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Cyril Charlier, T Reid Alderson, Joseph M Courtney, Jinfa Ying, Philip Anfinrud, Adriaan Bax
In general, small proteins rapidly fold on the timescale of milliseconds or less. For proteins with a substantial volume difference between the folded and unfolded states, their thermodynamic equilibrium can be altered by varying the hydrostatic pressure. Using a pressure-sensitized mutant of ubiquitin, we demonstrate that rapidly switching the pressure within an NMR sample cell enables study of the unfolded protein under native conditions and, vice versa, study of the native protein under denaturing conditions...
April 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
Albert Y Lau
The majority of excitatory synaptic transmission in the central nervous system is mediated by ionotropic glutamate receptors (iGluRs). These membrane-bound protein assemblies consist of modular domains that can be genetically isolated and expressed, which has resulted in a plethora of crystal structures of individual domains in different conformations bound to different ligands. These structures have presented opportunities for molecular dynamics (MD) simulation studies. To examine the free energies that govern molecular behavior, simulation strategies and algorithms have been developed, collectively called enhanced sampling methods This review focuses on the use of enhanced sampling MD simulations of isolated iGluR ligand-binding domains to characterize thermodynamic properties important to receptor function...
April 14, 2018: Neuroscience Letters
Moin Ishrat, Md Imtaiyaz Hassan, Faizan Ahmad, Asimul Islam
Organisms synthesize sugar osmolytes during environmental stresses to protect proteins against denaturation. These studies were carried out in dilute buffer whereas intracellular milieu within cells has cytoplasmic concentration of macromolecules in the range of 80-400 mg ml-1 . Is the stabilizing effect of sugar osmolytes on the protein in dilute buffer different from that when protein is in cellular environment? To answer this question, we have measured and analysed the effect of sugar osmolytes on the structural and thermodynamic stability of ribonuclease A in the presence of dextran 70 at multiple concentrations of six sugars at different pH values...
April 14, 2018: International Journal of Biological Macromolecules
Fatemeh S Mohseni-Shahri, Farid Moeinpour, Masoumeh Nosrati
The interaction of pepsin with sunset yellow food additive (SY) was studied by fluorescence spectroscopy and molecular dynamics simulation. The experimental results indicated that SY can quench the fluorescence of pepsin with static quenching. The apparent binding constant Ka and binding site number n were evaluated at different temperatures. Thermodynamic analysis suggests that SY interact with pepsin spontaneously by van der Waal's forces and hydrogen bond formation. Three-dimensional fluorescence spectra showed that pepsin undergoes a slightly conformation change when it interacts with SY...
April 14, 2018: International Journal of Biological Macromolecules
Jeong Yun Kim, Heather J Kulik
We present a detailed study of nearly 70 Zn molecular catalysts for CO2 hydration from four diverse ligand classes ranging from well-studied carbonic anhydrase mimics (e.g., cyclen) to new structures we obtain by leveraging diverse hits from large organic libraries. Using kinetic analysis and establishing linear free energy relationships, we confirm turnover to be sensitive to relative thermodynamic stability of reactive hydroxyl and bound bicarbonate moieties. We observe a wide range of thermodynamic stabilities for these intermediates, showing up to 6 kcal/mol improvement over well-studied cyclen catalysts...
April 17, 2018: Journal of Physical Chemistry. A
Franziska Ortner, Chantal Ruppli, Marco Mazzotti
A thermodynamically consistent description of binary adsorption in reversed phase chromatography is presented, accounting for thermodynamic nonidealities in the liquid and the adsorbed phase. The investigated system involves the adsorbent Zorbax 300SB-C18, as well as phenetole (PNT) and 4-tert-butylphenol (TBP) as solutes and methanol and water as inert components forming the eluent. The description is based on adsorption isotherms which are a function of the liquid phase activities, in order to account for non-idealities in the liquid phase...
April 17, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Andrés Arango-Restrepo, J Miguel Rubi, Daniel Barragán
Gel formation is described by a non-equilibrium self-assembly mechanism which considers the presence of precursors. Assuming that non-equilibrium structures appear and are maintained by entropy production, we developed a mesoscopic non-equilibrium thermodynamic model that describes the dynamic assembly of the structures. In the model, the evolution of the structures from the initially inactivated building blocks to the final agglomerates is governed by kinetic equations of the Fokker-Planck type. From these equations, we get the probability densities which enable one to know measurable quantities such as the concentrations of the different components and the dynamic structure factor obtained in light-scattering experiments...
