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https://www.readbyqxmd.com/read/28738645/competitive-fluorescence-anisotropy-polarization-assay-for-atp-using-aptamer-as-affinity-ligand-and-dye-labeled-atp-as-fluorescence-tracer
#1
Yapiao Li, Linlin Sun, Qiang Zhao
We developed an aptamer-based competitive fluorescence anisotropy (FA)/fluorescence polarization (FP) assay for adenosine triphosphate (ATP). Different from the traditional fluorescence polarization immunoassays for small molecules, here DNA aptamer against ATP was used as affinity ligand, and tetramethylrhodamine (TMR) labeled ATP served as fluorescent tracer. The binding between TMR-labeled ATP and aptamer gave large FA due to molecular volume increase and restricted rotation of the dye-labeled ATP. When ATP was added in solution, ATP competitively displaced the TMR-labeled ATP from aptamer affinity complex, causing decrease of FA of TMR-labeled ATP...
November 1, 2017: Talanta
https://www.readbyqxmd.com/read/28738444/protein-coating-of-dna-nanostructures-for-enhanced-stability-and-immunocompatibility
#2
Henni Auvinen, Hongbo Zhang, Nonappa, Alisa Kopilow, Elina H Niemelä, Sami Nummelin, Alexandra Correia, Hélder A Santos, Veikko Linko, Mauri A Kostiainen
Fully addressable DNA nanostructures, especially DNA origami, possess huge potential to serve as inherently biocompatible and versatile molecular platforms. However, their use as delivery vehicles in therapeutics is compromised by their low stability and poor transfection rates. This study shows that DNA origami can be coated by precisely defined one-to-one protein-dendron conjugates to tackle the aforementioned issues. The dendron part of the conjugate serves as a cationic binding domain that attaches to the negatively charged DNA origami surface via electrostatic interactions...
July 24, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28738244/dna-binding-and-unwinding-by-hel308-helicase-requires-dual-functions-of-a-winged-helix-domain
#3
Sarah J Northall, Ryan Buckley, Nathan Jones, J Carlos Penedo, Panos Soultanas, Edward L Bolt
Hel308 helicases promote genome stability linked to DNA replication in archaea, and have homologues in metazoans. In the crystal structure of archaeal Hel308 bound to a tailed DNA duplex, core helicase domains encircle single-stranded DNA (ssDNA) in a "ratchet" for directional translocation. A winged helix domain (WHD) is also present, but its function is mysterious. We investigated the WHD in full-length Hel308, identifying that mutations in a solvent exposed α-helix resulted in reduced DNA binding and unwinding activities...
July 16, 2017: DNA Repair
https://www.readbyqxmd.com/read/28738206/a-preliminary-study-on-the-effects-of-lanthanum-iii-on-plant-vitronectin-like-protein-and-its-toxicological-basis
#4
Lihong Wang, Jingfang He, Qing Yang, Xiaodong Li, Haiyan Wei, David D Y Chen, Xiaohua Huang
Vitronectin-like protein (VN) is widely found outside plant plasma membranes. The VN molecular surface contains a large number of active groups that combine strongly with rare earth elements (REEs), which means that VN is a preferential binding target for REEs exhibiting their toxic effects, but the toxicological mechanism remains unknown. This study used transmission electron microscopy, circular dichroism, fluorescence spectrometry, ultraviolet-visible spectroscopy, X-ray photoelectron spectroscopy, and calculational chemistry (homology modeling, molecular dynamics simulation and quantum chemical calculation) to preliminarily investigate the effect of lanthanum [La(III)] as an REE, on the structure of VN and its toxicological mechanism...
July 21, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28738155/engineering-aromatic-aromatic-interactions-to-nucleate-folding-in-intrinsically-disordered-regions-of-proteins
#5
Swati Balakrishnan, Siddhartha Peddibhotla Sarma
Aromatic interactions are known to be an important force in protein folding as they combine the stability of a hydrophobic interaction with the selectivity of a hydrogen bond. Much of our understanding of aromatic interactions comes from analyses of protein structures and from the contribution of these interactions to stabilizing secondary structure motifs in model peptides. In this study the structural consequences of aromatic interactions on protein folding have been explored in engineered mutants of the molten globule protein apo - cytochrome b5...
