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Journal of Physical Chemistry. B

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https://www.readbyqxmd.com/read/28650664/the-dynamical-transition-of-lipid-multi-lamellar-bilayers-as-a-matter-of-cooperativity
#1
Judith Peters, Jérémie Marion, Francesca Natali, Efim Kats, Dominique J Bicout
The present study is the application of a two-state model formerly developed by Bicout, D.J. and and Zaccai, G., Biophys J 2001, 80 (3), 1115-23 1 to describe the dynamical transition exhibited in the atomic mean square displacements of biological samples in terms of dynamic and thermodynamic parameters. Data were obtained by elastic incoherent neutron scattering on 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid membranes in various hydration states and on one partially per-deuterated lipid membrane. Fitting the data with the model allowed investigating which parts of lipid molecules were mainly involved in the dynamical transition, heads, tails or both...
June 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28650657/noncovalent-pegylation-through-protein-polyelectrolyte-interaction-kinetic-experiment-and-molecular-dynamics-simulation
#2
Takaaki Kurinomaru, Kengo Kuwada, Shunsuke Tomita, Tomoshi Kameda, Kentaro Shiraki
Noncovalent binding of polyethylene glycol (PEG) to a protein surface is a unique protein handling technique to control protein function and stability. A diblock copolymer containing PEG and polyelectrolyte chains (PEGylated polyelectrolyte) is a promising candidate for noncovalent attachment of PEG to a protein surface because of the binding through multiple electrostatic interactions without protein denaturation. To obtain a deeper understanding of protein-polyelectrolyte interaction at the molecular level, we investigated the manner in which cationic PEGylated polyelectrolyte binds to anionic α-amylase in enzyme kinetic experiments and molecular dynamics (MD) simulations...
June 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28650655/vibrational-relaxation-of-the-backbone-and-bases-modes-in-lacdna-complexes-by-uv-resonance-raman-spectroscopy
#3
Cristina M Muntean, Ioan Bratu, Antonio Hernanz
Vibrational band shape analysis through time correlation function concept is widely used to obtain experimental information on the molecular dynamics of medium size molecules in different environments. Interesting details are revealed by extending this technique to biomolecules such as functional groups of the nucleic acids in media approaching the physiological conditions. In this work a study into the UV resonance Raman (UVRR) vibrational half bandwidths of functional groups in LacDNA, upon lowering the pH (pH 6...
June 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28650636/orthogonal-electric-field-measurements-near-the-green-fluorescent-protein-fluorophore-through-stark-effect-spectroscopy-and-pka-shifts-provide-a-unique-benchmark-for-electrostatics-models
#4
Joshua D Slocum, Jeremy T First, Lauren J Webb
Measurement of the magnitude, direction, and functional importance of electric fields in biomolecules has been a longstanding experimental challenge. pKa shifts of titratable residues have been the most widely implemented measurements of local electrostatic environment around the labile proton, and experimental data sets of pKa shifts in a variety of systems have been used to test and refine computational prediction capabilities of protein electrostatic fields. A more direct and increasingly popular technique to measure electric fields in proteins is Stark effect spectroscopy, where the change in absorption energy of a chromophore relative to a reference state is related to the change in electric field felt by the chromophore...
June 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28650635/ternary-interactions-and-energy-transfer-between-fluorescein-isothiocyanate-adenosine-triphosphate-and-graphene-oxide-nanocarriers
#5
Katarzyna Ratajczak, Magdalena Stobiecka
The interactions of fluorescent probes and biomolecules with nanocarriers are of key importance to the emerging targeted drug delivery systems. Graphene oxide nanosheets (GONs) as the nanocarriers offer biocompatibility and robust drug binding capacity. The interactions of GONs with fluorophores lead to strong fluorescence quenching, which may interfere with fluorescence bioimaging and biodetection. Herein, we report on the interactions and energy transfers in a model ternary system: GONs-FITC-ATP, where FITC is a model fluorophore (fluorescein isothiocyanate) and ATP is a common biomolecule (adenosine-5'-triphosphate)...