April 17, 2018: Journal of Physical Chemistry. B
Seyed Hossein Jamali, Ludger Wolff, Tim M Becker, André Bardow, Thijs J H Vlugt, Othonas A Moultos
Molecular Dynamics simulations were performed for the prediction of the finite-size effects of Maxwell-Stefan diffusion coefficients of molecular mixtures and a wide variety of binary Lennard-Jones systems. A strong dependency of computed diffusivities on the system size was observed. Computed diffusivities were found to increase with the number of molecules. We propose a correction for the extrapolation of Maxwell-Stefan diffusion coefficients to the thermodynamic limit, based on the study by Yeh and Hummer (J...
April 17, 2018: Journal of Chemical Theory and Computation
Jamie M Baird-Titus, Mahendra Thapa, Thomas Doerdelmann, Kelly A Combs, Mark Rance
An important but poorly characterized contribution to the thermodynamics of protein-DNA interactions is the loss of entropy that occurs from restricting the conformational freedom of amino acid side chains. The effect of restricting the flexibility of several side chains at a protein-DNA interface may be comparable in many cases to the other factors that determine the binding thermodynamics, and may therefore play a key role in dictating the binding affinity and/or specificity. Because the entropic contributions, including the presence and influence of side-chain dynamics, are especially difficult to estimate based on structural information, it is important to pursue experimental and theoretical studies that can provide direct information regarding these issues...
April 17, 2018: Biochemistry
Xiang-He Kong, Qunyan Wu, Cong-Zhi Wang, Jianhui Lan, Zhi-Fang Chai, Changming Nie, Wei-Qun Shi
Separation of trivalent actinides (An(III)) and lanthanides (Ln(III)) is one of the most important steps in the spent nuclear fuel reprocessing. However, it is very difficult and challenging to separate them due to their similar chemical properties. Recently the pyridylpyrazole ligand (PypzH) has been identified to show good separation ability towards Am(III) over Eu(III). In this work, to explore the Am(III)/Eu(III) separation mechanism of PypzH at the molecular level, the geometrical structures, bonding nature, and thermodynamic behaviors of the Am(III) and Eu(III) complexes with PypzH ligands modified by alkyl chains (Cn-PypzH, n=2, 4, 8) have been systematically investigated using scalar relativistic density functional theory (DFT)...
April 17, 2018: Journal of Physical Chemistry. A
Nicola Gargiulo, Antonio Peluso, Paolo Aprea, Luca Micoli, Angelo Ausiello, Maria Turco, Ottavio Marino, Raffaele Cioffi, Elio Jannelli, Domenico Caputo
In this work, the potentialities of the amino-functionalized, chromium-based MIL-101 metal organic framework (NH2 -MIL-101) as a high capacity, fully regenerable hydrogen chloride adsorbent have been proved by a thorough adsorption thermodynamics investigation. The chosen adsorbent showed high gaseous HCl adsorption capacities and, to the best of our knowledge, it is the first example of a totally regenerable substrate for this kind of adsorbate, as evidenced by both experimental and modeling results. This paves the way to the implementation of greener, more energetically efficient pressure / temperature swing adsorption processes to purify biogas feeds for high temperature fuel cells...
April 17, 2018: ACS Applied Materials & Interfaces
Najoua Derbel, Olfa Ferchichi, Alexander Alijah
We present the results of a systematic investigation, at the BHandHLYP/AVTZ density functional (DFT) level, of the tautomeric equilibria of 1,2,3- and 1,2,4-triazoles and their reaction with hydroxyl radicals in the gas phase. A total of twenty-six chemical reactions has been studied, and thermodynamical data and rate constants are reported. The reactions can be classified in two categories: hydrogen abstraction and OH addition. It was found that OH addition proceeds more rapidly than hydrogen abstraction, by several orders of magnitude...
April 17, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Lu-Lu Zhang, Lei Zhang, Shi-Jun Li, De-Cai Fang
A series of density functional theory calculations have been carried out to investigate the detailed mechanisms of C-H activation and oxidation reactions, and further to disclose the distinct effects of mononuclear- and binuclear-palladium on these reaction pathways. The results of calculations demonstrated that the C-H activation of 2-phenylpyridine with mononuclear Pd(OAc)2 prefers the inner-shell proton-abstraction mechanism, while that with binuclear Pd2(μ-OAc)4 is biased to the outer-shell proton-abstraction mechanism...
April 17, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
Ambadas Rode, Tamaki Endoh, Naoki Sugimoto
In bacteria, the binding between riboswitch aptamer domain and ligand is regulated by environmental cues, such as low Mg2+ in macrophages during pathogenesis to ensure spatiotemporal expression of virulence genes. We investigated binding between the flavin mononucleotide (FMN) riboswitch aptamer and its anionic ligand in the presence of molecular crowding agent without Mg2+ ion, which mimics pathogenic conditions. Structural, kinetic, and thermodynamic analyses under the crowding revealed more dynamic conformational rearrangements of the FMN riboswitch aptamer compared to dilute Mg2+-containing solution...
