeulen, Daan P Geerke
BACKGROUND: Computational methods to predict binding affinities of small ligands toward relevant biological (off-)targets are helpful in prioritizing the screening and synthesis of new drug candidates, thereby speeding up the drug discovery process. However, use of ligand-based approaches can lead to erroneous predictions when structural and dynamic features of the target substantially affect ligand binding. Free energy methods for affinity computation can include steric and electrostatic protein-ligand interactions, solvent effects, and thermal fluctuations, but often they are computationally demanding and require a high level of supervision...
November 21, 2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29155577/identification-of-conserved-water-sites-in-protein-structures-for-drug-design
#2
Marko Jukic, Janez Konc, Stanislav Gobec, Dusanka Janezic
Identification of conserved waters in protein structures is a challenging task with applications in molecular docking and protein stability prediction. As an alternative to computationally demanding simulations of proteins in water, experimental co-crystallized waters in the Protein Data Bank (PDB) in combination with a local structure alignment algorithm can be used for reliable prediction of conserved water sites. We developed the ProBiS H2O approach based on previously developed ProBiS algorithm, which enables identification of conserved water sites in proteins using experimental protein structures from the PDB or a set of custom protein structures available to the user...
November 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29155427/pdb-wide-identification-of-biological-assemblies-from-conserved-quaternary-structure-geometry
#3
Sucharita Dey, David W Ritchie, Emmanuel D Levy
Protein structures are key to understanding biomolecular mechanisms and diseases, yet their interpretation is hampered by limited knowledge of their biologically relevant quaternary structure (QS). A critical challenge in inferring QS information from crystallographic data is distinguishing biological interfaces from fortuitous crystal-packing contacts. Here, we tackled this problem by developing strategies for aligning and comparing QS states across both homologs and data repositories. QS conservation across homologs proved remarkably strong at predicting biological relevance and is implemented in two methods, QSalign and anti-QSalign, for annotating homo-oligomers and monomers, respectively...
November 20, 2017: Nature Methods
https://www.readbyqxmd.com/read/29151691/parallel-mrna-proteomics-and-mirna-expression-analysis-in-cell-line-models-of-the-intestine
#4
Finbarr O'Sullivan, Joanne Keenan, Sinead Aherne, Fiona O'Neill, Colin Clarke, Michael Henry, Paula Meleady, Laura Breen, Niall Barron, Martin Clynes, Karina Horgan, Padraig Doolan, Richard Murphy
AIM: To identify miRNA-regulated proteins differentially expressed between Caco2 and HT-29: two principal cell line models of the intestine. METHODS: Exponentially growing Caco-2 and HT-29 cells were harvested and prepared for mRNA, miRNA and proteomic profiling. mRNA microarray profiling analysis was carried out using the Affymetrix GeneChip Human Gene 1.0 ST array. miRNA microarray profiling analysis was carried out using the Affymetrix Genechip miRNA 3.0 array...
November 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/29151207/rapid-prediction-of-multi-dimensional-nmr-data-sets-using-fandas
#5
Siddarth Narasimhan, Deni Mance, Cecilia Pinto, Markus Weingarth, Alexandre M J J Bonvin, Marc Baldus
Solid-state NMR (ssNMR) can provide structural information at the most detailed level and, at the same time, is applicable in highly heterogeneous and complex molecular environments. In the last few years, ssNMR has made significant progress in uncovering structure and dynamics of proteins in their native cellular environments [1-4]. Additionally, ssNMR has proven to be useful in studying large biomolecular complexes as well as membrane proteins at the atomic level [5]. In such studies, innovative labeling schemes have become a powerful approach to tackle spectral crowding...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29144742/successful-identification-of-cardiac-troponin-calcium-sensitizers-using-a-combination-of-virtual-screening-and-roc-analysis-of-known-troponin-c-binders
#6
Melanie L Aprahamian, Svetlana B Tikunova, Morgan V Price, Andres F Cuesta, Jonathan P Davis, Steffen Lindert
Calcium-dependent cardiac muscle contraction is regulated by the protein complex troponin. Calcium binds to the N-terminal domain of troponin C (cNTnC) which initiates the process of contraction. Heart failure is a consequence of a disruption of this process. With the prevalence of this condition, a strong need exists to find novel compounds to increase the calcium sensitivity of cNTnC. Desirable are small chemical molecules that bind to the interface between cTnC and the cTnI switch peptide and exhibit calcium sensitizing properties by possibly stabilizing cTnC in an open conformation...
