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https://www.readbyqxmd.com/read/28938568/senp3-grants-tight-junction-integrity-and-cytoskeleton-architecture-in-mouse-sertoli-cells
#1
Di Wu, Chun-Jie Huang, Faheem Ahmed Khan, Xiao-Fei Jiao, Xiao-Ming Liu, Nuruliarizki Shinta Pandupuspitasari, Rahim Dad Brohi, Li-Jun Huo
Germ cells develop in a sophisticated immune privileged microenvironment provided by specialized junctions contiguous the basement membrane of the adjacent Sertoli cells that constituted the blood-testis barrier (BTB) in seminiferous epithelium of testis in mammals. Deciphering the molecular regulatory machinery of BTB activity is central to improve male fertility and the role of post-translational modification including SUMOylation pathway is one of the key factors. Herein, we unveiled the mystery of the SUMO-2/3 specific protease SENP3 (Sentrin-specific protease 3) in BTB dynamics regulation...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938408/pioneer-factors-foxa1-and-foxa2-assist-selective-glucocorticoid-receptor-signaling-in-human-endometrial-cells
#2
Shannon Whirledge, Edwina P Kisanga, Robert N Taylor, John A Cidlowski
Successful pregnancy relies on dynamic control of cell signaling in order to achieve uterine receptivity and the necessary biological changes required for endometrial decidualization, embryo implantation, and fetal development. Glucocorticoids are master regulators of intracellular signaling and can directly regulate embryo implantation and endometrial remodeling during murine pregnancy. In immortalized human uterine cells, we have shown that glucocorticoids and estradiol co-regulate thousands of genes. Recently, glucocorticoids and estradiol were shown to co-regulate the expression of Left-right determination factor 1 (LEFTY1), previously implicated in the regulation of decidualization...
August 29, 2017: Endocrinology
https://www.readbyqxmd.com/read/28938164/multifunctional-superparamagnetic-nanoparticles-conjugated-with-fluorescein-labeled-designed-ankyrin-repeat-protein-as-an-efficient-her2-targeted-probe-in-breast-cancer
#3
Dong-Li Li, Jian-Er Tan, Ying Tian, Shun Huang, Peng-Hui Sun, Meng Wang, Yan-Jiang Han, Hong-Sheng Li, Hu-Bing Wu, Xing-Mei Zhang, Yi-Kai Xu, Quan-Shi Wang
Based on the discordance of human epidermal growth factor receptor-2 (HER2) expression between primary and metastatic/recurrent breast cancer, HER2 molecular imaging, which had potential to systemically assess and dynamically monitor HER2 expression, might improve the selection of patients for anti-HER2 therapy. In this study, designed ankyrin repeat protein (DARPin) G3, a novel binding protein with picomolar affinity for HER2, was used and multifunctional superparamagnetic nanoparticles modified with fluorescein-5-maleimide-labeled DARPin G3 (SPIO-G3-5MF) were developed for HER2 imaging...
September 8, 2017: Biomaterials
https://www.readbyqxmd.com/read/28938158/directional-migration-in-esophageal-squamous-cell-carcinoma-escc-is-epigenetically-regulated-by-set-nuclear-oncogene-a-member-of-the-inhibitor-of-histone-acetyltransferase-complex
#4
Xiang Yuan, Xinshuai Wang, Bianli Gu, Yingjian Ma, Yiwen Liu, Man Sun, Jinyu Kong, Wei Sun, Huizhi Wang, Fuyou Zhou, Shegan Gao
Directional cell migration is of fundamental importance to a variety of biological events, including metastasis of malignant cells. Herein, we specifically investigated SET oncoprotein, a subunit of the recently identified inhibitor of acetyltransferases (INHAT) complex and identified its role in the establishment of front-rear cell polarity and directional migration in Esophageal Squamous Cell Carcinoma (ESCC). We further define the molecular circuits that govern these processes by showing that SET modulated DOCK7/RAC1 and cofilin signaling events...
