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https://www.readbyqxmd.com/read/29334459/development-of-charmm-compatible-force-field-parameters-for-cobalamin-and-related-cofactors-from-quantum-mechanical-calculations
#1
Anna Pavlova, Jerry M Parks, James C Gumbart
Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co3+, Co2+ and Co1+, and with various axial ligands...
January 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29334456/building-ion-conduction-highways-in-polymeric-electrolytes-by-manipulating-protein-configuration
#2
Xuewei Fu, Chunhui Li, Yu Wang, Lucas Paul Kovatch, Louis Scudiero, Jin Liu, Wei-Hong Zhong
Solid polymer electrolytes play a critical role in the development of safe, flexible and all-solid-state energy storage devices. However, the low ion-conductivity has been the primary challenge impeding them from practical applications. Here, we propose a new biotechnology to fabricate novel protein-ceramic hybrid nanofillers for simultaneously boosting the ionic conductivity, mechanical properties and even adhesion properties of solid polymer electrolytes. This hybrid nanofiller is fabricated by coating ion-conductive soy-proteins onto TiO2 nanoparticles via a controlled denaturation process in appropriate solvent and conditions...
January 15, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29334397/recombinant-phosphatidylserine-binding-nanobodies-for-targeting-of-extracellular-vesicles-to-tumor-cells-a-plug-and-play-approach
#3
Sander A A Kooijmans, Jerney J J M Gitz-Francois, Raymond M Schiffelers, Pieter Vader
Extracellular vesicles (EVs) are increasingly being recognized as candidate drug delivery systems due to their ability to functionally transfer biological cargo between cells. However, manipulation of targeting properties of EVs through engineering of the producer cells can be challenging and time-consuming. As a novel approach to confer tumor targeting properties to isolated EVs, we generated recombinant fusion proteins of nanobodies against the epidermal growth factor receptor (EGFR) fused to phosphatidylserine (PS)-binding domains of lactadherin (C1C2)...
January 15, 2018: Nanoscale
https://www.readbyqxmd.com/read/29334383/a-simple-method-for-determining-the-ligand-affinity-toward-a-zinc-enzyme-model-by-using-a-tamra-tamra-interaction
#4
Hiroshi Kusamoto, Akio Shiba, Masaya Tsunehiro, Haruto Fujioka, Emiko Kinoshita-Kikuta, Eiji Kinoshita, Tohru Koike
Thiolate coordination to zinc(ii) ions occurs widely in such functional biomolecules as zinc enzymes or zinc finger proteins. Here, we introduce a simple method for determining the affinity of ligands toward the zinc-enzyme active-center model tetramethylrhodamine (TAMRA)-labeled 1,4,7,10-tetraazacyclododecane (cyclen)-zinc(ii) complex (TAMRA-ZnL). The 1 : 1 complexation of TAMRA-labeled cysteine (TAMRA-Cys) with TAMRA-ZnL (each at 2.5 μM), in which the TAMRA moieties approach one another closely, induces remarkable changes in the visible absorption and fluorescence spectra at pH 7...
January 15, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29334381/the-molecular-basis-of-subtype-selectivity-of-human-kinin-g-protein-coupled-receptors
#5
Lisa Joedicke, Jiafei Mao, Georg Kuenze, Christoph Reinhart, Tejaswi Kalavacherla, Hendrik R A Jonker, Christian Richter, Harald Schwalbe, Jens Meiler, Julia Preu, Hartmut Michel, Clemens Glaubitz
G-protein-coupled receptors (GPCRs) are the most important signal transducers in higher eukaryotes. Despite considerable progress, the molecular basis of subtype-specific ligand selectivity, especially for peptide receptors, remains unknown. Here, by integrating DNP-enhanced solid-state NMR spectroscopy with advanced molecular modeling and docking, the mechanism of the subtype selectivity of human bradykinin receptors for their peptide agonists has been resolved. The conserved middle segments of the bound peptides show distinct conformations that result in different presentations of their N and C termini toward their receptors...
