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Protein interface 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/28637867/full-length-cellular-beta-secretase-has-a-trimeric-subunit-stoichiometry-and-its-sulfur-rich-transmembrane-interaction-site-modulates-cytosolic-copper-compartmentalization
#2
Filip Liebsch, Mark R P Aurousseau, Tobias Bethge, Hugo McGuire, Silvia Scolari, Andreas Herrmann, Rikard Blunck, Derek Bowie, Gerd Multhaup
The beta-secretase (BACE1) initiates processing of the amyloid precursor protein (APP) into Aβ peptides, which have been implicated as central players in the pathology of Alzheimer disease. BACE1 has been described as a copper-binding protein and its oligomeric state as being monomeric, dimeric, and/or multimeric, but the native cellular stoichiometry has remained elusive. Here, by using single-molecule fluorescence and in vitro cross-linking experiments with photo-activatable unnatural amino acids, we show that full-length BACE1, independently of its subcellular localization, exists as trimers in human cells...
June 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28636918/actin-filament-strain-promotes-severing-and-cofilin-dissociation
#3
Anthony C Schramm, Glen M Hocky, Gregory A Voth, Laurent Blanchoin, Jean-Louis Martiel, Enrique M De La Cruz
Computational and structural studies have been indispensable in investigating the molecular origins of actin filament mechanical properties and modulation by the regulatory severing protein cofilin. All-atom molecular dynamics simulations of cofilactin filament structures determined by electron cryomicroscopy reveal how cofilin enhances the bending and twisting compliance of actin filaments. Continuum mechanics models suggest that buckled cofilactin filaments localize elastic energy at boundaries between bare and cofilin-decorated segments because of their nonuniform elasticity, thereby accelerating filament severing...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28602916/structural-investigation-of-a-c-terminal-epha2-receptor-mutant-does-mutation-affect-the-structure-and-interaction-properties-of-the-sam-domain
#4
Flavia A Mercurio, Susan Costantini, Concetta Di Natale, Luciano Pirone, Stefano Guariniello, Pasqualina L Scognamiglio, Daniela Marasco, Emilia M Pedone, Marilisa Leone
Ephrin A2 receptor (EphA2) plays a key role in cancer, it is up-regulated in several types of tumors and the process of ligand-induced receptor endocytosis, followed by degradation, is considered as a potential path to diminish tumor malignancy. Protein modulators of this mechanism are recruited at the cytosolic Sterile alpha motif (Sam) domain of EphA2 (EphA2-Sam) through heterotypic Sam-Sam associations. These interactions engage the C-terminal helix of EphA2 and close loop regions (the so called End Helix side)...
June 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28587924/prmt7-interacts-with-ass1-and-citrullinemia-mutations-disrupt-the-interaction
#5
Mamta Verma, Ramya Chandar M Charles, Baskar Chakrapani, Mohane Selvaraj Coumar, Gayathri Govindaraju, Arumugam Rajavelu, Sreenivas Chavali, Arunkumar Dhayalan
Protein Arginine Methyltransferase 7 (PRMT7) catalyzes the introduction of mono methylation marks at the arginine residues of substrate proteins. PRMT7 plays important roles in the regulation of gene expression, splicing, DNA damage, paternal imprinting, cancer and metastasis. However, little is known about the interaction partners of PRMT7. To address this, we performed yeast two hybrid screening of PRMT7 and identified argininosuccinate synthetase (ASS1) as a potential interaction partner of PRMT7. We confirmed that PRMT7 directly interacts with ASS1 using pull down studies...
June 3, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28587674/navise-superenhancer-navigator-integrating-epigenomics-signal-algebra
#6
Alex M Ascensión, Mikel Arrospide-Elgarresta, Ander Izeta, Marcos J Araúzo-Bravo
BACKGROUND: Superenhancers are crucial structural genomic elements determining cell fate, and they are also involved in the determination of several diseases, such as cancer or neurodegeneration. Although there are pipelines which use independent pieces of software to predict the presence of superenhancers from genome-wide chromatin marks or DNA-interaction protein binding sites, there is not yet an integrated software tool that processes automatically algebra combinations of raw data sequencing into a comprehensive final annotated report of predicted superenhancers...
