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Protein contact prediction

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https://www.readbyqxmd.com/read/28230370/coarse-grained-prediction-of-peptide-binding-to-g-protein-coupled-receptors
#1
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...
February 23, 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
#2
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
#3
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
#4
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
#5
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 14, 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
#6
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
https://www.readbyqxmd.com/read/28155083/the-long-zinc-finger-domain-of-prdm9-forms-a-highly-stable-and-long-lived-complex-with-its-dna-recognition-sequence
#7
Yasmin Striedner, Theresa Schwarz, Thomas Welte, Andreas Futschik, Ulrich Rant, Irene Tiemann-Boege
PR domain containing protein 9 (PRDM9) is a meiosis-specific, multi-domain protein that regulates the location of recombination hotspots by targeting its DNA recognition sequence for double-strand breaks (DSBs). PRDM9 specifically recognizes DNA via its tandem array of zinc fingers (ZnFs), epigenetically marks the local chromatin by its histone methyltransferase activity, and is an important tether that brings the DNA into contact with the recombination initiation machinery. A strong correlation between PRDM9-ZnF variants and specific DNA motifs at recombination hotspots has been reported; however, the binding specificity and kinetics of the ZnF domain are still obscure...
February 2, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28143938/sequence-structure-and-dynamics-based-comparisons-of-structurally-homologous-chey-like-proteins
#8
Yi He, Gia G Maisuradze, Yanping Yin, Khatuna Kachlishvili, S Rackovsky, Harold A Scheraga
We recently introduced a physically based approach to sequence comparison, the property factor method (PFM). In the present work, we apply the PFM approach to the study of a challenging set of sequences-the bacterial chemotaxis protein CheY, the N-terminal receiver domain of the nitrogen regulation protein NT-NtrC, and the sporulation response regulator Spo0F. These are all response regulators involved in signal transduction. Despite functional similarity and structural homology, they exhibit low sequence identity...
January 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28138060/rna-puzzles-round-iii-3d-rna-structure-prediction-of-five-riboswitches-and-one-ribozyme
#9
Zhichao Miao, Ryszard W Adamiak, Maciej Antczak, Robert T Batey, Alexander J Becka, Marcin Biesiada, Michał J Boniecki, Janusz Bujnicki, Shi-Jie Chen, Clarence Yu Cheng, Fang-Chieh Chou, Adrian R Ferré-D'Amaré, Rhiju Das, Wayne K Dawson, Ding Feng, Nikolay V Dokholyan, Stanisław Dunin-Horkawicz, Caleb Geniesse, Kalli Kappel, Wipapat Kladwang, Andrey Krokhotin, Grzegorz E Łach, François Major, Thomas H Mann, Marcin Magnus, Katarzyna Pachulska-Wieczorek, Dinshaw J Patel, Joseph A Piccirilli, Mariusz Popenda, Katarzyna J Purzycka, Aiming Ren, Greggory M Rice, John Santalucia, Joanna Sarzynska, Marta Szachniuk, Arpit Tandon, Jeremiah J Trausch, Siqi Tian, Jian Wang, Kevin M Weeks, Benfeard Williams, Yi Xiao, Xiaojun Xu, Dong Zhang, Tomasz Zok, Eric Westhof
RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF) and one set describes large conformational changes between ligand-free and ligand-bound states; the Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme...
January 30, 2017: RNA
https://www.readbyqxmd.com/read/28137713/hipred-an-integrative-approach-to-predicting-haploinsufficient-genes
#10
Hashem A Shihab, Mark F Rogers, Colin Campbell, Tom R Gaunt
MOTIVATION: A major cause of autosomal dominant disease is haploinsufficiency, whereby a single copy of a gene is not sufficient to maintain the normal function of the gene. A large proportion of existing methods for predicting haploinsufficiency incorporate biological networks, e.g. protein-protein interaction networks, that have recently been shown to introduce study bias. As a result, these methods tend to perform best on well studied genes, but underperform on less studied genes. The advent of large genome sequencing consortia, such as the 1,000 genomes project, NHLBI Exome Sequencing Project (ESP) and the Exome Aggregation Consortium (ExAC) creates an urgent need for unbiased haploinsufficiency prediction methods...
