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Protein interface prediction

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https://www.readbyqxmd.com/read/28548025/reprogramming-the-oncogenic-response-set-protein-as-a-potential-therapeutic-target-in-cancer
#1
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...
May 26, 2017: Expert Opinion on Therapeutic Targets
https://www.readbyqxmd.com/read/28541224/protein-protein-interaction-interface-residue-pair-prediction-based-on-deep-learning-architecture
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28499008/rippminer-a-bioinformatics-resource-for-deciphering-chemical-structures-of-ripps-based-on-prediction-of-cleavage-and-cross-links
#11
Priyesh Agrawal, Shradha Khater, Money Gupta, Neetu Sain, Debasisa Mohanty
Ribosomally synthesized and post-translationally modified peptides (RiPPs) constitute a rapidly growing class of natural products with diverse structures and bioactivities. We have developed RiPPMiner, a novel bioinformatics resource for deciphering chemical structures of RiPPs by genome mining. RiPPMiner derives its predictive power from machine learning based classifiers, trained using a well curated database of more than 500 experimentally characterized RiPPs. RiPPMiner uses Support Vector Machine to distinguish RiPP precursors from other small proteins and classify the precursors into 12 sub-classes of RiPPs...
May 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28497966/large-scale-analysis-of-hydrogen-bond-interaction-patterns-in-protein-ligand-interfaces
#12
Eva Nittinger, Therese Inhester, Stefan Bietz, Agnes Meyder, Karen T Schomburg, Gudrun Lange, Robert Klein, Matthias Rarey
Protein-ligand interactions are the fundamental basis for molecular design in pharmaceutical research, biocatalysis, and agrochemical development. Especially hydrogen bonds are known to have special geometric requirements and therefore deserve a detailed analysis. In modeling approaches a more general description of hydrogen bond geometries, using distance and directionality, is applied. A first study of their geometries was performed based on 15 protein structures in 1982. Currently there are about 95 000 protein-ligand structures available in the PDB, providing a solid foundation for a new large-scale statistical analysis...
May 12, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28495885/proteolytic-cleavage-of-the-hydrophobic-domain-in-the-cav%C3%AE-2%C3%AE-1-subunit-improves-assembly-and-activity-of-cardiac-cav1-2-channels
#13
Emilie Segura, Benoîte Bourdin, Marie-Philippe Tétreault, Julie Briot, Bruce G Allen, Gaétan Mayer, Lucie Parent
Voltage-gated L-type CaV1.2 channels in cardiomyocytes exist as heteromeric complexes with the pore-forming CaVα1, CaVβ, and CaVα2δ1 subunits. The full complement of subunits is required to reconstitute the native-like properties of L-type Ca(2+) currents but the molecular determinants responsible for the formation of the heteromeric complex are still being studied. Enzymatic treatment with PI-PLC, a phospholipase C specific for the cleavage of glycosyl-phosphatidylinositol (GPI)-anchored proteins, disrupted plasma membrane localization of the cardiac CaVα2δ1 prompting us to investigate deletions of its hydrophobic transmembrane domain...
May 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28495207/targeting-the-hsp90-c-terminal-domain-to-induce-allosteric-inhibition-and-selective-client-downregulation
#14
Kourtney M Goode, Dino Petrov, Renee E Vickman, Scott A Crist, Pete E Pascuzzi, Tim L Ratliff, V Jo Davisson, Tony R Hazbun
BACKGROUND: Inhibition of Hsp90 is desirable due to potential downregulation of oncogenic clients. Early generation inhibitors bind to the N-terminal domain (NTD) but C-terminal domain (CTD) inhibitors are a promising class because they do not induce a heat shock response. Here we present a new structural class of CTD binding molecules with a unique allosteric inhibition mechanism. METHODS: A hit molecule, NSC145366, and structurally similar probes were assessed for inhibition of Hsp90 activities...