January 15, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29334380/light-activated-chemical-probing-of-nucleobase-solvent-accessibility-inside-cells
#6
Chao Feng, Dalen Chan, Jojo Joseph, Mikko Muuronen, William H Coldren, Nan Dai, Ivan R Corrêa, Filipp Furche, Christopher M Hadad, Robert C Spitale
The discovery of functional RNAs that are critical for normal and disease physiology continues to expand at a breakneck pace. Many RNA functions are controlled by the formation of specific structures, and an understanding of each structural component is necessary to elucidate its function. Measuring solvent accessibility intracellularly with experimental ease is an unmet need in the field. Here, we present a novel method for probing nucleobase solvent accessibility, Light Activated Structural Examination of RNA (LASER)...
January 15, 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29334369/dual-gene-activation-and-knockout-screen-reveals-directional-dependencies-in-genetic-networks
#7
Michael Boettcher, Ruilin Tian, James A Blau, Evan Markegard, Ryan T Wagner, David Wu, Xiulei Mo, Anne Biton, Noah Zaitlen, Haian Fu, Frank McCormick, Martin Kampmann, Michael T McManus
Understanding the direction of information flow is essential for characterizing how genetic networks affect phenotypes. However, methods to find genetic interactions largely fail to reveal directional dependencies. We combine two orthogonal Cas9 proteins from Streptococcus pyogenes and Staphylococcus aureus to carry out a dual screen in which one gene is activated while a second gene is deleted in the same cell. We analyze the quantitative effects of activation and knockout to calculate genetic interaction and directionality scores for each gene pair...
January 15, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29334356/p53-suppresses-mutagenic-rad52-and-pol%C3%AE-pathways-by-orchestrating-dna-replication-restart-homeostasis
#8
Sunetra Roy, Karl-Heinz Tomaszowski, Jessica W Luzwick, Soyoung Park, Jun Li, Maureen Murphy, Katharina Schlacher
Classically, p53 tumor suppressor acts in transcription, apoptosis, and cell cycle arrest. Yet, replication-mediated genomic instability is integral to oncogenesis, and p53 mutations promote tumor progression and drug-resistance. By delineating human and murine separation-of-function p53 alleles, we find that p53 null and gain-of-function (GOF) mutations exhibit defects in restart of stalled or damaged DNA replication forks driving genomic instability genetically separable from transcription activation. By assaying protein-DNA fork interactions in single cells, we unveil a p53-MLL3-enabled recruitment of MRE11 DNA replication restart nuclease...
January 15, 2018: ELife
https://www.readbyqxmd.com/read/29334337/durable-responses-in-refractory-autoimmune-hemolytic-anemia-with-alemtuzumab
#9
Renee K McAlister, Mahsa S Talbott, Nishitha M Reddy
Autoimmune hemolytic anemia occurs due to an interaction of IgG antibodies with protein antigens expressed on red blood corpuscles. Glucocorticoids are the mainstay of treatment for autoimmune hemolytic anemia. For patients not responding to initial therapy, other agents such as rituximab, immunosuppressive therapy, or splenectomy are considered. When refractory to these treatment options, alemtuzumab is an alternative agent. However, long-term outcomes of patients supporting its use are lacking. We present three patients with refractory autoimmune hemolytic anemia treated with alemtuzumab...
January 1, 2018: Journal of Oncology Pharmacy Practice
https://www.readbyqxmd.com/read/29334217/characterization-of-an-hsp90-independent-interaction-between-the-co-chaperone-p23-and-the-transcription-factor-p53
#10
Huiwen Wu, Jashil Hyun, Maria A Martinez-Yamout, Sung Jean Park, Jane Dyson
The cancer-suppressing transcription factor p53 is regulated by a wide variety of cellular factors, including many chaperones. The DNA-binding domain (DBD) of p53 is known to interact with the chaperone Hsp90, but the role of other members of the chaperone network, including co-chaperones such as p23 is unknown. Using a combination of NMR titration, isothermal titration calorimetry, fluorescence anisotropy and native agarose gel electrophoresis, we have identified a direct interaction between the p53 DBD and the Hsp90 co-chaperone p23 that occurs in the absence of Hsp90...
January 15, 2018: Biochemistry
https://www.readbyqxmd.com/read/29334187/surveying-the-landscape-of-optogenetic-methods-for-detection-of-protein-protein-interactions
#11
REVIEW
Matthew D Wiens, Robert E Campbell
Mapping the protein-protein interaction (PPi) landscape is of critical importance to furthering our understanding how cells and organisms function. Optogenetic methods, that is, approaches that utilize genetically encoded fluorophores or fluorogenic enzyme reactions, uniquely enable the visualization of biochemical phenomena in live cells with high spatial and temporal accuracy. Applying optogenetic methods to the detection of PPis requires the engineering of protein-based systems in which an optical signal undergoes a substantial change when the two proteins of interest interact...