November 16, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29141686/anisotropic-m%C3%A3-ller-glial-scaffolding-supports-a-multiplex-lattice-mosaic-of-photoreceptors-in-zebrafish-retina
#7
Mikiko Nagashima, Jeremy Hadidjojo, Linda K Barthel, David K Lubensky, Pamela A Raymond
BACKGROUND: The multiplex, lattice mosaic of cone photoreceptors in the adult fish retina is a compelling example of a highly ordered epithelial cell pattern, with single cell width rows and columns of cones and precisely defined neighbor relationships among different cone types. Cellular mechanisms patterning this multiplex mosaic are not understood. Physical models can provide new insights into fundamental mechanisms of biological patterning. In earlier work, we developed a mathematical model of photoreceptor cell packing in the zebrafish retina, which predicted that anisotropic mechanical tension in the retinal epithelium orients planar polarized adhesive interfaces to align the columns as cone photoreceptors are generated at the retinal margin during post-embryonic growth...
November 15, 2017: Neural Development
https://www.readbyqxmd.com/read/29140522/ecodrug-a-database-connecting-drugs-and-conservation-of-their-targets-across-species
#8
Bas Verbruggen, Lina Gunnarsson, Erik Kristiansson, Tobias Österlund, Stewart F Owen, Jason R Snape, Charles R Tyler
Pharmaceuticals are designed to interact with specific molecular targets in humans and these targets generally have orthologs in other species. This provides opportunities for the drug discovery community to use alternative model species for drug development. It also means, however, there is potential for mode of action related effects in non-target wildlife species as many pharmaceuticals reach the environment through patient use and manufacturing wastes. Acquiring insight in drug target ortholog predictions across species and taxonomic groups has proven difficult because of the lack of an optimal strategy and because necessary information is spread across multiple and diverse sources and platforms...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29136213/knottin-the-database-of-inhibitor-cystine-knot-scaffold-after-10-years-toward-a-systematic-structure-modeling
#9
Guillaume Postic, Jérôme Gracy, Charlotte Périn, Laurent Chiche, Jean-Christophe Gelly
Knottins, or inhibitor cystine knots (ICKs), are ultra-stable miniproteins with multiple applications in drug design and medical imaging. These widespread and functionally diverse proteins are characterized by the presence of three interwoven disulfide bridges in their structure, which form a unique pseudoknot. Since 2004, the KNOTTIN database (www.dsimb.inserm.fr/KNOTTIN/) has been gathering standardized information about knottin sequences, structures, functions and evolution. The website also provides access to bibliographic data and to computational tools that have been specifically developed for ICKs...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29127686/the-challenge-of-modeling-protein-assemblies-the-casp12-capri-experiment
#10
Marc F Lensink, Sameer Velankar, Minkyung Baek, Lim Heo, Chaok Seok, Shoshana J Wodak
We present the quality assessment of 5613 models submitted by predictor groups from both CAPRI and CASP for the total of 15 most tractable targets from the second joint CASP-CAPRI protein assembly prediction experiment. These targets comprised 12 homo-oligomers and 3 hetero-complexes. The bulk of the analysis focuses on 10 targets (of CAPRI Round 37), which included all 3 hetero-complexes, and whose protein chains or the full assembly could be readily modeled from structural templates in the PDB. On average, 28 CAPRI groups and 10 CASP groups (including automatic servers), submitted models for each of these 10 targets...
