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Sunil Nath
As the chief energy source of eukaryotic cells, it is important to determine the thermodynamic efficiency of ATP synthesis in oxidative phosphorylation (OX PHOS). Previous estimates of the thermodynamic efficiency of this vital process have ranged from Lehninger's original back-of-the-envelope calculation of 38% to the often quoted value of 55-60% in current textbooks of biochemistry, to high values of 90% from recent information theoretic considerations, and reports of realizations of close to ideal 100% efficiencies by single molecule experiments...
October 15, 2016: Biophysical Chemistry
Shu-Yu Wu, Ping Zou, Alexandra W Fuller, Sanjay Mishra, Zhen Wang, Kevin L Schey, Hassane S Mchaourab
The refractivity and transparency of the ocular lens is dependent on the stability and solubility of the crystallins in the fiber cells. A number of mutations of lens crystallins have been associated with dominant cataracts in humans and mice. Of particular interest were γB- and γD-crystallin mutants linked to dominant cataracts in mouse models. While thermodynamically destabilized and aggregation-prone, these mutants were found to have weak affinity to the resident chaperone α-crystallin in vitro To better understand the mechanism of the cataract phenotype, we transgenically expressed different γD-crystallin mutants in the zebrafish lens, and observed a range of lens defects that arise primarily from the aggregation of the mutant proteins...
October 21, 2016: Journal of Biological Chemistry
Mansoore Hosseini-Koupaei, Behzad Shareghi, Ali Akbar Saboury, Fateme Davar
The alteration in structure, function and stability of proteinase K in the presence of spermine was investigated using spectroscopic methods and simulation techniques. The stability and enzyme activity of proteinase K-spermine complex were significantly enhanced as compared to that of the pure enzyme. The increase in the value of Vmax and the catalytic efficiency of Proteinase K in presence of spermine confirmed that the polyamine could bring the enzyme hyperactivation. UV-visible spectroscopy, intrinsic fluorescence and circular dichroism methods demonstrated that the binding of spermine changed the microenvironment and structure of proteinase K...
October 18, 2016: International Journal of Biological Macromolecules
Helen P Jarvie, Stephen M King, Colin Neal
River water-quality studies rarely measure dissolved inorganic carbon (DIC) routinely, and there is a gap in our knowledge of the contributions of DIC to aquatic carbon fluxes and cycling processes. Here, we present the THINCARB model (THermodynamic modelling of INorganic CARBon), which uses widely-measured determinands (pH, alkalinity and temperature) to calculate DIC concentrations, speciation (bicarbonate, HCO3(-); carbonate, CO3(2-); and dissolved carbon dioxide, H2CO3(⁎)) and excess partial pressures of carbon dioxide (EpCO2) in freshwaters...
October 18, 2016: Science of the Total Environment
Emilia Fisicaro, Carlotta Compari, Franco Bacciottini, Laura Contardi, Erika Pongiluppi, Nadia Barbero, Guido Viscardi, Pierluigi Quagliotto, Gaetano Donofrio, Marie Pierre Krafft
Biological and thermodynamic properties of a new homologous series of highly fluorinated bispyridinium cationic gemini surfactants, differing in the length of the spacer bridging the pyridinium polar heads in 1,1' position, are reported for the first time. Interestingly, gene delivery ability is closely associated with the spacer length due to a structural change of the molecule in solution. This conformation change is allowed when the spacer reaches the right length, and it is suggested by the trends of the apparent and partial molar enthalpies vs molality...
October 15, 2016: Journal of Colloid and Interface Science
Anirban Basu, Gopinatha Suresh Kumar
Interaction of proflavine with hemoglobin (Hgb) was studied employing spectroscopy, calorimetry, and atomic force microscopy. The equilibrium constant was found to be of the order 10(4)M(-1). The quenching of Hgb fluorescence by proflavine was due to the complex formation. Calculation of the molecular distance (r) between the donor (β-Trp37 of Hgb) and acceptor (proflavine) suggested that energy can be efficiently transferred from the β-Trp37 residue at the α1β2 interface of the protein to the dye. Proflavine induced significant secondary structural changes in Hgb...
