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Protein contact prediction

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https://www.readbyqxmd.com/read/28326907/skin-sensitizers-in-cosmetics-and-beyond-potential-multiple-mechanisms-of-action-and-importance-of-t-cell-assays-for-in-vitro-screening
#1
Stanislav Vukmanović, Nakissa Sadrieh
Allergic contact dermatitis (ACD) is a delayed-type hypersensitivity (DTH) reaction induced by repeated contact with sensitizers. The ability of a chemical to act as a sensitizer has most frequently been tested in animals. As the use of animals for these purposes is gradually and globally being phased out, there is a need for reliable in vitro surrogate assays. Currently proposed in vitro assays are designed to test four key events of the adverse outcome pathway (AOP) involving covalent modification of self-proteins by sensitizers (haptenation) and presentation of new antigens (hapten/carrier complexes) to the immune system...
March 22, 2017: Critical Reviews in Toxicology
https://www.readbyqxmd.com/read/28317069/deciphering-the-role-of-ectosomes-in-cancer-development-and-progression-focus-on-the-proteome
#2
REVIEW
Magdalena Surman, Ewa Stępień, Dorota Hoja-Łukowicz, Małgorzata Przybyło
Ectosomes are small heterogeneous membrane vesicles generated by budding from the plasma membrane in a variety of cell types and, more frequently, in tumor cells. They are shed into the extracellular space and are proposed as a novel form of intracellular communication in which information is transmitted from the originating cell to recipient cells without direct cell-to-cell contact. This review focuses on a single population of extracellular vesicles-ectosomes. We summarize recent studies of tumor-derived ectosomes which examine their biogenesis and protein cargo, and their influence on different aspects of cancer progression...
March 19, 2017: Clinical & Experimental Metastasis
https://www.readbyqxmd.com/read/28317030/blind-testing-cross-linking-mass-spectrometry-under-the-auspices-of-the-11-th-critical-assessment-of-methods-of-protein-structure-prediction-casp11
#3
Adam Belsom, Michael Schneider, Lutz Fischer, Mahmoud Mabrouk, Kolja Stahl, Oliver Brock, Juri Rappsilber
Determining the structure of a protein by any method requires various contributions from experimental and computational sides. In a recent study, high-density cross-linking/mass spectrometry (HD-CLMS) data in combination with ab initio structure prediction determined the structure of human serum albumin (HSA) domains, with an RMSD to X-ray structure of up to 2.5 Å, or 3.4 Å in the context of blood serum. This paper reports the blind test on the readiness of this technology through the help of Critical Assessment of protein Structure Prediction (CASP)...
December 9, 2016: Wellcome Open Res
https://www.readbyqxmd.com/read/28299733/mapping-lipid-bilayer-recognition-sites-of-metalloproteinases-and-other-prospective-peripheral-membrane-proteins
#4
Tara C Marcink, Rama K Koppisetti, Yan G Fulcher, Steven R Van Doren
Peripheral binding of proteins to lipid bilayers is critical not only in intracellular signaling but also in metalloproteinase shedding of signaling proteins from cell surfaces. Assessment of how proteins recognize fluid bilayers peripherally using crystallography or structure-based predictions has been important but incomplete. Assay of dynamic protein-bilayer interactions in solution has become feasible and reliable using paramagnetic NMR and site-directed fluor labeling. Details of preparations and assay protocols for these spectroscopic measurements of bilayer proximity or contact, respectively, are described...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28289198/large-scale-identification-of-coevolution-signals-across-homo-oligomeric-protein-interfaces-by-direct-coupling-analysis
#5
Guido Uguzzoni, Shalini John Lovis, Francesco Oteri, Alexander Schug, Hendrik Szurmant, Martin Weigt
Proteins have evolved to perform diverse cellular functions, from serving as reaction catalysts to coordinating cellular propagation and development. Frequently, proteins do not exert their full potential as monomers but rather undergo concerted interactions as either homo-oligomers or with other proteins as hetero-oligomers. The experimental study of such protein complexes and interactions has been arduous. Theoretical structure prediction methods are an attractive alternative. Here, we investigate homo-oligomeric interfaces by tracing residue coevolution via the global statistical direct coupling analysis (DCA)...
March 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28281928/amyloid-cores-in-prion-domains-key-regulators-for-prion-conformational-conversion
#6
María Rosario Fernández, Cristina Batlle, Marcos Gil-García, Salvador Ventura
Despite the significant efforts devoted to decipher the particular protein features that encode for a prion or prion-like behavior, they are still poorly understood. The well-characterized yeast prions constitute an ideal model system to address this question, because, in these proteins, the prion activity can be univocally assigned to a specific region of their sequence, known as the prion forming domain (PFD). These PFDs are intrinsically disordered, relatively long and, in many cases, of low complexity, being enriched in glutamine/asparagine residues...