April 16, 2018: Angewandte Chemie
Jamie Hicks, Petra Vasko, Jose M Goicoechea, Simon Aldridge
The reactivity of aluminium compounds is dominated by their electron deficiency and consequent electrophilicity; these compounds are archetypal Lewis acids (electron-pair acceptors). The main industrial roles of aluminium, and classical methods of synthesizing aluminium-element bonds (for example, hydroalumination and metathesis), draw on the electron deficiency of species of the type AlR3 and AlCl3 1,2 . Whereas aluminates, [AlR4 ]- , are well known, the idea of reversing polarity and using an aluminium reagent as the nucleophilic partner in bond-forming substitution reactions is unprecedented, owing to the fact that low-valent aluminium anions analogous to nitrogen-, carbon- and boron-centred reagents of the types [NX2 ]- , [CX3 ]- and [BX2 ]- are unknown3-5 ...
April 16, 2018: Nature
Jinhui Zhu, Xiangru Lu, Qingping Feng, Peter B Stathopulos
Store-operated calcium (Ca2+ ) entry (SOCE) is a major Ca2+ signaling pathway facilitating extracellular Ca2+ influx in response to the initial release of intracellular endo/sarcoplasmic reticulum (ER/SR) Ca2+ stores. Stromal interaction molecule-1 (STIM1) is the Ca2+ sensor which activates SOCE following ER/SR Ca2+ depletion. The EF-hand together with the adjacent sterile α motif (EFSAM) domains of STIM1 are essential for detecting changes in luminal Ca2+ concentrations. Low ER Ca2+ levels trigger STIM1 destabilization and oligomerization, culminating in the opening of Orai1-composed Ca2+ channels on the plasma membrane...
April 16, 2018: Journal of Biological Chemistry
Abdur Rashid, Dong-Xing Guan, Abida Farooqi, Sardar Khan, Salman Zahir, Shah Jehan, Seema Anjum Khattak, Muhammad Sufaid Khan, Raees Khan
This study investigated the fluoride (F- ) concentrations and physicochemical parameters of the groundwater in a fluorite mining area of the flood plain region of the River Swat, with particular emphasis on the fate and distribution of F- and the hydrogeochemistry. To better understand the groundwater hydrochemical profile and F- enrichment, groundwater samples (n=53) were collected from shallow (24-40m), mid-depth (48-65m) and deep (85-120m) aquifers, and then analysed using an ion-selective electrode. The lowest F- concentration (0...
April 13, 2018: Science of the Total Environment
R Bregier-Jarzębowska, L Łomozik, A Gąsowska
Potentiometric and NMR spectroscopic studies of the nucleotide (NucP)/polyamine (PA) system (where NucP = CDP, CTP, PA = putrescine or spermidine) revealed the formation of molecular complexes (NucP)(Hx+y )(PA) (where Hx+y  = number of protons; x - from NucP and y - from PA). Their thermodynamic parameters were determined and the modes of their interactions were proposed. The main reaction centers were found to be the protonated amine groups of polyamine (positive centers) and phosphate groups of nucleotide (negative centers)...
April 6, 2018: Journal of Inorganic Biochemistry
Pablo Ballester, Giulia Moncelsi, Luis Escobar, Henry Dube
We report the synthesis of two 2-(4'-pyridyl-N-oxide)-substituted hemithioindigos. We probed their photoisomerization using UV-Vis and 1H NMR spectroscopic techniques. Light irradiation at 450 nm provoked the isomerization of the HTI Z isomer to the E counterpart in a large extent (~80 % at the PSS). 1H NMR titration experiments revealed the formation of thermodynamically and kinetically stable 1:1 inclusion complexes of the Z-HTI isomers with a super aryl-extended host (Ka > 104 M-1). Photoirradiation at 450 nm of the inclusion complexes induced the isomerization of the bound HTI N-oxide affording the E-HTI⊂calix[4]pyrrole complex...
April 16, 2018: Chemistry, An Asian Journal
Sha Chen, Xiao-Xin Li, Fan Feng, Sumei Li, Jia-Hui Han, Zi-Yi Jia, Lun Shu, P Somsundaran, Jian-Rong Li
In this study, the baseline separations of xylene isomers and phthalate acid esters on a homemade DUT-67(Zr) packed column were achieved, respectively. The high selectivity for xylene isomers and phthalate acid esters was obtained with the increase of temperature and decrease of the retention time. The hydrophobicity of xylene isomers and phthalate acid esters caused the different separation time on the DUT-67(Zr) packed column. The relative standard deviation values of retention time, peak area, peak height and half peak width for five repeat separation of the xylene isomers were 0...
April 16, 2018: Journal of Separation Science
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