September 19, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28938095/dynamic-looping-interactions-setting-the-3d-stage-for-the-macrophage
#5
Mayuri Rege, Jennifer E Phillips-Cremins
The mechanisms by which 3D chromatin looping interactions mediate cell type-specific gene expression are an active area of investigation. In this issue of Molecular Cell, Phanstiel et al. (2017) annotate five classes of loops during macrophage development and predict candidate factors involved in their regulation.
September 21, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28938070/dynamics-of-water-monolayers-confined-by-chemically-heterogeneous-surfaces-observation-of-surface-induced-anisotropic-diffusion
#6
Mehdi Karzar Jeddi, Santiago Romero-Vargas Castrillón
Water present in confining geometries plays key roles in many systems of scientific and technological relevance. Prominent examples are living cells and nanofluidic devices. Despite its importance, a complete understanding of the dynamics of water in nanoscale confinement remains elusive. In this work, we use molecular dynamics (MD) simulation to investigate the diffusive dynamics of water monolayers confined in chemically heterogeneous silica slit pores. The effect of chemical heterogeneity is systematically investigated through the fraction f_SiOH of randomly distributed surface sites that possess hydroxyl functional groups...
September 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28938017/a-highly-conserved-amino-acid-in-vp1-regulates-maturation-of-enterovirus-71
#7
Yong-Xin Zhang, Yu-Ming Huang, Quan-Jie Li, Xiao-Yu Li, Yong-Dong Zhou, Fei Guo, Jin-Ming Zhou, Shan Cen
Enterovirus 71 (EV71) is the major causative agent of hand, foot and mouth disease (HFMD) in children, causing severe clinical outcomes and even death. Here, we report an important role of the highly conserved alanine residue at position 107 in the capsid protein VP1 (VP1A107) in the efficient replication of EV71. Substitutional mutations of VP1A107 significantly diminish viral growth kinetics without significant effect on viral entry, expression of viral genes and viral production. The results of mechanistic studies reveal that VP1A107 regulates the efficient cleavage of the VP0 precursor during EV71 assembly, which is required, in the next round of infection, for the transformation of the mature virion (160S) into an intermediate or A-particle (135S), a key step of virus uncoating...
September 22, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28937994/modeling-of-annexin-a2-membrane-interactions-by-molecular-dynamics-simulations
#8
Davit Hakobyan, Volker Gerke, Andreas Heuer
The annexins are a family of Ca2+-regulated phospholipid binding proteins that are involved in membrane domain organization and membrane trafficking. Although they are widely studied and crystal structures are available for several soluble annexins their mode of membrane association has never been studied at the molecular level. Here we obtained molecular information on the annexin-membrane interaction that could serve as paradigm for the peripheral membrane association of cytosolic proteins by Molecular Dynamics simulations...
2017: PloS One
https://www.readbyqxmd.com/read/28937762/projected-commutator-diis-method-for-accelerating-hybrid-functional-electronic-structure-calculations
#9
Wei Hu, Lin Lin, Chao Yang
The commutator direct inversion of the iterative subspace (commutator DIIS or C-DIIS) method developed by Pulay is an efficient and the most widely used scheme in quantum chemistry to accelerate the convergence of self consistent field (SCF) iterations in Hartree-Fock theory and Kohn-Sham density functional theory. The C-DIIS method requires the explicit storage of the density matrix, the Fock matrix and the commutator matrix. Hence the method can only be used for systems with a relatively small basis set, such as the Gaussian basis set...
September 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28937698/evolution-of-mechanics-in-%C3%AE-helical-peptide-conjugated-linear-and-star-block-peg
#10
S C O'Neill, Z H Bhuiyan, R S Tu
We have designed a peptide conjugated poly-ethylene glycol (PEG) bioconjugate system that allows us to examine the intra- and inter-molecular dynamics of gelation. We measure the kinetics of gelation for end-functionalized linear- and star-architectures, and we correlate the gelation behavior with the molecular structure and self-association. The 23-amino acid peptide sequence is known to form a coiled-coil structure as a function of the solution's electrolyte concentration, and the two topologies of the PEG are peptide end-functionalized to examine formation of supramolecular assemblies...
