Thermodynamics Research Today is a free monthly online journal that collates and summarizes the latest research about Thermodynamics, including details on enthalpy, entropy, energy transitions. | ||||||
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Incorporating nucleosomes into thermodynamic models of transcription regulation.Raveh-Sadka T, Levo M, Segal E Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel. Transcriptional control is central to many cellular processes, and, consequently, much effort has been devoted to understanding its underlying mechanisms. The organization of nucleosomes along promoter regions is important for this process, since most transcription factors cannot bind nucleosomal sequences and thus compete with nucleosomes for DNA access. This competition is governed by the relative concentrations of nucleosomes and transcription factors and by their respective sequence binding preferences. However, despite its importance, a mechanistic understanding of the quantitative effects that the competition between nucleosomes and factors has on transcription is still missing. Here we use a thermodynamic framework based on fundamental principles of statistical mechanics to explore theoretically the effect that different nucleosome organizations along promoters have on the activation dynamics of promoters in response to varying concentrations of the regulating factors. We show that even simple landscapes of nucleosome organization reproduce experimental results regarding the effect of nucleosomes as general repressors and as generators of obligate binding cooperativity between factors. Our modeling framework also allows us to characterize the effects that various sequence elements of promoters have on the induction threshold and on the shape of the promoter activation curves. Finally, we show that using only sequence preferences for nucleosomes and transcription factors, our model can also predict expression behavior of real promoter sequences, thereby underscoring the importance of the interplay between nucleosomes and factors in determining expression kinetics. Published 24 June 2009 in Genome Res. Articles on Thermodynamics published 24 June 2009: Standard electrode potential, Tafel equation, and the solvation thermodynamics. J Chem Phys, 130(23): 234704. Equilibrium in the electronic subsystem across the solution-metal interface is considered to connect the standard electrode potential to the statistics of localized electronic states in solution. We argue that a correct derivation of the Nernst equation for the electrode potential requires a careful separation of the relevant time scales. An equation for the standard metal potential is derived linking it to the thermodynamics of solvation. The Anderson-Newns model for electronic delocalization ... [Abstract] [Full-text] Articles on Thermodynamics published 23 June 2009: Kinetics and thermodynamics of DNA hybridization on gold nanoparticles. Nucleic Acids Res, 37(11): 3756-65. Hybridization of single-stranded DNA immobilized on the surface of gold nanoparticles (GNPs) into double stranded DNA and its subsequent dissociation into ssDNA were investigated. Melting curves and rates of dissociation and hybridization were measured using fluorescence detection based on hybridization-induced fluorescence change. Two distribution functions, namely the state distribution and the rate distribution, were proposed in order to take interfacial heterogeneity into account and to ... [Abstract] [Full-text] Specific thermodynamical potentials on surfaces under relativistic conditions. J Colloid Interface Sci. Expressions of specific thermodynamical potentials on surfaces (J/cm(2)) were obtained (for internal energy, enthalpy, free energy, and free enthalpy) under relativistic conditions. [Abstract] [Full-text] Articles on Thermodynamics published 22 June 2009: Tropoelastin as a thermodynamically unfolded premolten globule protein: The effect of trimethylamine N-oxide on structure and coacervation. Arch Biochem Biophys. Tropoelastin is the monomer building block of the biopolymer elastin, which is responsible for elasticity in arteries, lung and skin. Previous studies have shown that, in contrast to predictions made based on primary sequence, tropoelastin has little regular secondary structure in aqueous solution and displays considerable flexibility. This investigation defines the level of residual structure present in tropoelastin and uses the naturally-occurring structure-inducing osmolyte trimethylamine ... [Abstract] [Full-text] Contribution of the trifluoroacetyl group in the thermodynamics of antigen-antibody binding. J Mol Recognit. We analyzed the binding of the 7C8 antibody to the chloramphenicol phosphonate antigens-one containing a trifluoroacetyl group (CP-F) and the other containing an acetyl group (CP-H)-by using isothermal titration calorimetry (ITC). The thermodynamic difference due to the substitution of F by H was evaluated using free energy calculations based on molecular dynamics (MD) simulations. We have previously shown that another antibody, namely, 6D9, binds more weakly to CP-H than to CP-F, mainly due to ... [Abstract] [Full-text] Correlation of RNA Secondary Structure Statistics with Thermodynamic Stability and Applications to Folding. J Mol Biol. The accurate prediction of the secondary and tertiary structure of an RNA with different folding algorithms are dependent on several factors, including the energy functions. However, an RNA higher-order structure cannot be accurately predicted from its sequence based on a limited set of energy parameters. The inter- and intra-molecular forces between this RNA and other small molecules and macromolecules, in addition to other factors in the cell such as pH, ionic strength, and temperature ... [Abstract] [Full-text] Thermodynamic aspects of vitrification. Cryobiology. Vitrification is a process in which a liquid begins to behave as a solid during cooling without any substantial change in molecular arrangement or thermodynamic state variables. The physical phenomenon of vitrification is relevant to both cryopreservation by freezing, in which cells survive in glass between ice crystals, and cryopreservation by vitrification in which a whole sample is vitrified. The change from liquid to solid behavior is called the glass transition. It is coincident with ... [Abstract] [Full-text] To elucidate the applicability and effects of ionic liquids as reaction media for bioinorganic catalysis, detailed kinetic and mechanistic studies on the reversible binding of NO to the monohydroxo ligated iron(III) phorphyrin, (TMPS)Fe(III)(OH) were performed in the ionic liquid [emim][NTf(2)] as solvent. We report for the first time the determination of activation volumes via high pressure stopped flow methods in an ionic liquid. The studies clearly show that impurities of methylimidazole, ... [Abstract] [Full-text] © 2005-2009 Thermodynamics Research Today. All Rights Reserved. |
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