November 10, 2017: Proteins
https://www.readbyqxmd.com/read/29126218/libra-wa-a-web-application-for-ligand-binding-site-detection-and-protein-function-recognition
#11
Daniele Toti, Viet Hung Le, Valentina Tortosa, Valentina Brandi, Fabio Polticelli
Summary: Recently, LIBRA, a tool for active/ligand binding site prediction, was described. LIBRA's effectiveness was comparable to similar state-of-the-art tools; however, its scoring scheme, output presentation, dependence on local resources and overall convenience were amenable to improvements. To solve these issues, LIBRA-WA, a web application based on an improved LIBRA engine, has been developed, featuring a novel scoring scheme consistently improving LIBRA's performance, and a refined algorithm that can identify binding sites hosted at the interface between different subunits...
November 6, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29126202/activedriverdb-human-disease-mutations-and-genome-variation-in-post-translational-modification-sites-of-proteins
#12
Michal Krassowski, Marta Paczkowska, Kim Cullion, Tina Huang, Irakli Dzneladze, B F Francis Ouellette, Joseph T Yamada, Amelie Fradet-Turcotte, Jüri Reimand
Interpretation of genetic variation is needed for deciphering genotype-phenotype associations, mechanisms of inherited disease, and cancer driver mutations. Millions of single nucleotide variants (SNVs) in human genomes are known and thousands are associated with disease. An estimated 21% of disease-associated amino acid substitutions corresponding to missense SNVs are located in protein sites of post-translational modifications (PTMs), chemical modifications of amino acids that extend protein function. ActiveDriverDB is a comprehensive human proteo-genomics database that annotates disease mutations and population variants through the lens of PTMs...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29114958/evidence-for-multiple-modes-of-neutrophil-serine-protease-recognition-by-the-eap-family-of-staphylococcal-innate-immune-evasion-proteins
#13
Daphne A C Stapels, Jordan L Woehl, Fin J Milder, Angelino T Tromp, Aernoud A van Batenburg, Wilco C de Graaf, Samuel C Broll, Natalie M White, Suzan H M Rooijakkers, Brian V Geisbrecht
Neutrophils contain high levels of chymotrypsin-like serine proteases (NSPs) within their azurophilic granules that have a multitude of functions within the immune system. In response, the pathogen Staphylococcus aureus has evolved three potent inhibitors (Eap, EapH1, and EapH2) that protect the bacterium as well as several of its secreted virulence factors from the degradative action of NSPs. We previously showed that these so-called EAP domain proteins represent a novel class of NSP inhibitors characterized by a non-covalent inhibitory mechanism and a distinct target specificity profile...
November 7, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29110180/correlation-between-the-molecular-effects-of-mutations-at-the-dimer-interface-of-alanine-glyoxylate-aminotransferase-leading-to-primary-hyperoxaluria-type-i-and-the-cellular-response-to-vitamin-b6
#14
Mirco Dindo, Elisa Oppici, Daniele Dell'Orco, Rosa Montone, Barbara Cellini
Primary hyperoxaluria type I (PH1) is a rare disease caused by the deficit of liver alanine-glyoxylate aminotransferase (AGT). AGT prevents oxalate formation by converting peroxisomal glyoxylate to glycine. When the enzyme is deficient, progressive calcium oxalate stones deposit first in the urinary tract and then at the systemic level. Pyridoxal 5'-phosphate (PLP), the AGT coenzyme, exerts a chaperone role by promoting dimerization, as demonstrated by studies at protein and cellular level. Thus, variants showing a destabilized dimeric structure should, in principle, be responsive to vitamin B6, a precursor of PLP...
November 6, 2017: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/29109150/role-of-salt-bridges-in-the-dimer-interface-of-14-3-3%C3%AE-in-dimer-dynamics-n-terminal-%C3%AE-helical-order-and-molecular-chaperone-activity
#15
Joanna M Woodcock, Katy L Goodwin, Jarrod J Sandow, Carl Coolen, Matthew A Perugini, Andrew I Webb, Stuart M Pitson, Angel F Lopez, John A Carver
The 14-3-3 family of intracellular proteins are dimeric, multi-functional adaptor proteins that bind to and regulate the activities of many important signaling proteins. The subunits within 14-3-3 dimers are predicted to be stabilized by salt bridges that are largely conserved across the 14-3-3 protein family and allow the different isoforms to form heterodimers. Here, we have examined the contributions of conserved salt-bridging residues in stabilizing the dimeric state of 14-3-3ζ. Using analytical ultracentrifugation, our results revealed that Asp-21 and Glu-89 both play key roles in dimer dynamics and contribute to dimer stability...
