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Protein interface prediction

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https://www.readbyqxmd.com/read/28810664/bacterial-phosphoglycosyl-transferases-initiators-of-glycan-biosynthesis-at-the-membrane-interface
#1
Vinita Lukose, Marthe T C Walvoort, Barbara Imperiali
Phosphoglycosyl transferases (PGTs) initiate the biosynthesis of both essential and virulence-associated bacterial glycoconjugates including lipopolysaccharide, peptidoglycan and glycoproteins. PGTs catalyze the transfer of a phosphosugar moiety from a nucleoside diphosphate sugar to a polyprenol phosphate, to form a membrane-bound polyprenol diphosphosugar product. PGTs are integral membrane proteins, which include between 1 and 11 predicted transmembrane domains. Despite this variation, common motifs have been identified in PGT families through bioinformatics and mutagenesis studies...
September 1, 2017: Glycobiology
https://www.readbyqxmd.com/read/28791516/nlscore-a-novel-quantitative-algorithm-based-on-3-dimensional-structural-determinants-to-predict-the-probability-of-nuclear-localization-in-proteins-containing-classical-nuclear-localization-signals
#2
P S Hari, T S Sridhar, R Pravin Kumar
The presence of a nuclear localization signal (NLS) in proteins can be inferred by the presence of a stretch of basic amino acids (KRKK). These NLSs are termed classical NLS (cNLS). However, only a fraction of proteins containing the cNLS pattern are transported into the nucleus by binding to importin α. Hence, there must exist, additional structural determinants that guide the appropriate interaction between putative NLSs containing cargo and importin α. Using 52 protein structures containing cNLS obtained from RCSB PDB, we assembled a training set and a validation set such that both sets were comprised of a combination of proteins with proven nuclear localization and ones that were non-nuclear...
August 9, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28782718/merging-in-silico-and-in-vitro-salivary-protein-complex-partners-using-the-string-database-a-tutorial
#3
Karla Tonelli Bicalho Crosara, Eduardo Buozi Moffa, Yizhi Xiao, Walter Luiz Siqueira
Protein-protein interaction is a common physiological mechanism for protection and actions of proteins in an organism. The identification and characterization of protein-protein interactions in different organisms is necessary to better understand their physiology and to determine their efficacy. In a previous in vitro study using mass spectrometry, we identified 43 proteins that interact with histatin 1. Six previously documented interactors were confirmed and 37 novel partners were identified. In this tutorial, we aimed to demonstrate the usefulness of the STRING database for studying protein-protein interactions...
August 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28780861/characterization-of-protein-protein-interfaces-in-large-complexes-by-solid-state-nmr-solvent-paramagnetic-relaxation-enhancements
#4
Carl Öster, Simone Kosol, Christoph Hartlmüller, Jonathan M Lamley, Dinu Iuga, Andres Oss, Mai-Liis Org, Kalju Vanatalu, Ago Samoson, Tobias Madl, Józef R Lewandowski
Solid-state NMR is becoming a viable alternative for obtaining information about structures and dynamics of large biomolecular complexes including ones that are not accessible to other high resolution biophysical techniques. In this context, methods for probing protein-protein interfaces at atomic resolution are highly desirable. Solvent paramagnetic relaxation enhancements (sPREs) proved to be a powerful method for probing protein-protein interfaces in large complexes in solution but have not been employed towards this goal in the solid state...
August 7, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28777072/dissecting-the-protein-architecture-of-dna-binding-transcription-factors-in-bacteria-and-archaea
#5
Nancy Rivera-Gómez, Mario Alberto Martínez-Núñez, Nina Pastor, Katya Rodriguez-Vazquez, Ernesto Perez-Rueda
Gene regulation at the transcriptional level is a central process in all organisms where DNA-binding transcription factors play a fundamental role. This class of proteins binds specifically at DNA sequences, activating or repressing gene expression as a function of the cell's metabolic status, operator context and ligand-binding status, among other factors, through the DNA-binding domain (DBD). In addition, TFs may contain partner domains (PaDos), which are involved in ligand binding and protein-protein interactions...
August 4, 2017: Microbiology
https://www.readbyqxmd.com/read/28774292/rosetta-broker-for-membrane-protein-structure-prediction-concentrative-nucleoside-transporter-3-and-corticotropin-releasing-factor-receptor-1-test-cases
#6
Dorota Latek
BACKGROUND: Membrane proteins are difficult targets for structure prediction due to the limited structural data deposited in Protein Data Bank. Most computational methods for membrane protein structure prediction are based on the comparative modeling. There are only few de novo methods targeting that distinct protein family. In this work an example of such de novo method was used to structurally and functionally characterize two representatives of distinct membrane proteins families of solute carrier transporters and G protein-coupled receptors...