July 24, 2017: Biochemistry
https://www.readbyqxmd.com/read/28737894/dual-role-of-gold-nanorods-inhibition-dissolution-of-a%C3%AE-fibrils-induced-by-near-ir-laser
#6
Swathi Sudhakar, Poornima Budime Santhosh, Ethayaraja Mani
Extracellular plaques of amyloid beta (Aβ) fibrils and neurofibrillary tangles are known to be associated with neurological diseases such as Alzheimer's. Studies have shown that spherical nanoparticles inhibit the formation of Aβ fibrils by intercepting the nucleation and growth pathways of fibrillation. In this report, gold nanorods (AuNR) are used to inhibit the formation of Aβ fibrils and the shape-dependent plasmonic properties of AuNR are exploited to faciliate faster dissolution of mature Aβ fibrils...
July 24, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28737816/protein-stability-and-dynamics-influenced-by-ligands-in-extremophilic-complexes-a-molecular-dynamics-investigation
#7
Sara Khan, Umar Farooq, Maria Kurnikova
In this study, we explore the structural and dynamic adaptations of the Tryptophan synthase α-subunit in a ligand bound state in psychrophilic, mesophilic and hyperthermophilic organisms at different temperatures by MD simulations. We quantify the global and local fluctuations in the 40 ns time scale by analyzing the root mean square deviation/fluctuations. The distinct behavior of the active site and loop 6 is observed with the elevation of temperature. Protein stability relies more on electrostatic interactions, and these interactions might be responsible for the stability of varying temperature evolved proteins...
July 24, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28737710/cytoprotective-effect-of-the-ucp2-sirt3-signaling-pathway-by-decreasing-mitochondrial-oxidative-stress-on-cerebral-ischemia-reperfusion-injury
#8
REVIEW
Jing Su, Jie Liu, Xiao-Yu Yan, Yong Zhang, Juan-Juan Zhang, Li-Chao Zhang, Lian-Kun Sun
Recovered blood supply after cerebral ischemia for a certain period of time fails to restore brain function, with more severe dysfunctional problems developing, called cerebral ischemia-reperfusion injury (CIR). CIR involves several extremely complex pathophysiological processes in which the interactions between key factors at various stages have not been fully elucidated. Mitochondrial dysfunction is one of the most important mechanisms of CIR. The mitochondrial deacetylase, sirtuin 3 (SIRT3), can inhibit mitochondrial oxidative stress by deacetylation, to maintain mitochondrial stability...
July 24, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28737673/magnetic-nanoemulsions-comparison-between-nanoemulsions-formed-by-ultrasonication-and-by-spontaneous-emulsification
#9
Nathalia Rodríguez-Burneo, Maria Antònia Busquets, Joan Estelrich
Nanoemulsions are particularly suitable as a platform in the development of delivery systems. The type of nanoemulsion with a higher stability will offer an advantage in the preparation of a delivery system for lipophilic drugs. Nanoemulsions can be fabricated by different processing methods, which are usually categorized as either high- or low-energy methods. In this study, a comparison between two methods of preparing magnetic oil-in-water (O/W) nanoemulsions is described. The nanoemulsions were formed by sonication (the high-energy method) or by spontaneous emulsification (the low-energy method)...
July 22, 2017: Nanomaterials
https://www.readbyqxmd.com/read/28737513/loss-of-function-mutations-in-co-chaperone-bag3-destabilize-small-hsps-and-cause-cardiomyopathy
#10
Xi Fang, Julius Bogomolovas, Tongbin Wu, Wei Zhang, Canzhao Liu, Jennifer Veevers, Matthew J Stroud, Zhiyuan Zhang, Xiaolong Ma, Yongxin Mu, Dieu-Hung Lao, Nancy D Dalton, Yusu Gu, Celine Wang, Michael Wang, Yan Liang, Stephan Lange, Kunfu Ouyang, Kirk L Peterson, Sylvia M Evans, Ju Chen
Defective protein quality control (PQC) systems are implicated in multiple diseases. Molecular chaperones and co-chaperones play a central role in functioning PQC. Constant mechanical and metabolic stress in cardiomyocytes places great demand on the PQC system. Mutation and downregulation of the co-chaperone protein BCL-2-associated athanogene 3 (BAG3) are associated with cardiac myopathy and heart failure, and a BAG3 E455K mutation leads to dilated cardiomyopathy (DCM). However, the role of BAG3 in the heart and the mechanisms by which the E455K mutation leads to DCM remain obscure...