January 2, 2017: Prion
https://www.readbyqxmd.com/read/28272524/atomistic-structural-ensemble-refinement-reveals-non-native-structure-stabilizes-a-sub-millisecond-folding-intermediate-of-chey
#7
Jade Shi, R Paul Nobrega, Christian Schwantes, Sagar V Kathuria, Osman Bilsel, C Robert Matthews, T J Lane, Vijay S Pande
The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28265078/knowledge-based-entropies-improve-the-identification-of-native-protein-structures
#8
Kannan Sankar, Kejue Jia, Robert L Jernigan
Evaluating protein structures requires reliable free energies with good estimates of both potential energies and entropies. Although there are many demonstrated successes from using knowledge-based potential energies, computing entropies of proteins has lagged far behind. Here we take an entirely different approach and evaluate knowledge-based conformational entropies of proteins based on the observed frequencies of contact changes between amino acids in a set of 167 diverse proteins, each of which has two alternative structures...
March 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28264645/systematic-substitutions-at-blip-position-50-result-in-changes-in-binding-specificity-for-class-a-%C3%AE-lactamases
#9
Carolyn J Adamski, Timothy Palzkill
BACKGROUND: The production of β-lactamases by bacteria is the most common mechanism of resistance to the widely prescribed β-lactam antibiotics. β-lactamase inhibitory protein (BLIP) competitively inhibits class A β-lactamases via two binding loops that occlude the active site. It has been shown that BLIP Tyr50 is a specificity determinant in that substitutions at this position result in large differential changes in the relative affinity of BLIP for class A β-lactamases. RESULTS: In this study, the effect of systematic substitutions at BLIP position 50 on binding to class A β-lactamases was examined to further explore the role of BLIP Tyr50 in modulating specificity...
March 6, 2017: BMC Biochemistry
https://www.readbyqxmd.com/read/28263405/improving-prediction-of-helix-helix-packing-in-membrane-proteins-using-predicted-contact-numbers-as-restraints
#10
Bian Li, Jeffrey Mendenhall, Elizabeth Dong Nguyen, Brian E Weiner, Axel W Fischer, Jens Meiler
One of the challenging problems in computational prediction of tertiary structure of helical membrane proteins (HMPs) is the determination of rotation of α-helices around the helix normal. Incorrect prediction of rotation of α-helices around the helix normal substantially disrupts native residue-residue contacts while inducing only a relatively small effect on the overall fold. To address this problem, we previously developed a predictor for residue contact numbers (CNs), which measure the local packing density of residues within the protein tertiary structure...
March 6, 2017: Proteins
https://www.readbyqxmd.com/read/28263393/voromqa-assessment-of-protein-structure-quality-using-interatomic-contact-areas
#11
Kliment Olechnovič, Česlovas Venclovas
In the absence of experimentally determined protein structure many biological questions can be addressed using computational structural models. However, the utility of protein structural models depends on their quality. Therefore, the estimation of the quality of predicted structures is an important problem. One of the approaches to this problem is the use of knowledge-based statistical potentials. Such methods typically rely on the statistics of distances and angles of residue-residue or atom-atom interactions collected from experimentally determined structures...
March 6, 2017: Proteins
https://www.readbyqxmd.com/read/28259628/architecture-of-the-flagellar-switch-complex-of-escherichia-coli-conformational-plasticity-of-flig-and-implications-for-adaptive-remodeling
#12
Eun A Kim, Joseph Panushka, Trevor Meyer, Ryan Carlisle, Samantha Baker, Nicholas Ide, Michael Lynch, Brian R Crane, David F Blair
Structural models of the complex that regulates the direction of flagellar rotation assume either ~34 or ~25 copies of the protein FliG. Support for ~34 came from cross-linking experiments identifying an inter-subunit contact most consistent with that number; support for ~25 came from the observation that flagella can assemble and rotate when FliG is genetically fused to FliF, for which the accepted number is ~25. Here, we have undertaken cross-linking and other experiments to address more fully the question of FliG number...
March 1, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28254329/how-do-wettability-zeta-potential-and-hydroxylation-degree-affect-the-biological-response-of-biomaterials
#13
S Spriano, V Sarath Chandra, A Cochis, F Uberti, L Rimondini, E Bertone, A Vitale, C Scolaro, M Ferrari, F Cirisano, G Gautier di Confiengo, S Ferraris
It is well known that composition, electric charge, wettability and roughness of implant surfaces have great influence on their interaction with the biological fluids and tissues, but systematic studies of different materials in the same experimental conditions are still lacking in the scientific literature. The aim of this research is to investigate the correlations between some surface characteristics (wettability, zeta potential and hydroxylation degree) and the biological response (protein adsorption, blood wettability, cell and bacterial adhesion) to some model biomaterials...
