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Protein dynamic

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https://www.readbyqxmd.com/read/29224182/stable-and-rigid-dtpa-like-paramagnetic-tags-suitable-for-in-vitro-and-in-situ-protein-nmr-analysis
#1
Jia-Liang Chen, Yu Zhao, Yan-Jun Gong, Bin-Bin Pan, Xiao Wang, Xun-Cheng Su
Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein-ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond...
December 9, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29223917/molecular-dynamics-simulations-suggest-changes-in-electrostatic-interactions-as-a-potential-mechanism-through-which-serine-phosphorylation-inhibits-dna-polymerase-%C3%AE-s-activity
#2
Dirar Homouz, Kwee Hong Joyce-Tan, Mohd Shahir Shamsir, Ibrahim M Moustafa, Haitham Idriss
DNA polymerase β is a 39kDa enzyme that is a major component of Base Excision Repair in human cells. The enzyme comprises two major domains, a 31kDa domain responsible for the polymerase activity and an 8kDa domain, which bind ssDNA and has a deoxyribose phosphate (dRP) lyase activity. DNA polymerase β was shown to be phosphorylated in vitro with protein kinase C (PKC) at serines 44 and 55 (S44 and S55), resulting in loss of its polymerase enzymic activity, but not its ability to bind ssDNA. In this study, we investigate the potential phosphorylation-induced structural changes for DNA polymerase β using molecular dynamics...
November 7, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29223862/wave-regulates-cadherin-junction-assembly-and-turnover-during-epithelial-polarization
#3
Shashikala Sasidharan, Sofya Borinskaya, Falshruti Patel, Yelena Bernadskaya, Sailaja Mandalapu, Maria Agapito, Martha Soto
Actin is an integral component of epithelial apical junctions, yet the interactions of branched actin regulators with apical junction components are still not clear. Biochemical data have shown that α-catenin inhibits Arp2/3-dependent branched actin. These results suggested that branched actin is only needed at earliest stages of apical junction development. We use live imaging in developing C. elegans embryos to test models for how WAVE-induced branched actin collaborates with other apical junction proteins during the essential process of junction formation and maturation...
December 6, 2017: Developmental Biology
https://www.readbyqxmd.com/read/29223802/proteogenomic-insights-into-uranium-tolerance-of-a-chernobyl-s-microbacterium-bacterial-isolate
#4
Gallois Nicolas, Alpha-Bazin Béatrice, Ortet Philippe, Barakat Mohamed, Piette Laurie, Long Justine, Berthomieu Catherine, Armengaud Jean, Chapon Virginie
Microbacterium oleivorans A9 is a uranium-tolerant actinobacteria isolated from the trench T22 located near the Chernobyl nuclear power plant. This site is contaminated with different radionuclides including uranium. To observe the molecular changes at the proteome level occurring in this strain upon uranyl exposure and understand molecular mechanisms explaining its uranium tolerance, we established its draft genome and used this raw information to perform an in-depth proteogenomics study. High-throughput proteomics were performed on cells exposed or not to 10μM uranyl nitrate sampled at three previously identified phases of uranyl tolerance...
December 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29223737/synthesis-and-characterization-of-small-sized-gold-nanoparticles-coated-by-bovine-serum-albumin-bsa-for-cancer-photothermal-therapy
#5
Selma M H Al-Jawad, Ali A Taha, Mohammad M F Al-Habosiy, Lamyaa F A Al-Barram
In the present study, small gold nanoparticles <5nm coated with natural protein Bovine Serum Albumin (BSA) was synthesized and characterized using UV-Vis spectrophotometer, Dynamic Light Scattering (DLS), Transmission Electron Microscopy (TEM), zeta potential and scanning electron microscopy (SEM). Three types of cancer cell lines; Rhabdomyosarcoma (RD), Murine fibroblast (L20B) and RAW 264.7 monocyte-macrophage (MQ) were tested and treated by photothermal strategy, in vitro, by conjugating BSA-AuNPs complex of (0...
December 6, 2017: Photodiagnosis and Photodynamic Therapy
https://www.readbyqxmd.com/read/29223396/accelerated-dentinogenesis-by-inhibiting-the-mitochondrial-fission-factor-dynamin-related-protein-1
#6
Yumiko Matsuishi, Hiroki Kato, Keiji Masuda, Haruyoshi Yamaza, Yuta Hirofuji, Hiroshi Sato, Hiroko Wada, Tamotsu Kiyoshima, Kazuaki Nonaka
Undifferentiated odontogenic epithelium and dental papilla cells differentiate into ameloblasts and odontoblasts, respectively, both of which are essential for tooth development. These differentiation processes involve dramatic functional and morphological changes of the cells. For these changes to occur, activation of mitochondrial functions, including ATP production, is extremely important. In addition, these changes are closely related to mitochondrial fission and fusion, known as mitochondrial dynamics...
