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https://www.readbyqxmd.com/read/28092443/kinetics-and-structure-of-a-cold-adapted-hetero-octameric-atp-phosphoribosyltransferase
#1
Rozanne Stroek, Ying Ge, Paul D Talbot, Mateusz K Glok, Klaudia E Bernas, Catherine M Thomson, Eoin R Gould, Magnus S Alphey, Huanting Liu, Gordon J Florence, James H Naismith, Rafael Guimaraes da Silva
ATP-phosphoribosyltransferase (ATPPRT) catalyses the first step in histidine biosynthesis, the condensation of ATP and 5-phospho-α-D-ribosyl-1-pyrophosphate to generate N(1)-(5-phospho-β-D-ribosyl)-ATP and inorganic pyrophosphate. The enzyme is allosterically inhibited by histidine. Two forms of ATPPRT, encoded by the hisG gene, exist in nature, depending on the species. The long form, HisGL, is a single polypeptide chain with catalytic and regulatory domains. The short form, HisGS, lacks a regulatory domain, and cannot bind histidine...
January 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28092433/design-and-analysis-of-localized-dna-hybridization-chain-reactions
#2
Hieu Bui, Vincent Miao, Sudhanshu Garg, Reem Mokhtar, Tianqi Song, John Reif
Theoretical models of localized DNA hybridization reactions on nanoscale substrates indicate potential benefits over conventional DNA hybridization reactions. Recently, a few approaches have been proposed to speed-up DNA hybridization reactions; however, experimental confirmation and quantification of the acceleration factor have been lacking. Here, a system to investigate localized DNA hybridization reactions on a nanoscale substrate is presented. The system consists of six metastable DNA hairpins that are tethered to a long DNA track...
January 16, 2017: Small
https://www.readbyqxmd.com/read/28091811/charge-transfer-dissociation-ctd-mass-spectrometry-of-peptide-cations-study-of-charge-state-effects-and-side-chain-losses
#3
Pengfei Li, Glen P Jackson
1+, 2+, and 3+ precursors of substance P and bradykinin were subjected to helium cation irradiation in a 3D ion trap mass spectrometer. Charge exchange with the helium cations produces a variety of fragment ions, the number and type of which are dependent on the charge state of the precursor ions. For 1+ peptide precursors, fragmentation is generally restricted to C-CO backbone bonds (a and x ions), whereas for 2+ and 3+ peptide precursors, all three backbone bonds (C-CO, C-N, and N-Cα) are cleaved. The type of backbone bond cleavage is indicative of possible dissociation channels involved in CTD process, including high-energy, kinetic-based, and ETD-like pathways...
January 13, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28091668/effect-of-ammonia-on-chemical-vapour-deposition-and-carbon-nanotube-nucleation-mechanisms
#4
Clothilde A Eveleens, Alister J Page
Chemical vapour deposition (CVD) growth of carbon nanotubes is currently the most viable method for commercial-scale nanotube production. However, controlling the 'chirality', or helicity, of carbon nanotubes during CVD growth remains a challenge. Recent studies have shown that adding chemical 'etchants', such as ammonia and water, to the feedstock gas can alter the diameter and chirality of nanotubes produced with CVD. To date, this strategy for chirality control remains sub-optimal, since we have a poor understanding of how these etchants change the CVD and nucleation mechanisms...
January 16, 2017: Nanoscale
https://www.readbyqxmd.com/read/28088576/lid-domain-plasticity-and-lipid-flexibility-modulate-enzyme-specificity-in-human-monoacylglycerol-lipase
#5
Laura Riccardi, Jose M Arencibia, Luca Bono, Andrea Armirotti, Stefania Girotto, Marco De Vivo
Human monoacylglycerol lipase (MAGL) is a membrane-interacting enzyme that generates pro-inflammatory signaling molecules. For this reason, MAGL inhibition is a promising strategy to treat pain, cancer, and neuroinflammatory diseases. MAGL can hydrolyze monoacylglycerols bearing an acyl chain of different lengths and degrees of unsaturation, cleaving primarily the endocannabinoid 2-arachidonoylglycerol. Importantly, the enzymatic binding site of MAGL is confined by a 75-amino-acid-long, flexible cap domain, named 'lid domain', which is structurally similar to that found in several other lipases...
January 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28088328/altered-myocyte-contractility-and-calcium-homeostasis-in-alpha-myosin-heavy-chain-point-mutations-linked-to-familial-dilated-cardiomyopathy
#6
Matthew Klos, Lakshmi Mundada, Indroneal Banerjee, Sherry Morgenstern, Stephanie Myers, Michael Leone, Mark Kleid, Todd Herron, Eric Devaney
Mutations in the human cardiac motor protein beta-myosin heavy chain (βMHC) have been long recognized as a cause of familial hypertrophic cardiomyopathy. Recently, mutations (P830L and A1004S) in the less abundant but faster isoform alpha-myosin heavy chain (αMHC) have been linked to dilated cardiomyopathy (DCM). In this study, we sought to determine the cellular contractile phenotype associated with these point mutations. Ventricular myocytes were isolated from 2 month male Sprague Dawley rats. Cells were cultured in M199 media and infected with recombinant adenovirus containing the P830L or the A1004S mutant human αMHC at a MOI of 500 for 18 h...
