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https://www.readbyqxmd.com/read/27924262/mass-spectrometric-analysis-of-protein-ligand-interactions
#1
Kentaro Ishii, Masanori Noda, Susumu Uchiyama
The interactions of small molecules with proteins (protein-ligand interactions) mediate various biological phenomena including signal transduction and protein transcription and translation. Synthetic compounds such as drugs can also bind to target proteins, leading to the inhibition of protein-ligand interactions. These interactions typically accompany association-dissociation equilibrium according to the free energy difference between free and bound states; therefore, the quantitative biophysical analysis of the interactions, which uncovers the stoichiometry and dissociation constant, is important for understanding biological reactions as well as for rational drug development...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27917703/principles-of-the-kenzan-method-for-robotic-cell-spheroid-based-3d-bioprinting
#2
Nicanor I Moldovan, Narutoshi Hibino, Koichi Nakayama
Bioprinting is a technology with the prospect to change the way many diseases are treated, by replacing the damaged tissues with live, de novo created bio-similar constructs. However, after more than a decade of incubation and many proofs-of-concept, the field is still in its infancy. The current stagnation is the consequence of its early success: the first bioprinters, and most of those which followed, were modified versions of the 3D printers used in additive manufacturing, redesigned for layer-by-layer dispersion of biomaterials...
December 4, 2016: Tissue Engineering. Part B, Reviews
https://www.readbyqxmd.com/read/27901152/an-atomic-level-insight-into-the-basic-mechanism-responsible-for-the-enhancement-of-the-catalytic-oxidation-of-carbon-monoxide-on-a-cu-ceo2-surface
#3
Kenichi Koizumi, Katsuyuki Nobusada, Mauro Boero
The reaction mechanisms of CO molecules interacting with a Cu/CeO2 surface and related morphological modifications occurring upon removal of O atoms to generate CO2 are investigated by first-principles dynamical simulations complemented by a free-energy sampling technique. We show that the reactivity of oxygen atoms located in the first layer in the vicinity of the Cu site is remarkably high because of a reduction of the O coordination number. Moreover, we evidence that the doped Cu atoms are responsible for an enhancement of the exposure of other surrounding O atoms, even below the first surface layer, which can then easily react with CO and are gradually removed from the system in the oxidation process...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27896358/emergence-of-ordered-network-mesophases-in-kinetic-pathways-of-order-order-transition-for-linear-abc-triblock-terpolymers
#4
Tongjie Sun, Ping Tang, Feng Qiu, An-Chang Shi
Applying the string method to the self-consistent field theory (SCFT) of ABC linear triblock copolymers, we developed a new strategy to design kinetic pathways for the formation of stable or metastable network mesophases in order-order transition (OOT) processes. The design principle regarding the kinetic pathways between distinct mesophases is based on the matching relationships of both domain spacing and dominant Fourier components of the density distributions. The results suggest that complex ordered network mesophases, such as alternating diamond (D(A)) and alternating plumber's nightmare (P(A)) could be obtained in kinetic pathways between simple phases covering lamellae, cylinders and spheres...
November 29, 2016: Soft Matter
https://www.readbyqxmd.com/read/27896347/first-principles-study-of-pressure-induced-structural-phase-transitions-in-mnf2
#5
S López-Moreno, A H Romero, J Mejía-López, A Muñoz
In this work we report a complete structural and magnetic characterization of crystalline MnF2 under pressure obtained using first principle calculations. Density functional theory was used as the theoretical framework, within the generalized gradient approximation plus the Hubbard formalism (GGA+U) necessary to describe the strong correlations present in this material. The vibrational, the magnetic exchange couplings and the structural characterization of MnF2 in the rutile ground state structure and potential high pressure phases are reported...
November 29, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27886477/lattice-vibrations-change-the-solid-solubility-of-an-alloy-at-high-temperatures
#6
Nina Shulumba, Olle Hellman, Zamaan Raza, Björn Alling, Jenifer Barrirero, Frank Mücklich, Igor A Abrikosov, Magnus Odén
We develop a method to accurately and efficiently determine the vibrational free energy as a function of temperature and volume for substitutional alloys from first principles. Taking Ti_{1-x}Al_{x}N alloy as a model system, we calculate the isostructural phase diagram by finding the global minimum of the free energy corresponding to the true equilibrium state of the system. We demonstrate that the vibrational contribution including anharmonicity and temperature dependence of the mixing enthalpy have a decisive impact on the calculated phase diagram of a Ti_{1-x}Al_{x}N alloy, lowering the maximum temperature for the miscibility gap from 6560 to 2860 K...
