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computational structural biology

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https://www.readbyqxmd.com/read/28528214/nmr-structure-conformational-dynamics-and-biological-activity-of-psdef1-defensin-from-pinus-sylvestris
#1
Bulat I Khairutdinov, Elena A Ermakova, Yuri M Yusypovych, Elena K Bessolicina, Nadezhda B Tarasova, Yana Y Toporkova, Valentina Kovaleva, Yuriy F Zuev, Irina V Nesmelova
Plants have developed a complex defense response system against pests and pathogens. Defensins, produced by plants as part of their innate immune response, form the family of small, basic, cysteine-rich proteins with activity primarily directed against fungal pathogens. In addition, plant defensins can show antibacterial activity and protease and insect amylase inhibitory activities. However, in gymnosperms, only antifungal activity of defensins has been described thus far. Here, we report antibacterial and insect α-amylase inhibition activities for defensin PsDef1 from P...
May 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28524918/urotensin-ii-peptidomimetic-incorporating-a-non-reducible-1-5-triazole-disulfide-bond-reveals-a-pseudo-irreversible-covalent-binding-mechanism-to-the-urotensin-g-protein-coupled-receptor
#2
Salvatore Pacifico, Aidan Kerckhoffs, Andrew J Fallow, Rachel E Foreman, Remo Guerrini, John McDonald, David G Lambert, Andrew G Jamieson
The urotensin-II receptor (UTR) is a class A GPCR that predominantly binds to the pleiotropic cyclic peptide urotensin-II (U-II). U-II is constrained by a disulfide bridge that induces a β-turn structure and binds pseudo-irreversibly to UTR and is believed to result in a structural rearrangement of the receptor. However, it is not well understood how U-II binds pseudo-irreversibly and the nature of the reorganization of the receptor that results in G-protein activation. Here we describe a series of U-II peptidomimetics incorporating a non-reducible disulfide bond structural surrogate to investigate the feasibility that native U-II binds to the G protein-coupled receptor through disulfide bond shuffling as a mechanism of covalent interaction...
May 19, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28522865/lipoxygenase-2-from-cyanothece-sp-controls-dioxygen-insertion-by-steric-shielding-and-substrate-fixation
#3
Julia Newie, Piotr Neumann, Martin Werner, Ricardo A Mata, Ralf Ficner, Ivo Feussner
The biological function of lipoxygenases depends on the regio and stereo specific formation of fatty acid-derived hydroperoxides and different concepts exist to explain the mechanism that directs dioxygen to a specific carbon atom within the substrate. Here, we report the 1.8 Å resolution crystal structure of a cyanobacterial lipoxygenase that produces bis-allylic hydroperoxides (CspLOX2). Site directed mutagenesis experiments combined with computational approaches reveal that residues around the active site direct dioxygen to a preferred carbon atom and stereo configuration in the substrate fatty acid...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28521106/first-principles-models-for-biological-light-harvesting-phycobiliprotein-complexes-from-cryptophyte-algae
#4
Mi Kyung Lee, Ksenia B Bravaya, David F Coker
There have been numerous efforts, both experimental and theoretical, that have attempted to parameterize model Hamiltonians to describe excited state energy transfer in photosynthetic light harvesting systems. The Frenkel exciton model, with its set of electronically coupled two level chromophores that are each linearly coupled to dissipative baths of harmonic oscillators, has become the workhorse of this field. The challenges to parameterizing such Hamiltonians have been their uniqueness, and physical interpretation...
May 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28521011/translation-initiation-events-on-structured-eukaryotic-mrnas-generate-gene-expression-noise
#5
Estelle Dacheux, Naglis Malys, Xiang Meng, Vinoy Ramachandran, Pedro Mendes, John Eg McCarthy
Gene expression stochasticity plays a major role in biology, creating non-genetic cellular individuality and influencing multiple processes, including differentiation and stress responses. We have addressed the lack of knowledge about posttranscriptional contributions to noise by determining cell-to-cell variations in the abundance of mRNA and reporter protein in yeast. Two types of structural element, a stem-loop and a poly(G) motif, not only inhibit translation initiation when inserted into an mRNA 5΄ untranslated region, but also generate noise...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520533/a-fully-automated-high-throughput-zebrafish-behavioral-ototoxicity-assay
#6
Douglas W Todd, Rohit C Philip, Maki Niihori, Ryan A Ringle, Kelsey R Coyle, Sobia F Zehri, Jordan A Mudery, Ross H Francis, Jeffrey J Rodriguez, Abraham Jacob
Zebrafish animal models lend themselves to behavioral assays that can facilitate rapid screening of ototoxic, otoprotective, and otoregenerative drugs. Structurally similar to human inner ear hair cells, the mechanosensory hair cells on their lateral line allow the zebrafish to sense water flow and orient head-to-current in a behavior called rheotaxis. This rheotaxis behavior deteriorates in a dose-dependent manner with increased exposure to the ototoxin cisplatin, thereby establishing itself as an excellent biomarker for anatomic damage to lateral line hair cells...