November 6, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29106933/prediction-of-host-pathogen-interactions-for-helicobacter-pylori-by-interface-mimicry-and-implications-to-gastric-cancer
#16
Emine Guven-Maiorov, Chung-Jung Tsai, Buyong Ma, Ruth Nussinov
There is a strong correlation between some pathogens and certain cancer types. One example is Helicobacter pylori and gastric cancer. Exactly how they contribute to host tumorigenesis is however a mystery. Pathogens often interact with the host through proteins. To subvert defense, they may mimic host proteins at the sequence, structure, motif or interface levels. Interface similarity permits pathogen proteins to compete with those of the host for a target protein, and thereby alter the host signaling. Detection of host-pathogen interactions (HPIs) and mapping the re-wired superorganism HPI network - with structural details - can provide unprecedented clues to the underlying mechanisms and help therapeutics...
October 26, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29092940/dinc-2-0-a-new-protein-peptide-docking-webserver-using-an-incremental-approach
#17
Dinler A Antunes, Mark Moll, Didier Devaurs, Kyle R Jackson, Gregory Lizée, Lydia E Kavraki
Molecular docking is a standard computational approach to predict binding modes of protein-ligand complexes by exploring alternative orientations and conformations of the ligand (i.e., by exploring ligand flexibility). Docking tools are largely used for virtual screening of small drug-like molecules, but their accuracy and efficiency greatly decays for ligands with more than 10 flexible bonds. This prevents a broader use of these tools to dock larger ligands, such as peptides, which are molecules of growing interest in cancer research...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29091310/design-of-inhibitory-peptide-targeting-toxoplasma-gondii-ron4-human-%C3%AE-tubulin-interactions-by-implementing-structural-bioinformatics-methods
#18
Umashankar Vetrivel, Hemavathy Nagarajan, Indhuja Thirumudi
Toxoplasma gondii an obligate intracellular parasite causes toxoplasmosis in homeothermic animals. Host invasion of this parasite is mediated by the formation of Moving Junction (MJ) complex which encompasses a network of microneme and Rhoptry Neck proteins (RONs) 2/4/5/8. Among these proteins, RON4 is the only cytosolic secretory protein that is considered as a crucial member, as it directly facilitates the motility of MJ complex by interacting with host tubulin. It is also prominently localised at the host-pathogen interface during the invasion, thus projecting it as a potential drug target...
November 1, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29082672/critical-assessment-of-methods-of-protein-structure-prediction-casp-round-xii
#19
John Moult, Krzysztof Fidelis, Andriy Kryshtafovych, Torsten Schwede, Anna Tramontano
This paper reports the outcome of the 12th round of Critical Assessment of Structure Prediction (CASP12), held in 2016. CASP is a community experiment to determine the state of the art in modeling protein structure from amino acid sequence. Participants are provided sequence information and in turn provide protein structure models and related information. Analysis of the submitted structures by independent assessors provides a comprehensive picture of the capabilities of current methods, and allows progress to be identified...
October 30, 2017: Proteins
https://www.readbyqxmd.com/read/29071742/assessment-of-protein-assembly-prediction-in-casp12-casp12-assembly
#20
Aleix Lafita, Spencer Bliven, Andriy Kryshtafovych, Martino Bertoni, Bohdan Monastyrskyy, Jose M Duarte, Torsten Schwede, Guido Capitani
We present the results of the first independent assessment of protein assemblies in CASP. A total of 1,624 oligomeric models were submitted by 108 predictor groups for the 30 oligomeric targets in the CASP12 edition. The target assemblies were of diverse topology, composition and prediction difficulty, including eight heteromeric complexes, five viral fibre heads, four dihedral homomers and two membrane dimers. We evaluated the accuracy of oligomeric predictions by comparison to their experimentally determined reference structures at the interface patch and residue contact levels...
October 26, 2017: Proteins
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