January 30, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28137710/dscam1-web-server-online-prediction-of-dscam1-self-and-hetero-affinity
#11
Simone Marini, Nelson Nazzicari, Filippo Biscarini, Guang-Zhong Wang
MOTIVATION: Formation of homodimers by identical Dscam1 protein isomers on cell surface is the key factor for the self-avoidance of growing neurites. Dscam1 immense diversity has a critical role in the formation of arthropod neuronal circuit, showing unique evolutionary properties when compared to other cell surface proteins. Experimental measures are available for 89 self-binding and 1722 hetero-binding protein samples, out of more than 19 thousands (self-binding) and 350 millions (hetero-binding) possible isomer combinations...
January 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28135092/evolutionary-covariance-combined-with-molecular-dynamics-predicts-a-framework-for-allostery-in-the-muts-dna-mismatch-repair-protein
#12
Bharat Lakhani, Kelly Marie Thayer, Manju M Hingorani, David L Beveridge
Mismatch repair (MMR) is an essential, evolutionarily conserved pathway that maintains genome stability by correcting base-pairing errors in DNA. Here we examine the sequence and structure of MutS MMR protein to decipher the amino acid framework underlying its two key activities - recognizing mismatches in DNA and using ATP to initiate repair. Statistical Coupling Analysis (SCA) identified a network (sector) of co-evolved amino acids in the MutS protein family. The potential functional significance of this SCA sector was assessed by performing molecular dynamics (MD) simulations for alanine mutants of the top 5% of 160 residues in the distribution, and control non-sector residues...
January 30, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28130547/mitochondrial-protein-interactome-elucidated-by-chemical-cross-linking-mass-spectrometry
#13
Devin K Schweppe, Juan D Chavez, Chi Fung Lee, Arianne Caudal, Shane E Kruse, Rudy Stuppard, David J Marcinek, Gerald S Shadel, Rong Tian, James E Bruce
Mitochondrial protein interactions and complexes facilitate mitochondrial function. These complexes range from simple dimers to the respirasome supercomplex consisting of oxidative phosphorylation complexes I, III, and IV. To improve understanding of mitochondrial function, we used chemical cross-linking mass spectrometry to identify 2,427 cross-linked peptide pairs from 327 mitochondrial proteins in whole, respiring murine mitochondria. In situ interactions were observed in proteins throughout the electron transport chain membrane complexes, ATP synthase, and the mitochondrial contact site and cristae organizing system (MICOS) complex...
January 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28130237/identification-of-protein-complexes-by-integrating-multiple-alignment-of-protein-interaction-networks
#14
Cheng-Yu Ma, Yi-Ping Phoebe Chen, Bonnie Berger, Chung-Shou Liao
MOTIVATION: Protein complexes are one of the keys to studying the behavior of a cell system. Many biological functions are carried out by protein complexes. During the past decade, the main strategy used to identify protein complexes from high-throughput network data has been to extract near-cliques or highly dense subgraphs from a single protein-protein interaction (PPI) network. Although experimental PPI data has increased significantly over recent years, most PPI networks still have many false positive interactions and false negative edge loss due to the limitations of high-throughput experiments...
January 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28130235/ispred4-interaction-sites-prediction-in-protein-structures-with-a-refining-grammar-model
#15
Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio
MOTIVATION: The identification of Protein-Protein Interaction (PPI) sites is an important step towards the characterization of protein functional integration in the cell complexity. Experimental methods are costly and time-consuming and computational tools for predicting PPI sites can fill the gaps of PPI present knowledge. RESULTS: We present ISPRED4, an improved structure-based predictor of PPI sites on unbound monomer surfaces. ISPRED4 relies on machine-learning methods and incorporating features extracted from protein sequence and structure...