October 12, 2016: Journal of Photochemistry and Photobiology. B, Biology
Tobias Dornheim, Simon Groth, Travis Sjostrom, Fionn D Malone, W M C Foulkes, Michael Bonitz
We perform ab initio quantum Monte Carlo (QMC) simulations of the warm dense uniform electron gas in the thermodynamic limit. By combining QMC data with the linear response theory, we are able to remove finite-size errors from the potential energy over the substantial parts of the warm dense regime, overcoming the deficiencies of the existing finite-size corrections by Brown et al. [Phys. Rev. Lett. 110, 146405 (2013)]. Extensive new QMC results for up to N=1000 electrons enable us to compute the potential energy V and the exchange-correlation free energy F_{xc} of the macroscopic electron gas with an unprecedented accuracy of |ΔV|/|V|,|ΔF_{xc}|/|F|_{xc}∼10^{-3}...
October 7, 2016: Physical Review Letters
Jennifer Trinh, Ekkes Brück, Theo Siegrist, Rebecca Flint, Premala Chandra, Piers Coleman, Arthur P Ramirez
The heavy fermion compound URu_{2}Si_{2} continues to attract great interest due to the unidentified hidden order it develops below 17.5 K. The unique Ising character of the spin fluctuations and low-temperature quasiparticles is well established. We present detailed measurements of the angular anisotropy of the nonlinear magnetization that reveal a cos^{4}θ Ising anisotropy both at and above the ordering transition. With Landau theory, we show this implies a strongly Ising character of the itinerant hidden order parameter...
October 7, 2016: Physical Review Letters
Giuseppe Lanza, Maria A Chiacchio
Exploration of interfacial hydration networks of zwitterion and non-ionized trialanine has been performed using DFT-M062X quantum chemical computations explicitly considering up to 41 water molecules. The step-by-step water molecules peptide surrounding, carried out for unfolded extended (β), polyproline II (PPII) conformations reveals the crucial importance of explicit solvent effects in stabilizing the zwitterion form and the left-handed PPII-helix ubiquitously found at room temperature for short polyalanines...
October 21, 2016: Journal of Physical Chemistry. B
Fengjiao Chen, Qishan Zhu, Yeyun Wang, Wei Cui, Xiaodong Su, Yanguang Li
Increasing attention has now been focused on the photoelectrochemical (PEC) hydrogen evolution as a promising route to transform solar energy into chemical fuels. Silicon is one of the most studied PEC electrode materials, but its performance is still limited by its inherent PEC instability and electrochemical inertness toward water splitting. To achieve significant PEC activities, silicon-based photoelectrodes usually have to be coupled with proper cocatalysts, and thus formed semiconductor/cocatalyst interface represents a critical structural parameter in the rational design of efficient PEC devices...
October 21, 2016: ACS Applied Materials & Interfaces
R D Astumian
Molecular machines use external energy to drive transport, to do mechanical, osmotic, or electrical work on the environment, and to form structure. In this paper the fundamental difference between the design principles necessary for a molecular machine to use light or external modulation of thermodynamic parameters as an energy source vs. the design principle for using an exergonic chemical reaction as a fuel will be explored. The key difference is that for catalytically-driven motors microscopic reversibility must hold arbitrarily far from equilibrium...
October 21, 2016: Faraday Discussions
Girish G Ariga, Praveen N Naik, Sharanappa T Nandibewoor, Shivamurti A Chimatadar
The goal of this study was to investigate the interactions between meclizine (MEC) and human serum albumin (HSA) under physiological conditions by different spectroscopies and molecular modeling technique. The drug, MEC quenched the intrinsic fluorescence of HSA and the analysis of the results revealed that static quenching mechanism. The binding of MEC quenches the HSA fluorescence; stoichiometry was 1:1 interaction. Thermodynamic quantities were calculated at different temperatures suggested that hydrophobic and van der Waals interaction with HSA-MEC...
October 21, 2016: Journal of Biomolecular Structure & Dynamics
Petr Stadlbauer, Liuba Mazzanti, Tristan Cragnolini, David J Wales, Philippe Derreumaux, Samuela Pasquali, Jiri Sponer
G-quadruplexes are the most important non-canonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradicting models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach the thermodynamics equilibrium...