August 3, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28766075/protein-binding-hot-spots-prediction-from-sequence-only-by-a-new-ensemble-learning-method
#7
Shan-Shan Hu, Peng Chen, Bing Wang, Jinyan Li
Hot spots are interfacial core areas of binding proteins, which have been applied as targets in drug design. Experimental methods are costly in both time and expense to locate hot spot areas. Recently, in-silicon computational methods have been widely used for hot spot prediction through sequence or structure characterization. As the structural information of proteins is not always solved, and thus hot spot identification from amino acid sequences only is more useful for real-life applications. This work proposes a new sequence-based model that combines physicochemical features with the relative accessible surface area of amino acid sequences for hot spot prediction...
August 1, 2017: Amino Acids
https://www.readbyqxmd.com/read/28737906/role-of-protein-dimeric-interface-in-allosteric-inhibition-of-n-acetyl-aspartate-hydrolysis-by-human-aspartoacylase
#8
Ekaterina D Kots, Sofya V Lushchekina, Sergey D Varfolomeev, Alexander V Nemukhin
The results of molecular modeling suggest a mechanism of allosteric inhibition upon hydrolysis of N-acetyl-aspartate (NAA), one of the most abundant amino acid derivatives in brain, by human aspartoacylase (hAsp). Details of this reaction are important to suggest the practical ways to control the enzyme activity. Search for allosteric sites using the Allosite web server and SiteMap analysis allowed us to identify substrate binding pockets located at the interface between the subunits of the hAsp dimer molecule...
August 4, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28734179/computational-analysis-for-the-determination-of-deleterious-nssnps-in-human-mthfd1-gene
#9
Mansi Desai, J B Chauhan
Single nucleotide polymorphisms (SNPs) are the most common genetic polymorphisms and play a major role in many inherited diseases. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is one of the enzymes involved in folate metabolism. In the present study, the functional and structural consequences of nsSNPs of human MTHFD1 gene was analyzed using various computational tools like SIFT, PolyPhen2, PANTHER, PROVEAN, SNAP2, nsSNPAnalyzer, PhD-SNP, SNPs&GO, I-Mutant, MuPro, ConSurf, InterPro, NCBI Conserved Domain Search tool, ModPred, SPARKS-X, RAMPAGE, FT Site and PyMol...
July 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28726636/live-cell-visualization-of-gasdermin-d-driven-pyroptotic-cell-death
#10
Joseph K Rathkey, Bryan L Benson, Steven M Chirieleison, Jie Yang, Tsan S Xiao, George R Dubyak, Alex Y Huang, Derek W Abbott
Pyroptosis is a form of cell death important in defenses against pathogens, but which can also result in a potent and sometimes pathological inflammatory response. During pyroptosis, gasdermin D (GSDMD), the pore-forming effector protein, is cleaved, forms oligomers, and inserts into the membranes of the cell, resulting in rapid cell death. However, the potent cell death induction caused by GSDMD has complicated our ability to understand the biology of this protein. Studies aimed at visualizing GSDMD have relied on expression of GSDMD fragments in epithelial cell lines that naturally lack GSDMD expression and also lack the proteases necessary to cleave GSDMD...
July 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28718782/prediction-of-protein-hotspots-from-whole-protein-sequences-by-a-random-projection-ensemble-system
#11
Jinjian Jiang, Nian Wang, Peng Chen, Chunhou Zheng, Bing Wang
Hotspot residues are important in the determination of protein-protein interactions, and they always perform specific functions in biological processes. The determination of hotspot residues is by the commonly-used method of alanine scanning mutagenesis experiments, which is always costly and time consuming. To address this issue, computational methods have been developed. Most of them are structure based, i.e., using the information of solved protein structures. However, the number of solved protein structures is extremely less than that of sequences...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28717196/trib1-is-a-positive-regulator-of-hepatocyte-nuclear-factor-4-alpha
#12
Sébastien Soubeyrand, Amy Martinuk, Ruth McPherson
The TRIB1 locus has been linked to both cardiovascular disease and hepatic steatosis. Recent efforts have revealed TRIB1 to be a major regulator of liver function, largely, but not exclusively, via CEBPA degradation. We recently uncovered a functional interaction between TRIB1 and HNF4A, another key regulator of hepatic function, whose molecular underpinnings remained to be clarified. Here we have extended these findings. In hepatoma models, HNF4A levels were found to depend on TRIB1, independently of its impact on CEBPA...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28716627/membrane-proteins-structures-a-review-on-computational-modeling-tools
#13
REVIEW
Jose G Almeida, Antonio J Preto, Panagiotis I Koukos, Alexandre M J J Bonvin, Irina S Moreira
BACKGROUND: Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic organisms' genomes. In humans, their importance is emphasized as they represent 50% of all known drug targets. Nevertheless, experimental determination of their three-dimensional (3D) structure has proven to be both time consuming and rather expensive, which has led to the development of computational algorithms to complement the available experimental methods and provide valuable insights...
