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Protein dynamic

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https://www.readbyqxmd.com/read/28221844/evaluation-of-commercial-milk-specific-lateral-flow-devices
#1
Rachel C Courtney, Steve L Taylor, Joe L Baumert
The requirement for validation of allergen cleaning processes is increasing. The use of lateral flow devices (LFDs) to identify allergens has rapidly expanded, but the best practices for use of these devices are still developing. The goal of this study was to compare commercially available milk-specific LFDs and a general protein identification method. Five milk proteins and seven milk-derived ingredients were tested at several concentrations with eight milk-specific LFDs and a general protein identification kit...
October 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28221775/electrostatic-interactions-as-mediators-in-the-allosteric-activation-of-pka-ri%C3%AE
#2
Emilia Pecora de Barros, Robert D Malmstrom, Kimya Nourbakhsh, Jason Cruz Del Rio, Alexandr P Kornev, Susan S Taylor, Rommie E Amaro
Close-range electrostatic interactions that form salt bridges are key components of protein stability. Here we investigate the role of these charged interactions in modulating the allosteric activation of Protein Kinase A (PKA) via computational and experimental mutational studies on a conserved basic patch located in the regulatory subunit's B/C helix. Molecular dynamics simulations evidenced the presence of an extended network of fluctuating salt bridges spanning the helix and connecting the two cAMP binding domains in its extremities...
February 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28221767/construction-of-a-chassis-for-a-tripartite-protein-based-molecular-motor
#3
Lara Sioban Small, Marc Bruning, Andrew Thomson, Aimee L Boyle, Roberta Davies, Paul M G Curmi, Nancy R Forde, Heiner Linke, Derek N Woolfson, Elizabeth Bromley
Improving our understanding of biological motors, both to fully comprehend their activities in vital processes, and to exploit their impressive abilities for use in bionanotechnology, is highly desirable. One means of understanding these systems is through the production of synthetic molecular motors. We demonstrate the use of orthogonal coiled-coil dimers (including both parallel and anti-parallel coiled-coils) as a hub for linking other components of a previously described synthetic molecular motor, the Tumbleweed...
February 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28221352/dynamic-undocking-and-the-quasi-bound-state-as-tools-for-drug-discovery
#4
Sergio Ruiz-Carmona, Peter Schmidtke, F Javier Luque, Lisa Baker, Natalia Matassova, Ben Davis, Stephen Roughley, James Murray, Rod Hubbard, Xavier Barril
There is a pressing need for new technologies that improve the efficacy and efficiency of drug discovery. Structure-based methods have contributed towards this goal but they focus on predicting the binding affinity of protein-ligand complexes, which is notoriously difficult. We adopt an alternative approach that evaluates structural, rather than thermodynamic, stability. As bioactive molecules present a static binding mode, we devised dynamic undocking (DUck), a fast computational method to calculate the work necessary to reach a quasi-bound state at which the ligand has just broken the most important native contact with the receptor...
March 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28221348/self-assembly-of-nanoparticles-into-biomimetic-capsid-like-nanoshells
#5
Ming Yang, Henry Chan, Gongpu Zhao, Joong Hwan Bahng, Peijun Zhang, Petr Král, Nicholas A Kotov
Nanoscale compartments are one of the foundational elements of living systems. Capsids, carboxysomes, exosomes, vacuoles and other nanoshells easily self-assemble from biomolecules such as lipids or proteins, but not from inorganic nanomaterials because of difficulties with the replication of spherical tiling. Here we show that stabilizer-free polydispersed inorganic nanoparticles (NPs) can spontaneously organize into porous nanoshells. The association of water-soluble CdS NPs into self-limited spherical capsules is the result of scale-modified electrostatic, dispersion and other colloidal forces...
March 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28221344/chemoproteomic-profiling-and-discovery-of-protein-electrophiles-in-human-cells
#6
Megan L Matthews, Lin He, Benjamin D Horning, Erika J Olson, Bruno E Correia, John R Yates, Philip E Dawson, Benjamin F Cravatt
Activity-based protein profiling (ABPP) serves as a chemical proteomic platform to discover and characterize functional amino acids in proteins on the basis of their enhanced reactivity towards small-molecule probes. This approach, to date, has mainly targeted nucleophilic functional groups, such as the side chains of serine and cysteine, using electrophilic probes. Here we show that 'reverse-polarity' (RP)-ABPP using clickable, nucleophilic hydrazine probes can capture and identify protein-bound electrophiles in cells...