October 21, 2016: Journal of Chemical Theory and Computation
S Alipour, F Benatti, F Bakhshinezhad, M Afsary, S Marcantoni, A T Rezakhani
We provide a characterization of energy in the form of exchanged heat and work between two interacting constituents of a closed, bipartite, correlated quantum system. By defining a binding energy we derive a consistent quantum formulation of the first law of thermodynamics, in which the role of correlations becomes evident, and this formulation reduces to the standard classical picture in relevant systems. We next discuss the emergence of the second law of thermodynamics under certain-but fairly general-conditions such as the Markovian assumption...
October 21, 2016: Scientific Reports
Fei Pan, Jian Zhang, Hao-Long Chen, Yen-Hsun Su, Yen-Hao Su, Weng-Sing Hwang
Thermodynamic calculation has been applied to predict the inclusion formation in molten SS400 steel. When the Cerium addition in liquid iron is 70 ppm and the initial Oxygen and Sulphur are both 110 ppm, the formation of oxides containing Cerium would experience the transformation from Ce2O3 to CeO2 and also the formation of sulfides containing Cerium would experience the transformation from CeS to Ce2S3 and then to Ce3S4. Below 2000 K the most thermodynamic stable matter is CeO2 and the less thermodynamic stable inclusion is CeS...
October 21, 2016: Scientific Reports
Zhimin Xie, Dongliang Chai, Youshan Wang, Huifeng Tan
The effective potentials are of great importance for the coarse-grained (CG) simulations, which can be obtained by the structure-based iterative Boltzmann inversion (IBI) method. However, the standard IBI method is incapable of keeping the mechanical and thermodynamic properties of the CG model in consistence with those of the all-atom model. Unlike the existed techniques, such as introducing the friction force as the dissipative force to drop the superatom motion while the conservative force arising from the CG potential was kept intact, we directly modified the standard IBI nonbonded potential by adding an empirical function...
October 21, 2016: Journal of Physical Chemistry. B
Hahnbeom Park, Philip Bradley, Per Greisen, Yuan Liu, Vikram Khipple Mulligan, David E Kim, David Baker, Frank DiMaio
Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data...
October 21, 2016: Journal of Chemical Theory and Computation
Michel Alain Cuendet, Harel Weinstein, Michael V LeVine
Allostery plays a fundamental role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two collective variables is not a single number, but instead a two-dimensional thermodynamic coupling function that is directly related to the mutual information from information theory and the copula density function from probability theory. On this basis, we demonstrate how to quantify the contribution of specific energy terms to this thermodynamic coupling function, enabling an approximate decomposition that reveals the mechanism of allostery...
October 21, 2016: Journal of Chemical Theory and Computation
Ryo Amano, Kenta Takada, Yoichiro Tanaka, Yoshikazu Nakamura, Gota Kawai, Tomoko Kozu, Taiichi Sakamoto
AML1 (RUNX1) protein is an essential transcription factor involved in the development of hematopoietic cells. Several genetic aberrations that disrupt the function of AML1 have been frequently observed in human leukemia. AML1 contains a DNA-binding domain known as the Runt domain (RD), which recognizes the RD-binding double-stranded DNA element of target genes. In this study, we identified high-affinity RNA aptamers that bind to RD by SELEX. The binding assay using surface plasmon resonance indicated that a shortened aptamer retained the ability to bind to RD when 1 M potassium acetate was used...
October 21, 2016: Biochemistry
Qihui Chen
A temperature and anions induced coordination-driven self-assembly system based on dynamic Ag6L4 metallocage has been developed. Induced by SbF6- anions, both of kinetic-control [Ag3L2(SbF6)3]n and thermodynamic-control [Ag2L2(SbF6)2]n can be reassembled from discrete Ag6L4(SbF6)6 metallocages at 30 ℃, raising temperature up to 40 ℃ results to selective inhibition of their kinetic product. While driven by BF4- anions, dynamic Ag6L4(BF4)6 metallocages prior to self-assemble into thermodynamic-control polycage at 25 ℃, lowing the temperature down to 0℃ leads to selective inhibition of their thermodynamic product...
October 20, 2016: Chemistry: a European Journal
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