June 6, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28575181/deepsite-protein-binding-site-predictor-using-3d-convolutional-neural-networks
#7
J Jiménez, S Doerr, G Martínez-Rosell, A S Rose, G De Fabritiis
Motivation: An important step in structure-based drug design consists in the prediction of druggable binding sites. Several algorithms for detecting binding cavities, those likely to bind to a small drug compound, have been developed over the years by clever exploitation of geometric, chemical and evolutionary features of the protein. Results: Here we present a novel knowledge-based approach that uses state-of-the-art convolutional neural networks, where the algorithm is learned by examples...
May 31, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28573570/the-sticky-patch-model-of-crystallization-and-modification-of-proteins-for-enhanced-crystallizability
#8
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/28556501/a-three-gene-signature-from-protein-protein-interaction-network-of-loxl2-and-actin-related-proteins-for-esophageal-squamous-cell-carcinoma-prognosis
#9
Xiu-Hui Zhan, Ji-Wei Jiao, Hai-Feng Zhang, Chun-Quan Li, Jian-Mei Zhao, Lian-di Liao, Jian-Yi Wu, Bing-Li Wu, Zhi-Yong Wu, Shao-Hong Wang, Ze-Peng Du, Jin-Hui Shen, Hai-Ying Zou, Gera Neufeld, Li-Yan Xu, En-Min Li
Current staging is inadequate for predicting clinical outcome of esophageal squamous cell carcinoma (ESCC). Aberrant expression of LOXL2 and actin-related proteins plays important roles in ESCC. Here, we aimed to develop a novel molecular signature that exceeds the power of the current staging system in predicting ESCC prognosis. We found that LOXL2 colocalized with filamentous actin in ESCC cells, and gene set enrichment analysis (GSEA) showed that LOXL2 is related to the actin cytoskeleton. An ESCC-specific protein-protein interaction (PPI) network involving LOXL2 and actin-related proteins was generated based on genome-wide RNA-seq in 15 paired ESCC samples, and the prognostic significance of 14 core genes was analyzed...
May 29, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28553984/modulation-of-coiled-coil-dimer-stability-through-surface-residues-while-preserving-pairing-specificity
#10
Igor Drobnak, Helena Gradišar, Ajasja Ljubetič, Estera Merljak, Roman Jerala
The coiled-coil dimer is a widespread protein structural motif and, due to its designability, represents an attractive building block for assembling modular nanostructures. The specificity of coiled-coil dimer pairing is mainly based on hydrophobic and electrostatic interactions between residues at positions a, d, e, and g of the heptad repeat. Binding affinity, on the other hand, can also be affected by surface residues that face away from the dimerization interface. Here we show how design of the local helical propensity of interacting peptides can be used to tune the stabilities of coiled-coil dimers over a wide range...
June 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28548025/reprogramming-the-oncogenic-response-set-protein-as-a-potential-therapeutic-target-in-cancer
#11
Man-Hsin Hung, Kuen-Feng Chen
SET is a multitask oncoprotein that promotes the initiation and progression of cancer. Overexpression of SET has been characterized as being tumor-specific and is associated with adverse clinical outcomes in many different human malignant diseases. Notably, SET has been shown to promote the development of therapeutic resistance in cancer cells. Area covered: In this review, we summarized the currently available evidence relating to the oncogenic roles, biological functions and clinical relevance of SET protein in cancer...
June 6, 2017: Expert Opinion on Therapeutic Targets
https://www.readbyqxmd.com/read/28541224/protein-protein-interaction-interface-residue-pair-prediction-based-on-deep-learning-architecture
#12
Zhenni Zhao, Xinqi Gong
MOTIVATION: Proteins usually fulfill their biological functions by interacting with other proteins. Although some methods have been developed to predict the binding sites of a monomer protein, these are not sufficient for prediction of the interaction between two monomer proteins. The correct prediction of interface residue pairs from two monomer proteins is still an open question and has great significance for practical experimental applications in the life sciences. We hope to build a method for the prediction of interface residue pairs that is suitable for those applications...