May 18, 2017: Zebrafish
https://www.readbyqxmd.com/read/28518172/super-resolution-microscopy-with-dna-paint
#7
Joerg Schnitzbauer, Maximilian T Strauss, Thomas Schlichthaerle, Florian Schueder, Ralf Jungmann
Super-resolution techniques have begun to transform biological and biomedical research by allowing researchers to observe structures well below the classic diffraction limit of light. DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) offers an easy-to-implement approach to localization-based super-resolution microscopy, owing to the use of DNA probes. In DNA-PAINT, transient binding of short dye-labeled ('imager') oligonucleotides to their complementary target ('docking') strands creates the necessary 'blinking' to enable stochastic super-resolution microscopy...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28515680/trk-receptors-and-neurotrophin-cross-interactions-new-perspectives-toward-manipulating-therapeutic-side-effects
#8
Yazan Haddad, Vojtěch Adam, Zbyněk Heger
Some therapeutic side-effects result from simultaneous activation of homolog receptors by the same ligand. Tropomyosin receptor kinases (TrkA, TrkB and TrkC) play a major role in the development and biology of neurons through neurotrophin signaling. The wide range of cross-interactions between Trk receptors and neurotrophins vary in selectivity, affinity and function. In this study, we discuss new perspectives to the manipulation of side-effects via a better understanding of the cross-interactions at the molecular level, derived by computational methods...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28515050/the-mapping-of-predicted-triplex-dna-rna-in-the-drosophila-genome-reveals-a-prominent-location-in-development-and-morphogenesis-related-genes
#9
Claude Pasquier, Sandra Agnel, Alain Robichon
Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson-Crick duplex. The "triplex-forming oligonucleotide" (TFO) can be a short sequence of RNA that binds to the major groove of the targeted duplex only when this duplex presents a sequence of purine or pyrimidine bases in one of the DNA strands. Many nuclear proteins are known to bind triplex DNA or DNA:RNA, but their biological functions are unexplored...
May 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28513076/a-computational-assessment-of-the-predicted-structures-of-human-macrophage-migration-inhibitory-factor-1-orthologs-in-parasites-and-its-affinity-to-human-cd74-receptor
#10
REVIEW
Claudia Machicado, Luis A Marcos
The human macrophage migration inhibitory factor 1 (Hu-MIF-1) is a protein involved in the inflammatory and immunology response to parasite infection. In the present study, the existence of Hu-MIF-1 from parasites have been explored by mining WormBase. A total of 35 helminths were found to have Hu-MIF-1 homologs, including some parasites of importance for public health. Physicochemical, structural, and biological properties of Hu-MIF-1 were compared with its orthologs in parasites showing that most of these are secretory proteins, with positive net charge and presence of the Cys-Xaa-Xaa-Cys motif that is critical for its oxidoreductase activity...
May 17, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/28511148/computational-studies-of-membrane-proteins-from-sequence-to-structure-to-simulation
#11
REVIEW
Phillip J Stansfeld
In this review, I discuss the recent advances in computational approaches to studying membrane protein structures, covering the latest methods for predicting a protein structure from its amino acid sequence, through to methods for assessing the structural dynamics and lipid interactions within molecular simulations of complex biological membranes. These approaches have not only benefited from advances in the computational software and architectures, but have also been assisted by a prodigious rise in the number of both the molecular sequences and experimentally determined membrane protein structures...
May 13, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28510023/protein-rna-interactions-structural-biology-and-computational-modeling-techniques
#12
REVIEW
Susan Jones
RNA-binding proteins are functionally diverse within cells, being involved in RNA-metabolism, translation, DNA damage repair, and gene regulation at both the transcriptional and post-transcriptional levels. Much has been learnt about their interactions with RNAs through structure determination techniques and computational modeling. This review gives an overview of the structural data currently available for protein-RNA complexes, and discusses the technical issues facing structural biologists working to solve their structures...
December 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28507231/biological-modelling-of-a-computational-spiking-neural-network-with-neuronal-avalanches
#13
Xiumin Li, Qing Chen, Fangzheng Xue
In recent years, an increasing number of studies have demonstrated that networks in the brain can self-organize into a critical state where dynamics exhibit a mixture of ordered and disordered patterns. This critical branching phenomenon is termed neuronal avalanches. It has been hypothesized that the homeostatic level balanced between stability and plasticity of this critical state may be the optimal state for performing diverse neural computational tasks. However, the critical region for high performance is narrow and sensitive for spiking neural networks (SNNs)...