July 24, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28737508/targeting-nek2-attenuates-glioblastoma-growth-and-radioresistance-by-destabilizing-histone-methyltransferase-ezh2
#11
Jia Wang, Peng Cheng, Marat S Pavlyukov, Hai Yu, Zhuo Zhang, Sung-Hak Kim, Mutsuko Minata, Ahmed Mohyeldin, Wanfu Xie, Dongquan Chen, Violaine Goidts, Brendan Frett, Wenhao Hu, Hongyu Li, Yong Jae Shin, Yeri Lee, Do-Hyun Nam, Harley I Kornblum, Maode Wang, Ichiro Nakano
Accumulating evidence suggests that glioma stem cells (GSCs) are important therapeutic targets in glioblastoma (GBM). In this study, we identified NIMA-related kinase 2 (NEK2) as a functional binding protein of enhancer of zeste homolog 2 (EZH2) that plays a critical role in the posttranslational regulation of EZH2 protein in GSCs. NEK2 was among the most differentially expressed kinase-encoding genes in GSC-containing cultures (glioma spheres), and it was required for in vitro clonogenicity, in vivo tumor propagation, and radioresistance...
July 24, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28737389/glycosyl-cations-versus-allylic-cations-in-spontaneous-and-enzymatic-hydrolysis
#12
Phillip M Danby, Stephen G Withers
Enzymatic prenyl and glycosyl transfer are seemingly unrelated reactions that yield molecules and protein modifications with disparate biological functions. However, both reactions employ diphosphate-activated donors and each proceed via cationic spe-cies: allylic cations and oxocarbenium ions, respectively. In this study, we explore the relationship between these processes by preparing valienyl ethers to serve as glycoside mimics that are capable of allylic rather than oxocarbenium cation stabilization. Rate constants for spontaneous hydrolysis of aryl glycosides and their analogous valienyl ethers were found to be almost identical, as were the corresponding activation enthalpies and entropies...
July 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28737169/actomyosin-drives-cancer-cell-nuclear-dysmorphia-and-threatens-genome-stability
#13
Tohru Takaki, Marco Montagner, Murielle P Serres, Maël Le Berre, Matt Russell, Lucy Collinson, Karoly Szuhai, Michael Howell, Simon J Boulton, Erik Sahai, Mark Petronczki
Altered nuclear shape is a defining feature of cancer cells. The mechanisms underlying nuclear dysmorphia in cancer remain poorly understood. Here we identify PPP1R12A and PPP1CB, two subunits of the myosin phosphatase complex that antagonizes actomyosin contractility, as proteins safeguarding nuclear integrity. Loss of PPP1R12A or PPP1CB causes nuclear fragmentation, nuclear envelope rupture, nuclear compartment breakdown and genome instability. Pharmacological or genetic inhibition of actomyosin contractility restores nuclear architecture and genome integrity in cells lacking PPP1R12A or PPP1CB...
July 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28737009/non-additive-stabilization-by-halogenated-amino-acids-reveals-protein-plasticity-on-a-sub-angstrom-scale
#14
Azade S Hosseini, Christopher J Pace, Adam A Esposito, Jianmin Gao
It has been a long-standing goal to understand the structure-stability relationship of proteins, as optimal stability is essential for protein function and highly desirable for protein therapeutics. Halogenation has emerged as a minimally invasive strategy to probe the physical characteristics of proteins in solution, as well as enhance the structural stabilities of proteins for therapeutic applications. Although advances in synthetic chemistry and genetic code expansion have allowed for the rapid synthesis of proteins with diverse chemical sequences, much remains to be learned regarding the impact of these mutations on their structural integrity...
July 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28736891/heat-induced-native-dimerization-prevents-amyloid-formation-by-variable-domain-from-immunoglobulin-light-chain-rei
#15
Marina Nawata, Hirotaka Tsutsumi, Yuta Kobayashi, Satoru Unzai, Shouhei Mine, Tsutomu Nakamura, Koichi Uegaki, Hironari Kamikubo, Mikio Kataoka, Daizo Hamada
Amyloid light chain (AL) amyloidosis is a protein-misfolding disease characterized by accumulation of immunoglobulin light chains (LCs) into amyloid fibrils. Dimerization of full length or variable domain (VL ) of LC serves to stabilize the native state and prevent the formation of amyloid fibrils. We here analyzed the thermodynamic properties of dimerization and unfolding reactions by nonamyloidogenic VL from REI LC or its monomeric Y96K mutant using sedimentation velocity and circular dichroism. The data indicate that the equilibrium shifts to native dimerization for wild type REI VL by elevating temperature due to the negative enthalpy change for dimer dissociation (-81...