March 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28221042/on-the-internal-dynamics-of-the-3-pyrroline-n-oxide-ring-in-spin-labeled-proteins
#7
Philipp Consentius, Bernhard Loll, Ulrich Gohlke, Claudia Alings, Carsten Mueller, Robert Müller, Christian Teutloff, Udo Heinemann, Martin Kaupp, Markus C Wahl, Thomas Risse
Site-directed spin labeling is a versatile tool to study structure as well as dynamics of proteins using EPR spectroscopy. Methanethiosulfonate (MTS)-spin labels tethered through a disulfide linkage to an engineered cysteine residue were used in a large number of studies to extract structural as well as dynamic information of the protein from the rotational dynamics of the nitroxide moiety. The ring itself was always considered to be a rigid body. In this contribution, we present a combination of high-resolution X-ray crystallography and EPR spectroscopy of spin-labeled protein single crystals demonstrating that the nitroxide ring inverts fast at ambient temperature, while being characterized by a bent conformation at low temperature...
February 21, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28220785/c-edge-loops-of-arrestin-function-as-a-membrane-anchor
#8
Ciara C M Lally, Brian Bauer, Jana Selent, Martha E Sommer
G-protein-coupled receptors are membrane proteins that are regulated by a small family of arrestin proteins. During formation of the arrestin-receptor complex, arrestin first interacts with the phosphorylated receptor C terminus in a pre-complex, which activates arrestin for tight receptor binding. Currently, little is known about the structure of the pre-complex and its transition to a high-affinity complex. Here we present molecular dynamics simulations and site-directed fluorescence experiments on arrestin-1 interactions with rhodopsin, showing that loops within the C-edge of arrestin function as a membrane anchor...
February 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28220294/chromogranin-a-regulates-vesicle-storage-and-mitochondrial-dynamics-to-influence-insulin-secretion
#9
Joshua Wollam, Sumana Mahata, Matthew Riopel, Angelina Hernandez-Carretero, Angshuman Biswas, Gautam K Bandyopadhyay, Nai-Wen Chi, Lee E Eiden, Nitish R Mahapatra, Angelo Corti, Nicholas J G Webster, Sushil K Mahata
Chromogranin A (CgA) is a prohormone and a granulogenic factor that regulates secretory pathways in neuroendocrine tissues. In β-cells of the endocrine pancreas, CgA is a major cargo in insulin secretory vesicles. The impact of CgA deficiency on the formation and exocytosis of insulin vesicles is yet to be investigated. In addition, no literature exists on the impact of CgA on mitochondrial function in β-cells. Using three different antibodies, we demonstrate that CgA is processed to vasostatin- and catestatin-containing fragments in pancreatic islet cells...
February 20, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/28220073/enhanced-late-na-and-ca-currents-as-effective-antiarrhythmic-drug-targets
#10
REVIEW
Hrayr S Karagueuzian, Arash Pezhouman, Marina Angelini, Riccardo Olcese
While recent advances clarified the molecular and cellular modes of action of antiarrhythmic drugs (AADs), their link to suppression of dynamical arrhythmia mechanisms remains only partially understood. The current classifications of AADs (Classes I, III, and IV) rely on blocking peak Na, K and L-type calcium currents (ICa,L), with Class II with dominant beta receptor blocking activity and Class V including drugs with diverse classes of actions. The discovery that the calcium and redox sensor, cardiac Ca/calmodulin-dependent protein kinase II (CaMKII) enhances both the late Na (INa-L) and the late ICa,L in patients at high risk of VT/VF provided a new and a rational AAD target...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28220061/a-model-of-induction-of-cerebellar-long-term-depression-including-rkip-inactivation-of-raf-and-mek
#11
Iain Hepburn, Anant Jain, Himanshu Gangal, Yukio Yamamoto, Keiko Tanaka-Yamamoto, Erik De Schutter
We report an updated stochastic model of cerebellar Long Term Depression (LTD) with improved realism. Firstly, we verify experimentally that dissociation of Raf kinase inhibitor protein (RKIP) from Mitogen-activated protein kinase kinase (MEK) is required for cerebellar LTD and add this interaction to an earlier published model, along with the known requirement of dissociation of RKIP from Raf kinase. We update Ca(2+) dynamics as a constant-rate influx, which captures experimental input profiles accurately...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28219978/a-mutation-in-the-g-protein-gene-gnb2-causes-familial-sinus-node-and-atrioventricular-conduction-dysfunction
#12
Birgit Stallmeyer, Johanna Kuß, Stefan Kotthoff, Sven Zumhagen, Kirsty S Vowinkel, Susanne Rinne, Lina A Matschke, Corinna Friedrich, Ellen Schulze-Bahr, Stephan Rust, Guiscard Seebohm, Niels Decher, Eric Schulze-Bahr
Rationale: Familial sinus node and atrioventricular (AV) conduction dysfunction is a rare disorder that leads to paroxysmal dizziness, fatigue and syncope due to a temporarily or permanent reduced heart rate. To date, only a few genes for familial sinus and/or AV conduction dysfunction are known and the majority of cases remain etiologically unresolved. Objective: We aim to identify the disease gene in a large three-generation family (n=25) with autosomal dominant sinus node dysfunction (SND) and AV block (AVB) and to characterise the mutation-related pathomechanisms in familial SND+AVB...