July 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28713396/system-level-and-granger-network-analysis-of-integrated-proteomic-and-metabolomic-dynamics-identifies-key-points-of-grape-berry-development-at-the-interface-of-primary-and-secondary-metabolism
#14
Lei Wang, Xiaoliang Sun, Jakob Weiszmann, Wolfram Weckwerth
Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major developmental phases...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28710385/electron-transfer-chain-in-respiratory-complex-i
#15
Daniel R Martin, Dmitry V Matyushov
Complex I is a part of the respiration energy chain converting the redox energy into the cross-membrane proton gradient. The electron-transfer chain of iron-sulfur cofactors within the water-soluble peripheral part of the complex is responsible for the delivery of electrons to the proton pumping subunit. The protein is porous to water penetration and the hydration level of the cofactors changes when the electron is transferred along the chain. High reaction barriers and trapping of the electrons at the iron-sulfur cofactors are prevented by the combination of intense electrostatic noise produced by the protein-water interface with the high density of quantum states in the iron-sulfur clusters caused by spin interactions between paramagnetic iron atoms...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28694495/functional-determinants-of-protein-assembly-into-homomeric-complexes
#16
L Therese Bergendahl, Joseph A Marsh
Approximately half of proteins with experimentally determined structures can interact with other copies of themselves and assemble into homomeric complexes, the overwhelming majority of which (>96%) are symmetric. Although homomerisation is often assumed to a functionally beneficial result of evolutionary selection, there has been little systematic analysis of the relationship between homomer structure and function. Here, utilizing the large numbers of structures and functional annotations now available, we have investigated how proteins that assemble into different types of homomers are associated with different biological functions...
July 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28692290/top-down-atmospheric-ionization-mass-spectrometry-microscopy-combined-with-proteogenomics
#17
Cheng-Chih Hsu, Michael W Baker, Terry Gaasterland, Michael J Meehan, Eduardo R Macagno, Pieter C Dorrestein
Mass spectrometry-based protein analysis has become an important methodology for proteogenomic mapping by providing evidence for the existence of proteins predicted at the genomic level. However, screening and identification of proteins directly on tissue samples, where histological information is preserved, remain challenging. Here we demonstrate that the ambient ionization source, nanospray desorption electrospray ionization (nanoDESI), interfaced with light microscopy allows for protein profiling directly on animal tissues at the microscopic scale...
July 24, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28679759/mutational-analysis-of-lassa-virus-glycoprotein-highlights-regions-required-for-alpha-dystroglycan-utilization
#18
Marissa Acciani, Jacob T Alston, Guohui Zhao, Hayley Reynolds, Afroze M Ali, Brian Xu, Melinda A Brindley
Lassa virus (LASV) is an enveloped RNA virus endemic to West Africa and responsible for severe cases of hemorrhagic fever. Virus entry is mediated by the glycoprotein complex consisting of a stable signal peptide, a receptor-binding subunit GP1, and a viral-host membrane fusion subunit GP2. Several cellular receptors can interact with the GP1 subunit and mediate viral entry, including alpha-dystroglycan (αDG) and lysosomal associated membrane protein 1 (LAMP1). In order to define the regions within GP1 that interact with the cellular receptors, we implemented insertional mutagenesis, carbohydrate shielding, and alanine scanning mutagenesis...
July 5, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28671670/multimerin-2-is-a-ligand-for-group-14-family-c-type-lectins-clec14a-cd93-and-cd248-spanning-the-endothelial-pericyte-interface
#19
K A Khan, A J Naylor, A Khan, P J Noy, M Mambretti, P Lodhia, J Athwal, A Korzystka, C D Buckley, B E Willcox, F Mohammed, R Bicknell
The C-type lectin domain containing group 14 family members CLEC14A and CD93 are proteins expressed by endothelium and are implicated in tumour angiogenesis. CD248 (alternatively known as endosialin or tumour endothelial marker-1) is also a member of this family and is expressed by tumour-associated fibroblasts and pericytes. Multimerin-2 (MMRN2) is a unique endothelial specific extracellular matrix protein that has been implicated in angiogenesis and tumour progression. We show that the group 14 C-type lectins CLEC14A, CD93 and CD248 directly bind to MMRN2 and only thrombomodulin of the family does not...
July 3, 2017: Oncogene
https://www.readbyqxmd.com/read/28670277/nano-lazar-read-across-predictions-for-nanoparticle-toxicities-with-calculated-and-measured-properties
#20
Christoph Helma, Micha Rautenberg, Denis Gebele
The lazar framework for read across predictions was expanded for the prediction of nanoparticle toxicities, and a new methodology for calculating nanoparticle descriptors from core and coating structures was implemented. Nano-lazar provides a flexible and reproducible framework for downloading data and ontologies from the open eNanoMapper infrastructure, developing and validating nanoparticle read across models, open-source code and a free graphical interface for nanoparticle read-across predictions. In this study we compare different nanoparticle descriptor sets and local regression algorithms...
2017: Frontiers in Pharmacology
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