November 11, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27886307/a-simple-guiding-principle-for-the-temperature-dependence-of-the-solubility-of-light-gases-in-imidazolium-based-ionic-liquids-derived-from-molecular-simulations
#7
Daniela Kerlé, Majid Namayandeh Jorabchi, Ralf Ludwig, Sebastian Wohlrab, Dietmar Paschek
We have determined the temperature dependence of the solvation behavior of a large collection of important light gases in imidazolium-based ionic liquids with the help of extensive molecular dynamics simulations. The motivation of our study is to unravel common features of the temperature dependent solvation under well controlled conditions, and to provide a guidance for cases, where experimental data from different sources disagree significantly. The solubility of molecular hydrogen, oxygen, nitrogen, methane, krypton, argon, neon and carbon dioxide in the imidazolium based ionic liquids of type 1-n-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([Cnmim][NTf2]) with varying alkyl side chain lengths n = 2, 4, 6, 8 is computed for a temperature range between 300 K and 500 K at 1 bar...
November 25, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27886288/exploring-the-mechanochemical-cycle-of-dynein-motor-proteins-structural-evidence-of-crucial-intermediates
#8
Mandira Dutta, Biman Jana
Dyneins, a class of motor proteins consisting of six AAA+ modules (AAA1-AAA6), convert chemical energy derived from the hydrolysis of ATP into mechanical energy to walk along the microtubule track towards its minus end while accomplishing various cellular tasks including the transportation of various intracellular cargos. In a full mechanochemical cycle, dynein goes through ATP binding induced open to closed state transition of AAA1, hydrolysis of that ATP and closed to open state transition induced by the release of hydrolysed products along with linker remodelling in different nucleotide states...
November 25, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27886259/atomic-resolution-interfacial-structure-of-lead-free-ferroelectric-k0-5na0-5nbo3-thin-films-deposited-on-srtio3
#9
Chao Li, Lingyan Wang, Zhao Wang, Yaodong Yang, Wei Ren, Guang Yang
Oxide interface engineering has attracted considerable attention since the discovery of its exotic properties induced by lattice strain, dislocation and composition change at the interface. In this paper, the atomic resolution structure and composition of the interface between the lead-free piezoelectric (K0.5Na0.5)NbO3 (KNN) thin films and single-crystalline SrTiO3 substrate were investigated by means of scanning transmission electron microscopy (STEM) combining with electron energy loss spectroscopy (EELS)...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27875891/the-uhlenbeck-ford-model-exact-virial-coefficients-and-application-as-a-reference-system-in-fluid-phase-free-energy-calculations
#10
Rodolfo Paula Leite, Rodrigo Freitas, Rodolfo Azevedo, Maurice de Koning
The Uhlenbeck-Ford (UF) model was originally proposed for the theoretical study of imperfect gases, given that all its virial coefficients can be evaluated exactly, in principle. Here, in addition to computing the previously unknown coefficients B11 through B13, we assess its applicability as a reference system in fluid-phase free-energy calculations using molecular simulation techniques. Our results demonstrate that, although the UF model itself is too soft, appropriately scaled Uhlenbeck-Ford (sUF) models provide robust reference systems that allow accurate fluid-phase free-energy calculations without the need for an intermediate reference model...
November 21, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27874113/an-atomically-thin-layer-of-ru-mos2-heterostructure-structural-electronic-and-magnetic-properties
#11
Chenghuan Jiang, Rongqing Zhou, Zhaohui Peng, Jinfu Zhu, Qian Chen
The fabrication of a transition metal (TM) atomically thin layer with robust ferromagnetic ordering (FM) for the continuous miniaturization of spintronic and quantum computing devices is desired. Through first-principles calculations, we establish that Ru atoms can be epitaxially aligned on MoS2 monolayers, thus forming an atomically thin layer of 2D Ru/MoS2 heterostructure with high structural stability. The Ru layer possesses a robust FM (more than 300 K) and an out-of-plane easy axis with the magnetic anisotropy energy (MAE) of ∼3...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27870614/active-inference-a-process-theory
#12
Karl Friston, Thomas FitzGerald, Francesco Rigoli, Philipp Schwartenbeck, Giovanni Pezzulo
This article describes a process theory based on active inference and belief propagation. Starting from the premise that all neuronal processing (and action selection) can be explained by maximizing Bayesian model evidence-or minimizing variational free energy-we ask whether neuronal responses can be described as a gradient descent on variational free energy. Using a standard (Markov decision process) generative model, we derive the neuronal dynamics implicit in this description and reproduce a remarkable range of well-characterized neuronal phenomena...
November 21, 2016: Neural Computation
https://www.readbyqxmd.com/read/27851934/forced-unfolding-mechanism-of-bacteriorhodopsin-as-revealed-by-coarse-grained-molecular-dynamics
#13
Tatsuya Yamada, Takahisa Yamato, Shigeki Mitaku
Developments in atomic force microscopy have opened up a new path toward single-molecular phenomena; in particular, during the process of pulling a membrane protein out of a lipid bilayer. However, the characteristic features of the force-distance (F-D) curve of a bacteriorhodopsin in purple membrane, for instance, have not yet been fully elucidated in terms of physicochemical principles. To address the issue, we performed a computer simulation of bacteriorhodopsin with, to our knowledge, a novel coarse-grained (C-G) model...