January 11, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28076957/collapse-precedes-folding-in-denaturant-dependent-assembly-of-ubiquitin
#7
Govardhan Reddy, Dave Thirumalai
The folding of small protein Ubiquitin (Ub), which plays an indispensable role in targeting proteins for degradation and DNA damage response is complex. A number of experiments on Ub folding have reached differing conclusions regarding the relation between collapse and folding, and whether intermediates are populated. In order to resolve these vexing issues, we elucidate the denaturant-dependent thermodynamics and kinetics of Ub folding at low and neutral pH as a function of Guanidinium chloride and Urea using coarse-grained molecular simulations...
January 11, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28076454/a-broad-ph-range-and-processive-chitinase-from-a-metagenome-library
#8
S S Thimoteo, A Glogauer, H Faoro, E M de Souza, L F Huergo, B M Moerschbacher, F O Pedrosa
Chitinases are hydrolases that degrade chitin, a polymer of N-acetylglucosamine linked β(1-4) present in the exoskeleton of crustaceans, insects, nematodes and fungal cell walls. A metagenome fosmid library from a wastewater-contaminated soil was functionally screened for chitinase activity leading to the isolation and identification of a chitinase gene named metachi18A. The metachi18A gene was subcloned and overexpressed in Escherichia coli BL21 and the MetaChi18A chitinase was purified by affinity chromatography as a 6xHis-tagged fusion protein...
January 5, 2017: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/28074656/atomistic-modeling-of-ion-conduction-through-the-voltage-sensing-domain-of-the-shaker-k-ion-channel
#9
Mona L Wood, J Alfredo Freites, Francesco Tombola, Douglas J Tobias
Voltage-sensing domains (VSDs) are modular membrane protein units that sense changes in the membrane electrostatic potential, and through conformational changes, regulate a specific function. The VSDs of voltage-dependent K+, Na+, and Ca2+ channels do not conduct ions under physiological conditions, but they can become ion-permeable under pathological conditions through mutations in the voltage sensor, particularly of basic residues (mostly arginines) in the S4 helix. Relatively little is known about the underlying mechanisms of conduction through VSDs...
January 11, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28074646/differences-in-protein-concentration-dependence-for-nucleation-and-elongation-in-light-chain-amyloid-formation
#10
Luis Miguel Blancas-Mejía, Pinaki Misra, Marina Ramirez-Alvarado
Light chain (AL) amyloidosis is a lethal disease characterized by the deposition of the immunoglobulin light chain into amyloid fibrils, resulting in organ dysfunction and failure. Amyloid fibrils have the ability to self-propagate recruiting soluble protein into the fibril by a nucleation-polymerization mechanism, characteristic of auto-catalytic reactions. Experimental data suggest the existence of a critical concentration to initiate fibril formation. As such, the initial concentration of soluble amyloidogenic protein is expected to have a profound effect on the rate of fibril formation...
January 11, 2017: Biochemistry
https://www.readbyqxmd.com/read/28071908/mechanically-induced-homochirality-in-nucleated-enantioselective-polymerization
#11
Celia Blanco, Michael Stich, David Hochberg
Understanding how biological homochirality may have emerged during chemical evolution remains a challenge for origin of life research. In keeping with this goal, we introduce and solve numerically a kinetic rate equation model of nucleated cooperative enantioselective polymerization in closed systems. The microreversible scheme includes (i) solution phase racemization of the monomers, (ii) linear chain growth by stepwise monomer attachment, in both the nucleation and elongation phases, and (iii) annealing or fusion of homochiral chains...
January 10, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28067272/the-mechanism-of-catalysis-by-type-ii-nadh-quinone-oxidoreductases
#12
James N Blaza, Hannah R Bridges, David Aragão, Elyse A Dunn, Adam Heikal, Gregory M Cook, Yoshio Nakatani, Judy Hirst
Type II NADH:quinone oxidoreductase (NDH-2) is central to the respiratory chains of many organisms. It is not present in mammals so may be exploited as an antimicrobial drug target or used as a substitute for dysfunctional respiratory complex I in neuromuscular disorders. NDH-2 is a single-subunit monotopic membrane protein with just a flavin cofactor, yet no consensus exists on its mechanism. Here, we use steady-state and pre-steady-state kinetics combined with mutagenesis and structural studies to determine the mechanism of NDH-2 from Caldalkalibacillus thermarum...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28066550/a-microfluidic-based-cell-encapsulation-platform-to-achieve-high-long-term-cell-viability-in-photopolymerized-pegnb-hydrogel-microspheres
#13
Zhongliang Jiang, Bingzhao Xia, Ralph McBride, John Oakey
Cell encapsulation within photopolymerized polyethylene glycol (PEG)-based hydrogel scaffolds has been demonstrated as a robust strategy for cell delivery, tissue engineering, regenerative medicine, and developing in vitro platforms to study cellular behavior and fate. Strategies to achieve spatial and temporal control over PEG hydrogel mechanical properties, chemical functionalization, and cytocompatibility have advanced considerably in recent years. Recent microfluidic technologies have enabled the miniaturization of PEG hydrogels, thus enabling the fabrication of miniaturized cell-laden vehicles...