July 24, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28736824/evaluation-of-lumazine-synthase-from-bacillus-anthracis-as-a-presentation-platform-for-polyvalent-antigen-display
#16
Yangjie Wei, Newton Wahome, Greta VanSlyke, Neal Whitaker, Prashant Kumar, Michael L Barta, Wendy L Picking, David B Volkin, Nicholas J Mantis, C Russell Middaugh
Polyvalent antigen display is an effective strategy to enhance the immunogenicity of subunit vaccines by clustering them in an array-like manner on a scaffold system. This strategy results in a higher local density of antigens, increased high avidity interactions with B cells and other antigen presenting cells, and therefore a more effective presentation of vaccine antigens. In the present study, we used lumazine synthase (LS), an icosahedral symmetry capsid derived from Bacillus anthracis, as a scaffold to present 60 copies of a linear B cell epitope (PB10) from the ricin toxin fused to the C terminus of LS via four different linkers...
July 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28736525/pharmaceutical-chaperones-and-proteostasis-regulators-in-the-therapy-of-lysosomal-storage-disorders-current-perspective-and-future-promises
#17
REVIEW
Fedah E Mohamed, Lihadh Al-Gazali, Fatma Al-Jasmi, Bassam R Ali
Different approaches have been utilized or proposed for the treatment of lysosomal storage disorders (LSDs) including enzyme replacement and hematopoietic stem cell transplant therapies, both aiming to compensate for the enzymatic loss of the underlying mutated lysosomal enzymes. However, these approaches have their own limitations and therefore the vast majority of LSDs are either still untreatable or their treatments are inadequate. Missense mutations affecting enzyme stability, folding and cellular trafficking are common in LSDs resulting often in low protein half-life, premature degradation, aggregation and retention of the mutant proteins in the endoplasmic reticulum...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28735897/radx-promotes-genome-stability-and-modulates-chemosensitivity-by-regulating-rad51-at-replication-forks
#18
Huzefa Dungrawala, Kamakoti P Bhat, Rémy Le Meur, Walter J Chazin, Xia Ding, Shyam K Sharan, Sarah R Wessel, Aditya A Sathe, Runxiang Zhao, David Cortez
RAD51 promotes homology-directed repair (HDR), replication fork reversal, and stalled fork protection. Defects in these functions cause genomic instability and tumorigenesis but also generate hypersensitivity to cancer therapeutics. Here we describe the identification of RADX as an RPA-like, single-strand DNA binding protein. RADX is recruited to replication forks, where it prevents fork collapse by regulating RAD51. When RADX is inactivated, excessive RAD51 activity slows replication elongation and causes double-strand breaks...
July 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28735869/dhu1-negatively-regulates-uv-b-signaling-via-its-direct-interaction-with-cop1-and-rup1
#19
Sang-Hoon Kim, Hani Kim, Sunglan Chung, Jae-Hoon Lee
Although DWD HYPERSENSITIVE TO UV-B 1 (DHU1) is reported to be a negative regulator in UV-B mediated cellular responses, its detailed role in UV-B signaling is still elusive. To further understand the action mechanism of DHU1 in UV-B response, physical and genetic interactions of DHU1 with various UV-B signaling components were investigated. Yeast two hybrid assay results suggested that DHU1 directly interacts with COP1 and RUP1, implying a functional connection with both COP1 and RUP1. In spite of the physical association between DHU1 and COP1, loss of DHU1 did not affect protein stability of COP1...
July 20, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28735865/rps27a-enhances-ebv-encoded-lmp1-mediated-proliferation-and-invasion-by-stabilizing-of-lmp1
#20
Seung-Woo Hong, Seung-Mi Kim, Dong-Hoon Jin, Yeong Seok Kim, Dae Young Hur
Epstein-Barr virus (EBV)-encoded latent membrane protein 1 (LMP1) is an oncoviral protein that plays a pivotal role in EBV-induced oncogenic transformation. The function of LMP1 in EBV-induced oncogenesis has been well studied. However, the molecular mechanisms underlying LMP1 protein stability remain poorly understood. In this study, we found that ribosomal protein s27a (RPS27a) regulates LMP1 stability by a tandem affinity purification analysis. RPS27a interacts directly with LMP1 in vitro and in vivo. Furthermore, overexpression of RPS27a increases the half-life of LMP1 in 293T cells, whereas downregulation of RPS27a using lentiviral shRNA technology accelerates the decrease in LMP1 protein level in EBV-transformed B cells...
July 20, 2017: Biochemical and Biophysical Research Communications
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