June 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28650169/increasing-protein-production-rates-can-decrease-the-rate-at-which-functional-protein-is-produced-and-their-steady-state-levels
#6
Ajeet K Sharma, Edward P O'Brien
The rate at which soluble, functional protein is produced by the ribosome has recently been found to vary in complex and unexplained ways as various translation-associated rates are altered through synonymous codon substitutions. To understand this phenomenon, here, we combine a well-established ribosome-traffic model with a master-equation model of co-translational domain folding to explore the scenarios that are possible for the protein production rate, J , and the functional-nascent protein production rate, F , as the rates of various translation processes are altered for five different E...
June 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28598621/roughness-in-surface-force-measurements-extension-of-dlvo-theory-to-describe-the-forces-between-hafnia-surfaces
#7
Namsoon Eom, Drew F Parsons, Vincent S J Craig
The interaction between colloidal particles is commonly viewed through the lens of DLVO theory, whereby the interaction is described as the sum of the electrostatic and dispersion forces. For similar materials acting across a medium at pH values remote from the isoelectric point the theory typically involves an electrostatic repulsion that is overcome by dispersion forces at very small separations. However, the dominance of the dispersion forces at short separations is generally not seen in force measurements, with the exception of the interaction between mica surfaces...
June 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28648071/elucidation-of-the-catalytic-mechanism-of-a-miniature-zinc-finger-hydrolase
#8
Abir Ganguly, Trung Quan Luong, Oliver Brylski, Michael Dirkmann, David Möller, Simon Ebbinghaus, Frank Schulz, Roland Winter, Elsa Sanchez-Garcia, Walter Thiel
To improve our mechanistic understanding of zinc metalloenzymes, we report a joint computational and experimental study of a minimal carbonic anhydrase (CA) mimic, a 22-residue Zn-finger hydrolase. We combine classical molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) geometry optimizations, and QM/MM free energy simulations with ambient and high-pressure kinetic measurements to investigate the mechanism of the hydrolysis of the substrate p-nitrophenylacetate (pNPA). The zinc center of the hydrolase prefers a pentacoordinated geometry, as found in most naturally occurring CAs and CA-like enzymes...
June 24, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28644027/speckle-visibility-spectroscopy-of-depolarized-dynamic-light-scattering
#9
David Bossert, Jens Christoph Natterodt, Dominic Andreas Urban, Christoph Weder, Alke Petri-Fink, Sandor Balog
We show that the statistical analysis of the photon counts in depolarized dynamic light scattering experiments allows for the accurate characterization of the rotational Brownian dynamics of particles. Unlike photon correlation spectroscopy, the technique is accurate even at low temporal resolution and enables discontinuous data acquisition, which offers several advantages. To demonstrate the usefulness of the method, we present a case study in which we analyze aqueous suspensions of tunicate cellulose nanocrystals and silica particles, and discuss aspects that are specific to particle sizing...
June 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28644023/kinetics-of-interlayer-expansion-of-a-layered-silicate-driven-by-caffeine-intercalation-in-the-water-phase-using-transmission-x-ray-diffraction
#10
Tomohiko Okada, Takumi Yoshida, Taku Iiyama
The kinetics of caffeine uptake into the interlayer nanospace of silicate nanosheets modified with benzylammonium was evaluated by in situ monitoring the basal spacing in aqueous media using transmission X-ray diffraction. An interlayer spacing of 0.58 nm in water before caffeine uptake indicates a monomolecular layer of benzylammonium and a few water layers in each interlayer. The interlayer space expanded by 0.10 nm upon caffeine uptake (intercalation) and saturated even in the presence of excess caffeine...