February 20, 2017: Circulation Research
https://www.readbyqxmd.com/read/28219947/phosphorylation-potential-of-drosophila-e-cadherin-intracellular-domain-is-essential-for-development-and-regulating-adherens-junction-biosynthetic-dynamics
#13
Yi-Jiun Chen, Juan Huang, Lynn Huang, Erin Austin, Yang Hong
E-Cadherin intracellular domain contains a highly conserved serine cluster whose phosphorylations are essential for binding to β-Catenin in vitro. In cultured cells phosphorylations of specific serine residues within the cluster are also required for regulating adherens junction (AJ) stability and dynamics. However, much less is known how such phosphorylations of E-Cadherin regulate the AJ formation and dynamics in vivo. In this report we generated an extensive array of Drosophila E-Cadherin (DE-Cad) endogenous knock-in alleles that carry mutations targeting this highly conserved serine cluster...
February 20, 2017: Development
https://www.readbyqxmd.com/read/28219929/hsp70-displaces-small-heat-shock-proteins-from-aggregates-to-initiate-protein-refolding
#14
Szymon Żwirowski, Agnieszka Kłosowska, Igor Obuchowski, Nadinath B Nillegoda, Artur Piróg, Szymon Ziętkiewicz, Bernd Bukau, Axel Mogk, Krzysztof Liberek
Small heat shock proteins (sHsps) are an evolutionary conserved class of ATP-independent chaperones that protect cells against proteotoxic stress. sHsps form assemblies with aggregation-prone misfolded proteins, which facilitates subsequent substrate solubilization and refolding by ATP-dependent Hsp70 and Hsp100 chaperones. Substrate solubilization requires disruption of sHsp association with trapped misfolded proteins. Here, we unravel a specific interplay between Hsp70 and sHsps at the initial step of the solubilization process...
February 20, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28219123/identification-of-core-gene-networks-and-hub-genes-associated-with-progression-of-nonalcoholic-fatty-liver-disease-by-rna-sequencing
#15
Kikuko Hotta, Masataka Kikuchi, Takuya Kitamoto, Aya Kitamoto, Yuji Ogawa, Yasushi Honda, Takaomi Kessoku, Kaori Kobayashi, Masato Yoneda, Kento Imajo, Wataru Tomeno, Akihiro Nakaya, Yutaka Suzuki, Satoru Saito, Atsushi Nakajima
AIM: Nonalcoholic fatty liver disease (NAFLD) progresses because of the interaction between numerous genes. Thus, we performed weighted gene co-expression network analysis to identify core gene networks and key genes associated with NAFLD progression. METHODS: We enrolled 39 patients with mild NAFLD (fibrosis stages 0 to 2) and 21 with advanced NAFLD (fibrosis stages 3 or 4). Total RNA was extracted from frozen liver biopsies, and sequenced to capture a large dynamic range of expression levels...