January 15, 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29334167/cross-linking-mass-spectrometry-for-studying-protein-structures-and-protein-protein-interactions-where-are-we-now-and-where-should-we-go-from-here
#12
Andrea Sinz
Structural mass spectrometry (MS) is gaining increasing importance in deriving valuable three-dimensional structural information on proteins and protein complexes and complements existing techniques, such as NMR spectroscopy and X-ray crystallography. Structural MS unites different MS-based techniques, i.e, hydrogen-deuterium exchange, native MS, ion-mobility MS, protein footprinting, and chemical cross-linking/MS, and allows fundamental questions in structural biology to be addressed. In this article, I will focus on the cross-linking/MS strategy...
January 15, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29334122/inhibition-of-hsp90%C3%AE-protects-cultured-neurons-from-oxygen-glucose-deprivation-induced-necroptosis-by-decreasing-rip3-expression
#13
Zhen Wang, Li-Min Guo, Yong Wang, Hong-Kang Zhou, Shu-Chao Wang, Dan Chen, Ju-Fang Huang, Kun Xiong
Heat shock protein 90α (HSP90α) maintains cell stabilization and regulates cell death, respectively. Recent studies have shown that HSP90α is involved in receptor interacting protein 3 (RIP3)-mediated necroptosis in HT29 cells. It is known that oxygen and glucose deprivation (OGD) can induce necroptosis, which is regulated by RIP3 in neurons. However, it is still unclear whether HSP90α participates in the process of OGD-induced necroptosis in cultured neurons via the regulation of RIP3. Our study found that necroptosis occurs in primary cultured cortical neurons and PC-12 cells following exposure to OGD insult...
November 20, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29334118/markers-of-proliferation-and-invasiveness-in-somatotropinomas
#14
Agata Baldys-Waligorska, Iga Wierzbicka, Grzegorz Sokolowski, Dariusz Adamek, Filip Golkowski
IntroductionIn the search for markers of invasiveness of pituitary adenomas, we studied the expression of Ki-67 antigen, TOPO 2A (topoisomerase 2 alpha), AIP (Aryl Hydrocarbon Receptor-Interacting Protein) and VEGF (Vascular Endothelial Growth Factor) in somatotropinomas.Material and MethodsWe retrospectively studied a group of 31 patients who underwent pituitary tumour surgery. Expression of Ki-67, TOPO 2A, AIP and VEGF in surgical specimens was determined by immunohistochemistry. Relations between quantitatively determined markers and clinical symptoms, tumour features, and MR imaging, were analysed...
January 15, 2018: Endokrynologia Polska
https://www.readbyqxmd.com/read/29333953/the-irreversible-erbb1-2-4-inhibitor-neratinib-interacts-with-the-bcl-2-inhibitor-venetoclax-to-kill-mammary-cancer-cells
#15
Laurence Booth, Jane L Roberts, Francesca Avogadri-Connors, Richard E CutlerJr, Alshad S Lalani, Andrew Poklepovic, Paul Dent
The irreversible ERBB1/2/4 inhibitor, neratinib, down-regulates the expression of ERBB1/2/4 as well as the levels of MCL-1 and BCL-XL. Venetoclax (ABT199) is a BCL-2 inhibitor. At physiologic concentrations neratinib interacted in a synergistic fashion with venetoclax to kill HER2+ and TNBC mammary carcinoma cells. This was associated with the drug-combination: reducing the expression and phosphorylation of ERBB1/2/3; in an eIF2α-dependent fashion reducing the expression of MCL-1 and BCL-XL and increasing the expression of Beclin1 and ATG5; and increasing the activity of the ATM-AMPKα-ULK1 S317 pathway which was causal in the formation of toxic autophagosomes...
January 15, 2018: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/29333944/mir-155-promotes-uveal-melanoma-cell-proliferation-and-invasion-by-regulating-ndfip1-expression
#16
Jing Peng, Honglei Liu, Cuihong Liu
MicroRNAs refer to small RNA molecules that destroy the messenger RNA by binding on them inhibiting the production of protein. However, the role of miR-155 in uveal melanoma metastasis remains largely unknown. In this study, we found that miR-155 was upregulated in both uveal melanoma cells and tissues. Transfection of miR-155 mimic into uveal melanoma cells led to an increase in cell growth and invasion; in contrast, inhibition of miR-155 resulted in opposite effects. Also, we identified Nedd4-family interacting protein 1 as a direct target of miR-155, and the expression of Nedd4-family interacting protein 1 was inhibited by miR-155...