January 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28119472/pseudomonas-aeruginosa-pore-forming-exolysin-and-type-iv-pili-cooperate-to-induce-host-cell-lysis
#16
Pauline Basso, Michel Ragno, Sylvie Elsen, Emeline Reboud, Guillaume Golovkine, Stephanie Bouillot, Philippe Huber, Stephen Lory, Eric Faudry, Ina Attrée
: Clinical strains of Pseudomonas aeruginosa lacking the type III secretion system genes employ a toxin, exolysin (ExlA), for host cell membrane disruption. Here, we demonstrated that ExlA export requires a predicted outer membrane protein, ExlB, showing that ExlA and ExlB define a new active two-partner secretion (TPS) system of P. aeruginosa In addition to the TPS signals, ExlA harbors several distinct domains, which include one hemagglutinin domain, five arginine-glycine-aspartic acid (RGD) motifs, and a C-terminal region lacking any identifiable sequence motifs...
January 24, 2017: MBio
https://www.readbyqxmd.com/read/28118389/rapid-design-of-knowledge-based-scoring-potentials-for-enrichment-of-near-native-geometries-in-protein-protein-docking
#17
Alexander Sasse, Sjoerd J de Vries, Christina E M Schindler, Isaure Chauvot de Beauchêne, Martin Zacharias
Protein-protein docking protocols aim to predict the structures of protein-protein complexes based on the structure of individual partners. Docking protocols usually include several steps of sampling, clustering, refinement and re-scoring. The scoring step is one of the bottlenecks in the performance of many state-of-the-art protocols. The performance of scoring functions depends on the quality of the generated structures and its coupling to the sampling algorithm. A tool kit, GRADSCOPT (GRid Accelerated Directly SCoring OPTimizing), was designed to allow rapid development and optimization of different knowledge-based scoring potentials for specific objectives in protein-protein docking...
2017: PloS One
https://www.readbyqxmd.com/read/28108520/rna-binding-specificity-landscape-of-the-pentatricopeptide-repeat-protein-ppr10
#18
Rafael G Miranda, Margarita Rojas, Michael P Montgomery, Kyle P Gribbin, Alice Barkan
Pentatricopeptide repeat (PPR) proteins comprise a large family of helical repeat proteins that influence gene expression in mitochondria and chloroplasts. PPR tracts can bind RNA via a modular one repeat-one nucleotide mechanism in which the nucleotide is specified by the identities of several amino acids in each repeat. This mode of recognition, the so-called PPR code, offers opportunities for the prediction of native PPR binding sites and the design of proteins to bind specified RNAs. However, a deep understanding of the parameters that dictate the affinity and specificity of PPR-RNA interactions is necessary to realize these goals...
January 20, 2017: RNA
https://www.readbyqxmd.com/read/28108305/efficient-dynamic-programming-algorithm-with-prior-knowledge-for-protein-%C3%AE-strand-alignment
#19
Mostafa Sabzekar, Mahmoud Naghibzadeh, Javad Sadri
One of the main tasks towards the prediction of protein β-sheet structure is to predict the native alignment of β-strands. The alignment of two β-strands defines similar regions that may reflect functional, structural, or evolutionary relationships between them. Therefore, any improvement in β-strands alignment not only reduces the computational search space but also improves β-sheet structure prediction accuracy. To define the alignment scores, previous studies utilized predicted residue-residue contacts (contact maps)...
January 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28104891/protein-structure-determination-using-metagenome-sequence-data
#20
Sergey Ovchinnikov, Hahnbeom Park, Neha Varghese, Po-Ssu Huang, Georgios A Pavlopoulos, David E Kim, Hetunandan Kamisetty, Nikos C Kyrpides, David Baker
Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank...
January 20, 2017: Science
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