May 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28236234/highly-flexible-protein-peptide-docking-using-cabs-dock
#14
Maciej Paweł Ciemny, Mateusz Kurcinski, Konrad Jakub Kozak, Andrzej Kolinski, Sebastian Kmiecik
Protein-peptide molecular docking is a difficult modeling problem. It is even more challenging when significant conformational changes that may occur during the binding process need to be predicted. In this chapter, we demonstrate the capabilities and features of the CABS-dock server for flexible protein-peptide docking. CABS-dock allows highly efficient modeling of full peptide flexibility and significant flexibility of a protein receptor. During CABS-dock docking, the peptide folding and binding process is explicitly simulated and no information about the peptide binding site or its structure is used...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28230370/coarse-grained-prediction-of-peptide-binding-to-g-protein-coupled-receptors
#15
Bartholomé Delort, Pedro Renault, Landry Charlier, Florent Raussin, Jean Martinez, Nicolas Floquet
In this study, we used the Martini Coarse-Grained model with no applied restraints to predict the binding mode of some peptides to G-Protein Coupled Receptors (GPCRs). Both the Neurotensin-1 and the chemokine CXCR4 receptors were used as test cases. Their ligands, NTS8-13 and CVX15 peptides, respectively, were initially positioned in the surrounding water box. Using a protocol based on Replica Exchange Molecular Dynamics (REMD), both opening of the receptors and entry of the peptides into their dedicated pockets were observed on the μs time-scale...
March 7, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28221352/dynamic-undocking-and-the-quasi-bound-state-as-tools-for-drug-discovery
#16
Sergio Ruiz-Carmona, Peter Schmidtke, F Javier Luque, Lisa Baker, Natalia Matassova, Ben Davis, Stephen Roughley, James Murray, Rod Hubbard, Xavier Barril
There is a pressing need for new technologies that improve the efficacy and efficiency of drug discovery. Structure-based methods have contributed towards this goal but they focus on predicting the binding affinity of protein-ligand complexes, which is notoriously difficult. We adopt an alternative approach that evaluates structural, rather than thermodynamic, stability. As bioactive molecules present a static binding mode, we devised dynamic undocking (DUck), a fast computational method to calculate the work necessary to reach a quasi-bound state at which the ligand has just broken the most important native contact with the receptor...
March 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28213880/detection-of-digestive-malignancies-and-post-gastrectomy-complications-via-gastrointestinal-fluid-examination
#17
REVIEW
Lei Huang, Aman Xu
To date, gastric carcinoma (GC) is one of the common and fatal digestive malignancies worldwide. The prognosis of GC is not always satisfactory because of late diagnosis. Scholars are keen on discovering novel accurate and economical biomarkers in body liquids for GC screening to detect and evaluate the lesion before the results of imaging techniques are obtained. While traditional serum assays have limited sensitivity and specificity, gastrointestinal juice may provide relevant specific biomarkers because of its close contact with the tumor...
February 17, 2017: Frontiers of Medicine
https://www.readbyqxmd.com/read/28205569/heteroaryldihydropyrimidine-hap-and-sulfamoylbenzamide-sba-inhibit-hepatitis-b-virus-replication-by-different-molecular-mechanisms
#18
Zheng Zhou, Taishan Hu, Xue Zhou, Steffen Wildum, Fernando Garcia-Alcalde, Zhiheng Xu, Daitze Wu, Yi Mao, Xiaojun Tian, Yuan Zhou, Fang Shen, Zhisen Zhang, Guozhi Tang, Isabel Najera, Guang Yang, Hong C Shen, John A T Young, Ning Qin
Heteroaryldihydropyrimidine (HAP) and sulfamoylbenzamide (SBA) are promising non-nucleos(t)ide HBV replication inhibitors. HAPs are known to promote core protein mis-assembly, but the molecular mechanism of abnormal assembly is still elusive. Likewise, the assembly status of core protein induced by SBA remains unknown. Here we show that SBA, unlike HAP, does not promote core protein mis-assembly. Interestingly, two reference compounds HAP_R01 and SBA_R01 bind to the same pocket at the dimer-dimer interface in the crystal structures of core protein Y132A hexamer...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28196882/trade-offs-between-enzyme-fitness-and-solubility-illuminated-by-deep-mutational-scanning
#19
Justin R Klesmith, John-Paul Bacik, Emily E Wrenbeck, Ryszard Michalczyk, Timothy A Whitehead
Proteins are marginally stable, and an understanding of the sequence determinants for improved protein solubility is highly desired. For enzymes, it is well known that many mutations that increase protein solubility decrease catalytic activity. These competing effects frustrate efforts to design and engineer stable, active enzymes without laborious high-throughput activity screens. To address the trade-off between enzyme solubility and activity, we performed deep mutational scanning using two different screens/selections that purport to gauge protein solubility for two full-length enzymes...
February 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28196116/the-scoring-bias-in-reverse-docking-and-the-score-normalization-strategy-to-improve-success-rate-of-target-fishing
#20
Qiyao Luo, Liang Zhao, Jianxing Hu, Hongwei Jin, Zhenming Liu, Liangren Zhang
Target fishing often relies on the use of reverse docking to identify potential target proteins of ligands from protein database. The limitation of reverse docking is the accuracy of current scoring funtions used to distinguish true target from non-target proteins. Many contemporary scoring functions are designed for the virtual screening of small molecules without special optimization for reverse docking, which would be easily influenced by the properties of protein pockets, resulting in scoring bias to the proteins with certain properties...
2017: PloS One
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