February 20, 2017: Hepatology Research: the Official Journal of the Japan Society of Hepatology
https://www.readbyqxmd.com/read/28218996/hypoxia-stimulated-membrane-trafficking-requires-t-plastin
#16
Marieke Wottawa, Stephanie Naas, Johannes Böttger, Gijsbert J van Belle, Wiebke Möbius, Natalia H Revelo, Doris Heidenreich, Melanie von Ahlen, Anke Zieseniss, Katharina Kröhnert, Susanne Lutz, Christof Lenz, Henning Urlaub, Silvio O Rizzoli, Dörthe M Katschinski
Traffic between the plasma membrane and the endomembrane compartments is an essential feature of eukaryotic cells. The secretory pathway sends cargoes from biosynthetic compartments to the plasma membrane. This is counterbalanced by a retrograde endocytotic route and is essential for cell homeostasis. Cells need to adapt rapidly to environmental challenges like the reduction of pO2 which, however, has not been analyzed in relation to membrane trafficking in detail. Therefore we determined changes in the plasma membrane trafficking in normoxia, hypoxia, and after reoxygenation METHODS: Membrane trafficking was analyzed by using the bulk membrane endocytosis marker FM 1-43, the newly developed membrane probe mCLING, wheat germ agglutinin as well as fluorescently labeled choleratoxin subunit B...
February 20, 2017: Acta Physiologica
https://www.readbyqxmd.com/read/28218679/mcm10-a-dynamic-scaffold-at-eukaryotic-replication-forks
#17
REVIEW
Ryan M Baxley, Anja-Katrin Bielinsky
To complete the duplication of large genomes efficiently, mechanisms have evolved that coordinate DNA unwinding with DNA synthesis and provide quality control measures prior to cell division. Minichromosome maintenance protein 10 (Mcm10) is a conserved component of the eukaryotic replisome that contributes to this process in multiple ways. Mcm10 promotes the initiation of DNA replication through direct interactions with the cell division cycle 45 (Cdc45)-minichromosome maintenance complex proteins 2-7 (Mcm2-7)-go-ichi-ni-san GINS complex proteins, as well as single- and double-stranded DNA...
February 17, 2017: Genes
https://www.readbyqxmd.com/read/28218519/probing-the-dynamic-interaction-between-damaged-dna-and-a-cellular-responsive-protein-using-a-piezoelectric-mass-biosensor
#18
Yulong Jin, Yunfeng Xie, Kui Wu, Yanyan Huang, Fuyi Wang, Rui Zhao
The binding events between damaged DNA and recognition biomolecules are of great interest for understanding of the activity of DNA-damaging drugs and the related DNA repair networks. Herein, a simple and sensitive sensor system was tailored for real-time probing the dynamic molecular recognition between cisplatin-damaged DNA (cisPt-DNA) and a cellular responsive protein, high mobility group box 1 (HMGB1). By integrating of flow injection analysis (FIA) with quartz crystal microbalance (QCM), the interaction time-course of cisPt-DNA and HMGB1 domain A (HMGB1a) was investigated...
February 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28218299/expression-and-distribution-of-extensins-and-agps-in-susceptible-and-resistant-banana-cultivars-in-response-to-wounding-and-fusarium-oxysporum
#19
Yunli Wu, Wei Fan, Xiaoquan Li, Houbin Chen, Tomáš Takáč, Olga Šamajová, Musana Rwalinda Fabrice, Ling Xie, Juan Ma, Jozef Šamaj, Chunxiang Xu
Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is soil-borne disease of banana (Musa spp.) causing significant economic losses. Extensins and arabinogalactan proteins (AGPs) are cell wall components important for pathogen defence. Their significance for Foc resistance in banana was not reported so far. In this study, two banana cultivars differing in Foc sensitivity were used to monitor the changes in transcript levels, abundance and distribution of extensins and AGPs after wounding and Foc inoculation...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28218293/plasma-exosome-profiling-of-cancer-patients-by-a-next-generation-systems-biology-approach
#20
Valeriy Domenyuk, Zhenyu Zhong, Adam Stark, Nianqing Xiao, Heather A O'Neill, Xixi Wei, Jie Wang, Teresa T Tinder, Sonal Tonapi, Janet Duncan, Tassilo Hornung, Andrew Hunter, Mark R Miglarese, Joachim Schorr, David D Halbert, John Quackenbush, George Poste, Donald A Berry, Günter Mayer, Michael Famulok, David Spetzler
Technologies capable of characterizing the full breadth of cellular systems need to be able to measure millions of proteins, isoforms, and complexes simultaneously. We describe an approach that fulfils this criterion: Adaptive Dynamic Artificial Poly-ligand Targeting (ADAPT). ADAPT employs an enriched library of single-stranded oligodeoxynucleotides (ssODNs) to profile complex biological samples, thus achieving an unprecedented coverage of system-wide, native biomolecules. We used ADAPT as a highly specific profiling tool that distinguishes women with or without breast cancer based on circulating exosomes in their blood...
February 20, 2017: Scientific Reports
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