June 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28506989/fgf-signaling-refines-wnt-gradients-to-regulate-patterning-of-taste-papillae
#14
Michaela Prochazkova, Teemu J Häkkinen, Jan Prochazka, Frantisek Spoutil, Andrew H Jheon, Youngwook Ahn, Robb Krumlauf, Jukka Jernvall, Ophir D Klein
The patterning of repeated structures is a major theme in developmental biology, and the interrelationship between spacing and size of such structures is an open question. Fungiform papillae are repeated epithelial structures that house taste buds on the anterior tongue. Here, we report that FGF signaling is a critical regulator of fungiform papillae development. We found that mesenchymal FGF10 controls the size of the papillary area, while overall patterning remains unchanged. Our results show that FGF signaling negatively affects the extent of canonical Wnt signaling, which is the main activation pathway during fungiform papillae development, but this effect does not occur at the level of gene transcription...
May 15, 2017: Development
https://www.readbyqxmd.com/read/28504081/dissecting-physical-structure-of-calreticulin-an-intrinsically-disordered-ca-2-buffering-chaperone-from-endoplasmic-reticulum
#15
Anna Rita Migliaccio, Vladimir N Uversky
Calreticulin (CALR) is a Ca(2+) binding multifunctional protein that mostly resides in the endoplasmic reticulum (ER) and plays a number of important roles in various physiological and pathological processes. Although the major functions ascribed to CALR are controlling the Ca(2+) homeostasis in ER and acting as a lectin-like ER chaperon for many glycoproteins, this moonlighting protein can be found in various cellular compartments where it has many non-ER functions. To shed more light on the mechanisms underlying polyfunctionality of this moonlighting protein that can be found in different cellular compartments and that possesses a wide spectrum of unrelated biological activities, being able to interact with Ca(2+) (and potentially other metal ions), RNA, oligosaccharides, and numerous proteins, we used a set of experimental and computational tools to evaluate the intrinsic disorder status of CALR and the role of calcium binding on structural properties and conformational stability of the full-length CALR and its isolated P- and C-domains...
May 13, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28502001/clustering-and-network-analysis-of-reverse-phase-protein-array-data
#16
Adam Byron
Molecular profiling of proteins and phosphoproteins using a reverse phase protein array (RPPA) platform, with a panel of target-specific antibodies, enables the parallel, quantitative proteomic analysis of many biological samples in a microarray format. Hence, RPPA analysis can generate a high volume of multidimensional data that must be effectively interrogated and interpreted. A range of computational techniques for data mining can be applied to detect and explore data structure and to form functional predictions from large datasets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28501650/prober-provides-a-general-toolkit-for-analyzing-sequencing-based-toeprinting-assays
#17
Bo Li, Akshay Tambe, Sharon Aviran, Lior Pachter
A number of sequencing-based transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and RNA modification. Although these assays survey a diverse set of epitranscriptomic marks, we use the term toeprinting assays since they share methodological similarities. Their interpretation is predicated on addressing a similar computational challenge: how to learn isoform-specific chemical modification profiles in the face of complex read multi-mapping...
May 9, 2017: Cell Systems
https://www.readbyqxmd.com/read/28501339/x-ray-free-electron-laser-single-particle-analysis-for-biological-systems
#18
REVIEW
Osamu Miyashita, Yasumasa Joti
The X-ray free electron laser (XFEL) is a new light source that can produce coherent, ultra-brilliant, femtosecond X-ray pulses. This X-ray beam provides new possibilities for studies in structural biology. In this review, we survey the applications of XFEL to biological systems, with an emphasis on studies of noncrystalline samples. Although atomic-level modeling is not yet achievable, this method enables high-throughput, damage-free imaging of biological samples under near-physiological conditions and is being rapidly developed...
May 10, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28500031/labeling-glycans-on-living-cells-by-a-chemoenzymatic-glycoengineering-approach
#19
Ruben T Almaraz, Yanhong Li
Structural glycobiology has traditionally been a challenging field due to a limited set of tools available to investigate the diverse and complexity of Glycan molecules. However, we cannot ignore that glycans play critical roles in health as well as in disease, are present in more than 50% of all proteins and on over 80% of all surface proteins. Chemoenzymatic Glycoengineering (CEG) methods are a powerful set of tools to synthesize complex glycans but its full potential has not been explored in cell biology yet...
May 12, 2017: Biology Open
https://www.readbyqxmd.com/read/28499419/across-proteome-modeling-of-dimer-structures-for-the-bottom-up-assembly-of-protein-protein-interaction-networks
#20
Surabhi Maheshwari, Michal Brylinski
BACKGROUND: Deciphering complete networks of interactions between proteins is the key to comprehend cellular regulatory mechanisms. A significant effort has been devoted to expanding the coverage of the proteome-wide interaction space at molecular level. Although a growing body of research shows that protein docking can, in principle, be used to predict biologically relevant interactions, the accuracy of the across-proteome identification of interacting partners and the selection of near-native complex structures still need to be improved...
May 12, 2017: BMC Bioinformatics
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