September 22, 2017: Soft Matter
https://www.readbyqxmd.com/read/28937675/coherent-singlet-fission-activated-by-symmetry-breaking
#11
Kiyoshi Miyata, Yuki Kurashige, Kazuya Watanabe, Toshiki Sugimoto, Shota Takahashi, Shunsuke Tanaka, Jun Takeya, Takeshi Yanai, Yoshiyasu Matsumoto
Singlet fission, in which a singlet exciton is converted to two triplet excitons, is a process that could be beneficial in photovoltaic applications. A full understanding of the dynamics of singlet fission in molecular systems requires detailed knowledge of the relevant potential energy surfaces and their (conical) intersections. However, obtaining such information is a nontrivial task, particularly for molecular aggregates. Here we investigate singlet fission in rubrene crystals using transient absorption spectroscopy and state-of-the-art quantum chemical calculations...
October 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28937668/complete-protein-protein-association-kinetics-in-atomic-detail-revealed-by-molecular-dynamics-simulations-and-markov-modelling
#12
Nuria Plattner, Stefan Doerr, Gianni De Fabritiis, Frank Noé
Protein-protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein-protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling...
October 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28937662/glucose-responsive-insulin-by-molecular-and-physical-design
#13
Naveed A Bakh, Abel B Cortinas, Michael A Weiss, Robert S Langer, Daniel G Anderson, Zhen Gu, Sanjoy Dutta, Michael S Strano
The concept of a glucose-responsive insulin (GRI) has been a recent objective of diabetes technology. The idea behind the GRI is to create a therapeutic that modulates its potency, concentration or dosing relative to a patient's dynamic glucose concentration, thereby approximating aspects of a normally functioning pancreas. From the perspective of the medicinal chemist, the GRI is also important as a generalized model of a potentially new generation of therapeutics that adjust potency in response to a critical therapeutic marker...
September 22, 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28937216/relative-contributions-of-core-protein-and-solvatation-shell-in-the-terahertz-dielectric-properties-of-protein-solutions
#14
Marianne Grognot, Guilhem Gallot
The properties of the solvation shell surrounding biomolecules in solution are fundamental to understand the modifications of the dynamics of the water molecules by peptides and proteins. The dynamics of the hydrogen bonding network typically occurs at the picosecond time scale, then terahertz spectroscopy is a unique tool to investigate the solvation shell. Here, we present terahertz measurements of the refractive index and extinction coefficient of solutions of biomolecules of various molecular weights. We observe a clear correlation between the terahertz dielectric properties and the weight of the molecules...
September 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28937170/photochemistry-and-aggregation-behavior-of-triethylene-glycol-teg-terminated-stilbene-dendrimers
#15
Hiroya Sakurai, Takashi Maruyama, Tatsuo Arai
The photochemical properties of stilbene cored amphiphilic dendrimers (G0-G3) in THF and water were investigated. The solvation dynamics in water depended on the generation, while the behavior is almost the same in THF. Dendrimers G1 and G2 form molecular assemblies and undergo photodimerization reaction in addition to photoisomerization. G3 has enough TEG groups on the surface to cover the hydrophobic moiety within a single molecule. These dendrimers have free space around the core to undergo mutual isomerization even in water...