November 15, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27847872/blind-protein-structure-prediction-using-accelerated-free-energy-simulations
#14
Alberto Perez, Joseph A Morrone, Emiliano Brini, Justin L MacCallum, Ken A Dill
We report a key proof of principle of a new acceleration method [Modeling Employing Limited Data (MELD)] for predicting protein structures by molecular dynamics simulation. It shows that such Boltzmann-satisfying techniques are now sufficiently fast and accurate to predict native protein structures in a limited test within the Critical Assessment of Structure Prediction (CASP) community-wide blind competition.
November 2016: Science Advances
https://www.readbyqxmd.com/read/27844507/probing-the-binding-mechanism-of-mercaptoguanine-derivatives-as-inhibitors-of-hppk-by-docking-and-molecular-dynamics-simulations
#15
Parthiban Marimuthu, Kalaimathy Singaravelu, Vigneshwaran Namasivayam
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a promising antimicrobial target involved in the folate biosynthesis pathway. Although, the results from crystallographic studies of HPPK have attracted a great interest in the design of novel HPPK inhibitors, the mechanism of action of HPPK due to inhibitor binding remains questionable. Recently, mercaptoguanine derivatives were reported to inhibit the pyrophosphoryl transfer mechanism of Staphylococcus aureus HPPK (SaHPPK). The present study is an attempt to understand the SaHPPK-inhibitors binding mechanism and to highlight the key residues that possibly involve in the complex formation...
November 30, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27827496/predicting-molecular-self-assembly-at-surfaces-a-statistical-thermodynamics-and-modeling-approach
#16
Simone Conti, Marco Cecchini
Molecular self-assembly at surfaces and interfaces is a prominent example of self-organization of matter with outstanding technological applications. The ability to predict the equilibrium structure of a self-assembled monolayer (SAM) is of fundamental importance and would boost the development of bottom-up strategies in a number of fields. Here, we present a self-consistent theory for a first-principles interpretation of 2D self-assembly based on modeling and statistical thermodynamics. Our development extends the treatment from finite-size to infinite supramolecular objects and delineates a general framework in which previous approaches can be recovered as particular cases...
November 9, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27819055/entropy-driven-structural-transition-and-kinetic-trapping-in-formamidinium-lead-iodide-perovskite
#17
Tianran Chen, Benjamin J Foley, Changwon Park, Craig M Brown, Leland W Harriger, Jooseop Lee, Jacob Ruff, Mina Yoon, Joshua J Choi, Seung-Hun Lee
A challenge of hybrid perovskite solar cells is device instability, which calls for an understanding of the perovskite structural stability and phase transitions. Using neutron diffraction and first-principles calculations on formamidinium lead iodide (FAPbI3), we show that the entropy contribution to the Gibbs free energy caused by isotropic rotations of the FA(+) cation plays a crucial role in the cubic-to-hexagonal structural phase transition. Furthermore, we observe that the cubic-to-hexagonal phase transition exhibits a large thermal hysteresis...
October 2016: Science Advances
https://www.readbyqxmd.com/read/27804272/how-strongly-does-appetite-counter-weight-loss-quantification-of-the-feedback-control-of-human-energy-intake
#18
David Polidori, Arjun Sanghvi, Randy J Seeley, Kevin D Hall
OBJECTIVE: To quantify the feedback control of energy intake in response to long-term covert manipulation of energy balance in free-living humans. METHODS: A validated mathematical method was used to calculate energy intake changes during a 52-week placebo-controlled trial in 153 patients treated with canagliflozin, a sodium glucose co-transporter inhibitor that increases urinary glucose excretion, thereby resulting in weight loss without patients being directly aware of the energy deficit...
November 2016: Obesity
https://www.readbyqxmd.com/read/27801443/study-of-entropic-characteristics-of-strongly-correlated-systems-using-vo2-as-a-model-case
#19
Asaya Fujita, Yoshiaki Kinemuchi, Wataru Yamaguchi
To explain the huge caloric effects often observed in the first-order electronic phase transition in the strongly correlated oxides, the entropic characteristics are investigated in VO2. By evaluating the spin and charge fluctuations based on the local moment model and the Sommerfeld coefficient in the high-temperature rutile phase, it is found that these fluctuations of the high-temperature phase are the main source of the entropic change during the transition. This mode of entropic change is realized by the quenching of these fluctuations owing to the formation of a singlet bonding state in the low-temperature monoclinic phase...
November 1, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27796304/how-ef-tu-can-contribute-to-efficient-proofreading-of-aa-trna-by-the-ribosome
#20
Jeffrey K Noel, Paul C Whitford
It has long been recognized that the thermodynamics of mRNA-tRNA base pairing is insufficient to explain the high fidelity and efficiency of aminoacyl-tRNA (aa-tRNA) selection by the ribosome. To rationalize this apparent inconsistency, Hopfield proposed that the ribosome may improve accuracy by utilizing a multi-step kinetic proofreading mechanism. While biochemical, structural and single-molecule studies have provided a detailed characterization of aa-tRNA selection, there is a limited understanding of how the physical-chemical properties of the ribosome enable proofreading...
October 31, 2016: Nature Communications
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