June 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28644022/hot-spot-residues-to-be-mutated-common-in-g-protein-coupled-receptors-of-class-a-identification-of-thermostabilizing-mutations-followed-by-determination-of-three-dimensional-structures-for-two-example-receptors
#11
Satoshi Yasuda, Yuta Kajiwara, Yosuke Toyoda, Kazushi Morimoto, Ryoji Suno, So Iwata, Takuya Kobayashi, Takeshi Murata, Masahiro Kinoshita
G protein-coupled receptors (GPCRs), which are indispensable to life and also implicated in a number of diseases, construct important drug targets. For the efficient structure-guided drug design, however, their structural stabilities must be enhanced. An amino-acid mutation is known to possibly lead to the enhancement, but currently available experimental and theoretical methods for identifying stabilizing mutations suffer such drawbacks as the incapability of exploring the whole mutational space with minor effort and the unambiguous physical origin of the enhanced or lowered stability...
June 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28598176/reaction-kinetics-of-phenolic-antioxidants-toward-photoinduced-pyranine-free-radicals-in-biological-models
#12
Alexis Aspée, Christian Aliaga, Luca Maretti, Daniel Zúñiga-Núñez, Jessica Godoy, Eduardo Pino, Gloria Cárdenas-Jirón, Camilo Lopez-Alarcon, Juan C Scaiano, Emilio I Alarcon
8-Hydroxy-1,3,6-pyrenetrisulfonic acid (pyranine, PyOH) free radicals were induced by laser excitation at visible wavelengths (470 nm). The photochemical process involves photoelectron ejection from PyO- to produce PyO• and PyO•- with maxima absorption at 450 and 510 nm, respectively. The kinetic rate constants for phenolic antioxidants with PyO•, determined by nanosecond time-resolved spectroscopy, were largely reliant on the ionic strength depending on the antioxidant phenol/phenolate dissociation constant...
June 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28558209/aminopolymer-mobility-and-support-interactions-in-silica-pei-composites-for-co2-capture-applications-a-quasielastic-neutron-scattering-study
#13
Adam Holewinski, Miles A Sakwa-Novak, Jan-Michael Y Carrillo, Matthew E Potter, Nathan Ellebracht, Gernot Rother, Bobby G Sumpter, Christopher W Jones
Composite gas sorbents, formed from an active polymer phase and a porous support, are promising materials for the separation of acid gases from a variety of gas streams. Significant changes in sorption performance (capacity, rate, stability etc.) can be achieved by tuning the properties of the polymer and the nature of interactions between polymer and support. Here we utilize quasielastic neutron scattering (QENS) and coarse-grained molecular dynamics (MD) simulations to characterize the dynamic behavior of the most commonly reported polymer in such materials, poly(ethylenimine) (PEI), both in bulk form and when supported in a mesoporous silica framework...
June 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28640620/using-complementary-nmr-data-sets-to-detect-inconsistencies-and-model-flaws-in-the-structure-determination-of-human-interleukin-4
#14
Lorna J Smith, Wilfred F van Gunsteren, Niels Hansen
The derivation of protein structure from values of observable quantities measured in NMR experiments is a rather non-trivial task due to (i) the limited number of data compared to degrees of freedom of a protein, (ii) the uncertainty inherent to the function connecting an observable quantity to molecular structure, (iii) the finite quality of biomolecular models and force fields used in structure refinement, and (iv) the conformational freedom of a protein in aqueous solution, which requires extensive conformational sampling and appropriate conformational averaging when calculating or restraining to sets of NMR data...
June 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28640619/optimization-and-automation-of-the-construction-of-smooth-free-energy-profiles
#15
Jeremy Schofield
An adaptive procedure is introduced to construct smooth analytical profiles of the free energy along a reaction coordinate using sampled data from multiple biased simulations. The procedure is based upon identifying problematic regions encountered in maximum likelihood estimators of the profile where there are statistically relevant discrepancies between the empirical and parameterized cumulative distribution functions and preferentially improving the construction of the parametric profile in these regions...