December 6, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29223166/protein-poly-adp-ribosyl-ation-system-changes-in-development-and-aging-as-well-as-due-to-restriction-of-cell-proliferation
#7
REVIEW
G A Shilovsky, S I Shram, G V Morgunova, A N Khokhlov
It is well known that the number of dividing cells in an organism decreases with age. The average rate of cell division in tissues and organs of a mature organism sharply decreases, which is probably a trigger for accumulation of damage leading to disturbance of genome integrity. This can be a cause for the development of many age-related diseases and appearance of phenotypic and physiological signs of aging. In this connection, the protein poly(ADP-ribosyl)ation system, which is activated in response to appearance of various DNA damage, attracts great interest...
November 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29223157/self-organization-of-recombinant-membrane-porin-ompf-from-yersinia-pseudotuberculosis-in-aqueous-environments
#8
E V Sidorin, V A Khomenko, N Yu Kim, P S Dmitrenok, A M Stenkova, O D Novikova, T F Solov'eva
Recombinant porin OmpF (an integral protein of bacterial outer membrane) from Yersinia pseudotuberculosis was synthesized in Escherichia coli cells as inclusion bodies. By combining the methods of anion-exchange and gel filtration chromatographies, recombinant OmpF (rOmpF) was isolated as an individual protein in its denatured state, and its characteristic properties (molecular mass, N-terminal amino acid sequence, and hydrodynamic radius of the protein in 8 M urea solution) were determined. According to the data of gel filtration, dynamic light scattering, optical spectroscopy, and binding of the hydrophobic fluorescent probe 8-anilino-1-naphthalenesulfonic acid, the rOmpF is fully unfolded in 8 M urea and exists in random coil conformation...
November 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29222784/methods-for-quantitative-analysis-of-axonal-cargo-transport
#9
Matias Alloatti, Luciana Bruno, Tomas L Falzone
Neurons rely on complex axonal transport mechanisms that mediate the intracellular dynamics of proteins, vesicles, and mitochondria along their high polarized structure. The fast improvement of live imaging techniques of fluorescent cargos allowed the identification of the diverse motion properties of different transported molecules. These properties arise as the result of molecular interactions between many players involved in axonal transport. Motor proteins, microtubule tracks, cargo association, and even axonal viscosity contribute to the proper axonal dynamics of different cargos...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222758/differential-proteomics-based-on-2d-difference-in-gel-electrophoresis-and-tandem-mass-spectrometry-for-the-elucidation-of-biological-processes-in-antibiotic-producer-bacterial-strains
#10
Giuseppe Gallo, Andrea Scaloni
Proteomics based on 2D-Difference In Gel Electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) procedures can be considered a "gold standard" to determine quantitatively and comparatively protein abundances in cell extracts from different biological sources/conditions according to a gel-based approach. In particular, 2D-DIGE is used for protein specie separation, detection, and relative quantification, whenever tandem MS is used to obtain peptide sequence information that is managed according to bioinformatic procedures to identify the differentially represented protein species...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222589/production-optimization-for-concentration-and-volume-limited-fed-batch-reactors-in-biochemical-processes
#11
Ping Liu, Xinggao Liu, Zeyin Zhang, Yalin Wang, Chunhua Yang, Weihua Gui
Since a very slight violation of constraint could cause process safety and product quality problems in biochemical processes, an adaptive approach of fed-batch reactor production optimization that can strictly satisfy constraints over the entire operating time is presented. In this approach, an improved smooth function is proposed such that the inequality constraints can be transformed into smooth constraints. Based on this, only an auxiliary state is needed to monitor violations in the augmented performance index...
December 8, 2017: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/29222519/virtual-screening-for-inhibitors-of-the-human-tslp-tslpr-interaction
#12
Dries Van Rompaey, Kenneth Verstraete, Frank Peelman, Savvas N Savvides, Koen Augustyns, Pieter Van Der Veken, Hans De Winter
The pro-inflammatory cytokine thymic stromal lymphopoietin (TSLP) plays a pivotal role in the pathophysiology of various allergy disorders that are mediated by type 2 helper T cell (Th2) responses, such as asthma and atopic dermatitis. TSLP forms a ternary complex with the TSLP receptor (TSLPR) and the interleukin-7-receptor subunit alpha (IL-7Rα), thereby activating a signaling cascade that culminates in the release of pro-inflammatory mediators. In this study, we conducted an in silico characterization of the TSLP:TSLPR complex to investigate the drugability of this complex...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222445/model-based-genome-wide-determination-of-rna-chain-elongation-rates-in-escherichia-coli
#13
Peter Großmann, Anja Lück, Christoph Kaleta
Dynamics in the process of transcription are often simplified, yet they play an important role in transcript folding, translation into functional protein and DNA supercoiling. While the modulation of the speed of transcription of individual genes and its role in regulation and proper protein folding has been analyzed in depth, the functional relevance of differences in transcription speeds as well as the factors influencing it have not yet been determined on a genome-wide scale. Here we determined transcription speeds for the majority of E...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29222167/cytoplasmic-linker-protein-clip170-negatively-regulates-tlr4-signaling-by-targeting-the-tlr-adaptor-protein-tirap
#14
Padmaja Jakka, Bindu Bhargavi, Swapna Namani, Subathra Murugan, Gary Splitter, Girish Radhakrishnan
Cytoplasmic linker protein 170 (CLIP170) is a CAP-Gly domain-containing protein that is associated with the plus end of growing microtubules and implicated in various cellular processes, including the regulation of microtubule dynamics, cell migration, and intracellular transport. Our studies revealed a previously unrecognized property and role of CLIP170. We identified CLIP170 as one of the interacting partners of Brucella effector protein TcpB that negatively regulates TLR2 and TLR4 signaling. In this study, we demonstrate that CLIP170 interacts with the TLR2 and TLR4 adaptor protein TIRAP...