May 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28494966/mechanotransduction-dynamics-at-the-cell-matrix-interface
#15
Seth H Weinberg, Devin B Mair, Christopher A Lemmon
The ability of cells to sense and respond to mechanical cues from the surrounding environment has been implicated as a key regulator of cell differentiation, migration, and proliferation. The extracellular matrix (ECM) is an oft-overlooked component of the interface between cells and their surroundings. Cells assemble soluble ECM proteins into insoluble fibrils with unique mechanical properties that can alter the mechanical cues a cell receives. In this study, we construct a model that predicts the dynamics of cellular traction force generation and subsequent assembly of fibrils of the ECM protein fibronectin (FN)...
May 9, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28472372/proteinsplus-a-web-portal-for-structure-analysis-of-macromolecules
#16
Rainer Fährrolfes, Stefan Bietz, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Thomas Otto, Andrea Volkamer, Matthias Rarey
With currently more than 126 000 publicly available structures and an increasing growth rate, the Protein Data Bank constitutes a rich data source for structure-driven research in fields like drug discovery, crop science and biotechnology in general. Typical workflows in these areas involve manifold computational tools for the analysis and prediction of molecular functions. Here, we present the ProteinsPlus web server that offers a unified easy-to-use interface to a broad range of tools for the early phase of structure-based molecular modeling...
May 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28469201/flagellar-hooks-and-hook-protein-flge-participate-in-host-microbe-interactions-at-immunological-level
#17
Ying Shen, Lin Chen, Meixiang Wang, Dandan Lin, Zhongjie Liang, Peiqing Song, Qing Yuan, Hua Tang, Weihua Li, Kangmin Duan, Baiyan Liu, Ge Zhao, Yiqiang Wang
Host-microbe interactions determine the outcome of host responses to commensal and pathogenic microbes. Previously, two epithelial cell-binding peptides were found to be homologues of two sites (B, aa168-174; F, aa303-309) in the flagellar hook protein FlgE of Pseudomonas aeruginosa. Tertiary modeling predicted these sites at the interface of neighboring FlgE monomers in the fully formed hook. Recombinant FlgE protein stimulated proinflammatory cytokine production in a human cell line and in murine lung organoid culture as detected with real-time RT-PCR and ELISA assays...
May 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28464870/comparative-analysis-of-the-predicted-secretomes-of-rosaceae-scab-pathogens-venturia-inaequalis-and-v-pirina-reveals-expanded-effector-families-and-putative-determinants-of-host-range
#18
Cecilia H Deng, Kim M Plummer, Darcy A B Jones, Carl H Mesarich, Jason Shiller, Adam P Taranto, Andrew J Robinson, Patrick Kastner, Nathan E Hall, Matthew D Templeton, Joanna K Bowen
BACKGROUND: Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuticular space without penetrating plant cells, it is assumed that effectors that contribute to virulence and determination of host range will be secreted into this plant-pathogen interface...
May 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28460610/a-perspective-on-water-site-prediction-methods-for-structure-based-drug-design
#19
Alan P Graves, Ian D Wall, Colin M Edge, James M Woolven, Guanglei Cui, Armelle Le Gall, Xuan Hong, Kaushik Raha, Eric S Manas
Over the last decade a number of computational methods have been developed, which attempt to evaluate the thermodynamic properties of individual water molecules at the solute-solvent interface, in order to assess contributions to protein-ligand binding. In some cases these tools tell us what we already know, e.g. that hydrophobic pockets prefer lipophilic substituents, and in other cases the methods only seem to add clarity when retrospectively applied. Hence we have grappled with how to utilize such approaches to understand non-intuitive results and to generate chemistry ideas that otherwise would not have been developed...
April 26, 2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/28453653/the-bologna-annotation-resource-bar-3-0-improving-protein-functional-annotation
#20
Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio
BAR 3.0 updates our server BAR (Bologna Annotation Resource) for predicting protein structural and functional features from sequence. We increase data volume, query capabilities and information conveyed to the user. The core of BAR 3.0 is a graph-based clustering procedure of UniProtKB sequences, following strict pairwise similarity criteria (sequence identity ≥40% with alignment coverage ≥90%). Each cluster contains the available annotation downloaded from UniProtKB, GO, PFAM and PDB. After statistical validation, GO terms and PFAM domains are cluster-specific and annotate new sequences entering the cluster after satisfying similarity constraints...
April 27, 2017: Nucleic Acids Research
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