June 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28574718/calibration-of-1-2-4-triazole-3-thione-an-original-zn-binding-group-of-metallo-%C3%AE-lactamase-inhibitors-validation-of-a-polarizable-mm-md-potential-by-quantum-chemistry
#16
Karolina Kwapien, Mirna Damergi, Serge Nader, Léa El Khoury, Zeina Hobaika, Richard G Maroun, Jean-Philip Piquemal, Laurent Gavara, Dorothée Berthomieu, Jean-François Hernandez, Nohad Gresh
In the context of the SIBFA polarizable molecular mechanics/dynamics (PMM/PMD) procedure, we report the calibration and a series of validation tests for the 1,2,4-triazole-3-thione (TZT) heterocycle. TZT acts as the chelating group of inhibitors of dizinc metallo-β-lactamases (MBL), an emerging class of Zn-dependent bacterial enzymes, which by cleaving the β-lactam bond of most β-lactam antibiotics are responsible for the acquired resistance of bacteria to these drugs. Such a study is indispensable prior to performing PMD simulations of complexes of TZT-based inhibitors with MBL's, on account of the anchoring role of TZT in the dizinc MBL recognition site...
June 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28636820/experimental-and-theoretical-study-of-ionic-pair-dissociation-in-lithium-ion-linear-polyethyleneimine-polyacrylonitrile-blend-for-solid-polymer-electrolytes
#17
Fernando Pignanelli, Mariano Romero, Ricardo Faccio, Álvaro W Mombrú
Herein, we report the preparation and characterization of novel polymeric blend between linear polyethylene imine (PEI) and polyacrylonitrile (PAN), with the purpose to facilitate the dissociation of lithium perchlorate salt (LiClO4) and thus to enhance Li-ion transport. It is a joint theoretical and experimental procedure for evaluating and thus demonstrating, the lithium salt dissociation. The procedure implies the correlation between theoretical pair distribution function (PDF) and conventional X-rays diffraction (XRD) by means of molecular dynamics (MD) approach...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28636818/critical-temperature-of-1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine-monolayers-and-its-possible-biological-relevance
#18
Jordi Hernandez Borrell, Oscar Domenech
Since transmembrane proteins (TMPs) can be obtained with sufficient purity for x-ray diffraction studies more frequently than decades ago, their mechanisms of action may now be elucidated. One of the pending issues is the actual interplay between transmembrane proteins and membrane lipids. There is strong evidence of the involvement of specific lipids with some membrane proteins, such as the potassium crystallographically sited activation channel (KcsA) of Streptomyces lividans and the secondary transporter of lactose LacY of Escherichia coli, the activities of which are associated with the presence of anionic phospholipids such as the phosphatidylglycerol (PG) and phosphatidyethanolamine (PE), respectively...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28636397/a-comparison-of-the-structural-response-to-pressure-of-ils-with-ether-and-alkyl-functionalities
#19
Kamal B Dhungana, Claudio Javier Margulis
The response of ionic liquids to external perturbations including elevated pressure is a topic of current interest for applications such as tribology. Ionic liquids come in many classes, including those that are amphiphilic and some that are mostly polar having either cationic or anionic tails that are functionalized. The current study compares the effect of elevated pressure on two ionic liquids with different types of cationic tail. 1-decyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide (C10mim+/NTf2-) is amphiphilic whereas isoelectronic ether-functionalized 1-(2-(2-(2-methoxyethoxy)ethoxy)ethyl)-3-methylimidazolium bis(trifluoromethylsulfonyl)amide (C7O3mim+/NTf2-) has cationic tails that are more polar and conformationally different...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28636376/on-the-mechanism-of-the-iodide-triiodide-exchange-reaction-in-a-solid-state-ionic-liquid
#20
Joás Grossi, Jorge J Kohanoff, Niall J English, Eduardo M Bringa, Mario G Del Pópolo
Efficient charge transport has been observed in iodide-based room-temperature ionic liquids when doped with iodine. To investigate preferred pathways for the iodide (I(-))-to-triiodide (I3(-)) exchange reaction and to clarify the origin of this high ionic conductivity, we have conducted electronic structure calculations in the crystal state of 1-butyl-3-methylimidazolium iodide ([BMIM][I]). Energy barriers for the different stages of the iodine-swapping process, including the reorientation of the I(-)···I3(-) moiety, were determined from minimum energy paths as a function of a reaction coordinate...
June 21, 2017: Journal of Physical Chemistry. B
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