December 8, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29222055/autophagy-plays-a-protective-role-in-mn-induced-toxicity-in-pc12-cells
#15
Qian Zhou, Xiaolong Fu, Xueting Wang, Qin Wu, Yuanfu Lu, Jingshan Shi, James E Klaunig, Shaoyu Zhou
Excessive environmental or occupational exposure to manganese (Mn) is associated with increased risk of neuron degenerative disorders. Oxidative stress and mitochondrial dysfunction are the main mechanisms of Mn mediated neurotoxicity. Selective removal of damaged mitochondria by autophagy has been proposed as a protective mechanism against neuronal toxicant-induced neurotoxicity. Whether autophagic flux plays a role in Mn-induced cytotoxicity remains to be fully elucidated. The present study was designed to investigate the effect of Mn exposure on autophagy, and how modulation of autophagic flux alters the sensitivities of cells to Mn-elicited cytotoxicity...
December 6, 2017: Toxicology
https://www.readbyqxmd.com/read/29221925/detecting-protein-aggregation-and-interactions-in-live-cells-a-guide-to-number-and-brightness
#16
REVIEW
Rory Nolan, Maro Iliopoulou, Luis Alvarez, Sergi Padilla-Parra
The possibility to detect and quantify protein-protein interactions with good spatial and temporal resolutions in live cells is crucial in biology. Number and Brightness is a powerful approach to detect both protein aggregation/desegregation dynamics and stoichiometry in live cells. Importantly, this technique can be applied in commercial set ups: both camera based and laser scanning microscopes. It provides pixel-by-pixel information on protein oligomeric states. If performed with two colours, the technique can retrieve the stoichiometry of the reaction under study...
December 5, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29221924/unraveling-co-translational-protein-folding-concepts-and-methods
#17
REVIEW
Anton A Komar
Advances in techniques such as nuclear magnetic resonance spectroscopy, cryo-electron microscopy, and single-molecule and time-resolved fluorescent approaches are transforming our ability to study co-translational protein folding both in vivo in living cells and in vitro in reconstituted cell-free translation systems. These approaches provide comprehensive information on the spatial organization and dynamics of nascent polypeptide chains and the kinetics of co-translational protein folding. This information has led to an improved understanding of the process of protein folding in living cells and should allow remaining key questions in the field, such as what structures are formed within nascent chains during protein synthesis and when, to be answered...
December 5, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29221897/comparative-mechanical-unfolding-studies-of-spectrin-domains-r15-r16-and-r17
#18
Anna V Glyakina, Ilya V Likhachev, Nikolay K Balabaev, Oxana V Galzitskaya
Spectrins belong to repetitive three-helix bundle proteins that have vital functions in multicellular organisms and are of potential value in nanotechnology. To reveal the unique physical features of repeat proteins we have studied the structural and mechanical properties of three repeats of chicken brain α-spectrin (R15, R16 and R17) at the atomic level under stretching at constant velocities (0.01, 0.05 and 0.1Å·ps-1) and constant forces (700 and900pN) using molecular dynamics (MD) simulations at T = 300K...
December 5, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29221402/transition-path-time-distributions
#19
M Laleman, E Carlon, H Orland
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the barrier. Average transition path times and, recently, their full probability distribution have been measured for several biomolecular systems, e.g., in the folding of nucleic acids or proteins. Motivated by these experiments, we have calculated the full transition path time distribution for a single stochastic particle crossing a parabolic barrier, including inertial terms which were neglected in previous studies...
December 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29221399/long-range-coupling-between-atp-binding-and-lever-arm-regions-in-myosin-via-dielectric-allostery
#20
Takato Sato, Jun Ohnuki, Mitsunori Takano
A protein molecule is a dielectric substance, so the binding of a ligand is expected to induce dielectric response in the protein molecule, considering that ligands are charged or polar in general. We previously reported that binding of adenosine triphosphate (ATP) to molecular motor myosin actually induces such a dielectric response in myosin due to the net negative charge of ATP. By this dielectric response, referred to as "dielectric allostery," spatially separated two regions in myosin, the ATP-binding region and the actin-binding region, are allosterically coupled...
December 7, 2017: Journal of Chemical Physics
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