December 2017: Technology in Cancer Research & Treatment
https://www.readbyqxmd.com/read/29333942/six1-and-dach1-influence-the-proliferation-and-apoptosis-of-hepatocellular-carcinoma-through-regulating-p53
#17
Qi Cheng, Deng Ning, Jin Chen, Xue Li, Xiaoping Chen, Li Jiang
ABSTRACTS This research aimed to explore effects of SIX1 and DACH1 on hepatocellular carcinoma (HCC) cell proliferation, apoptosis and cell cycle. Fifty paired hepatocellular carcinoma tissues were screened for differentially expressed genes. SIX1 and DACH1 expressions were subjected to qRT-PCR and western blot in tumor tissues and cells. The knockdown efficiency of siRNAs and transfection efficiency of cDNAs and siRNAs were validated by qRT-PCR and western blot as well. Then colony formation assay and flow cytometry were applied to observe cell proliferation, cell apoptosis and cell cycle changes...
January 15, 2018: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/29333723/nandrolone-induced-nuclear-accumulation-of-myod-protein-is-mediated-by-numb-a-notch-inhibitor-in-c2c12-myoblasts
#18
Xin-Hua Liu, Rita De Gasperi, William A Bauman, Christopher P Cardozo
Signaling via the androgen receptor (AR) stimulates myogenic progenitor differentiation. In addition, myogenic differentiation factor D (MyoD) and Numb, a Notch inhibitor, play key roles in regulating myogenic differentiation. Nandrolone, an anabolic steroid, upregulates both MyoD and Numb expression in myogenic cells. However, the molecular mechanisms by which MyoD is upregulated by nandrolone are unclear. Moreover, the potential crosstalk between nandrolone, MyoD, and Numb is not well understood. With these considerations in mind, we examined the effects of nandrolone on the expression of MyoD mRNA and protein, and determined the interactions of MyoD and Numb in the presence or absence of nandrolone in differentiating C2C12 myoblasts...
January 2018: Physiological Reports
https://www.readbyqxmd.com/read/29333604/adiponectin-inhibits-inflammatory-cytokines-production-by-beclin-1-phosphorylation-and-bcl-2-mrna-destabilization-role-for-autophagy-induction
#19
Nirmala Tilija Pun, Pil-Hoon Park
BACKGROUND AND PURPOSE: Adiponectin potently suppresses inflammatory mediator production. Autophagy is known to play a critical role in modulating inflammatory responses by adiponectin. However, the underlying mechanisms are not clearly understood. Interaction between Beclin-1 and Bcl-2 is a critical event in autophagy induction. We examined the effects of globular adiponectin (gAcrp) on the Beclin-1/Bcl-2 association and its underlying mechanisms. EXPERIMENTAL APPROACH: The effect of gAcrp on the interaction between Beclin-1 and Bcl-2 was examined by immunoprecipitation followed by Western blotting...
January 14, 2018: British Journal of Pharmacology
https://www.readbyqxmd.com/read/29333119/phytotherapeutics-oridonin-and-ponicidin-show-additive-effects-combined-with-irradiation-in-pancreatic-cancer-in-vitro
#20
Jakob Liermann, Patrick Naumann, Franco Fortunato, Thomas E Schmid, Klaus-Josef Weber, Jürgen Debus, Stephanie E Combs
Background: Chemoradiation of locally advanced non-metastatic pancreatic cancer can lead to secondary operability by tumor mass reduction. Here, we analyzed radiomodulating effects of oridonin and ponicidin in pancreatic cancer in vitro. Both agents are ent-kaurane diterpenoids, extracted from Isodon rubescens, a plant that is well known in Traditional Chinese Medicine. Cytotoxic effects have recently been shown in different tumor entities for both agents. Materials and methods: Pancreatic cancer cell lines AsPC-1, BxPC-3, Panc-1 and MIA PaCa-2 were pretreated with oridonin or ponicidin and irradiated with 2 Gy to 6 Gy...
December 2017: Radiology and Oncology
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