September 22, 2017: Photochemical & Photobiological Sciences
https://www.readbyqxmd.com/read/28936651/in-vivo-ploidy-determination-of-arabidopsis-thaliana-male-and-female-gametophytes
#16
Burcu Nur Keçeli, Nico De Storme, Danny Geelen
Organ- or tissue-specific ploidy level determination is often used for answering biological, molecular, genetic, or evolutionary questions in plant sciences. However, current techniques for ploidy determination either cannot provide information on single cell level, require destructive sample preparation, or are laborious and time-consuming. Here, we present a new approach developed in Arabidopsis thaliana, which is not only less labor intensive but also allows in vivo ploidy determination on single cell level...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28936467/peroxisome-motility-measurement-and-quantification-assay
#17
Jeremy Metz, Inês G Castro, Michael Schrader
Organelle movement, distribution and interaction contribute to the organisation of the eukaryotic cell. Peroxisomes are multifunctional organelles which contribute to cellular lipid metabolism and ROS homeostasis. They distribute uniformly in mammalian cells and move along microtubules via kinesin and dynein motors. Their metabolic cooperation with mitochondria and the endoplasmic reticulum (ER) is essential for the β-oxidation of fatty acids and the synthesis of myelin lipids and polyunsaturated fatty acids...
September 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28936355/theoretical-and-experimental-study-of-the-antifreeze-protein-afp752-trehalose-and-dimethyl-sulfoxide-cryoprotection-mechanism-correlation-with-cryopreserved-cell-viability
#18
Irena Kratochvílová, Martin Golan, Karel Pomeisl, Jan Richter, Silvia Sedláková, Jakub Šebera, Júlia Mičová, Martin Falk, Iva Falková, David Řeha, K Wade Elliott, Krisztina Varga, Shelby E Follett, Daniel Šimek
In this work the physico-chemical properties of selected cryoprotectants (antifreeze protein TrxA-AFP752, trehalose and dimethyl sulfoxide) were correlated with their impact on the constitution of ice and influence on frozen/thawed cell viability. The freezing processes and states of investigated materials solutions were described and explained from a fundamental point of view using ab-initio modelling (molecular dynamics, DFT), Raman spectroscopy, Differential Scanning Calorimetry and X-Ray Diffraction. For the first time, in this work we correlated the microscopic view (modelling) with the description of the frozen solution states and put these results in the context of human skin fibroblast viability after freezing and thawing...
2017: RSC Advances
https://www.readbyqxmd.com/read/28936215/omics-approaches-for-understanding-grapevine-berry-development-regulatory-networks-associated-with-endogenous-processes-and-environmental-responses
#19
REVIEW
Alejandra Serrano, Carmen Espinoza, Grace Armijo, Claudio Inostroza-Blancheteau, Evelyn Poblete, Carlos Meyer-Regueiro, Anibal Arce, Francisca Parada, Claudia Santibáñez, Patricio Arce-Johnson
Grapevine fruit development is a dynamic process that can be divided into three stages: formation (I), lag (II), and ripening (III), in which physiological and biochemical changes occur, leading to cell differentiation and accumulation of different solutes. These stages can be positively or negatively affected by multiple environmental factors. During the last decade, efforts have been made to understand berry development from a global perspective. Special attention has been paid to transcriptional and metabolic networks associated with the control of grape berry development, and how external factors affect the ripening process...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28935965/aromatic-side-chain-conformational-switch-on-the-surface-of-the-rna-recognition-motif-enables-rna-discrimination
#20
Nana Diarra Dit Konté, Miroslav Krepl, Fred F Damberger, Nina Ripin, Olivier Duss, Jiří Šponer, Frédéric H-T Allain
The cyclooxygenase-2 is a pro-inflammatory and cancer marker, whose mRNA stability and translation is regulated by the CUG-binding protein 2 interacting with AU-rich sequences in the 3' untranslated region. Here, we present the solution NMR structure of CUG-binding protein 2 RRM3 in complex with 5'-UUUAA-3' originating from the COX-2 3'-UTR. We show that RRM3 uses the same binding surface and protein moieties to interact with AU- and UG-rich RNA motifs, binding with low and high affinity, respectively. Using NMR spectroscopy, isothermal titration calorimetry and molecular dynamics simulations, we demonstrate that distinct sub-states characterized by different aromatic side-chain conformations at the RNA-binding surface allow for high- or low-affinity binding with functional implications...
September 21, 2017: Nature Communications
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