May 19, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28528879/functional-annotation-and-analysis-of-the-ornithodoros-moubata-midgut-genes-differentially-expressed-after-blood-feeding
#13
Ana Oleaga, Prosper Obolo-Mvoulouga, Raúl Manzano-Román, Ricardo Pérez-Sánchez
The argasid tick Ornithodoros moubata is the main vector of the African swine fever and the human relapsing fever in Africa. As part of the host-parasite-pathogen interface, the tick midgut expresses key proteins for tick survival and tick-borne pathogen transmission. Accordingly, midgut proteins are potential targets for the development of new drugs and vaccines aimed at tick control, and obtaining proteomic and transcriptomic data from the O. moubata midgut would facilitate the identification of such target candidates...
May 13, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28514864/application-of-advanced-sampling-and-analysis-methods-to-predict-the-structure-of-adsorbed-protein-on-a-material-surface
#14
Tigran M Abramyan, David L Hyde-Volpe, Steven J Stuart, Robert A Latour
The use of standard molecular dynamics simulation methods to predict the interactions of a protein with a material surface have the inherent limitations of lacking the ability to determine the most likely conformations and orientations of the adsorbed protein on the surface and to determine the level of convergence attained by the simulation. In addition, standard mixing rules are typically applied to combine the nonbonded force field parameters of the solution and solid phases the system to represent interfacial behavior without validation...
May 17, 2017: Biointerphases
https://www.readbyqxmd.com/read/28513090/benchmarking-a-computational-design-method-for-the-incorporation-of-metal-ion-binding-sites-at-symmetric-protein-interfaces
#15
William A Hansen, Sagar D Khare
The design of novel metal-ion binding sites along symmetric axes in protein oligomers could provide new avenues for metalloenzyme design, construction of protein-based nanomaterials and novel ion transport systems. Here, we describe a computational design method, Symmetric Protein Recursive Ion-cofactor Sampling (SyPRIS), for locating constellations of backbone positions within oligomeric protein structures that are capable of supporting desired symmetrically coordinated metal ion(s) chelated by sidechains (chelant model)...
May 15, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28512576/applications-of-contact-predictions-to-structural-biology
#16
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/28507948/characterizing-the-hot-spots-involved-in-ron-msp%C3%AE-complex-formation-using-in-silico-alanine-scanning-mutagenesis-and-molecular-dynamics-simulation
#17
Omid Zarei, Maryam Hamzeh-Mivehroud, Silvia Benvenuti, Fulya Ustun-Alkan, Siavoush Dastmalchi
Purpose: Implication of protein-protein interactions (PPIs) in development of many diseases such as cancer makes them attractive for therapeutic intervention and rational drug design. RON (Recepteur d'Origine Nantais) tyrosine kinase receptor has gained considerable attention as promising target in cancer therapy. The activation of RON via its ligand, macrophage stimulation protein (MSP) is the most common mechanism of activation for this receptor. The aim of the current study was to perform in silico alanine scanning mutagenesis and to calculate binding energy for prediction of hot spots in protein-protein interface between RON and MSPβ chain (MSPβ)...
April 2017: Advanced Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28505313/structural-study-of-the-fox-1-rrm-protein-hydration-reveals-a-role-for-key-water-molecules-in-rrm-rna-recognition
#18
Miroslav Krepl, Markus Blatter, Antoine Cléry, Fred F Damberger, Frédéric H T Allain, Jiri Sponer
The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface...
May 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28505312/soda-prediction-of-protein-solubility-from-disorder-and-aggregation-propensity
#19
Lisanna Paladin, Damiano Piovesan, Silvio C E Tosatto
Solubility is an important, albeit not well understood, feature determining protein behavior. It is of paramount importance in protein engineering, where similar folded proteins may behave in very different ways in solution. Here we present SODA, a novel method to predict the changes of protein solubility based on several physico-chemical properties of the protein. SODA uses the propensity of the protein sequence to aggregate as well as intrinsic disorder, plus hydrophobicity and secondary structure preferences to estimate changes in solubility...
May 13, 2017: Nucleic Acids Research
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
#20
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 2017: PLoS Genetics
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