January 7, 2017: Journal of Materials Chemistry. B, Materials for Biology and Medicine
https://www.readbyqxmd.com/read/28063273/mechanisms-of-compensation-in-the-gait-of-patients-with-drop-foot
#14
Błażkiewicz Michalina, Wiszomirska Ida, Kaczmarczyk Katarzyna, Grażyna Brzuszkiewicz-Kuźmicka, Wit Andrzej
BACKGROUND: Drop foot is a complex syndrome, with multiple interactions between joints and muscles. Abnormalities in movement patterns can be measured using motion capture techniques, but identifying compensation mechanisms remains challenging. METHODS: In order to identify compensatory mechanisms in patients with drop foot, this study evaluated a sample of 15 such patients using a computerized gait analysis system, as compared to a group of 15 healthy subjects...
January 3, 2017: Clinical Biomechanics
https://www.readbyqxmd.com/read/28062560/the-amyloid-phenomenon-and-its-links-with-human-disease
#15
Christopher M Dobson
The ability of normally soluble proteins to convert into amyloid fibrils is now recognized to be a generic phenomenon. The overall cross-β architecture of the core elements of such structures is closely similar for different amino acid sequences, as this architecture is dominated by interactions associated with the common polypeptide main chain. In contrast, the multiplicity of complex and intricate structures of the functional states of proteins is dictated by specific interactions involving the variable side chains, the sequence of which is unique to a given protein...
January 6, 2017: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/28049327/molecular-simulation-of-flow-enhanced-nucleation-in-n-eicosane-melts-under-steady-shear-and-uniaxial-extension
#16
David A Nicholson, Gregory C Rutledge
Non-equilibrium molecular dynamics is used to study crystal nucleation of n-eicosane under planar shear and, for the first time, uniaxial extension. A method of analysis based on the mean first-passage time is applied to the simulation results in order to determine the effect of the applied flow field type and strain rate on the steady-state nucleation rate and a characteristic growth rate, as well as the effects on kinetic parameters associated with nucleation: the free energy barrier, critical nucleus size, and monomer attachment pre-factor...
December 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28049087/sequestration-of-dyes-from-artificially-prepared-textile-effluent-using-rsm-ccd-optimized-hybrid-backbone-based-adsorbent-kinetic-and-equilibrium-studies
#17
Sukriti, Jitender Sharma, Amritpal Singh Chadha, Vaishali Pruthi, Prerna Anand, Jaspreet Bhatia, B S Kaith
Present work reports the synthesis of semi-Interpenetrating Network Polymer (semi-IPN) using Gelatin-Gum xanthan hybrid backbone and polyvinyl alcohol in presence of l-tartaric acid and ammonium persulphate as the crosslinker-initiator system. Reaction parameters were optimized with Response Surface Methodology (RSM) in order to maximize the percent gel fraction of the synthesized sample. Polyvinyl alcohol, l-Tartaric acid, ammonium persulphate, reaction temperature, time and pH of the reaction medium were found to make an impact on the percentage gel fraction obtained...
December 31, 2016: Journal of Environmental Management
https://www.readbyqxmd.com/read/28045924/effects-of-spatial-localization-on-microbial-consortia-growth
#18
Michael Venters, Ross P Carlson, Tomas Gedeon, Jeffrey J Heys
Microbial consortia are commonly observed in natural and synthetic systems, and these consortia frequently result in higher biomass production relative to monocultures. The focus here is on the impact of initial spatial localization and substrate diffusivity on the growth of a model microbial consortium consisting of a producer strain that consumes glucose and produces acetate and a scavenger strain that consumes the acetate. The mathematical model is based on an individual cell model where growth is described by Monod kinetics, and substrate transport is described by a continuum-based, non-equilibrium reaction-diffusion model where convective transport is negligible (e...
2017: PloS One
https://www.readbyqxmd.com/read/28045229/thioether-bearing-hyperbranched-polyether-polyols-with-methionine-like-side-chains-a-versatile-platform-for-orthogonal-functionalization
#19
Jan Seiwert, Jana Herzberger, Daniel Leibig, Holger Frey
The synthesis of thioether-bearing hyperbranched polyether polyols based on an AB/AB2 type copolymerization (cyclic latent monomers) is introduced. The polymers are prepared by anionic ring-opening multibranching copolymerization of glycidol and 2-(methylthio)ethyl glycidyl ether (MTEGE), which is conveniently accessible in a single etherification step. Slow monomer addition provides control over molecular weights. Moderate dispersities (Đ = 1.48-1.85) are obtained, given the hyperbranched structure. In situ (1) H NMR copolymerization kinetics reveal reactivity ratios of rG = 3...
January 2017: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/28045147/reactions-driving-conformational-movements-molecular-motors-in-gels-conformational-and-structural-chemical-kinetics
#20
Toribio F Otero
In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (Ea), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction...
January 3, 2017: Physical Chemistry Chemical Physics: PCCP
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